pdf_store_loader.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "884d6f8a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# pip install langchain chromadb\n",
    "# What we want is an environment for procesing pdfs and loading them\n",
    "# into a local vector store. We want a vector store that is fast. We\n",
    "# want to process the pdfs into smart chunks. Finally, an outstanding\n",
    "# question is how the pdf is represented in the vector store. More to \n",
    "# come on that."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "2f5fb5bc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2023-12-11 21:39:07.893468\t2.0742416381835938e-05\tStart.\n",
      "file_count: 316\n",
      "2023-12-11 21:39:07.940644\t0.04710674285888672\tLoading documents\n"
     ]
    },
    {
     "ename": "NameError",
     "evalue": "name 'ArxivLoader' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[7], line 38\u001b[0m\n\u001b[1;32m     32\u001b[0m page_count \u001b[38;5;241m=\u001b[39m page_count \u001b[38;5;241m+\u001b[39m \u001b[38;5;28mlen\u001b[39m(pages)\n\u001b[1;32m     34\u001b[0m \u001b[38;5;66;03m# print(f\"loading {pdf}\")\u001b[39;00m\n\u001b[1;32m     35\u001b[0m \u001b[38;5;66;03m# print(f'page_count: {page_count}')\u001b[39;00m\n\u001b[1;32m     36\u001b[0m \n\u001b[1;32m     37\u001b[0m \u001b[38;5;66;03m# Need to get the falcon embeddings and embed these new pages\u001b[39;00m\n\u001b[0;32m---> 38\u001b[0m docs \u001b[38;5;241m=\u001b[39m \u001b[43mArxivLoader\u001b[49m(query\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAntibiotic design using deep learning\u001b[39m\u001b[38;5;124m\"\u001b[39m, load_max_docs\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m10\u001b[39m)\u001b[38;5;241m.\u001b[39mload()\n\u001b[1;32m     39\u001b[0m text_splitter \u001b[38;5;241m=\u001b[39m RecursiveCharacterTextSplitter(chunk_size\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1000\u001b[39m, chunk_overlap\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m200\u001b[39m)\n\u001b[1;32m     40\u001b[0m splits \u001b[38;5;241m=\u001b[39m text_splitter\u001b[38;5;241m.\u001b[39msplit_documents(docs)\n",
      "\u001b[0;31mNameError\u001b[0m: name 'ArxivLoader' is not defined"
     ]
    }
   ],
   "source": [
    "from langchain.document_loaders import PyPDFLoader\n",
    "from os import listdir\n",
    "from os.path import isfile, join\n",
    "import datetime\n",
    "import time\n",
    "from langchain.vectorstores import FAISS\n",
    "from langchain.embeddings.openai import OpenAIEmbeddings\n",
    "\n",
    "def _print(txt=\"HERE\", last_time=time.time()):\n",
    "    this_time = time.time()\n",
    "    print(\"{}\\t{}\\t{}\".format(datetime.datetime.now(),\n",
    "                              this_time-last_time,\n",
    "                              txt)\n",
    "         )\n",
    "    return time.time()\n",
    "\n",
    "t = _print(\"Start.\")\n",
    "\n",
    "\n",
    "mypath=\"pdfs\"\n",
    "onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]\n",
    "print(f'file_count: {len(onlyfiles)}')\n",
    "\n",
    "# This needs to run parallel\n",
    "t = _print(\"Loading documents\", t)\n",
    "page_count = 0\n",
    "pages = []\n",
    "for pdf in onlyfiles:\n",
    "    if pdf.endswith(\".pdf\"):\n",
    "        loader = PyPDFLoader(\"pdfs/\" + pdf)\n",
    "        pages = loader.load_and_split()\n",
    "        page_count = page_count + len(pages)\n",
    "        \n",
    "        # print(f\"loading {pdf}\")\n",
    "        # print(f'page_count: {page_count}')\n",
    "        \n",
    "        # Need to get the falcon embeddings and embed these new pages\n",
    "\n",
    "        # Then should investigate the best way to embed. How big of chunks.\n",
    "\n",
    "        # Then need to load into a vector store\n",
    "        \n",
    "t = _print(\"Done loading documents\", t)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "caa5c31f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pages: 27\n",
      "[Document(page_content='Morbidity and Mortality Weekly Report\\nWeekly / Vol. 72 / No. 1  Januar y 6, 2023\\nINSIDE\\n9 M pox Cases Among Cisgender Women and Pregnant \\nPersons — United States, May 11–November 7, 2022\\n16 QuickStats\\nContinuing Education examination available at  \\nhttps://www.cdc.gov/mmwr/mmwr_continuingEducation.html\\nU.S. Department of Health and Human Services\\nCenters for Disease Control and PreventionRacial and Ethnic Differences in COVID-19 Vaccination Coverage Among \\nChildren and Adolescents Aged 5–17 Years and Parental Intent to Vaccinate \\nTheir Children — National Immunization Survey–Child COVID Module, \\nUnited States, December 2020–September 2022\\nMadeleine R. Valier, MPH1,2; Laurie D. Elam-Evans, PhD1; Yi Mu, PhD1; Tammy A. Santibanez, PhD1; David Yankey, PhD1; Tianyi Zhou, MPH1,3; \\nCassandra Pingali, MPH, MS1; James A. Singleton, PhD1\\nSome racial and ethnic groups are at increased risk for \\nCOVID-19 and associated hospitalization and death because \\nof systemic and structural inequities contributing to higher \\nprevalences of high-risk conditions and increased exposure \\n(1). Vaccination is the most effective prevention intervention against COVID-19–related morbidity and mortality*; ensur -\\ning more equitable vaccine access is a public health priority. Differences in adult COVID-19 vaccination coverage by race and ethnicity have been previously reported (2,3), but \\nsimilar information for children and adolescents is limited \\n(4,5). CDC analyzed data from the National Immunization Survey–Child COVID Module (NIS-CCM) to describe racial and ethnic differences in vaccination status, parental intent to vaccinate their child, and behavioral and social drivers of \\nvaccination among children and adolescents aged 5–17 years. \\nBy August 31, 2022, approximately one third (33.2%) of children aged 5–11 years, more than one half (59.0%) of children and adolescents aged 12–15 years, and more than two thirds (68.6%) of adolescents aged 16–17 years had received ≥1 COVID-19 vaccine dose. Vaccination coverage was highest \\namong non-Hispanic Asian (Asian) children and adolescents, \\nranging from 63.4% among those aged 5–11 years to 91.8% \\n* CDC’ s Advisory Committee on Immunization Practices (ACIP) issued an \\ninterim recommendation for use of the Pfizer-BioNTech COVID-19 vaccine \\nfor persons aged ≥16 years on December 12, 2020, 12–15 years on May 12, \\n2021, and 5–11 years on November 2, 2021. ACIP recommended use of an \\nadditional homologous primary dose of Pfizer-BioNTech vaccine after an initial series in immunocompromised persons aged ≥12 years on August 13, 2021. ACIP recommended monovalent booster doses for persons aged \\n16–17 years on December 9, 2021, 12–15 years on January 5, 2022, and \\n5–11 years on May 19, 2022.among those aged 16–17 years. Coverage was next highest \\namong Hispanic or Latino (Hispanic) children and adolescents (34.5%–77.3%). Coverage was similar for non-Hispanic Black \\nor African American (Black), non-Hispanic White (White), \\nand non-Hispanic other race\\n† or multiple race (other/multiple \\nrace) children and adolescents aged 12–15 and 16–17 years. Among children aged 5–11 years, coverage among Black \\nchildren was lower than that among Hispanic, Asian, and \\nother/multiple race children. Enhanced public health efforts are needed to increase COVID-19 vaccination coverage for all children and adolescents. To address disparities in child and adolescent COVID-19 vaccination coverage, vaccination providers and trusted messengers should provide culturally \\n† Race and ethnicity of the child or adolescent w ere reported by the parent or \\nguardian and were available for all study participants. Asian, Black, White, or \\nother/multiple race children and adolescents were reported by the parent or \\nguardian to be non-Hispanic. Other/multiple race children and adolescents', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 0}), Document(page_content='other/multiple race children and adolescents were reported by the parent or \\nguardian to be non-Hispanic. Other/multiple race children and adolescents \\nhad more than one race category selected, or were identified as American Indian or Alaska Native, or Native Hawaiian or other Pacific Islander. Hispanic children and adolescents might be of any race.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 0}), Document(page_content='Morbidity and Mortality Weekly Report2 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionThe MMWR series of publications is published by the Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention (CDC), \\nU.S. Department of Health and Human Services, Atlanta, GA 30329-4027.\\nSuggested citation: [Author names; first three, then et al., if more than six.] [Report title]. MMWR Morb Mortal Wkly Rep 2023;72:[inclusive page numbers].\\nCenters for Disease Control and Prevention\\nRochelle P . Walensky, MD, MPH, Director\\nDebra Houry, MD, MPH, Acting Principal Deputy Director\\nJennifer Layden, MD, PhD, Acting Deputy Director for Public Health Science and Surveillance\\nRebecca Bunnell, PhD, MEd, Director, Office of Science\\nLeslie Dauphin, PhD, Director, Center for Surveillance, Epidemiology, and Laboratory Services\\nMMWR Editorial and Production Staff (Weekly)\\nCharlotte K. Kent, PhD, MPH, Editor in Chief \\nJacqueline Gindler, MD, Editor\\nTegan K. Boehmer, PhD, MPH, Guest Science Editor\\nPaul Z. Siegel, MD, MPH, Associate Editor\\nMary Dott, MD, MPH, Online Editor\\nTerisa F . Rutledge, Managing Editor \\nTeresa M. Hood, MS, Lead T echnical Writer-Editor\\nLeigh Berdon, Glenn Damon,\\nTiana Garrett-Cherry, PhD, MPH,\\nStacy Simon, MA, Morgan Thompson, Suzanne Webb, PhD\\nT echnical Writer-EditorsMartha F . Boyd, Lead Visual Information Specialist\\nAlexander J. Gottardy, Maureen A. Leahy,\\nJulia C. Martinroe, Stephen R. Spriggs, Tong Yang,\\nVisual Information Specialists\\nQuang M. Doan, MBA, Phyllis H. King, \\nTerraye M. Starr, Moua Yang, \\nInformation T echnology Specialists\\nMMWR Editorial Board\\nTimothy F . Jones, MD, Chairman\\nMatthew L. Boulton, MD, MPH\\nCarolyn Brooks, ScD, MA \\nJay C. Butler, MD \\nVirginia A. Caine, MD \\nJonathan E. Fielding, MD, MPH, MBADavid W. Fleming, MD \\nWilliam E. Halperin, MD, DrPH, MPH\\nJewel Mullen, MD, MPH, MPA\\nJeff Niederdeppe, PhD\\nCeleste Philip, MD, MPHPatricia Quinlisk, MD, MPH \\nPatrick L. Remington, MD, MPH \\nCarlos Roig, MS, MA\\nWilliam Schaffner, MD \\nMorgan Bobb Swanson, BSIan Branam, MA, \\nActing Lead Health Communication Specialist\\nKiana Cohen, MPH, Symone Hairston, MPH,  \\nLeslie Hamlin, Lowery Johnson, \\nHealth Communication Specialists\\nDewin Jimenez, Will Yang, MA,\\nVisual Information Specialistsrelevant information and vaccine recommendations and build \\na higher level of trust among those groups with lower coverage.\\nNIS-CCM is a nationally representative random-digit–dialed \\nmobile telephone survey of households with children and adolescents aged 6 months–17 years. NIS-CCM interview data collected from 94,838 respondents during September 26, 2021–September 30, 2022,\\n§ were used to assess racial and \\nethnic differences in COVID-19 vaccination coverage, parental intent to vaccinate, and behavioral and social drivers of vaccina -\\ntion among children and adolescents aged 5–17 years. Survey respondents were those who reported being knowledgeable about the child’s or adolescent’s vaccination status (parent). Interviews with parents of an unvaccinated child or adolescent, or a child or adolescent who received ≥1 COVID-19 vaccine dose\\n¶ during December 2020–September 2022 were included. \\nWhite persons were designated as the referent group for most racial and ethnic comparisons because this group has the largest \\npopulation size and the most social advantage (6).\\nKaplan-Meier estimation methods were used to calculate \\ncumulative ≥1-dose COVID-19 vaccination coverage as of \\n§ R espondents interviewed during September 26, 2021–September 30, 2022, were \\nincluded; month and year of vaccination occurred during December 2020–\\nSeptember 2022.\\n¶ Assessed b y response to the question, “Has [child’s name] received at least one \\ndose of a COVID-19 vaccine?” Month and year of first dose was assessed by asking, “During what month and year did [child’s name] receive [his/her] first', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 1}), Document(page_content='dose of a COVID-19 vaccine?” Month and year of first dose was assessed by asking, “During what month and year did [child’s name] receive [his/her] first \\nCOVID-19 vaccine?”August 31, 2022.** First-dose vaccination month and year \\nwere hot deck imputed†† for 20.2% of children and adolescents \\nwith parent-reported vaccination but without a vaccination date (7). Differences in ≥1-dose coverage were assessed by race \\nand ethnicity and stratified by sociodemographic subgroups. \\nPairwise comparisons were conducted to assess differences in ≥1-dose estimates for all races and ethnicities. Survey data during July 1–September 30, 2022,\\n§§ (26,961) were pooled \\nto calculate proportions of children and adolescents who 1) were unvaccinated, but parental intent to vaccinate was \\nascertained, 2) initiated COVID-19 vaccination (received \\n≥1 dose), 3) completed the primary series (received ≥2 doses), \\n * * K aplan-Meier estimation methods were used to calculate estimated cumulative \\nvaccination coverage as of the end of each month from December 2020 \\nthrough August 2022 using data from interviews conducted during \\nSeptember 26, 2021–September 30, 2022, in which the event was defined as \\nthe month and year of receipt of first dose of COVID-19 vaccine and was censored by date of interview. Vaccination status was assigned as of the end of the month before the interview.\\n †† D ata were imputed using hot deck imputation (replacing missing values \\nwith observed values from a respondent with similar characteristics) from donor pools matched for month of interview, age group, region, and race \\nand ethnicity.\\n §§ I nterview data were restricted to the previous 3 months (July 1–September 30, \\n2022) to provide the most current assessment of vaccination coverage, parental \\nintent, and behavioral and social drivers of vaccination. Estimates of \\nvaccination coverage represent the cumulative percentage of children and \\nadolescents vaccinated as of approximately the midpoint of this interview period (mid-August 2022), and estimates of coverage with ≥1 dose might differ from the Kaplan-Meier estimates as of August 31, 2022.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 1}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  3\\nUS Department of Health and Human Services/Centers for Disease Control and Prevention4) received a monovalent booster (≥3 doses),¶¶ or 5) had an \\nassessment of behavioral and social drivers of vaccination.*** \\nFor all analyses, p-values <0.05 were considered statistically \\nsignificant. Analyses were performed using SAS (version 9.4; \\nSAS Institute) and SAS-callable SUDAAN (version 11.0.3; Research T riangle Institute). Survey weights were used to adjust to the noninstitutionalized U.S. population of children and adolescents and to calibrate to CDC vaccine administration data. The cumulative Council of American Survey Research \\nOrganizations (CASRO) response rate\\n††† was 18.1%. This \\nactivity was reviewed by CDC and was conducted consistent \\nwith applicable federal law and CDC policy.§§§\\nBy August 31, 2022, 33.2%, 59.0%, and 68.6% of persons \\naged 5–11, 12–15, and 16–17 years, respectively, had received ≥1 COVID-19 vaccine dose ( Table 1 ). Coverage among \\nAsian persons was higher than that among persons of other races and ethnicities, ranging from 63.4% (aged 5–11 years) to 91.8% (16–17 years), followed by Hispanic persons, with coverage ranging from 34.5% to 77.3% (Figure). Coverage was similar for Black, White, and other/multiple race persons aged 12–15 and 16–17 years. Coverage in Black children aged \\n5–11 years was 4.0 to 33.6 percentage points lower than that \\namong Asian, Hispanic, and other/multiple race children of the same age (Supplementary Table 1, https://stacks.cdc.gov/\\nview/cdc/122810).\\nCoverage with ≥1 COVID-19 vaccine dose by August 31, 2022, \\nwas higher among children and adolescents aged 12–17 years, those whose mothers had obtained a college degree, who lived in a household with yearly income ≥$75,000, who always or often wore a mask in public during the previous 7 days, and who had received ≥1 influenza vaccine dose (Table 1). Coverage among Asian and Hispanic children and adolescents was higher \\nin most sociodemographic subgroups compared with coverage \\namong White children and adolescents. Black, White, and other/multiple race children and adolescents had the largest variation in coverage by sociodemographic and behavioral characteristics.\\n ¶¶ I nformation on whether the child or adolescent was immunocompromised \\nwas not ascertained in NIS-CCM; thus, booster dose coverage estimates \\nmight include immunocompromised children and adolescents who received \\n3 primary COVID-19 vaccine doses.\\n *** Assessed b y responses to six questions covering 1) concern about the child \\nor adolescent getting COVID-19, 2) confidence in COVID-19 vaccine \\nsafety, 3) confidence in COVID-19 vaccine importance, 4) percentage of \\nfriends and family who had vaccinated their children (social norms), 5) health \\ncare provider recommendation for COVID-19 vaccination, and 6) school COVID-19 vaccination requirements. https://www.cdc.gov/vaccines/imz-managers/nis/downloads/NIS-CCM-Questionnaire-Q3-2022.pdf\\n ††† The CASR O response rate is the product of three rates: 1) the proportion of \\ntelephone numbers that can be identified as either for business or residence (resolution rate), 2) the proportion of qualified households that complete the \\nscreening process (screening rate), and 3) the proportion of contacted eligible \\nhouseholds for which a completed interview is obtained (cooperation rate).\\n §§§ 45 C.F .R. part 46.102(l)(2), 21 C.F .R. part 56; 42 U.S.C. Sect. 241(d); \\n5 U.S.C. Sect. 552a; 44 U.S.C. Sect. 3501 et seq.Data collected during July 1–September 30, 2022, indi -\\ncate that overall, 47.2% of children and adolescents received \\n≥1 COVID-19 vaccine dose; 43.3% completed the primary \\nseries (≥2 doses) ( Table 2). Among children and adolescents \\naged 5–17 years, primary series coverage was highest among', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 2}), Document(page_content='≥1 COVID-19 vaccine dose; 43.3% completed the primary \\nseries (≥2 doses) ( Table 2). Among children and adolescents \\naged 5–17 years, primary series coverage was highest among \\nAsian persons. Monovalent booster dose coverage was low overall (14.7%) and was highest among Asian children and adolescents (22.4%) and lowest among Black children and adolescents (9.3%). Parents of White children and adolescents \\nof all ages reported the highest level of reluctance\\n¶¶¶ (40.3%) \\nto have their child vaccinated.\\nParents of vaccinated children and adolescents reported \\nhigh levels of confidence in the importance (93.1%) and \\nsafety (78.8%) of vaccination overall and by race and eth -\\nnicity (Supplementary Table 2, https://stacks.cdc.gov/view/\\ncdc/122811 ). Confidence in vaccine importance remained \\nhigh (76.7%), but confidence in vaccine safety was consider -\\nably lower (40.2%) among parents of unvaccinated children \\nand adolescents who might get their child vaccinated (reach-\\nable children****). Parents of reluctant and reachable children and adolescents reported substantially lower percentages of friends and family had vaccinated their children and adoles -\\ncents (reflection of social norms) (6.4%–21.2%) and reported \\nhaving received a provider recommendation (27.9%–35.9%) \\nfor vaccination compared with parents of vaccinated children (72.9% and 61.8%, respectively). The magnitude of these differences was similar by race and ethnicity.\\nOverall, reluctant parents expressed less favorable attitudes \\nand opinions regarding vaccination than did parents of vac -\\ncinated and unvaccinated but reachable children. Among all reluctant parents, those of Black and Hispanic children and adolescents reported the highest levels of concern about their child getting COVID-19 and expressed the most confidence in the importance of the vaccine.\\nDiscussion\\nCOVID-19 vaccination coverage was low among children \\nand adolescents aged 5–17 years overall, but highest among Asian and Hispanic children and adolescents. By August 31, \\n2022, Asian children and adolescents had substantially higher \\ncoverage than did all other children and adolescents overall and when stratified by factors associated with lower coverage for all children and adolescents, indicating a willingness across demographic and behavioral characteristics in this population to receive vaccination. During July 1–September 30, 2022, \\n ¶¶¶ U nvaccinated children and adolescents whose parents responded that they \\ndefinitely or probably will not vaccinate their child (reluctant).\\n **** U nvaccinated children and adolescents whose parents responded that they \\ndefinitely, probably will, or are unsure if they will vaccinate their child \\n(reachable).', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 2}), Document(page_content='Morbidity and Mortality Weekly Report 4 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionTABLE 1. COVID–19 vaccination coverage with ≥1 dose as of August 31, 2022, among children and adolescents aged 5–17 years, by race and \\nethnicity * and demographic characteristics — National Immunization Survey–Child COVID Module, United States, September 26, 2021–\\nSeptember 30, 2022\\nCharacteristicRespondent distribution Vaccinated,† weighted % (95% CI)\\nUnweighted \\nno.Weighted %§ \\n (95% CI)Total \\n(N = 94,838)Asian \\n(n = 4,962)Black or African \\nAmerican \\n(n = 10,103)Hispanic or Latino \\n(n = 19,805)White (Ref)¶ \\n(n = 51,606)Other or  \\nmultiple race \\n(n = 8,362)\\nTotal 94,838 100.0 47.1 (46.5–47.7) 75.2 (72.3–78.0)** 43.1 (41.4–44.8)** 49.1 (47.7–50.5)** 45.0 (44.2–45.8) 48.3 (46.0–50.6)**\\nAge group, yrs\\n5–11 (Ref) 59,502 52.9 (52.4–53.5) 33.2 (32.5–33.9) 63.4 (59.3–67.5)** 29.8 (28.0–31.7) 34.5 (32.9–36.2)** 31.2 (30.3–32.0) 33.8 (31.2–36.6)\\n12–15 26,652 31.4 (30.9–32.0) 59.0 (57.9–60.2)††89.2 (85.3–92.5)**,††56.6 (53.3–60.0)††63.9 (61.3–66.5)**,††55.5 (54.0–57.1)††58.6 (54.4–62.8)††\\n16–17 8,684 15.6 (15.2–16.1) 68.6 (66.8–70.5)††91.8 (84.4–96.6)**,††65.5 (60.0–71.0)††77.3 (72.8–81.5)**,††64.6 (62.3–66.9)††67.8 (60.8–74.7)††\\nSexFemale 45,380 48.9 (48.3–49.4) 48.1 (47.2–49.0)\\n††75.9 (71.9–79.8)** 42.9 (40.6–45.3)** 49.9 (47.9–52.0)** 46.5 (45.3–47.6)††47.6 (44.3–51.0)\\nMale (Ref) 48,974 51.1 (50.6–51.7) 46.1 (45.2–46.9) 74.3 (70.2–78.3)** 43.1 (40.8–45.5) 48.2 (46.2–50.1)** 43.7 (42.6–44.7) 48.7 (45.5–52.0)**\\nMother’s highest education level\\nCollege degree or higher (Ref) 48,451 37.2 (36.6–37.7) 63.6 (62.7–64.6) 83.4 (80.3–86.3)** 55.4 (52.3–58.5)** 66.2 (63.6–68.7)** 62.0 (60.9–63.2) 70.6 (67.0–74.2)**\\nSome college 22,949 30.9 (30.3–31.4) 38.8 (37.8–39.9)††66.2 (58.1–74.2)**,††40.4 (37.7–43.3)**,††44.2 (41.8–46.7)**,††34.8 (33.4–36.2)†† 40.1 (36.6–43.9)**,††\\nHigh school or equivalent 15,714 20.5 (20.0–21.0) 35.5 (34.2–36.9)††68.9 (59.9–77.5)**,††37.1 (33.7–40.7)**,††43.0 (40.3–45.8)**,††28.3 (26.7–30.0)††34.2 (29.5–39.4)**,††\\nLess than high school 4,958 11.4 (11.0–11.9) 39.0 (36.6–41.4)†† NR§§ 29.4 (24.4–35.2)†† 46.6 (43.1–50.4)**,††25.1 (22.2–28.3)†† 36.5 (27.9–46.8)**,††\\nPoverty status and household income\\nAbove poverty, ≥$75,000 (Ref) 43,645 39.7 (39.1–40.2) 55.8 (54.8–56.7) 82.3 (77.6–86.4)** 53.4 (50.2–56.6) 56.9 (54.5–59.4)** 53.5 (52.4–54.7) 62.4 (58.8–66.0)**\\nAbove poverty, <$75,000 21,269 24.9 (24.4–25.4) 39.3 (38.1–40.5)††62.6 (55.3–69.9)**,††39.8 (36.9–42.8)**,††47.6 (44.9–50.4)**,††32.8 (31.3–34.4)††34.8 (30.9–39.0)††\\nBelow poverty 8,965 13.2 (12.8–13.6) 38.2 (36.3–40.1)†† NR§§ 34.0 (30.2–38.1)**,††46.5 (43.1–50.0)**,††28.0 (25.4–30.7)†† 34.0 (28.1–40.8)††\\nUnknown income 20,959 22.2 (21.7–22.7) 45.5 (44.2–46.8)††75.9 (71.1–80.4)** 41.8 (38.5–45.3)††43.4 (40.5–46.3)††44.2 (42.5–45.9)††47.8 (42.9–52.9)††\\nHealth insurance\\nOther insurance (Ref) 65,506 63.4 (62.9–64.0) 51.8 (51.0–52.6) 79.6 (76.3–82.7)** 48.2 (45.8–50.6) 51.1 (49.2–53.1) 50.4 (49.5–51.3) 55.9 (52.9–59.0)**\\nAny Medicaid 21,601 32.1 (31.5–32.6) 40.2 (39.1–41.4)††69.1 (62.0–76.0)**,††38.4 (36.0–41.0)**,††48.4 (46.1–50.8)** 32.5 (31.0–34.1)††36.5 (32.8–40.4)††\\nUninsured 3,458 4.5 (4.2–4.7) 34.6 (31.3–38.1)†† NR§§ 34.8 (26.8–44.2)†† 38.5 (32.9–44.6)**,††25.3 (21.3–29.9)†† NR§§\\nUrbanicity¶¶\\nMSA, principal city (Ref) 29,633 32.6 (32.0–33.1) 52.1 (51.0–53.3) 74.2 (69.6–78.6)** 42.3 (39.9–44.9)** 52.7 (50.4–55.1) 53.7 (52.0–55.3) 53.3 (49.2–57.4)\\nMSA, nonprincipal city 45,475 53.5 (52.9–54.1) 47.8 (47.0–48.7)††77.1 (73.4–80.7)** 43.8 (41.4–46.2)** 45.6 (43.7–47.7)††47.6 (46.5–48.6)††48.7 (45.5–52.0)\\nNon-MSA 14,688 13.9 (13.5–14.3) 29.7 (28.4–31.1)††NR§§43.4 (37.5–49.7)** 35.0 (31.0–39.3)**,††26.3 (24.9–27.8)††35.6 (31.0–40.8)**,††', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 3}), Document(page_content='Non-MSA 14,688 13.9 (13.5–14.3) 29.7 (28.4–31.1)††NR§§43.4 (37.5–49.7)** 35.0 (31.0–39.3)**,††26.3 (24.9–27.8)††35.6 (31.0–40.8)**,††\\nU.S. Census Bureau region***Northeast (Ref) 18,269 15.2 (14.9–15.5) 57.7 (56.3–59.1) 82.4 (76.8–87.4)** 45.3 (41.4–49.3)** 53.4 (50.2–56.6)** 60.4 (58.6–62.2) 52.9 (47.5–58.6)**\\nMidwest 18,223 21.3 (20.9–21.6) 40.4 (39.2–41.6)\\n††66.3 (58.9–73.5)**,††36.8 (33.1–40.9)††40.7 (37.4–44.2)††40.4 (39.0–41.9)††37.1 (32.9–41.7)††\\nSouth 34,023 38.6 (38.2–39.1) 42.3 (41.4–43.2)††71.2 (65.9–76.2)**,††45.0 (42.9–47.2)** 45.6 (43.4–47.8)**,††38.5 (37.3–39.7)††40.4 (37.2–43.9)††\\nWest 19,281 24.9 (24.4–25.4) 52.2 (50.7–53.7)††76.8 (71.6–81.7)** 39.0 (32.9–45.7)** 49.7 (47.2–52.4) 50.9 (48.9–52.9)††60.7 (56.2–65.2)**,††\\nSVI of county of residence†††\\nLow (Ref) 31,027 28.0 (27.6–28.5) 51.6 (50.6–52.7) 77.6 (72.3–82.5)** 48.5 (44.6–52.6) 48.5 (45.6–51.4) 51.5 (50.2–52.7) 48.6 (44.8–52.6)\\nModerate 31,119 37.3 (36.8–37.9) 47.2 (46.1–48.2)††77.9 (73.5–82.0)** 44.9 (42.1–47.8) 48.5 (45.9–51.2)** 44.4 (43.1–45.7)††50.7 (47.0–54.6)**\\nHigh 24,156 34.6 (34.1–35.2) 44.1 (43.0–45.3)††70.3 (63.3–77.0)** 40.5 (38.0–43.1)††49.0 (46.8–51.3)** 39.0 (37.4–40.6)††46.1 (41.8–50.7)**\\nSee table footnotes on the next page.\\noverall and among all racial and ethnic groups, most children \\nand adolescents who initiated a primary COVID-19 vaccina -\\ntion series also completed the primary series, an encouraging \\nsign of COVID-19 vaccine access and acceptance among par -\\nents who intend to vaccinate, but efforts are needed to achieve \\nmuch higher coverage levels for all children and adolescents.\\nLower coverage with ≥1 COVID-19 vaccine dose associated \\nwith some demographic and behavioral characteristics point to opportunities to improve coverage. Frequent mask use in public \\nand receipt of influenza vaccine were associated with higher \\nCOVID-19 vaccination coverage among all children and adolescents; however, among Black and Hispanic children and adolescents with these characteristics, the increase in coverage was smaller. Less than one half of parents of Black and Hispanic \\nchildren and adolescents had confidence in COVID-19 vaccine \\nsafety, which might indicate reluctance to be vaccinated among a population receptive to other public health behaviors. During July 1–September 30, 2022, large proportions of Hispanic and \\nBlack children and adolescents were unvaccinated but reachable \\n(26% and 29%, respectively), suggesting that coverage might increase over time with strengthened public health interven-tions. A higher proportion of parents of other/multiple race and White children and adolescents were reluctant to vaccinate their child (36% and 40%, respectively) than were considered \\nreachable (15%), suggesting potential difficulty achieving high \\nvaccination coverage among these children and adolescents.\\nImplementation of evidence-based practices described in \\nCDC’s COVID-19 Vaccination Field Guide\\n†††† could help \\nincrease vaccine coverage. Community members should serve as trusted messengers to advocate for vaccination among parents \\nof unvaccinated children and adolescents and should deliver \\ntailored messages to strengthen confidence in vaccine safety and \\n †††† https://www.cdc.gov/vaccines/covid-19/downloads/vaccination-strategies.pdf', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 3}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  5\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionTABLE 1. (Continued) COVID–19 vaccination coverage with ≥1 dose as of August 31, 2022, among children and adolescents aged 5–17 years, \\nby race and ethnicity * and demographic characteristics — National Immunization Survey–Child COVID Module, United States, September 26, \\n2021–September 30, 2022\\nCharacteristicRespondent distribution Vaccinated,† weighted % (95% CI)\\nUnweighted \\nno.Weighted %§ \\n (95% CI)Total \\n(N = 94,838)Asian \\n(n = 4,962)Black or African \\nAmerican \\n(n = 10,103)Hispanic or Latino \\n(n = 19,805)White (Ref)¶ \\n(n = 51,606)Other or  \\nmultiple race \\n(n = 8,362)\\nMask-wearing in indoor public spaces during previous 7 days\\nAlways/Often wore mask (Ref) 49,336 51.0 (50.4–51.6) 56.3 (55.3–57.3) 77.4 (73.9–80.8)** 45.0 (43.0–47.1)** 54.8 (52.8–56.8)** 60.1 (58.6–61.6) 57.8 (54.5–61.1)\\nSometimes/Rarely/\\nNever wore mask44,475 49.0 (48.4–49.6) 38.8 (38.0–39.6)††70.7 (65.5–75.7)**,††38.4 (35.5–41.5)†† 40.9 (38.8–43.0)**,††37.1 (36.2–38.1)†† 38.1 (35.0–41.4)††\\nInfluenza vaccination status since July 1, 2021§§§\\n≥1 dose influenza vaccine \\n(Ref)34,630 43.0 (42.3–43.7) 63.4 (62.4–64.5) 83.6 (79.6–87.2)** 53.9 (50.9–57.1)** 61.3 (58.9–63.6)** 64.6 (63.3–66.0) 65.8 (62.2–69.3)\\nDid not receive \\ninfluenza vaccine31,596 57.0 (56.3–57.7) 32.2 (31.4–33.1)††55.3 (49.6–61.1)**,††31.9 (29.7–34.3)†† 36.6 (34.6–38.6)**,††29.4 (28.3–30.5)†† 31.2 (28.2–34.4)††\\nChild/Adolescent ever had COVID–19\\nNo (Ref) 61,551 63.4 (62.9–64.0) 50.2 (49.4–51.0) 75.8 (72.2–79.1)** 43.2 (41.2–45.2)** 51.2 (49.4–53.0) 49.4 (48.4–50.4) 52.2 (49.3–55.2)\\nYes 32,310 36.6 (36.0–37.1) 42.3 (41.3–43.3)††74.1 (68.8–79.0)** 42.9 (39.9–46.0)** 45.7 (43.4–48.0)**,††38.9 (37.7–40.2)†† 42.7 (39.0–46.5)††\\nMental health of child/adolescentExcellent, very good, or good \\n(Ref)88,245 92.2 (91.9–92.5) 46.6 (46.0–47.2) 76.3 (73.4–79.1)** 42.8 (41.1–44.5) 48.4 (46.9–49.8)** 44.3 (43.5–45.1) 48.5 (46.1–50.9)**\\nFair or poor 6,056 7.8 (7.5–8.1) 53.3 (50.8–55.8)\\n†† NR§§ 47.2 (40.5–54.5) 57.9 (51.1–64.9)†† 53.9 (50.9–57.0)†† 47.0 (39.8–54.8)\\nAbbreviations:  MSA  = metropolitan statistical area; NR  = not reported; Ref  = referent group; SVI  = Social Vulnerability Index.\\n * R ace and ethnicity were reported by the parent or guardian. Children and adolescents identified as Asian, Black or African American, White, or other or multiple races were reported by \\nthe parent or guardian as non-Hispanic. Children and adolescents identified as being of other or multiple races had more than one race category selected, or were identified as American \\nIndian or Alaska Native, or Native Hawaiian or other Pacific Islander. Children and adolescents identified as Hispanic might be of any race.\\n † C umulative percentage vaccinated with ≥1 dose was estimated using Kaplan Meier survival analysis techniques with the event defined as the month and year of vaccination and the \\ncensoring variable defined as the date of interview.\\n § C olumn percentages might not sum to 100 because of rounding.\\n ¶ W hite persons were designated as the Ref for racial and ethnic comparisons because this group has the largest population size and the most social advantage. https://pubmed.ncbi.\\nnlm.nih.gov/26599027/\\n ** Sta tistically significant (p<0.05) difference compared with the indicated Ref (column) level (White).\\n †† Sta tistically significant (p<0.05) difference compared with the indicated Ref (row) level.\\n §§ Estima tes were suppressed because they did not meet standards for data reliability (CI >20, relative SE >30, or sample size <30).\\n ¶¶ Ur banicity was determined from household reported city and county of residence and was grouped into three categories: MSA principal city, MSA nonprincipal city, and non-MSA. MSA', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 4}), Document(page_content='¶¶ Ur banicity was determined from household reported city and county of residence and was grouped into three categories: MSA principal city, MSA nonprincipal city, and non-MSA. MSA \\nand MSA principal city were as defined by the U.S. Census Bureau ( https://www.census.gov/programs-surveys/metro-micro.html). Non-MSA areas include urban populations not located \\nwithin an MSA and completely rural areas.\\n *** https://www2.census.gov/geo/pdfs/maps-data/maps/reference/us_regdiv.pdf\\n ††† C ategorization of National Immunization Survey–Child COVID Module data into an SVI level was based on zip code of residence reported by the respondent. https://www.atsdr.cdc.gov/\\nplaceandhealth/svi/index.html\\n §§§ Da ta on receipt of influenza vaccine were collected via interviews conducted during October 1, 2021–June 30, 2022.\\nimportance. Provider recommendation is an impactful driver \\nof vaccination (8 ). A multifaceted approach with community \\ncollaboration and provider recommendation are essential to \\nincreasing childhood COVID-19 vaccination coverage.\\nThe findings in this report are subject to at least five \\nlimitations. First, the survey response rate was low (18.1%). \\nData were weighted to account for household and provider nonresponse and for households without telephones and weighted to the COVID-19 vaccine administration data \\n(≥1 doses) reported by jurisdictions to CDC. However, some \\nbias might remain. Second, child and adolescent COVID-19 vaccination receipt was parent-reported and might be subject to recall or social desirability biases. However, limited recall bias is expected because of the recency of COVID-19 vac -\\ncination recommendations. Third, small sample sizes were available for American Indian or Alaska Native and for Native Hawaiian or other Pacific Islander children and adolescents; therefore, these data were aggregated in the other/multiple race category. Fourth, aggregated racial and ethnic data might Summary\\nWhat is already known about this topic?\\nSome racial and ethnic groups are at increased risk for \\nCOVID-19–associated morbidity and mortality because of systemic and structural inequities. Vaccination is effective in preventing severe COVID-19–related outcomes.\\nWhat is added by this report?\\nAmong children and adolescents aged 5–17 years, ≥1-dose \\nCOVID-19 vaccination coverage was low overall, but highest \\namong Asian and Hispanic or Latino children and adolescents. Parental intent to vaccinate their child varied by the child’s age, race, and ethnicity. Parents of unvaccinated children and \\nadolescents reported low confidence in vaccine safety, and a \\nlow percentage reported receipt of a provider vaccination recommendation.\\nWhat are the implications for public health practice?\\nTo increase overall coverage and address disparities in child and \\nadolescent COVID-19 vaccination coverage, providers and \\ntrusted messengers should provide culturally relevant informa-\\ntion and vaccine recommendations.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 4}), Document(page_content='Morbidity and Mortality Weekly Report 6 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionFIGURE. COVID-19 vaccination coverage estimates,* by race and ethnicity,† among persons aged 5–11 years (A), 12–15 years (B), and  \\n16–17 years (C) during December 2020–August 2022 — National Immunization Survey–Child COVID Module, United States, September 26, \\n2021–September 30, 2022\\nAsian\\nBlackHispanicWhiteOther or multiple races\\n020406080100\\nDec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul AugCoverage (%)\\nMonth and year of vaccination\\n020406080100\\nDec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul AugCoverage (%)\\n020406080100\\nDec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul AugCoverage (%)Month and year of vaccination\\nMonth and year of vaccination2020 2021 2022\\n2020 2021 2022\\n2020 2021 2022A. 5–11 yrs\\nB. 12–15 yrs\\nC. 16–17 yrsAsian\\nBlackHispanicWhiteOther or multiple races\\nAsianBlackHispanicWhiteOther or multiple races\\nAbbreviations: Black = Black or African American; Hispanic = Hispanic or Latino.\\n* ≥1 dose coverage; Kaplan-Meier survival analysis was used to estimate vaccination coverage based on the month and year of first dose receipt; estimates reflect \\nthe cumulative percentage vaccinated as of the end of each month. \\n† R ace and ethnicity were reported by the parent or guardian. Children and adolescents identified as Asian, Black, White, or other or multiple races were reported by \\nthe parent or guardian as non-Hispanic. Children and adolescents identified as being of other or multiple races had more than one race category selected or were \\nidentified as American Indian or Alaska Native, or Native Hawaiian or other Pacific Islander. Children and adolescents identified as Hispanic might be of any race.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 5}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  7\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionTABLE 2. COVID-19 vaccination status among children and adolescents aged 5–17 years, and parental intent to vaccinate their children, by \\nrace and ethnicity * — National Immunization Survey–Child COVID Module, United States, July 1–September 30, 2022\\nAge group and race/ethnicityWeighted % (95% CI)\\nVaccinated, doses received Unvaccinated, parents’ intent\\nVaccinated  \\n≥1 dose†Primary series \\n≥2 dosesBooster, \\nmonovalent \\n≥3 dosesDefinitely, probably, or \\nunsure if will get child/\\nadolescent vaccinatedDefinitely or probably \\nwill not get child/\\nadolescent vaccinated\\nAll, 5–17 yrs 47.2 (46.1–48.3) 43.3 (42.2–44.4) 14.7 (13.9–15.5) 19.5 (18.5–20.4) 33.4 (32.3–34.5)\\nAsian 73.4 (68.4–77.8)§ 69.3 (64.3–73.9)§ 22.4 (18.3–27.0)§ 14.9 (11.6–19.0) 11.7 (8.5–15.8)§\\nBlack or African American 44.7 (41.6–47.8) 39.1 (36.2–42.1) 9.3 (7.8–11.1)§ 28.9 (26.0–32.0)§ 26.4 (23.5–29.5)§\\nHispanic or Latino 49.0 (46.6–51.4)§43.5 (41.2–45.9) 13.4 (11.9–15.0)§26.2 (24.0–28.5)§24.8 (22.7–27.1)§\\nWhite (Ref)¶ 45.0 (43.5–46.5) 42.3 (40.9–43.8) 15.9 (14.9–17.0) 14.8 (13.6–15.9) 40.3 (38.7–41.8)\\nOther or multiple race 49.0 (44.8–53.3) 45.4 (41.2–49.7) 16.4 (13.3–20.1) 14.6 (12.1–17.5) 36.4 (32.3–40.7)\\n5–11 yrs 34.1 (33.0–35.3) 29.7 (28.6–30.8) 5.5 (5.0–6.0) 25.3 (24.1–26.6) 40.6 (39.2–41.9)\\nAsian 63.5 (57.3–69.2)§ 57.1 (51.1–62.9)§ 10.9 (8.0–14.7)§ 20.2 (15.7–25.6) 16.3 (11.8–22.0)§\\nBlack or African American 32.7 (29.6–35.9) 27.3 (24.4–30.3) 4.5 (3.4–5.8)§ 36.3 (32.6–40.1)§ 31.1 (27.5–34.8)§\\nHispanic or Latino 35.2 (32.6–37.8)§ 28.8 (26.5–31.2) 4.6 (3.7–5.7)§ 33.3 (30.5–36.3)§ 31.5 (28.7–34.4)§\\nWhite (Ref)¶32.0 (30.5–33.5) 29.0 (27.5–30.4) 6.0 (5.3–6.7) 19.1 (17.5–20.7) 49.0 (47.1–50.8)\\nOther or multiple race 33.0 (28.8–37.4) 28.8 (24.9–33.1) 5.0 (3.7–6.7) 19.7 (16.3–23.7) 47.3 (42.3–52.4)\\n12–15 yrs 58.2 (56.0–60.5) 55.1 (52.8–57.3) 21.8 (20.1–23.5) 14.9 (13.2–16.7) 26.9 (24.8–29.1)\\nAsian 87.3 (78.6–92.8)§ 86.6 (77.9–92.2)§ 33.7 (24.6–44.3)§ 8.2 (3.7–17.0) 4.5 (2.1–9.5)§\\nBlack or African American 58.2 (51.4–64.7) 53.1 (46.5–59.6) 15.2 (11.6–19.6)§20.0 (15.1–26.0)§21.7 (16.2–28.5)§\\nHispanic or Latino 61.8 (56.9–66.4)§ 57.8 (52.9–62.5) 20.7 (17.5–24.3) 20.8 (16.9–25.3)§ 17.5 (13.9–21.6)§\\nWhite (Ref)¶ 54.5 (51.5–57.5) 52.2 (49.2–55.2) 22.4 (20.2–24.8) 12.0 (10.1–14.4) 33.5 (30.5–36.5)\\nOther or multiple race 62.0 (53.6–69.7) 57.5 (49.2–65.5) 26.1 (19.4–34.2) 10.0 (6.4–15.4) 28.0 (20.9–36.4)\\n16–17 yrs 68.8 (65.3–72.1) 65.6 (62.1–68.9) 31.3 (28.5–34.3) 9.0 (7.0–11.4) 22.2 (19.3–25.6)\\nAsian 87.3 (66.1–96.1)§86.2 (65.9–95.3)§46.7 (31.3–62.8) 6.2 (1.2–26.3) 6.4 (1.1–29.8)§\\nBlack or African American 66.4 (55.5–75.8) 59.5 (48.9–69.2) 17.5 (11.9–25.2)§ 16.7 (10.0–26.6)§ 16.9 (9.8–27.6)§\\nHispanic or Latino 75.0 (66.7–81.8)§ 70.4 (62.1–77.6) 32.3 (26.0–39.3) 9.8 (5.6–16.4) 15.2 (9.8–23.0)§\\nWhite (Ref)¶65.8 (61.1–70.1) 63.5 (58.9–67.9) 33.5 (29.7–37.5) 7.0 (4.8–10.1) 27.2 (23.1–31.7)\\nOther or multiple race 68.6 (55.8–79.0) 67.9 (55.2–78.3) 29.1 (19.5–41.1) 9.3 (4.4–18.7) 22.1 (13.1–34.9)\\nAbbreviation:  Ref = referent group.\\n* Race and ethnicity were reported by the parent or guardian. Children and adolescents identified as Asian, Black or African American, White, or other or multiple races \\nwere reported by the parent or guardian as non-Hispanic. Children and adolescents identified as being of other or multiple races had more than one race category \\nselected, or were identified as American Indian or Alaska Native, or Native Hawaiian or other Pacific Islander. Children and adolescents identified as Hispanic might be of any race.\\n† P roportions of children and adolescents who received ≥1 dose COVID-19 vaccine based on July–September 2022 interview data might not match Kaplan-Meier', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 6}), Document(page_content='† P roportions of children and adolescents who received ≥1 dose COVID-19 vaccine based on July–September 2022 interview data might not match Kaplan-Meier \\nvaccination coverage estimates, which use more months of data (September 26, 2021–September 30, 2022) and a different analytic method.\\n§ Sta tistically significant (p<0.05) difference compared with White persons.\\n¶ W hite persons were designated as the Ref for racial and ethnic comparisons because this group has the largest population size and the most social advantage. \\nhttps://pubmed.ncbi.nlm.nih.gov/26599027/\\nobscure differences in coverage that are apparent in disag -\\ngregated subgroups (9 ). Data on racial and ethnic subgroups \\nwere collected, but the sample size was inadequate to analyze \\nthe disaggregated data. Finally, reporting of month and year \\nof vaccination was incomplete for one fifth of children and adolescents who were reported to be vaccinated, requiring imputation of missing dates.\\nPublic health efforts to increase coverage with the primary \\nCOVID-19 vaccination series in all age groups and the bivalent \\nCOVID-19 booster dose\\n§§§§ among eligible persons should \\ncontinue. These efforts should be tailored to differences in \\nparental intent, behavioral and social drivers of vaccination, and by the child’s or adolescent’s age, race, and ethnicity. Programs should provide culturally relevant information and employ evidence-based strategies, including tailored messages \\ndelivered by trusted messengers and strong recommendations \\nfrom vaccination providers, to increase vaccine confidence and coverage among all groups, and to eliminate the disparities for those with lower vaccination coverage.\\nAcknowledgments\\nJanet Cleveland, Jennifer Kriss, CDC.\\nCorresponding author: Madeleine R. Valier, rtf3@cdc.gov .\\n 1Immunization Services Division, National Center for Immunization and \\nRespiratory Diseases, CDC; 2Oak Ridge Institute for Science and Education, \\nOak Ridge, Tennessee; 3Leidos Inc., Atlanta, Georgia.\\nAll authors have completed and submitted the International \\nCommittee of Medical Journal Editors form for disclosure of potential \\nconflicts of interest. No potential conflicts of interest were disclosed. §§§§ As of D ecember 9, 2022, persons aged ≥6 months are recommended to \\nreceive a bivalent booster dose, even if they already received a monovalent \\nbooster dose. https://www.cdc.gov/coronavirus/2019-ncov/vaccines/stay-\\nup-to-date.html', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 6}), Document(page_content='Morbidity and Mortality Weekly Report 8 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionReferences\\n1. CDC. CO VID-19. Risk for COVID-19 infection, hospitalization, and \\ndeath by race/ethnicity. Atlanta, GA: US Department of Health and \\nHuman Services, CDC; 2022. Accessed October 20, 2022. https://www.\\ncdc.gov/coronavirus/2019-ncov/covid-data/investigations-discovery/hospitalization-death-by-race-ethnicity.html\\n2. K riss JL, Hung M-C, Srivastav A, et al. COVID-19 vaccination coverage, \\nby race and ethnicity—National Immunization Survey Adult COVID Module, United States, December 2020–November 2021. MMWR Morb Mortal Wkly Rep 2022;71:757–63.  PMID:35679179  https://doi.\\norg/10.15585/mmwr.mm7123a2\\n3. Ndugga N, H ill L, Artiga S, Haldar S. Latest data on COVID-19 \\nvaccinations by race/ethnicity. Oakland, CA: Kaiser Family Foundation; 2021. https://www.kff.org/coronavirus-covid-19/issue-brief/\\nlatest-data-on-covid-19-vaccinations-by-race-ethnicity/\\n4. S antibanez TA, Lendon JP , Singleton JA, et al. Factors associated with \\nreceipt and parental intent for COVID-19 vaccination of children ages 5–11 years. medRxiv [Preprint posted online June 27, 2022]. https://doi.\\norg/10.1101/2022.06.24.22276865\\n5. M urthy BP , Zell E, Saelee R, et al. COVID-19 vaccination coverage among \\nadolescents aged 12–17 years—United States, December 14, 2020–July 31, 2021. MMWR Morb Mortal Wkly Rep 2021;70:1206–13.  \\nPMID:34473680 https://doi.org/10.15585/mmwr.mm7035e16. P enman-Aguilar A, Talih M, Huang D, Moonesinghe R, Bouye K, \\nBeckles G. Measurement of health disparities, health inequities, and social determinants of health to support the advancement of health equity. J Public Health Manag Pract 2016;22(Suppl 1):S33–42.  PMID:26599027  \\nhttps://doi.org/10.1097/PHH.0000000000000373\\n7. Andridge RR, Little RJ. A r eview of hot deck imputation for survey non-\\nresponse. Int Stat Rev 2010;78:40–64.  PMID:21743766  https://doi.\\norg/10.1111/j.1751-5823.2010.00103.x\\n8. B rewer NT. What works to increase vaccination uptake. Acad Pediatr \\n2021;21(4S):S9–16.  PMID:33958099  https://doi.org/10.1016/j.\\nacap.2021.01.017\\n9. Q uint JJ, Van Dyke ME, Maeda H, et al. Disaggregating data to measure \\nracial disparities in COVID-19 outcomes and guide community response—Hawaii, March 1, 2020–February 28, 2021. MMWR Morb Mortal Wkly Rep 2021;70:1267–73.  PMID:34529634  https://doi.\\norg/10.15585/mmwr.mm7037a1', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 7}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  9\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionMpox Cases Among Cisgender Women and Pregnant Persons —  \\nUnited States, May 11–November 7, 2022\\nLisa P . Oakley, PhD1,*; Kaitlin Hufstetler, MD1,2,*; Jesse O’Shea, MD1; J. Danielle Sharpe, PhD1,3; Cristin McArdle, PhD1,3; Varsha Neelam, MPH1; \\nNicole M. Roth, MPH1; Emily O. Olsen, PhD1; Maren Wolf, MPH1,3; Leah Zilversmit Pao, PhD1; Jeremy A. W. Gold, MD1; K. Meryl Davis, MD1,2; \\nDana Perella, MPH4; Shara Epstein, MD4; Maura K. Lash, MPH5; Olivia Samson, MPH5; Jessica Pavlick, DrPH6; Amanda Feldpausch, DVM6; \\nJennifer Wallace, MD7; Atmaram Nambiar, MD7; Van Ngo, MPH8; Umme-Aiman Halai, MD8; Claudia W. Richardson, MD9; T raci Fowler, DNP10; \\nBurnestine P . Taylor, MD11; Joyce Chou, MSPH12; Lindsey Brandon, MSN13; Rose Devasia, MD14; Erin K. Ricketts, MD3,15; Catherine Stockdale16; \\nMellisa Roskosky, PhD3,16; Rachel Ostadkar17; Yeng Vang17; Romeo R. Galang, MD1; Kiran Perkins, MD1; Melanie Taylor, MD1;  \\nMary Joung Choi, MD1; Paul J. Weidle, PharmD1; Patrick Dawson, PhD1; Sascha Ellington, PhD1; CDC Mpox Analytics Team\\nMonkeypox (mpox) cases in the 2022 outbreak have pri -\\nmarily occurred among adult gay, bisexual, and other men \\nwho have sex with men (MSM); however, other popula -\\ntions have also been affected ( 1). To date, data on mpox in \\ncisgender women and pregnant persons have been limited. Understanding transmission in these populations is critical for mpox prevention. In addition, among pregnant persons, Monkeypox virus can be transmitted to the fetus during preg-nancy or to the neonate through close contact during or after \\nbirth (2–5). Adverse pregnancy outcomes, including sponta-\\nneous abortion and stillbirth, have been reported in previous mpox outbreaks ( 3). During May 11–November 7, 2022, \\nCDC and U.S. jurisdictional health departments identified mpox in 769 cisgender women aged ≥15 years, representing \\n2.7% of all reported mpox cases.\\n† Among cases with available \\ndata, 44% occurred in cisgender women who were non-\\nHispanic Black or African American (Black), 25% who were \\nnon-Hispanic White (White), and 23% who were Hispanic \\nor Latino (Hispanic). Among cisgender women with available data, 73% reported sexual activity or close intimate contact as the likely route of exposure, with mpox lesions most frequently reported on the legs, arms, and genitals. T wenty-three mpox cases were reported in persons who were pregnant or recently \\npregnant\\n§; all identified as cisgender women based on the mpox \\ncase report form.¶ Four pregnant persons required hospitaliza -\\ntion for mpox. Eleven pregnant persons received tecovirimat, \\nand no adverse reactions were reported. Continued studies on \\nmpox transmission risks in populations less commonly affected \\nduring the outbreak, including cisgender women and pregnant persons, are important to assess and understand the impact of mpox on sexual, reproductive, and overall health.\\n* These authors contributed equally to this r eport.\\n† https://www.cdc.gov/poxvirus/monkeypox/response/2022/demographics.html  \\n(Accessed November 7, 2022).\\n§ R ecently pregnant persons had confirmed or probable Monkeypox virus  infection \\nwithin 21 days of delivery.\\n¶ https://www.cdc.gov/poxvirus/monkeypox/health-departments/case-reporting.htmlData on confirmed and probable cases of mpox are electroni-\\ncally reported as part of national case surveillance through a standardized case report form or the National Notifiable \\nDiseases Surveillance System.** Data are collected by health \\ndepartments and include demographic characteristics, possible exposure routes, and signs and symptoms. CDC analyzed case report data for probable or confirmed\\n†† cases among \\ncisgender women aged ≥15 years and pregnant persons during May 11–November 7, 2022. In addition, CDC identified all \\npersons with mpox reported to CDC through national case', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 8}), Document(page_content='†† cases among \\ncisgender women aged ≥15 years and pregnant persons during May 11–November 7, 2022. In addition, CDC identified all \\npersons with mpox reported to CDC through national case \\nsurveillance and clinical consultations who were pregnant or recently pregnant regardless of gender identity. Detailed data regarding maternal and neonatal outcomes were obtained through enhanced pregnancy surveillance.\\n§§ Statistical analyses \\nwere conducted using SAS statistical software (version 9.4; SAS Institute) and restricted to cases with available data. This \\nactivity was reviewed by CDC and was conducted consistent \\nwith applicable federal law and CDC policy.\\n¶¶\\nCases Among Cisgender Women\\nDuring May 11–November 7, 2022, a total of 769 cases \\nof mpox among cisgender women, including 23 (3%) who were pregnant, were reported by 42 public health jurisdictions \\n(Table 1). The median age was 32 years (IQR  = 25–40 years). \\nAmong the 717 (93%) cisgender women with information on race and ethnicity, 313 (44%) were Black, 182 (25%) were White, and 167 (23%) were Hispanic. Among 463 \\n(60%) cisgender women with information on recent sexual \\nbehaviors, 329 (71%) reported recent sexual activity or close intimate contact,*** including 296 (90%) who had recent \\n ** https://www.cdc.gov/nndss/index.html\\n †† https://www.cdc.gov/poxvirus/monkeypox/clinicians/case-definition.html\\n §§ E nhanced pregnancy surveillance data were collected through direct \\ncommunication with jurisdictions, under an Assurance of Confidentiality, \\nleveraging existing mother-baby linked surveillance. https://www.cdc.gov/\\nncbddd/set-net/index.html\\n ¶¶ 45 C.F .R. part 46.102(l)(2), 21 C.F .R. part 56; 42 U.S.C. Sect. 241(d); \\n5 U.S.C. Sect. 552a; 44 U.S.C. Sect. 3501 et seq.\\n * ** D efined as any sex or close intimate contact during the 3 weeks before \\nsymptom onset.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 8}), Document(page_content='Morbidity and Mortality Weekly Report 10 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionTABLE 1. Characteristics of cisgender women with mpox, by current or recent* pregnancy status — United States, May 11–November 7, 2022†\\nCharacteristic (no. with available information)No. (%)§ of cisgender women with mpox\\nAll Not currently or \\nrecently pregnantCurrently or  \\nrecently pregnant\\nTotal (769)¶ 769 (100.0) 746 (97.0) 23 (3.0)\\nGender identity (769)\\nCisgender woman 769 (100.0) 746 (100.0) 23 (100.0)\\nAge (765)Median, yrs (IQR) (range) 32 (25–40) (15–89) 32 (25–40) (15–89) 28.5 (23–32) (20–35)\\nMissing 4 4 0\\nRace and ethnicity (717) 717 (100.0) 696 (93.3) 21 (91.3)\\nAmerican Indian or Alaska Native, non-Hispanic 4 (0.6) 4 (0.6) 0 (—)\\nAsian, non-Hispanic 18 (2.5) 18 (2.6) 0 (—)\\nBlack or African American, non-Hispanic 313 (43.7) 298 (42.8) 15 (71.4)\\nHispanic or Latino 167 (23.3) 165 (23.7) 2 (9.5)\\nNative Hawaiian or other Pacific Islander, non-Hispanic 1 (0.1) 1 (0.1) 0 (—)\\nWhite, non-Hispanic 182 (25.4) 179 (25.7) 3 (14.3)\\nMultiple races, non-Hispanic 10 (1.4) 10 (1.4) 0 (—)\\nOther race, non-Hispanic 22 (3.1) 21 (3.0) 1 (4.8)\\nMissing 52 50 2\\nRecent sexual partners (463)\\n**463 (100.0) 446 (60.0) 17 (73.9)\\nHad a recent sexual partner 329 (71.1) 317 (71.1) 12 (70.6)\\nGender of recent sexual partners††\\nCisgender man 296 (90.0) 284 (89.6) 12 (100.0)\\nCisgender woman 18 (5.5) 18 (5.7) 0 (—)\\nTransgender man 2 (0.6) 2 (0.6) 0 (—)\\nTransgender woman 0 (—) 0 (—) 0 (—)\\nOther gender identity 2 (0.6) 2 (0.6) 0 (—)\\nExposure (73)§§ 73 (100.0) 61 (8.2) 12 (52.2)\\nSexual or intimate 53 (72.6) 44 (72.1) 9 (75.0)\\nHousehold or caregiving 16 (21.9) 13 (21.3) 3 (25.0)\\nShared food, utensils, or dishes 12 (18.2) 12 (19.7) 0 (—)\\nShared towels or bedding 16 (24.2) 16 (26.2) 0 (—)\\nShared transportation 10 (15.2) 10 (16.4) 0 (—)\\nFace-to-face 14 (21.2) 14 (23.0) 0 (—)\\nShared bathrooms 15 (22.7) 15 (24.6) 0 (—)\\nOther 16 (24.2) 16 (26.2) 0 (—)\\nHealth conditionsImmunocompromised (excluding HIV) (378)\\n¶¶35 (9.3) 34 (9.3)*** 1 (7.1)†††\\nHIV infection (173) 13 (7.5) 13 (8.1)§§§ 0 (—)¶¶¶\\nAbbreviation: mpox  = monkeypox .\\n * R ecently pregnant persons had confirmed or probable mpox infection within 21 days of delivery.\\n † Data as of November 9, 2022.\\n § Percentages calculated using nonmissing data.\\n ¶ Information on pregnant and recently pregnant persons was gathered by the national surveillance form, clinical consultation, and enhanced pregnancy surveillance.\\n ** S exual partner during the 3 weeks before symptom onset.\\n †† Percentage of those who had a sexual partner during the 3 weeks before symptom onset.\\n §§ Exposur es are not mutually exclusive.\\n ¶¶ I mmunocompromising conditions include diseases (e.g., diabetes, lupus, organ transplants, stem cell transplants, and cancer) or certain medicines (e.g., \\nchemotherapy, biologic therapies, and steroids).\\n *** P ercentage among the 364 cisgender women who are not currently or recently pregnant with data available on any known immunocompromising conditions.\\n ††† P ercentage among the 14 pregnant or recently pregnant persons with data available on any known immunocompromising conditions.\\n §§§ P ercentage among the 161 cisgender women who are not currently or recently pregnant with data available on HIV status.\\n ¶¶¶ P ercentage among the 12 pregnant or recently pregnant persons with data available on HIV status.\\nsexual contact with a cisgender man and 18 (6%) who had \\nrecent sexual contact with a cisgender woman. Among the 18 patients who had recent sexual contact with a woman, 12 \\nalso had a recent male sex partner. Of the 73 cisgender women', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 9}), Document(page_content='recent sexual contact with a cisgender woman. Among the 18 patients who had recent sexual contact with a woman, 12 \\nalso had a recent male sex partner. Of the 73 cisgender women \\nwho had complete exposure data, 53 (73%) reported recent sexual or intimate contact as the likely route of exposure. Among the 16 who reported household contact or caregiving as the likely route of exposure, five reported recent sexual or intimate contact. Among the 378 cisgender women with available data on immunocompromising conditions, 35 (9%) \\nreported any known immunocompromising condition other \\nthan HIV infection. Information on HIV status was available for 173 cisgender women, 13 (8%) of whom had HIV infec-tion; no cisgender women with HIV infection were pregnant.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 9}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  11\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionAmong all cisgender women with mpox and available data, \\nthe most frequently reported signs and symptoms were rash \\n(93%), headache (54%), pruritis (57%), malaise (54%), fever \\n(49%), and chills (49%) (Table 2). Among 376 (49%) cisgen -\\nder women with data on rash location, rash was most frequently \\nreported on the legs (48%), arms (47%), genitals (36%), and trunk (33%); 50 (16%) reported rash in one region, 63 (20%) in two regions, 57 (18%) in three regions, and 140 (45%) in four or more regions. Rash location was similar when com-\\nparing cisgender women who reported recent sexual exposure \\nwith those who did not.\\nCases in Currently and Recently Pregnant Persons\\nDuring May 11–November 7, 2022, 23 cases of mpox were \\nreported during pregnancy (21) or within 3 weeks of pregnancy (two); all pregnant and recently pregnant persons with mpox \\nidentified as cisgender women on the mpox case report form\\n††† \\n(Table 1). Among 12 currently or recently pregnant persons \\nwith available exposure data, nine reported sexual contact and three reported household contact. Among 10 cases in \\npregnant persons with information on trimester of infection, three occurred during the first, four during the second, and three during the third trimester (Table 3). Rash was present in all persons. Genital lesions were reported by four currently or recently pregnant persons; none reported genital lesions near \\nthe time of delivery.\\nEleven (48%) pregnant persons received tecovirimat \\n(administered during all trimesters of pregnancy); no \\nmedication-related adverse events were reported. Four preg-nant persons were hospitalized related to symptoms from \\nMonkeypox virus  infection (pain control and treatment of \\nsuperimposed cellulitis) and remained pregnant at discharge. \\nNo pregnant person required intensive care, intubation, or unplanned delivery. None of the pregnant persons received vaccinia immune globulin intravenous (VIGIV) for treatment.  \\nOf the 21 persons who received an mpox diagnosis during \\npregnancy, three have reported outcomes, including two full-\\nterm deliveries without complications (including no transmis -\\nsion to the infant) and one spontaneous abortion at 11 weeks’ gestation. T wo pregnant persons experienced mpox symptoms within 3 days after delivery; their newborns developed lesions \\nwithin 1 week of their symptom onset. Both newborns received \\noral tecovirimat within 48 hours of developing lesions and were treated for 10–14 days; one received VIGIV. Both newborns responded to treatment, appeared to be in good health, and were discharged home.\\n ††† CDC r ecognizes that not all pregnant persons are cisgender women. However, \\nin the study, all cases of mpox in pregnant persons, recently pregnant persons, \\nand breastfeeding persons occurred in persons who identified as cisgender \\nwomen based on the mpox case report form.One recently pregnant person who was breastfeeding devel -\\noped lesions 4 days postpartum, including under the breast; this \\nperson’s newborn developed symptoms with lesions on the face \\nand chest 6 days later. T wo other cisgender women who were \\nnot pregnant or recently pregnant were breastfeeding at the time of mpox diagnosis. One woman’s infant was exposed to a symptomatic household contact; she experienced symptoms 2 weeks after the infant’s diagnosis. The second woman received an mpox diagnosis following an occupational exposure; breast \\nmilk samples from this person were tested and were negative for \\nMonkeypox virus  DNA by polymerase chain reaction testing.\\n§§§\\nDiscussion\\nMonkeypox virus  infections in cisgender women during \\nMay 11–November 7 constituted <3% of total U.S. cases. Consistent with disparities observed overall during the ongo -', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 10}), Document(page_content='§§§\\nDiscussion\\nMonkeypox virus  infections in cisgender women during \\nMay 11–November 7 constituted <3% of total U.S. cases. Consistent with disparities observed overall during the ongo -\\ning mpox epidemic, the proportion of Black and Hispanic women with mpox was higher than the proportion of Black and Hispanic women in the U.S. population ( 6). This finding \\nis similar to disparities among mpox cases in the United States overall and underscores the continued need for public health efforts to provide education on prevention of mpox and ensure \\nequitable access to mpox vaccination, testing, and treatment.\\nSex or close intimate contact within 3 weeks of symptom \\nonset was reported by nearly three quarters of cisgender women \\nwith mpox, and genital lesions were frequently reported, sug-gesting sexual exposure as a likely primary route of transmis-\\nsion. Obstetrician-gynecologists and other providers should \\nconsider mpox when examining new genital, oral, or breast lesions. Patient education regarding risks for transmission of Monkeypox virus  and other sexually transmitted infections \\nshould be provided.\\nGenital lesions in pregnant persons pose a risk for Monkeypox \\nvirus transmission to the fetus during vaginal delivery.\\n¶¶¶ A thor-\\nough skin and mucosal (e.g., anal, vaginal, and oral) examination for mpox lesions should be performed in persons with possible \\nmpox near the time of delivery to identify lesions of which they \\nmight be unaware. When mpox lesions, including genital lesions, are present, shared decision-making should be considered when discussing route of delivery. Because there might be an increased risk for severe disease in newborns, breastfeeding should be temporarily delayed until criteria for discontinuing isolation \\nhave been met (lesions have resolved, the scabs have fallen off, \\nand a fresh layer of intact skin has formed).****\\n \\n §§§ This br eastfeeding mother was a health care worker who cared for a \\nsymptomatic patient. She later developed atypical features of mpox.\\n ¶¶¶ https://www.cdc.gov/poxvirus/monkeypox/about/science-behind-\\ntransmission.html\\n **** https://www.cdc.gov/poxvirus/monkeypox/clinicians/pregnancy.html#contact-breastfeeding', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 10}), Document(page_content='Morbidity and Mortality Weekly Report 12 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionTABLE 2. Signs and symptoms and rash sites among all cisgender women with mpox (N = 769) — United States, May 11–November 7, 2022*\\nCharacteristicPresence or absence of signs or symptoms, no. (%)†\\nNo. missing \\n(% of total sample) Present Absent Unknown\\nSign or symptom\\nRash 376 (92.6) 17 (4.2) 13 (3.2) 363 (47.2)\\nHeadache 182 (54.3) 122 (36.4) 31 (9.3) 434 (56.4)\\nMalaise 176 (53.5) 115 (35.0) 38 (11.6) 440 (57.2)\\nFever 165 (48.5) 139 (40.9) 36 (10.6) 429 (55.8)\\nChills 162 (49.2) 135 (41.0) 32 (9.7) 440 (57.2)\\nPruritis 164 (56.8) 91 (31.5) 34 (11.8) 480 (62.4)\\nMyalgia 142 (45.1) 142 (45.1) 31 (9.8) 454 (59.0)\\nEnlarged lymph nodes 137 (41.8) 153 (46.7) 38 (11.6) 441 (57.3)\\nVomiting or nausea 63 (24.3) 161 (62.2) 35 (13.5) 510 (66.3)\\nAbdominal pain 57 (19.2) 198 (66.7) 42 (14.1) 472 (61.4)\\nRectal pain 39 (12.8) 229 (74.8) 38 (12.4) 463 (60.2)\\nTenesmus 22 (8.5) 199 (76.8) 38 (14.7) 510 (66.3)\\nConjunctivitis 14 (5.7) 199 (80.2) 35 (14.1) 521 (67.8)\\nPus or blood in stools 12 (4.6) 210 (80.5) 39 (14.9) 508 (66.1)\\nRectal bleeding 11 (3.7) 246 (82.8) 40 (13.5) 472 (61.4)\\nProctitis 8 (3.3) 185 (76.5) 49 (20.3) 527 (68.5)\\nRash site§\\nLegs 182 (48.4) NA NA NA\\nArms 178 (47.3)\\nTrunk 125 (33.2)\\nGenitals 137 (36.4)\\nFace 116 (30.9)\\nPalms 81 (21.5)\\nHead 79 (21.0)\\nHand 73 (19.4)\\nNeck 54 (14.4)\\nMouth 57 (15.2)\\nPerianal 53 (14.1)\\nSoles 44 (11.7)\\nOther 100 (26.6)\\nAbbreviation: NA = not applicable.\\n* Da ta as of November 9, 2022.\\n† P ercentages calculated using nonmissing data.\\n§ P ercentages among the 376 cisgender women who reported experiencing rash.\\nClinicians caring for cisgender women and pregnant per -\\nsons should become familiar with clinical considerations for \\nthe prevention, diagnosis, and treatment of mpox†††† and \\nshould provide pre- and postexposure prophylaxis if indicated. Vaccination with JYNNEOS should be provided to eligible \\npersons, including those who are pregnant or breastfeeding, \\nand providers should discuss vaccination risks and benefits.\\n§§§§\\nThe findings in this report are subject to at least three limita -\\ntions. First, data for some variables such as exposure risk and HIV status were frequently missing (≤92%). Thus, these data \\nmight not represent the characteristics of the overall sample. \\nSecond, the small sample size of currently and recently preg -\\nnant persons with mpox might limit the generalizability of outcomes. Finally, additional time is needed for pregnancy completion to describe outcomes among all cases of mpox during pregnancy.\\n ††††  https://www.cdc.gov/poxvirus/monkeypox/clinicians/pregnancy.html\\n §§§§  https://www.cdc.gov/poxvirus/monkeypox/interim-considerations/jynneos-\\nvaccine.htmlCases of mpox have occurred primarily among adult gay, \\nbisexual, and other MSM during the current outbreak; how -\\never, any person, including cisgender women, can also acquire \\ninfection. Public health efforts should include more emphasis \\non cisgender women who might be at increased risk for expo -\\nsure. In addition, although most reported cases of mpox in pregnant persons have been managed in the outpatient setting, some persons might require hospitalization, and there is a risk for perinatal transmission. To mitigate this risk, pregnant, \\nrecently pregnant, and breastfeeding persons should be offered \\nprophylaxis or treatment if indicated. Continued collection of information is critical to evaluating the risk for transmission, informing infection prevention and control, and assessing the impact of mpox on the sexual, reproductive, and overall health \\nof cisgender women. In addition, collection of longitudinal \\ndata among pregnant persons and their infants is critical to understanding the effects of mpox on maternal and neonatal outcomes. CDC, in collaboration with health departments,', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 11}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  13\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionTABLE 3. Characteristics of currently and recently pregnant persons* \\nwith mpox (N = 23) — United States, May 11–November 7, 2022\\nCharacteristic No. (%)†\\nCurrently pregnant 21 (91.3)\\nRecently pregnant 2 (8.7)\\nPregnancy trimester when Monkeypox virus infection occurred (10)\\nFirst 3 (30.0)\\nSecond 4 (40.0)\\nThird 3 (30.0)\\nMissing 11\\nSign or symptom§\\nFever 6 (26.1)\\nRash 23 (100.0)\\nGenital or breast lesions 4 (17.4)\\nMyalgia 2 (8.7)\\nPruritis 6 (26.1)\\nLymphadenopathy 3 (13.0)\\nDisease severity\\nHospitalized\\nYes 4 (17.4)\\nNo 19 (82.6)\\nAdmitted to ICU 0 (—)\\nMpox-directed therapy¶\\nTecovirimat (oral or IV) 11 (47.8)\\nVIGIV 0 (—)\\nPostexposure prophylaxisReceived JYNNEOS 0 (—)\\nAbbreviations:\\n ICU  =  in tensive care unit; IV = intravenous; mpox = monkeypox; \\nVIGIV= vaccinia immune globulin intravenous.\\n* R ecently pregnant persons had confirmed or probable Monkeypox virus  \\ninfection within 21 days of delivery.\\n† P ercentages calculated among nonmissing values.\\n§ Sig ns and symptoms are not mutually exclusive.\\n¶ T wo women who received tecovirimat also received other treatments (e.g., \\nacyclovir or antibiotics).\\nwill continue to follow cases in pregnant and recently pregnant \\npersons and provide updates as data become available.\\nAcknowledgments\\nMpox response teams from state and local health departments; \\nhospital and clinical providers involved in CDC clinical consultations; \\nSuzanne Newton, Ruth Stefanos, CDC; Thandiwe Bobb, Georgia Department of Public Health; Kay Hooshmand, Chase Israel, Claire Park, Jasmine Sharma, Los Angeles County Department of Public Health; mpox case investigation and response staff members at Acute Communicable Disease Control Program and Community Field Services Division, Los Angeles County Department of Public Health; Marcie Babcock, Victor Cruz, Minnesota Department of Health; Jennifer MacFarquhar, CDC Career Epidemiology Field Officer, North Carolina Department of Health and Human Services; Karen Alroy, Ellen Lee, New York City Department of Health and Mental Hygiene; Lisa McHugh, W. Gina Pang, Nottasorn Plipate, Kumar Nalluswami, Arlene Seid, Pennsylvania Department of Summary\\nWhat is already known about this topic?\\nData from the ongoing monkeypox (mpox) outbreak on cases in \\ncisgender women and in pregnancy are limited.\\nWhat is added by this report?\\nAmong 769 mpox cases reported among U.S. cisgender women, \\nBlack or African American and Hispanic or Latino women were disproportionately affected. Most cisgender women reported \\nrecent sexual activity with men. Twenty-three cases among \\npregnant or recently pregnant persons were reported and all recovered. Four pregnant persons were hospitalized for mpox, and tecovirimat was tolerated with no adverse reactions.\\nWhat are the implications for public health practice?\\nContinued monitoring of mpox risk in cisgender women and \\nduring pregnancy is critical to assessing the impacts of mpox on sexual, reproductive, and overall health and to better under -\\nstand perinatal outcomes.\\nHealth; Lenore Asbel, Aasta Mehta, Ayomide Sokale, Philadelphia \\nDepartment of Public Health; Division of Disease Control Response Team, Philadelphia Department of Public Health; Hospital Obstetrics/Gynecology and Infectious Disease Partners, Philadelphia, Pennsylvania; Public Health - Seattle & King County Communicable Disease Investigations Team; Liz Harris, Robertson Nash, Pamela Talley, Tennessee Department of Health; Nicholas Hysmith, LeBonheur Children’s Hospital; Sandra Castejon-Ramirez, St. Jude Children’s Research Hospital, LeBonheur Children’s Hospital.\\nCDC Mpox Analytics Team\\nCori Dennison , CDC; Ian Hennessee , CDC; Aspen  Riser, CDC; \\nLaT weika  Salmon-T rejo , CDC; Gail Scogin , CDC; Emily  Sims, CDC; \\nPenelope  Strid, CDC; Raquel  Velazquez-Kronen , CDC; Claire  Xu, CDC; \\nCarla Zelaya , CDC.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 12}), Document(page_content='LaT weika  Salmon-T rejo , CDC; Gail Scogin , CDC; Emily  Sims, CDC; \\nPenelope  Strid, CDC; Raquel  Velazquez-Kronen , CDC; Claire  Xu, CDC; \\nCarla Zelaya , CDC.\\nCorresponding author: Sascha Ellington, sellington@cdc.gov .\\n 1CDC Mpox Emergency Response Team; 2CDC Foundation, Atlanta, Georgia; \\n3Epidemic Intelligence Service, CDC; 4Philadelphia Department of Public \\nHealth, Philadelphia, Pennsylvania; 5New York City Department of Health \\nand Mental Hygiene, New York, New York; 6Georgia Department of Public \\nHealth; 7Pennsylvania Department of Health; 8Los Angeles County Department \\nof Public Health, Los Angeles, California; 9Detroit Health Department, Detroit, \\nMichigan; 10Michigan Department of Health & Human Services; 11Alabama \\nDepartment of Public Health; 12Missouri Department of Health and Senior \\nServices; 13Shelby County Health Department, Memphis, Tennessee; \\n14Tennessee Department of Health; 15North Carolina Department of Health \\nand Human Services; 16Communicable Disease, Epidemiology and \\nImmunizations, Public Health – Seattle & King County, Seattle, Washington; \\n17Minnesota Department of Health.\\nAll authors have completed and submitted the International \\nCommittee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 12}), Document(page_content='Morbidity and Mortality Weekly Report 14 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionReferences\\n1. B lackburn D, Roth NM, Gold JA, et al. Epidemiologic and clinical \\nfeatures of mpox in transgender and gender-diverse adults—United States, \\nMay–November 2022. MMWR Morb Mortal Wkly Rep 2022;71:1605–9. http://dx.doi.org/10.15585/mmwr.mm715152a1 \\n2. M eaney-Delman DM, Galang RR, Petersen BW, Jamieson DJ. A primer \\non Monkeypox virus for obstetrician-gynecologists: diagnosis, prevention, \\nand treatment. Obstet Gynecol 2022;140:391–7.  PMID:36356237  \\nhttps://doi.org/10.1097/AOG.0000000000004909\\n3. D’Antonio F , Pagani G, Buca D, Khalil A. Monkeypox infection in \\npregnancy: a systematic review and metaanalysis. Am J Obstet Gynecol MFM 2023;5:100747.  PMID:36096413  https://doi.org/10.1016/j.\\najogmf.2022.1007474. Thornhill JP , Palich R, Ghosn J, et al.; Share-Net writing group. Human \\nMonkeypox virus infection in women and non-binary individuals during the 2022 outbreaks: a global case series. Lancet 2022;400:1953–65.  \\nPMID:36403584 https://doi.org/10.1016/S0140-6736(22)02187-0\\n5. Ramnarayan P , Mitting R, Whittaker E, et al.; National Health Service \\nEngland High Consequence Infectious Diseases (Airborne) Network. Neonatal monkeypox virus infection. N Engl J Med 2022;387:1618–20.  \\nPMID:36223535 https://doi.org/10.1056/NEJMc2210828\\n6. P hilpott D, Hughes CM, Alroy KA, et al.; CDC Multinational \\nMonkeypox Response Team. Epidemiologic and clinical characteristics of monkeypox cases—United States, May 17–July 22, 2022. MMWR Morb Mortal Wkly Rep 2022;71:1018–22.  PMID:35951487 https://\\ndoi.org/10.15585/mmwr.mm7132e3', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 13}), Document(page_content='Morbidity and Mortality Weekly ReportMMWR  / January 6, 2023  / V ol. 72  /  No. 1  15\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionErratum\\nVol. 71, No. 46\\nIn the report “Measles, Mumps, Rubella Vaccine \\n(PRIORIX): Recommendations of the Advisory Committee \\non Immunization Practices — United States, 2022,” on page \\n1465, the second sentence of the first footnote should have \\nread, “In addition, measles postexposure prophylaxis is an \\noff-label indicated use for PRIORIX; measles postexposure prophylaxis is an on-label indicated use for M-M-R II.”', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 14}), Document(page_content='Morbidity and Mortality Weekly Report 16 MMWR  /  January 6, 2023  /  V ol. 72  /  No. 1\\nUS Department of Health and Human Services/Centers for Disease Control and PreventionQuickStats\\nFROM THE NATIONAL CENTER FOR HEALTH STATISTICS\\nPercentage of Mothers with Gestational Diabetes,* by Maternal Age — \\nNational Vital Statistics System, United States, 2016 and 2021\\n02468101214161820100\\nAll mothers <20 20–24 25–29 30–34 35–39 ≥40Age group of  mother, yrsPercentage2016 2021\\n* Diabet es diagnosed during the pregnancy as reported on the birth certificate. National information on \\ngestational diabetes became available for the first time in 2016 and might be underreported.\\nThe percentage of mothers giving birth who received a diagnosis of diabetes during pregnancy (gestational diabetes) increased \\nfrom 6.0% in 2016 to 8.3% in 2021. Increases in gestational diabetes were seen in each maternal age group, and rates rose steadily with maternal age; in 2021, the rate for mothers aged ≥40 years (15.6%) was nearly six times as high as the rate for \\nmothers aged <20 years (2.7%). \\nSource:  National Center for Health Statistics, National Vital Statistics System, Natality Data.  https://www.cdc.gov/nchs/nvss/births.htm\\nReported by: Joyce A. Martin, jcm9@cdc.gov , 301-458-4362; Elizabeth C. W. Gregory.\\nFor more information on this topic, CDC recommends the following link: https://www.cdc.gov/pregnancy/diabetes.html', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 15}), Document(page_content='Morbidity and Mortality Weekly Report \\nISSN: 0149-2195 (Print)The Morbidity and Mortality Weekly Report (MMWR) Series is prepared by the Centers for Disease Control and Prevention (CDC) and is available free \\nof charge in electronic format. To receive an electronic copy each week, visit MMWR at https://www.cdc.gov/mmwr/index.html. \\nReaders who have difficulty accessing this PDF file may access the HTML file at https://www.cdc.gov/mmwr/index2023.html . Address all inquiries about \\nthe MMWR Series to Editor-in-Chief, MMWR Series, Mailstop V25-5, CDC, 1600 Clifton Rd., N.E., Atlanta, GA 30329-4027 or to mmwrq@cdc.gov.\\nAll material in the MMWR Series is in the public domain and may be used and reprinted without permission; citation as to source, however, is appreciated.MMWR and Morbidity and Mortality Weekly Report are service marks of the U.S. Department of Health and Human Services.Use of trade names and commercial sources is for identification only and does not imply endorsement by the U.S. Department of Health and Human Services.References to non-CDC sites on the Internet are provided as a service to MMWR readers and do not constitute or imply endorsement of these organizations \\nor their programs by CDC or the U.S. Department of Health and Human Services. CDC is not responsible for the content of these sites. URL addresses \\nlisted in MMWR were current as of the date of publication.', metadata={'source': 'pdfs/mm7201-H.pdf', 'page': 19})]\n"
     ]
    }
   ],
   "source": [
    "print(f'pages: {len(pages)}')\n",
    "print(pages)\n",
    "# Need to get the falcon embeddings and embed these new pages\n",
    "# from transformers import AutoTokenizer, AutoModelForCausalLM\n",
    "# model_id = \"tiiuae/falcon-180B\"\n",
    "# tokenizer = AutoTokenizer.from_pretrained(model_id)\n",
    "\n",
    "# Then should investigate the best way to embed. How big of chunks.\n",
    "# Then need to load into a vector store"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "669e7b73",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2023-12-11 21:44:25.038267\t317.14482069015503\tCreating FAISS index\n"
     ]
    },
    {
     "ename": "ValidationError",
     "evalue": "1 validation error for OpenAIEmbeddings\n__root__\n  Did not find openai_api_key, please add an environment variable `OPENAI_API_KEY` which contains it, or pass  `openai_api_key` as a named parameter. (type=value_error)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValidationError\u001b[0m                           Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[8], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m _print(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCreating FAISS index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 2\u001b[0m faiss_index \u001b[38;5;241m=\u001b[39m FAISS\u001b[38;5;241m.\u001b[39mfrom_documents(pages, \u001b[43mOpenAIEmbeddings\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m)\n\u001b[1;32m      3\u001b[0m _print(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mDone creating FAISS index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      5\u001b[0m \u001b[38;5;66;03m# docs = faiss_index.similarity_search(\"How will the community be engaged?\", k=2)\u001b[39;00m\n\u001b[1;32m      6\u001b[0m \u001b[38;5;66;03m# for doc in docs:\u001b[39;00m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;66;03m#     print(str(doc.metadata[\"page\"]) + \":\", doc.page_content[:300])\u001b[39;00m\n",
      "File \u001b[0;32m/rbscratch/brettin/conda_envs/openai-rag-arxiv/lib/python3.11/site-packages/pydantic/v1/main.py:341\u001b[0m, in \u001b[0;36mBaseModel.__init__\u001b[0;34m(__pydantic_self__, **data)\u001b[0m\n\u001b[1;32m    339\u001b[0m values, fields_set, validation_error \u001b[38;5;241m=\u001b[39m validate_model(__pydantic_self__\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__class__\u001b[39m, data)\n\u001b[1;32m    340\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m validation_error:\n\u001b[0;32m--> 341\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m validation_error\n\u001b[1;32m    342\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m    343\u001b[0m     object_setattr(__pydantic_self__, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m__dict__\u001b[39m\u001b[38;5;124m'\u001b[39m, values)\n",
      "\u001b[0;31mValidationError\u001b[0m: 1 validation error for OpenAIEmbeddings\n__root__\n  Did not find openai_api_key, please add an environment variable `OPENAI_API_KEY` which contains it, or pass  `openai_api_key` as a named parameter. (type=value_error)"
     ]
    }
   ],
   "source": [
    "\n",
    "\n",
    "_print(\"Creating FAISS index\")\n",
    "faiss_index = FAISS.from_documents(pages, OpenAIEmbeddings())\n",
    "_print(\"Done creating FAISS index\")\n",
    "\n",
    "# docs = faiss_index.similarity_search(\"How will the community be engaged?\", k=2)\n",
    "# for doc in docs:\n",
    "#     print(str(doc.metadata[\"page\"]) + \":\", doc.page_content[:300])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bd4dc1ca",
   "metadata": {},
   "outputs": [],
   "source": [
    "_print(\"Creating Chroma vector store\")\n",
    "vectorstore = Chroma.from_documents(documents=splits, embedding=OpenAIEmbeddings())\n",
    "_print(\"Done creating vector store\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3ea57a7f",
   "metadata": {},
   "source": [
    "System: Add an optional system prompt here\n",
    "User: This is the user input\n",
    "Falcon: This is what the model generates\n",
    "User: This might be a second turn input\n",
    "Falcon: and so on"
   ]
  }
 ],
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