CORD-19_Custom_license_subset  

CORD-19:373474bd0d2c88363e7fad85fa0ca0863687a791 JSONTXT 11 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T1 0-21 Sentence denotes Author affi liations:
T2 22-70 Sentence denotes University of North Carolina Health Care Sys-tem
T3 72-80 Sentence denotes Abstract
T4 81-308 Sentence denotes Despite widespread use of communicable disease surveillance data to inform public health intervention and control measures, the reporting completeness of the notifiable disease surveillance system remains incompletely assessed.
T5 309-541 Sentence denotes Therefore, we conducted a comprehensive study of reporting completeness with an analysis of 53 diseases reported by 8 health care systems across North Carolina, USA, during 1995USA, during -1997USA, during and 2000USA, during -2006.
T6 542-762 Sentence denotes All patients who were assigned an International Classifi cation of Diseases, 9th Revision, Clinical Modifi cation, diagnosis code for a state-required reportable communicable disease were matched to surveillance records.
T7 763-878 Sentence denotes We used logistic regression techniques to estimate reporting completeness by disease, year, and health care system.
T8 879-984 Sentence denotes The completeness of reporting varied among the health care systems from 2% to 30% and improved over time.
T9 985-1172 Sentence denotes Disease-specifi c reporting completeness proportions ranged from 0% to 82%, but were generally low even for diseases with great public health importance and opportunity for interventions.
T10 1174-1371 Sentence denotes S urveillance has been the cornerstone of public health since the US Congress authorized the Public Health Service to collect morbidity data for cholera, smallpox, plague, and yellow fever in 1878.
T11 1372-1572 Sentence denotes Currently, all states conduct notifi able disease surveillance following guidelines from the Centers for Disease Control and Prevention (CDC) and the Council for State and Territorial Epidemiologists.
T12 1573-2081 Sentence denotes The current list of nationally notifi able communicable diseases has expanded to >60 diseases and includes vaccine-preventable diseases (e.g., pertussis, measles), emerging infectious diseases (e.g., severe acute respiratory syndrome, West Nile virus encephalitis), foodborne diseases (e.g., Shiga toxinproducing Escherichia coli and Salmonella spp. infections), sexually transmitted diseases (e.g., syphilis, HIV), and aerosol and droplet transmitted diseases (e.g., tuberculosis, meningococcal meningitis).
T13 2082-2268 Sentence denotes Active surveillance programs conducted by CDC in conjunction with certain states include Active Bacterial Core surveillance, FoodNet, and infl uenza-related hospitalization surveillance.
T14 2269-2648 Sentence denotes Surveillance of epidemiologically important diseases provides critical information to clinicians and public health offi cials for use in measuring disease incidence in communities, recognizing disease outbreaks, assessing prevention and control measure effectiveness, allocating public health resources, and further clarifying the epidemiology of new and emerging pathogens (1) .
T15 2649-2769 Sentence denotes Like all US states, North Carolina has state laws and regulations mandating communicable disease reporting (2) (3) (4) .
T16 2770-2949 Sentence denotes The state relies on physicians and laboratories to comply with the directive to report diseases and laboratory results indicative of diseases considered a threat to public health.
T17 2950-3105 Sentence denotes During the periods of this study (1995) (1996) (1997) (2000) (2001) (2002) (2003) (2004) (2005) (2006) , mandatory reporting was required for >60 diseases.
T18 3106-3270 Sentence denotes Conditions and disease reports consisted of paper communicable-disease report forms that contained demographic, clinical, and risk factor data for the case-patient.
T19 3271-3448 Sentence denotes These reports were required to be submitted to the health department within a specifi ed period (i.e., immediately, within 24 hours, or within 7 days), depending on the disease.
T20 3449-3815 Sentence denotes An important change to the communicable disease surveillance system of the North Carolina Department of Health and Human Services (NC DHHS) occurred when the state administrative code was amended in September 1998 to require that persons in charge of diagnostic laboratories report positive laboratory results for most diseases already reportable by physicians (2) .
T21 3816-3925 Sentence denotes This dual reporting mechanism was intended to improve completeness, timeliness, and accuracy of surveillance.
T22 3926-4098 Sentence denotes More recently, in 2002, surveillance efforts have also expanded with the introduction of 7 regional public health teams and 11 hospital-based public health epidemiologists.
T23 4099-4272 Sentence denotes Despite the widespread use of these surveillance data, systematic data collection based on mandatory physician and laboratory reporting has never been extensively evaluated.
T24 4273-4361 Sentence denotes To date, only 2 evaluations have examined reporting proportions for >5 diseases (5, 6) .
T25 4362-4923 Sentence denotes Previous studies examining the completeness of disease reporting have differed considerably in terms of the following factors: size of geographic region (e.g., from clinics at a single university to multiple states), range of study period (e.g., several months to several years), heterogeneity of reporting systems (e.g., health care provider-based passive reporting vs. health care provider-and laboratory-based passive reporting), and various patient ascertainment methods (e.g., laboratory records, billing records, active surveillance, death certifi cates).
T26 4924-4998 Sentence denotes This variability renders study results diffi cult to compare or aggregate.
T27 4999-5384 Sentence denotes Therefore, we undertook a comprehensive study of reporting completeness with an analysis of 53 reportable diseases and conditions in selected health care systems across North Carolina over a 10-year period to estimate disease-specifi c reporting proportions, describe changes to reporting over time, and examine the variability of reporting completeness between health care facilities.
T28 5385-5581 Sentence denotes A retrospective cohort study was conducted at 8 large nonfederal acute care health care systems that experience 32% of all inpatient visits and 23% of all outpatient visits in North Carolina (7) .
T29 5582-5868 Sentence denotes These health care systems ranged in size from 581 to 1,324 site-licensed beds, spanned the Eastern Coastal, Central Piedmont, and Western Mountain regions of the state, and were selected from a network of 11 health care systems staffed with hospital-based public health epidemiologists.
T30 5869-6267 Sentence denotes The study cohort was defi ned as all inpatients and outpatients at the 8 health care systems who were assigned a discharge diagnostic code from the International Classifi cation of Diseases, 9th Revision, Clinical Modifi cation (ICD-9-CM), that corresponded with a reportable communicable diseases during a 10-year time period (1995) (1996) (1997) (2000) (2001) (2002) (2003) (2004) (2005) (2006) .
T31 6268-6442 Sentence denotes The years 1998-1999 were excluded from the study because this period marked the transition when the state law was changed to include a reporting requirement for laboratories.
T32 6443-6839 Sentence denotes Diseases were excluded if they were chronic infectious diseases that resulted in a recurring assignment of ICD-9-CM code (e.g., HIV, hepatitis B carrier), if no spe-cifi c ICD-9-CM code was available (e.g., for viral hemorrhagic fever), or if the NC DHHS did not record patient identifi ers in their surveillance database during the entire study period (e.g., for syphilis, gonorrhea, chlamydia).
T33 6840-7099 Sentence denotes Approval for the study was granted by the institutional review boards of all health care systems as well as by the North Carolina Division of Public Health because identifi able patient data were required to match the hospital and health department databases.
T34 7100-7481 Sentence denotes The cohort of patients assigned ICD-9-CM diagnostic codes by the health care systems for a reportable communicable disease were matched to the NC DHHS reported case-patients by using a unique identifi er created by either Social Security number, or a combination of the fi rst 2 letters of the last name, fi rst letter of the fi rst name, date of birth, and a 2-digit disease code.
T35 7482-7752 Sentence denotes Repeat patient visits within a 31-day window for the same disease were enumerated and only the fi rst visit was retained, with the exception of tuberculosis, which had a 365-day window, and hepatitis A and paralytic polio, which were restricted to only the fi rst visit.
T36 7753-7935 Sentence denotes Patients who had dates of reporting to the NC DHHS before the date of diagnosis at the health care system were excluded because they represented cases that had already been reported.
T37 7936-8228 Sentence denotes Unadjusted disease-specifi c reporting completeness proportions were calculated by dividing the number of case-patients that were reported to NC DHHS by the total number of patients identifi ed in the health care systems who were assigned an ICD-9-CM diagnostic code for a reportable disease.
T38 8229-8519 Sentence denotes In addition, completeness proportions were estimated by year (1995) (1996) (1997) (2000) (2001) (2002) (2003) (2004) (2005) (2006) for the 3 health care systems that had complete data available for all 10 years, and generalized linear regression models were used to examine the time trends.
T39 8520-8825 Sentence denotes For the years 2000-2006, reporting completeness proportions and 95% confi dence intervals (CIs) were estimated for each health care system by using a binomial logistic regression model that included as covariates whether or not specifi c health care system personnel were designated for disease reporting.
T40 8826-8967 Sentence denotes For disease-specifi c completeness proportions, empirical continuity corrections were used when no patients were reported for a disease (8) .
T41 8968-9200 Sentence denotes In addition, adjusted completeness proportions and 95% uncertainty intervals (UIs) were calculated by using semi-Bayesian analysis (9) as recommended to reduce the mean squared error when an ensemble of measures are estimated (10) .
T42 9201-9390 Sentence denotes This semi-Bayesian hierarchical regression analysis uses prior covariates that help explain the mean of the ensemble of estimates and a specifi ed prior variance (τ 2 ) of the distribution.
T43 9391-9577 Sentence denotes Traditional maximumlikelihood estimates (i.e., unadjusted estimates as presented here) can be viewed as a special case of semi-Bayesian analysis in which the prior variance is infi nite.
T44 9578-9990 Sentence denotes By specifying even a moderately informative prior variance such as a τ 2 indicating that 95% of all completeness proportions lie between 7.3% and 85%, an appreciable reduction in the overall mean squared error can be expected with a shift in the point estimate and a narrowing of the 95% UI for each completeness proportion, with the relative degree of narrowing being greater for diseases with less information.
T45 9991-10192 Sentence denotes A sensitivity analysis was conducted on the specifi ed prior variance, τ 2 , by using high, medium, and low τ 2 values that assumed 95% of the completeness proportions were within the following ranges:
T46 10193-10241 Sentence denotes 2.2%-95%, 7.3%-85%, and 12.9%-75%, respectively.
T47 10242-10741 Sentence denotes Sensitivity analyses were also conducted on the inclusion or exclusion of prior covariates, which were the time frame for reporting the disease (i.e., 24 hours vs. 7 days), whether or not the disease had a reportable laboratory result, whether or not the disease had reportable serologic test results, whether or not the disease is classifi ed as a CDC category A bioterrorism agent, and the mode of transmission of the disease (person-to-person, arthropod-borne, food/water-borne, droplet/aerosol).
T48 10742-10887 Sentence denotes Unadjusted and adjusted disease-specifi c completeness proportions for 2000-2006 with 95% CIs and UIs, respectively, are summarized in the Table.
T49 10888-11036 Sentence denotes The adjusted disease-specifi c, completeness proportions ranged from 0% to 82.0%, and almost all diseases (49/53) had completeness proportions <50%.
T50 11037-11321 Sentence denotes Eleven diseases accounted for 90% of disease reporting: salmonellosis, tuberculosis, meningococcal disease, Rocky Mountain spotted fever, campylobacteriosis, shigellosis, acute hepatitis A, pneumococcal meningitis, legionellosis, malaria, and Haemophilus infl uenzae invasive disease.
T51 11322-11557 Sentence denotes Some unexpected diseases had cases identifi ed with an ICD-9-CM code; for example, anthrax had 14 cases identifi ed, paralytic polio had 32 cases identifi ed, human rabies had 12 cases identifi ed, and smallpox had 9 cases identifi ed.
T52 11558-11815 Sentence denotes The most dramatic adjustments in the unadjusted to adjusted point estimates were noted for staphylococcal foodborne disease, and for foodborne diseases caused by Vibrio vulnifi cus and other Vibrio spp., with an ≈80% change in point estimate for the latter.
T53 11816-11878 Sentence denotes However, wide UIs refl ect the imprecision in these estimates.
T54 11879-12101 Sentence denotes Figure 1 displays the overall reporting proportions by year for the 2 periods, 1995-1997, when only physicians were required to report most diseases, and 2000-2006, when laboratories and physicians were required to report.
T55 12102-12249 Sentence denotes Reporting increased signifi cantly in the second period, but was still low overall; the linear trend line slope was ≈0 and the intercept was 10.2%.
T56 12250-12356 Sentence denotes Figure 2 The completeness proportions ranged from 1.8% to 29.7% with an overall median proportion of 8.0%.
T57 12357-12516 Sentence denotes The covariates that described whether or not each health care system designated persons to report had no effect on a health care system's reporting proportion.
T58 12517-13186 Sentence denotes The sensitivity analysis of the τ 2 values showed that the point estimates and UIs were relatively insensitive to dramatic changes in τ 2 ; for example, for meningococcal meningitis with a low τ 2 , the reporting proportion was estimated as 21% (95% UI 16%-28%), with a medium τ 2 , 22% (95% UI 16%-28%); and with a high τ 2 , 22% (95% UI 16%-29%), and the sensitivity analyses examining the use of prior covariates were shown only to have effects on the reporting proportion and 95% UI for diseases with sparse data; for example, cholera with all prior covariates 22% (95% UI 3%-74%), no prior covariates 10% (95% UI 1%-51%), time covariate alone 50% (95% UI 10%-89%).
T59 13187-13526 Sentence denotes The public health surveillance system in North Carolina is similar to surveillance systems used nationwide, and, although federal funding in addition to state and local budgets support the infrastructure and maintenance of these systems, they are rarely evaluated with respect to the completeness of the communicable disease data reported.
T60 13527-13763 Sentence denotes North Carolina's size (ranked 11th in the 2000 US Census) and population diversity enabled a thorough evaluation of the completeness of reporting many reportable communicable diseases that have rarely been evaluated in previous studies.
T61 13764-13882 Sentence denotes Disease-specifi c reporting completeness proportions were estimated to be low and varied greatly according to disease.
T62 13883-14096 Sentence denotes Notably, even for diseases that require immediate public health intervention, we found that a low proportion of cases were reported to the health department (e.g., meningococcal meningitis 21.2%, pertussis 20.3%).
T63 14097-14316 Sentence denotes Further research studies should be undertaken to focus on methods to improve completeness and timeliness of case reporting, especially for these diseases that are severe and require immediate public health intervention.
T64 14317-14379 Sentence denotes Variations in disease reporting can occur for several reasons.
T65 14380-14595 Sentence denotes First, clinicians may have the perception that some diseases are a greater public health threat based on communicability or severity of the illness and the likelihood of death (e.g., tuberculosis vs. salmonellosis).
T66 14596-15173 Sentence denotes Second, some diseases have relatively straightforward and primarily laboratory-based case defi nitions (e.g., stool culture positive for Salmonella spp. infections with a clinically compatible illness), whereas others are more complex, either requiring multiple laboratory results (e.g., 4-fold increase between acute-phase and convalescent-phase serologic results for Rocky Mountain spotted fever) or a combination of multiple clinical signs and symptoms without any specifi c laboratory result (e.g., toxic shock syndrome which, requires the presence of at least 4 symptoms).
T67 15174-15406 Sentence denotes One clear pattern that emerged in our fi ndings was that diseases with fewer clini- cal criteria and laboratory-based case defi nitions tended to have higher reporting rates (e.g., salmonellosis 44.8% vs. toxic shock syndrome 3.2%).
T68 15407-15618 Sentence denotes Laboratory-based case defi nitions ensure that a dual reporting system exists, and the process is more straightforward because less time is required for reviewing medical records for clinical signs and symptoms.
T69 15619-15765 Sentence denotes This fi nding underscores the need for simplicity of case defi nitions, an essential attribute in surveillance system development and maintenance.
T70 15766-15941 Sentence denotes Future research on predictors for reporting completeness would be useful for designing interventions to improve reporting and for guiding the future direction of surveillance.
T71 15942-16185 Sentence denotes Notably, we identifi ed some patients by ICD-9-CM diagnostic codes for some diseases known to be eliminated in the United States (e.g., smallpox and polio) and others that were highly unlikely to have occurred (e.g., anthrax and human rabies).
T72 16186-16448 Sentence denotes Numerous previous studies that have evaluated reporting completeness have also used ICD-9-CM codes (5,6,11) because they are standard codes that can be queried relatively easily and should capture clinical cases of disease regardless of laboratory confi rmation.
T73 16449-16524 Sentence denotes The accuracy of the ICD-9-CM codes was a potential limitation in our study.
T74 16525-16801 Sentence denotes Therefore, we also conducted a separate validation study of the positive predictive values of ICD-9-CM codes for communicable disease surveillance by using as the standard a complete medical record review and concordance with published CDC case classifi cation criteria (12) .
T75 16802-17030 Sentence denotes These results showed that for most diseases with higher incidence and relatively straightforward diagnoses, the positive predictive values (PPVs) were high (>80%) with the exception of tuberculosis, which had a PPV of 29% (13) .
T76 17031-17355 Sentence denotes For diseases with low PPVs, the estimates we present here are likely to be underestimates of the true reporting completeness because the completeness proportion denominator, or the number of patients identifi ed by ICD-9-CM codes for reportable diseases, is likely to be an overestimate (i.e., contain false-positive cases).
T77 17356-17536 Sentence denotes However, an additional limitation of this study was that we were unable to assess the sensitivity of ICD-9-CM codes (i.e., false-negative cases) for communicable disease reporting.
T78 17537-17835 Sentence denotes Quantifi cation of the sensitivity and PPVs of ICD-9-CM codes for communicable disease surveillance is essential in the interpretation of all ICD-9-CM data because these codes are used frequently for research studies and have been proposed as adjuncts to electronic, automated surveillance systems.
T79 17836-18035 Sentence denotes Bayesian analyses have been shown in theory, simulation, and prediction problems to offer better estimates for measures as varied as baseball batting averages (14) and toxoplasmosis prevalence (15) .
T80 18036-18174 Sentence denotes We believe that the semi-Bayesian adjusted estimates offer improved overall accuracy for our ensemble of reporting completeness estimates.
T81 18175-18277 Sentence denotes For example, for completeness proportions where the maximum-likelihood estimation methods result in 0%
T82 18278-18346 Sentence denotes proportions, it is unlikely that the true proportion is actually 0%.
T83 18347-18541 Sentence denotes The use of semi-Bayesian methods enables us to incorporate additional prior covariate data to produce results that are likely better and more plausible than maximumlikelihood estimation results.
T84 18542-18659 Sentence denotes However, for estimates that were based on less information, we still observed wide UIs around the adjusted estimates.
T85 18660-18895 Sentence denotes Specifi cally, we did note a dramatic shift in the reporting completeness proportions after semi-Bayesian adjustments for several diseases, including staphylococcal foodborne disease and V. vulnifi cus and other Vibrio spp. infections.
T86 18896-19173 Sentence denotes This shift refl ects the imprecision in each disease's measured estimates of reporting completeness and the adjustment or shrinkage of their proportions to the mean of the prior covariate probability groups (i.e., food/water-borne transmission, and reporting time of 24 hours).
T87 19174-19381 Sentence denotes These estimates are shrunk toward the mean of the food/water-borne transmission group of diseases which includes many of those with the highest reporting proportion (e.g., campylobacteriosis, salmonellosis).
T88 19382-19602 Sentence denotes This fi nding reinforces the importance of careful specifi cation of prior covariates as well as judicious examination and interpretation of the unadjusted and semi-Bayesian adjusted estimates along with their precision.
T89 19603-19843 Sentence denotes The reporting variation seen among health care systems ( Figure 2 ) may be explained in part by health care systems' internal policies that assign the responsibility for communicable disease reporting to the infection prevention department.
T90 19844-20263 Sentence denotes For example, the health care system with the highest reporting proportion (health care system A) has hospital-based public health epidemiologists or infection preventionists responsible for disease reporting, and the health care system with the lowest reporting proportion (health care system G) does not assign any additional reporting responsibility beyond the state-mandated reporting by physicians and laboratories.
T91 20264-20346 Sentence denotes However, adjusting for these Emerging Infectious Diseases • www.cdc.gov/eid • Vol.
T92 20347-20432 Sentence denotes 17 health care system policies did not modify the reporting completeness proportions.
T93 20433-20616 Sentence denotes Currently, the North Carolina general statute states that medical facilities may report (16) as opposed to physicians and persons in charge of laboratories who shall report (17, 18) .
T94 20617-20932 Sentence denotes Because infection preventionists typically receive laboratory data daily, are well-trained on case defi nition application, and share disease prevention goals with the health department, they can serve as partners to the local health department in ensuring that diseases are reported and investigated appropriately.
T95 20933-21112 Sentence denotes However, redundancy in disease reporting responsibilities could also cause reporting fatigue and the mistaken assumption that someone else has reported the case-patient (19, 20) .
T96 21113-21523 Sentence denotes In addition, external generalizations of these fi ndings to other health care systems should be approached with caution because the participating sites were part of an existing network that includes the largest health care systems in North Carolina and therefore may have been more likely to treat patients who had more severe illnesses or who did not receive a diagnosis at a local clinic or smaller hospital.
T97 21524-21662 Sentence denotes The general trend of the yearly reporting completeness proportions suggests that disease reporting has improved over time yet remains low.
T98 21663-21755 Sentence denotes Several notable changes occurred in North Carolina's surveillance system during this period.
T99 21756-21923 Sentence denotes First, in 1998, the inclusion of laboratory-mandated reporting served as a secondary reporting mechanism in addition to the already mandated physician-based reporting.
T100 21924-22036 Sentence denotes Regional public health teams were established in 2002 to assist health departments with outbreak investigations.
T101 22037-22472 Sentence denotes In 2003, a network of public health epidemiologists (funded through the state's Public Health Emergency Preparedness cooperative agreement with CDC) were placed in hospitals to facilitate disease reporting and case investigation, and, also in 2003, a statewide emergency department-based syndromic surveillance system (North Carolina Disease Event Tracking and Epidemiologic Collection Tool) was created for early case identifi cation.
T102 22473-22708 Sentence denotes Despite the likely positive effects of these regulatory and programmatic changes on disease reporting, the proportion of diseases reported remains low, as is consistent with data from other passive reporting surveillance systems (21) .
T103 22709-23110 Sentence denotes More recently, automated alerting and data collection for case-patients with reportable diseases (e.g., a positive blood culture result with gram-negative diplococci triggers an alert with case-patient contact information to infection preventionists, local health department staff, or both) has been shown to increase reporting rates when applied to traditional passive surveillance systems (22, 23) .
T104 23111-23427 Sentence denotes Although North Carolina, like many states, has developed and implemented an electronic disease surveillance system, the reporting of communicable diseases by local health departments still remains largely passive in that reporting is accomplished by accessing a secure Internet site and entering patient information.
T105 23428-23521 Sentence denotes Physicians who practice outside local health departments currently use paper-based reporting.
T106 23522-23694 Sentence denotes When health information exchange becomes a reality, public health surveillance can benefi t signifi cantly by automating processes that currently rely on manual data entry.
T107 23695-23999 Sentence denotes Disease reporting could be automated by standardized queries directly from the electronic health records for key laboratory results (e.g., positive acid-fast bacillus sputum smear) and for simplifi ed or proxy clinical case defi nitions by using ICD-9-CM diagnosis codes or free-text admission diagnoses.
T108 24000-24344 Sentence denotes Upon recognition of these potential casepatients, automating surveillance data collection directly from electronic health records to populate data fi elds for basic patient demographics and laboratory results could also reduce administrative time for physicians and health department offi cials and expedite communicable disease investigations.
T109 24345-24682 Sentence denotes This type of automated technology for electronic health records is consistent with The American Recovery and Reinvestment Act of 2009, which authorizes the Centers for Medicare and Medicaid Services to provide reimbursement incentives for health care entities who are "meaningful users" of certifi ed electronic health record technology.
T110 24683-24980 Sentence denotes In fact, the recent draft recommendations for defi ning "meaningful use" from the Health Information Technology Policy Council to the National Coordinator propose that hospitals be capable of providing electronic submission of reportable laboratory results to public health agencies by 2011 (24) .
T111 24981-25208 Sentence denotes Such an undertaking will require implementation of national laboratory reporting standards for hospitals and can only be accomplished with resource allocation and partnerships between health departments and health care systems.
T112 25209-25487 Sentence denotes Furthermore, additional surveillance research should investigate the sensitivity, specifi c- ity, and feasibility of using different key laboratory results and proxy clinical case defi nitions (e.g., ICD-9-CM codes) for automating the identifi cation of potential case-patients.
T113 25488-25795 Sentence denotes The "meaningful use" of the electronic health record for automated case-fi nding and data collection will transition our current public health surveillance system from passive to active and thereby overcome the major barriers to complete, accurate and timely communicable disease reporting and surveillance.