A proposed metric set for evaluation of genome assembly quality.

Quality control is essential for genome assemblies; however, a consensus has yet to be reached on what metrics should be adopted for the evaluation of assembly quality. N50 is widely used for contiguity measurement, but its effectiveness is constantly in question. Prevailing metrics for the completeness evaluation focus on gene space, yet challenging areas such as tandem repeats are commonly overlooked. Achieving correctness has become an indispensable dimension for quality control, while prevailing assembly releases lack scores reflecting this aspect. We propose a metric set with a set of statistic indexes for effective, comprehensive evaluation of assemblies and provide a score of a finished assembly for each metric, which can be utilized as a benchmark for achieving high-quality genome assemblies.

Assessment of Intraoperative Scoring Systems for Predicting Cytoreduction Outcome in Peritoneal Metastatic Disease: A Systematic Review and Meta-analysis.

BACKGROUND: Cytoreductive surgery (CRS) is a widely acknowledged treatment approach for peritoneal metastasis, showing favorable prognosis and long-term survival. Intraoperative scoring systems quantify tumoral burden before CRS and may predict complete cytoreduction (CC). This study reviews the intraoperative scoring systems for predicting CC and optimal cytoreduction (OC) and evaluates the predictive performance of the Peritoneal Cancer Index (PCI) and Predictive Index Value (PIV). METHODS: Systematic searches were conducted in Embase, MEDLINE, and Web of Science. Meta-analyses of extracted data were performed to compare the absolute predictive performances of PCI and PIV. RESULTS: Thirty-eight studies (5834 patients) focusing on gynecological (n = 34; 89.5%), gastrointestinal (n = 2; 5.3%) malignancies, and on tumors of various origins (n = 2; 5.3%) were identified. Seventy-seven models assessing the predictive performance of scoring systems (54 for CC and 23 for OC) were identified with PCI (n = 39/77) and PIV (n = 16/77) being the most common. Twenty models (26.0%) reinterpreted previous scoring systems of which ten (13%) used a modified version of PIV (reclassification). Meta-analyses of models predicting CC based on PCI (n = 21) and PIV (n = 8) provided an AUC estimate of 0.83 (95% confidence interval [CI] 0.79-0.86; Q = 119.6, p = 0.0001; I2 = 74.1%) and 0.74 (95% CI 0.68-0.81; Q = 7.2, p = 0.41; I2 = 11.0%), respectively. CONCLUSIONS: Peritoneal Cancer Index models demonstrate an excellent estimate of CC, while PIV shows an acceptable performance. There is a need for high-quality studies to address management differences, establish standardized cutoff values, and focus on non-gynecological malignancies.

The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems.

A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.

Pandemic preparedness improves national-level SARS-CoV-2 infection and mortality data completeness: a cross-country ecologic analysis.

BACKGROUND: Heterogeneity in national SARS-CoV-2 infection surveillance capabilities may compromise global enumeration and tracking of COVID-19 cases and deaths and bias analyses of the pandemic's tolls. Taking account of heterogeneity in data completeness may thus help clarify analyses of the relationship between COVID-19 outcomes and standard preparedness measures. METHODS: We examined country-level associations of pandemic preparedness capacities inventories, from the Global Health Security (GHS) Index and Joint External Evaluation (JEE), on SARS-CoV-2 infection and COVID-19 death data completion rates adjusted for income. Analyses were stratified by 100, 100-300, 300-500, and 500-700 days after the first reported case in each country. We subsequently reevaluated the relationship of pandemic preparedness on SARS-CoV-2 infection and age-standardized COVID-19 death rates adjusted for cross-country differentials in data completeness during the pre-vaccine era. RESULTS: Every 10% increase in the GHS Index was associated with a 14.9% (95% confidence interval 8.34-21.8%) increase in SARS-CoV-2 infection completion rate and a 10.6% (5.91-15.4%) increase in the death completion rate during the entire observation period. Disease prevention (infections: ß = 1.08 [1.05-1.10], deaths: ß = 1.05 [1.04-1.07]), detection (infections: ß = 1.04 [1.01-1.06], deaths: ß = 1.03 [1.01-1.05]), response (infections: ß = 1.06 [1.00-1.13], deaths: ß = 1.05 [1.00-1.10]), health system (infections: ß = 1.06 [1.03-1.10], deaths: ß = 1.05 [1.03-1.07]), and risk environment (infections: ß = 1.27 [1.15-1.41], deaths: ß = 1.15 [1.08-1.23]) were associated with both data completeness outcomes. Effect sizes of GHS Index on infection completion (Low income: ß = 1.18 [1.04-1.34], Lower Middle income: ß = 1.41 [1.16-1.71]) and death completion rates (Low income: ß = 1.19 [1.09-1.31], Lower Middle income: ß = 1.25 [1.10-1.43]) were largest in LMICs. After adjustment for cross-country differences in data completeness, each 10% increase in the GHS Index was associated with a 13.5% (4.80-21.4%) decrease in SARS-CoV-2 infection rate at 100 days and a 9.10 (1.07-16.5%) decrease at 300 days. For age-standardized COVID-19 death rates, each 10% increase in the GHS Index was with a 15.7% (5.19-25.0%) decrease at 100 days and a 10.3% (- 0.00-19.5%) decrease at 300 days. CONCLUSIONS: Results support the pre-pandemic hypothesis that countries with greater pandemic preparedness capacities have larger SARS-CoV-2 infection and mortality data completeness rates and lower COVID-19 disease burdens. More high-quality data of COVID-19 impact based on direct measurement are needed.

Improvements in data completeness in health information systems reveal racial inequalities: longitudinal national data from hospital admissions in Brazil 2010-2022.

BACKGROUND: Race and ethnicity are important drivers of health inequalities worldwide. However, the recording of race/ethnicity in data systems is frequently insufficient, particularly in low- and middle-income countries. The aim of this study is to descriptively analyse trends in data completeness in race/color records in hospital admissions and the rates of hospitalizations by various causes for Blacks and Whites individuals. METHODS: We conducted a longitudinal analysis, examining hospital admission data from Brazil's Hospital Information System (SIH) between 2010 and 2022, and analysed trends in reporting completeness and racial inequalities. These hospitalization records were examined based on year, quarter, cause of admission (using International Classification of Diseases (ICD-10) codes), and race/color (categorized as Black, White, or missing). We examined the patterns in hospitalization rates and the prevalence of missing data over a period of time. RESULTS: Over the study period, there was a notable improvement in data completeness regarding race/color in hospital admissions in Brazil. The proportion of missing values on race decreased from 34.7% in 2010 to 21.2% in 2020. As data completeness improved, racial inequalities in hospitalization rates became more evident - across several causes, including assaults, tuberculosis, hypertensive diseases, at-risk hospitalizations during pregnancy and motorcycle accidents. CONCLUSIONS: The study highlights the critical role of data quality in identifying and addressing racial health inequalities. Improved data completeness has revealed previously hidden inequalities in health records, emphasizing the need for comprehensive data collection to inform equitable health policies and interventions. Policymakers working in areas where socioeconomic data reporting (including on race and ethnicity) is suboptimal, should address data completeness to fully understand the scale of health inequalities.

Oncologic outcomes and surgical completeness of remote-access thyroidectomy: a systematic review and network meta-analysis.

BACKGROUND: The oncologic safety and surgical completeness of remote-access thyroidectomies are not yet clearly established. This study evaluates the oncologic outcomes and surgical completeness of three prevalent remote-access thyroidectomies: the gasless transaxillary approach (GTAA), bilateral axillo-breast approach (BABA), and transoral approach (TOA), in comparison with conventional transcervical thyroidectomy (CTT). METHODS: Literature searches were conducted in PubMed, EMBASE, and the Cochrane Library databases, covering the period from 2000 to 2023. Network meta-analyses were performed on selected studies, focusing on recurrence and surgical completeness. Surgical completeness was assessed using stimulated serum thyroglobulin levels and the count of retrieved lymph nodes. RESULTS: The review included 48 studies, encompassing a total of 16,356 patients. The number of retrieved lymph nodes was comparable among BABA, TOA, and CTT, while GTAA might be less effective. Stimulated serum thyroglobulin levels showed no significant differences across the four groups. However, the proportion of patients with stimulated thyroglobulin levels below 1.0 ng/mL was significantly lower in GTAA compared to the other groups. The overall recurrence rates were 1.31% for CTT, 0.89% for GTAA, 0.62% for BABA, and 0% for TOA, with no significant differences in recurrence rates when adjusted for follow-up duration. CONCLUSIONS: This study demonstrated that the oncologic outcomes of GTAA, BABA, and TOA are comparable to those of CTT, based on recurrence rates. In terms of surgical completeness, BABA and TOA showed equivalence to CTT, whereas GTAA might be inferior to the other techniques.

Assessing the accuracy and completeness of artificial intelligence language models in providing information on methotrexate use.

We aimed to assess Large Language Models (LLMs)-ChatGPT 3.5-4, BARD, and Bing-in their accuracy and completeness when answering Methotrexate (MTX) related questions for treating rheumatoid arthritis. We employed 23 questions from an earlier study related to MTX concerns. These questions were entered into the LLMs, and the responses generated by each model were evaluated by two reviewers using Likert scales to assess accuracy and completeness. The GPT models achieved a 100% correct answer rate, while BARD and Bing scored 73.91%. In terms of accuracy of the outputs (completely correct responses), GPT-4 achieved a score of 100%, GPT 3.5 secured 86.96%, and BARD and Bing each scored 60.87%. BARD produced 17.39% incorrect responses and 8.7% non-responses, while Bing recorded 13.04% incorrect and 13.04% non-responses. The ChatGPT models produced significantly more accurate responses than Bing for the "mechanism of action" category, and GPT-4 model showed significantly higher accuracy than BARD in the "side effects" category. There were no statistically significant differences among the models for the "lifestyle" category. GPT-4 achieved a comprehensive output of 100%, followed by GPT-3.5 at 86.96%, BARD at 60.86%, and Bing at 0%. In the "mechanism of action" category, both ChatGPT models and BARD produced significantly more comprehensive outputs than Bing. For the "side effects" and "lifestyle" categories, the ChatGPT models showed significantly higher completeness than Bing. The GPT models, particularly GPT 4, demonstrated superior performance in providing accurate and comprehensive patient information about MTX use. However, the study also identified inaccuracies and shortcomings in the generated responses.

The diagnosis of cerebral palsy in two Danish national registries: a validation study.

AIMS: To determine the quality of prospectively collected data from the highly specialized Danish Cerebral Palsy Follow-up Program (CPOP), and to establish the validity of a reported cerebral palsy (CP) diagnosis in the Danish National Patient Registry (NPR), regularly used as a proxy for neurodevelopmental disorders in epidemiological research. METHODS: We compared data from the two registries on children with registered CP, born in Denmark between 2008 and 2009, with information from medical records verified by two experienced physicians specializing in pediatric neurology. Data accuracy was estimated by completeness, correctness, and reliability. Completeness was calculated as the number of cases with correctly registered CP diagnoses divided by the total number of true CP diagnoses (similar to sensitivity). Correctness was calculated as the number of cases with correct registrations divided by the total number of cases (similar to positive predictive value). Reliability was estimated using kappa statistics. RESULTS: Registered CP diagnoses in the CPOP had high accuracy, with 94% correctness and 91% completeness. Furthermore, most key variables in the CPOP showed excellent reliability, especially variables defining the severity of the condition. In the Danish NPR, only 225 of 348 children with a noted CP diagnosis fulfilled the diagnostic criteria for CP, resulting in 65% correctness. CONCLUSIONS: Danish CPOP data are a valid source for epidemiological research. Conversely, a noted CP diagnosis in the Danish NPR was, at best, correct in only two out of three patients.

Evaluation of Focused Assessment With Sonography for Trauma Completeness of Children in the Clinical Setting.

OBJECTIVES: We evaluated the completeness of real-world Focused Assessment with Sonography for Trauma (FAST) in children after blunt abdominal trauma by benchmarking against established expert guidelines. METHODS: We conducted a retrospective cohort study, analyzing a random sample of FASTs from two urban pediatric emergency departments. Two experts reviewed and labeled all FASTs for completeness using a predefined guideline of 5 anatomic views and 30 landmarks. We compared frequencies of views and landmarks as medians with interquartile ranges. RESULTS: We analyzed 200 FASTs, consisting of 1636 video clips, performed by 31 clinicians representing 198 children with a median age of 10 years (IQR 5,14). Over half of FASTs (52%) had all 5 views. The right upper quadrant view was most commonly visualized (96.5%), and suprapubic sagittal was least (65%). None of the FASTs included all 30 landmarks, ranging from 0 to 28 and median of 19 (IQR 15,23). The least visualized landmark of the right and left upper quadrants was caudal liver edge (60%) and splenic tip (64%), respectively. In the pericardial view, it was left atrium (45%). In both transverse and sagittal pelvic views, retro-uterine space was least visualized in girls, 21 and 29% respectively. CONCLUSIONS: In our study, most FAST views and landmarks were visualized. However, the pelvic sagittal view was the least frequently visualized view, and caudal liver edge was the least visualized landmark. Future research should evaluate if variability in visualizing FAST views and landmarks correlates with inconsistencies in diagnostic test performance.

Differences in changes of data completeness after the implementation of an electronic medical record in three surgical departments of a German hospital-a longitudinal comparative document analysis.

PURPOSE: The European health data space promises an efficient environment for research and policy-making. However, this data space is dependent on high data quality. The implementation of electronic medical record systems has a positive impact on data quality, but improvements are not consistent across empirical studies. This study aims to analyze differences in the changes of data quality and to discuss these against distinct stages of the electronic medical record's adoption process. METHODS: Paper-based and electronic medical records from three surgical departments were compared, assessing changes in data quality after the implementation of an electronic medical record system. Data quality was operationalized as completeness of documentation. Ten information that must be documented in both record types (e.g. vital signs) were coded as 1 if they were documented, otherwise as 0. Chi-Square-Tests were used to compare percentage completeness of these ten information and t-tests to compare mean completeness per record type. RESULTS: A total of N = 659 records were analyzed. Overall, the average completeness improved in the electronic medical record, with a change from 6.02 (SD = 1.88) to 7.2 (SD = 1.77). At the information level, eight information improved, one deteriorated and one remained unchanged. At the level of departments, changes in data quality show expected differences. CONCLUSION: The study provides evidence that improvements in data quality could depend on the process how the electronic medical record is adopted in the affected department. Research is needed to further improve data quality through implementing new electronical medical record systems or updating existing ones.

Comparison of endoscopic thyroidectomy via the oral vestibule approach and the areola approach for papillary thyroid carcinoma.

BACKGROUND: The endoscopic thyroidectomy areola approach (ETAA) has been widely applied for papillary thyroid carcinoma (PTC), but leaves scars and is not truly minimally invasive. The oral vestibular approach (ETOVA) leaves no scars and is even more minimally invasive. However, there have been few comparative studies of ETAA and ETOVA for PTC. The purpose of our research was to compare two PTC treatment methods in terms of feasibility, safety, efficacy, and cosmetic results. METHODS: A total of 129 patients with PTC underwent thyroidectomy combined with central lymph node dissection by the same surgeon. Among them, 79 patients underwent the ETOVA, and the others underwent the ETAA. We compared the two groups in terms of operative outcomes, postoperative complications, and cosmetic results. RESULTS: No significant differences were found in the clinical characteristics between the ETOVA and ETAA groups. There were no significant differences in the number of removed lymph nodes (P = 0.279) or the number of positive lymph nodes (P = 0.569), but the ETOVA group had a higher number of removed lymph nodes. There was also no significant difference in blood loss volume(P = 0.180), postoperative drainage volume (P = 0.063), length of hospital stay (P = 0.182), transient RLN injury rate (P = 1.000), permanent RLN injury rate (P = 1.000), or recurrence rate (P = 1.000). The ETOVA was a longer operation than the ETAA was (P < 0.01). The ETOVA group had less pain (VAS 1: P < 0.01, VAS 3: P = 0.001), less neck discomfort (1 month after surgery: P = 0.009, 3 months after surgery: P = 0.033), and better cosmetic results (P = 0.001). CONCLUSIONS: The ETOVA is not inferior to the ETAA in terms of safety and curability of PTC and is advantageous in terms of central lymph node dissection, minimal invasiveness, and cosmetic results. TRIAL REGISTRATION: This study was approved by the Ethics Committee of Zhongshan Hospital of Xiamen University (2017 V1.0). No funding was received.

Secondary analysis of hand-offs in internal medicine using the I-PASS mnemonic.

BACKGROUND: Miscommunications account for up to 80% of preventable medical errors. Mnemonics like I-PASS (Illness severity, Patient summary, Actions list, Situation awareness, Synthesis) have demonstrated a positive impact on reducing error rates. Currently, physicians at our hospital do not follow a specific structure during hand-offs. We aimed to compare current hand-offs without prior training to a gold standard and the I-PASS tool in terms of content and sequence. METHODS: This study is a secondary analysis of data collected during a simulation study of a Friday evening hand-off to the night resident at University Hospitals of Geneva. Thirty physicians received a hand-off of four patients and managed two other patients through nursing pages at the start of the night shift, generating six sign-outs each, totaling 177 sign-outs. A focus group of three senior doctors defined the gold standard (GS) by consensus on the essential content of each sign-out. The analysis focused on the rates of relevance (ratio of information considered relevant by the GS) and completeness (proportion of transmitted elements out of all expected elements of the GS), and the distribution and sequence of the first four I-PASS categories. RESULTS: Relevance and completeness rates were 37.2% ± 0.07 and 51.9% ± 0.1, respectively, with no significant difference between residents and supervisors. There was a positive correlation between total hand-off time and relevance (residents: R2 = 0.62; supervisors: R2 = 0.67) and completeness (residents: R2 = 0.32; supervisors: R2 = 0.56). The distribution of I-PASS categories was highly skewed in both the GS (I = 2%, P = 72%, A = 17%, S = 9%) and participants (I = 6%, P = 73%, A = 14%, S = 7%), with significant differences in categories A (p = 0.046) and I (p ≤ 0.001). Sequences of I-PASS categories generally followed a P-A-S-I pattern. The first S category was frequently absent, and only one participant began by announcing the case severity as suggested by I-PASS. CONCLUSION: We identified gaps between current medical sign-outs in our institution's general internal medicine division and the I-PASS structure. We recommend implementing the I-PASS mnemonic, emphasizing the "I" category at the start and the "S" category to anticipate and prevent complications. Future studies should assess the impact of this recommendation, adapt the mnemonic elements to the context, and introduce specific hand-off training for senior medical students.

The impact of intraoperative neural monitoring during papillary thyroid cancer surgery on completeness of thyroidectomy and thyroglobulin response: a propensity-score matched study.

BACKGROUND: Intraoperative neural monitoring (IONM) has been utilized for a variety of thyroid pathologies, including papillary thyroid carcinoma (PTC). Remnant thyroid tissue following total thyroidectomy (TT) in patients with PTC is associated with increased recurrence. The aim of this study is to investigate whether the use of IONM in PTC surgery has an impact on the completeness of thyroidectomy. METHODS: Retrospectively, patients with preoperative diagnosis of PTC, who underwent TT in a tertiary center were reviewed. They were grouped based on the IONM usage, and 1:1 propensity-score match was performed. Primary outcome was the completeness of thyroidectomy, determined by measuring postoperative stimulated thyroglobulin levels (sTg). RESULTS: Among 274 clinically node-negative PTC patients who underwent TT and ipsilateral prophylactic central lymph-node dissection, a total of 170 patients (85:85) were matched. Postoperative sTg levels were significantly lower in the IONM group (1 ng/dL vs. 0.4 ng/dL; p < 0.01) with higher percentage of the patients with sTg levels <1 ng/ml (50.6% vs. 69.4%; p = 0.01). More patients in the no-IONM group received RAI ablation with significantly higher doses (mean mci: 120 vs. 102; p = 0.02). CONCLUSION: The use of IONM during thyroidectomy provides improvement in the completeness of thyroidectomy and reduction in postoperative sTg levels which can be used as a guide by clinicians to avoid RAI ablation in selected PTC patients and to adjust low ablative doses in patients who are scheduled for remnant ablation.

Examining the Completeness of Breast Cancer Pathology Reports Registered in the Population-Based Cancer Registration System in Iran during 2016 to 2018.

Background: Ensuring the comprehensive and accurate representation of data within cancer registries holds paramount significance across various facets of public health decision-making. This study delves into the evaluation of data completeness in breast cancer (BC) pathology reports within a population-based cancer registration system in Iran, spanning the period from 2016 to 2018. Methods: Employing a retrospective and descriptive analytical approach, we harnessed secondary data extracted from pathology reports encompassing breast cancer diagnoses, which were duly recorded in the Integrated Cancer Information Management System database during 2016-2018. A total of 4000 pathology reports were thoughtfully selected from each of the three years. The spectrum of pathology information encompassed tumor type, site grade, size (T), and involvement of lymph nodes (N). Summary statistics were provided as percentages of categorical variables and mean with standard deviation of continuous variables. A comparison of categorical variables was performed using the Chi-squared test. Results: The participants' mean age was 51.8±12.5 years. Among the 12,000 studied patients, 5744 (47.9%) were ≤ 50 years old, 5233 (43.6%) were aged 50-69 years, and 1023 (8.5%) were >60 years old. The completeness of BC pathology reports varied for different variables. Interestingly, the completeness of these variables increased with older age groups. The proportion of specific tumor types differed significantly among age groups (P = 0.001). Notably, the prevalence of invasive ductal carcinoma was higher in the ≤ 50 years age group compared to the older cohorts. Likewise, notable variations in tumor sizes were observed (P = 0.009), with a higher prevalence of missing tumor size data noted in the age group ≤ 50 years. On the other hand, pathologic T stage also demonstrated age-dependent variations (P = 0.014), indicating a higher prevalence of missing stages in the ≤ 50 years age group. Finally, tumor grade exhibited a statistically significant difference (P < 0.001), with a higher proportion of grade 1 tumors observed in the 50-69 years age group. Conclusion: Tumor grade had the highest completeness rate, while tumor size, pathologic T stage, and pathologic N stage had the lowest. Therefore, a good understanding of completeness of pathology reports, as well as improvement in the registration of stage, integrated system at the national level for BC is warranted.

Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification and Compartment and Process Coverage and Enables More Reflective Protein-Level Label-Free Quantitation.

The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement, with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Herein, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition methods. Analysis of offline fractionated cell line digests using both separations revealed an increase in peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. RAW proteomic data have been uploaded to the MassIVE repository with the primary accession code MSV000091495.

Completeness of regional cancer registry data in Northwest Russia 2008-2017.

BACKGROUND: A national framework for population-based cancer registration was established in Russia in the late 1990s. Data comparability and validity analyses found substantial differences across ten population-based cancer registries (PBCRs)in Northwest Russia, and only four out of ten met international standards. This study aimed to assess the completeness of the PBCR data of those registries. METHODS: Qualitative and quantitative methods recommended for completeness and timeliness assessment were applied to the data from ten Russian regional PBCRs in Northwest Russia, covering a population of 13 million. We used historic data methods (using several European PBCRs reference rates), mortality-to-incidence ratios (M:I) comparison, and death certificate methods to calculate the proportion of unregistered cases (Lincoln-Petersen estimator and Ajiki formula). RESULTS: Incidence rate trends of different cancer types were stable over time (except one region - Leningrad oblast). A slight drop in incidence rates in older age groups for several sites in the Northwestern regions was observed compared to the reference from European countries. Comparing M:I ratios against five-year survival revealed systematic differences in Leningrad oblast and Vologda oblast. Assessment of completeness revealed low or unrealistic estimates in Leningrad oblast and completeness below 90% in St. Petersburg. In other regions, the completeness was above 90%. The national annual report between 2008-2017 did not include about 10% of the cases collected later in the registry database of St. Petersburg. This difference was below 3% for Arkhangelsk oblast, Murmansk oblast, Novgorod oblast, Vologda oblast and the Republic of Karelia. CONCLUSIONS: Eight out of ten regional PBCRs in Northwest Russia collected data with an acceptable degree of completeness. Mostly populated St. Petersburg and Leningrad oblast did not reach such completeness. PBCR data from several regions in Northwest Russia are suitable for epidemiological research and monitoring cancer control activities.

Hemispherotomy in children: A retrospective analysis of 152 surgeries at a single center and predictors for long-term seizure outcome.

OBJECTIVE: Completeness as a predictor of seizure freedom is broadly accepted in epilepsy surgery. We focused on the requirements for a complete hemispherotomy and hypothesized that the disconnection of the insula contributes to a favorable postoperative seizure outcome. We analyzed surgical and nonsurgical predictors influencing long-term seizure outcome before and after a modification of our hemispherotomy technique. METHODS: We retrospectively studied surgical procedures, electroclinical parameters, magnetic resonance imaging (MRI) results, and follow-up data in all children who had undergone hemispherotomy between 2001 and 2018 at our institution. We used logistic regression models to analyze the influence of different factors on seizure outcome. RESULTS: A total of 152 patients were eligible for seizure outcome analysis only. Of these, 140 cases had complete follow-up data for ≥24 months and provide the basis for the following results. The median age at surgery was 4.3 years (range = .3-17.9 years). Complete disconnection (including the insular tissue) was achieved in 63.6% (89/140). At 2-year follow-up, seizure freedom (Engel class IA) was observed in 34.8% (8/23) with incomplete insular disconnection, whereas this was achieved in 88.8% (79/89) with complete surgical disconnection (p < .001, odds ratio [OR] = 10.41). In the latter group (n = 89), a potentially epileptogenic contralateral MRI lesion was the strongest predictor for postoperative seizure recurrence (OR = 22.20). SIGNIFICANCE: Complete surgical disconnection is the most important predictor of seizure freedom following hemispherotomy and requires disconnection of the insular tissue at the basal ganglia level. Even if the hemispherotomy is performed surgically completely, a potentially epileptogenic contralateral lesion on preoperative MRI significantly reduces the chances of postoperative seizure freedom.

Comparison of paediatric infectious disease deaths in public sector health facilities using different data sources in the Western Cape, South Africa (2007-2021).

BACKGROUND: Routinely collected population-wide health data are often used to understand mortality trends including child mortality, as these data are often available more readily or quickly and for lower geographic levels than population-wide mortality data. However, understanding the completeness and accuracy of routine health data sources is essential for their appropriate interpretation and use. This study aims to assess the accuracy of diagnostic coding for public sector in-facility childhood (age < 5 years) infectious disease deaths (lower respiratory tract infections [LRTI], diarrhoea, meningitis, and tuberculous meningitis [TBM]) in routine hospital information systems (RHIS) through comparison with causes of death identified in a child death audit system (Child Healthcare Problem Identification Programme [Child PIP]) and the vital registration system (Death Notification [DN] Surveillance) in the Western Cape, South Africa and to calculate admission mortality rates (number of deaths in admitted patients per 1000 live births) using the best available data from all sources. METHODS: The three data sources: RHIS, Child PIP, and DN Surveillance are integrated and linked by the Western Cape Provincial Health Data Centre using a unique patient identifier. We calculated the deduplicated total number of infectious disease deaths and estimated admission mortality rates using all three data sources. We determined the completeness of Child PIP and DN Surveillance in identifying deaths recorded in RHIS and the level of agreement for causes of death between data sources. RESULTS: Completeness of recorded in-facility infectious disease deaths in Child PIP (23/05/2007-08/02/2021) and DN Surveillance (2010-2013) was 70% and 69% respectively. The greatest agreement in infectious causes of death were for diarrhoea and LRTI: 92% and 84% respectively between RHIS and Child PIP, and 98% and 83% respectively between RHIS and DN Surveillance. In-facility infectious disease admission mortality rates decreased significantly for the province: 1.60 (95% CI: 1.37-1.85) to 0.73 (95% CI: 0.56-0.93) deaths per 1000 live births from 2007 to 2020. CONCLUSION: RHIS had accurate causes of death amongst children dying from infectious diseases, particularly for diarrhoea and LRTI, with declining in-facility admission mortality rates over time. We recommend integrating data sources to ensure the most accurate assessment of child deaths.

Validity of self-reported educational level in the Tromsø Study.

BACKGROUND: Self-reported data on educational level have been collected for decades in the Tromsø Study, but their validity has yet to be established. AIM: To investigate the completeness and correctness of self-reported educational level in the Tromsø Study, using data from Statistics Norway. In addition, we explored the consequence of using these two data sources on educational trends in cardiometabolic diseases. METHODS: We compared self-reported and Statistics Norway-recorded educational level (primary, upper secondary, college/university <4 years, and college/university ⩾4 years) among 20,615 participants in the seventh survey of the Tromsø Study (Tromsø7, 2015-2016). Sensitivity, positive predictive value and weighted kappa were used to measure the validity of self-reported educational level in three age groups (40-52, 53-62, 63-99 years). Multivariable logistic regression was used to compare educational trends in cardiometabolic diseases between self-reported and Statistics Norway-recorded educational level. RESULTS: Sensitivity of self-reported educational level was highest among those with a college/university education of 4 years or more (⩾97% in all age groups and both sexes). Sensitivity for primary educational level ranged from 67% to 92% (all age groups and both sexes). The lowest positive predictive value was observed among women with a college/university education of 4 years or more (29-46%). Weighted kappa was substantial (0.52-0.59) among men and moderate to substantial (0.41-0.51) among women. Educational trends in the risk of cardiometabolic diseases were less pronounced when self-reported educational level was used. CONCLUSIONS: Self-reported educational level in Tromsø7 is adequately complete and correct. Self-reported data may produce weaker associations between educational level and cardiometabolic diseases than registry-based data.

Timeliness and completeness of weekly surveillance data reporting on epidemic prone diseases in Uganda, 2020-2021.

INTRODUCTION: Disease surveillance provides vital data for disease prevention and control programs. Incomplete and untimely data are common challenges in planning, monitoring, and evaluation of health sector performance, and health service delivery. Weekly surveillance data are sent from health facilities using mobile tracking (mTRAC) program, and synchronized into the District Health Information Software version 2 (DHIS2). The data are then merged into district, regional, and national level datasets. We described the completeness and timeliness of weekly surveillance data reporting on epidemic prone diseases in Uganda, 2020-2021. METHODS: We abstracted data on completeness and timeliness of weekly reporting of epidemic-prone diseases from 146 districts of Uganda from the DHIS2.Timeliness is the proportion of all expected weekly reports that were submitted to DHIS2 by 12:00pm Monday of the following week. Completeness is the proportion of all expected weekly reports that were completely filled and submitted to DHIS2 by 12:00pm Wednesday of the following week. We determined the proportions and trends of completeness and timeliness of reporting at national level by year, health region, district, health facility level, and facility ownership. RESULTS: National average reporting timeliness and completeness was 44% and 70% in 2020, and 49% and 75% in 2021. Eight of the 15 health regions achieved the target for completeness of ≥ 80%; Lango attained the highest (93%) in 2020, and Karamoja attained 96% in 2021. None of the regions achieved the timeliness target of ≥ 80% in either 2020 or 2021. Kampala District had the lowest completeness (38% and 32% in 2020 and 2021, respectively) and the lowest timeliness (19% in both 2020 and 2021). Referral hospitals and private owned health facilities did not attain any of the targets, and had the poorest reporting rates throughout 2020 and 2021. CONCLUSION: Weekly surveillance reporting on epidemic prone diseases improved modestly over time, but timeliness of reporting was poor. Further investigations to identify barriers to reporting timeliness for surveillance data are needed to address the variations in reporting.