bluuebunny/crossref_metadata_2025_split huggingface dataset:
P-smoother: efficient PBWT smoothing of large haplotype panels
Authors: Yue William , Naseri Ardalan , Wang Victor , Shakya Pramesh , Zhang Shaojie , Zhi Degui 
Published: June 2022

Abstract

Motivation
As large haplotype panels become increasingly available, efficient string matching algorithms such as positional Burrows-Wheeler transformation (PBWT) are promising for identifying shared haplotypes. However, recent mutations and genotyping errors create occasional mismatches, presenting challenges for exact haplotype matching. Previous solutions are based on probabilistic models or seed-and-extension algorithms that passively tolerate mismatches.

Results
Here, we propose a PBWT-based smoothing algorithm, P-smoother, to actively ‘correct’ these mismatches and thus ‘smooth’ the panel. P-smoother runs a bidirectional PBWT-based panel scanning that flips mismatching alleles based on the overall haplotype matching context, which we call the IBD (identical-by-descent) prior. In a simulated panel with 4000 haplotypes and a 0.2% error rate, we show it can reliably correct 85% of errors. As a result, PBWT algorithms running over the smoothed panel can identify more pairwise IBD segments than that over the unsmoothed panel. Most strikingly, a PBWT-cluster algorithm running over the smoothed panel, which we call PS-cluster, achieves state-of-the-art performance for identifying multiway IBD segments, a challenging problem in the computational community for years. We also showed that PS-cluster is adequately efficient for UK Biobank data. Therefore, P-smoother opens up new possibilities for efficient error-tolerating algorithms for biobank-scale haplotype panels.

Availability and implementation
Source code is available at github.com/ZhiGroup/P-smoother.
A rarefaction-without-resampling extension of PERMANOVA for testing presence–absence associations in the microbiome
Authors: Hu Yi-Juan , Satten Glen A 
Published: June 2022

AbstractMotivationPERMANOVA is currently the most commonly used method for testing community-level hypotheses about microbiome associations with covariates of interest. PERMANOVA can test for associations that result from changes in which taxa are present or absent by using the Jaccard or unweighted UniFrac distance. However, such presence–absence analyses face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias but at the potential costs of information loss and the introduction of a stochastic component into the analysis.ResultsHere, we develop a non-stochastic approach to PERMANOVA presence–absence analyses that aggregates information over all potential rarefaction replicates without actual resampling, when the Jaccard or unweighted UniFrac distance is used. We compare this new approach to three possible ways of aggregating PERMANOVA over multiple rarefactions obtained from resampling: averaging the distance matrix, averaging the (element-wise) squared distance matrix and averaging the F-statistic. Our simulations indicate that our non-stochastic approach is robust to confounding by library size and outperforms each of the stochastic resampling approaches. We also show that, when overdispersion is low, averaging the (element-wise) squared distance outperforms averaging the unsquared distance, currently implemented in the R package vegan. We illustrate our methods using an analysis of data on inflammatory bowel disease in which samples from case participants have systematically smaller library sizes than samples from control participants.Availability and implementationWe have implemented all the approaches described above, including the function for calculating the analytical average of the squared or unsquared distance matrix, in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.Supplementary informationSupplementary data are available at Bioinformatics online.
PrISM: precision for integrative structural models
Authors: Ullanat Varun , Kasukurthi Nikhil , Viswanath Shruthi 
Published: June 2022

AbstractMotivationA single-precision value is currently reported for an integrative model. However, precision may vary for different regions of an integrative model owing to varying amounts of input information.ResultsWe develop PrISM (Precision for Integrative Structural Models) to efficiently identify high- and low-precision regions for integrative models.Availability and implementationPrISM is written in Python and available under the GNU General Public License v3.0 at https://github.com/isblab/prism; benchmark data used in this paper are available at doi:10.5281/zenodo.6241200.Supplementary informationSupplementary data are available at Bioinformatics online.
Role of right temporoparietal junction for counterfactual evaluation of partner’s decision in ultimatum game
Authors: Ogawa Akitoshi , Asano Saki , Osada Takahiro , Tanaka Masaki , Tochigi Reia , Kamagata Koji , Aoki Shigeki , Konishi Seiki 
Published: June 2022

AbstractHumans assess the distributions of resources based on their aversion to unfairness. If a partner distributes in an unfair manner even though the partner had a less unfair distribution option, a recipient will believe that the partner should have chosen the counterfactual option. In this study, we investigated the neural basis for fairness evaluation of actual and counterfactual options in the ultimatum game. In this task, a partner chose one distribution option out of two options, and a participant accepted or rejected the option. The behavioral results showed that the acceptance rate was influenced by counterfactual evaluation (CE), among others, as defined by the difference of monetary amount between the actual and counterfactual options. The functional magnetic resonance imaging results showed that CE was associated with the right ventral angular gyrus (vAG) that provided one of convergent inputs to the supramarginal gyrus related to decision utility, which reflects gross preferences for the distribution options. Furthermore, inhibitory repetitive transcranial magnetic stimulation administered to the right vAG reduced the behavioral component associated with CE. These results suggest that our acceptance/rejection of distribution options relies on multiple processes (monetary amount, disadvantageous inequity, and CE) and that the right vAG causally contributes to CE.
Effects of contraction bias on the decision process in the macaque prefrontal cortex
Authors: Benozzo Danilo , Ferrucci Lorenzo , Genovesio Aldo 
Published: June 2022

AbstractOur representation of magnitudes such as time, distance, and size is not always veridical because it is affected by multiple biases. From a Bayesian perspective, estimation errors are considered to be the result of an optimization mechanism for the behavior in a noisy environment by integrating previous experience with the incoming sensory information. One influence of the distribution of past stimuli on perceptual decisions is represented by the regression toward the mean, a type of contraction bias. Using a spatial discrimination task with 2 stimuli presented sequentially at different distances from the center, we show that this bias is also present in macaques when comparing the magnitude of 2 distances. We found that the contraction of the first stimulus magnitude toward the center of the distribution accounted for some of the changes in performance, even more so than the effect of difficulty related to the ratio between stimulus magnitudes. At the neural level in the dorsolateral prefrontal cortex, the coding of the decision after the presentation of the second stimulus reflected the effect of the contraction bias on the discriminability of the stimuli at the behavioral level.
Delayed Recognition of Coronavirus Disease 2019 (COVID-19) in New York City: A Descriptive Analysis of COVID-19 Illness Prior to 29 February 2020
Authors: Keating Page , Sell Jessica , Chen Judy , Ackelsberg Joel , Wu Winfred , Tsoi Benjamin , Weiss Don 
Published: June 2022

Abstract

Background
On 30 January 2020, COVID-19 was declared a Public Health Emergency of International Concern (PHEIC) by the World Health Organization. Almost a month later, on 29 February 2020, the first case in New York City (NYC) was diagnosed.

Methods
Three hundred sixty persons with COVID-19–like illness were reported to the NYC Department of Health and Mental Hygiene (DOHMH) before 29 February, but 37 of these tested negative and 237 were never tested for severe acute respiratory syndrome coronavirus 2. Records of 86 persons with confirmed COVID-19 and reported symptom onset prior to 29 February 2020 were reviewed by 4 physician-epidemiologists. Case-patients were classified as possible delayed recognition (PDR) of COVID-19 when upon medical review the reported onset date was believed to reflect the initial symptoms of COVID-19, or insufficient evidence to classify, when the onset could not be determined with confidence. Clinical and epidemiological factors collected by DOHMH and supplemented with emergency department records were analyzed.

Results
Thirty-nine PDR COVID-19 cases were identified. The majority had severe disease with 69% presenting to an emergency department within 2 weeks of symptom onset. The first PDR COVID-19 case had symptom onset on 28 January 2020. Only 7 of the 39 cases (18%) had traveled internationally within 14 days of onset (none to China).

Conclusions
COVID-19 was in NYC before being classified as a PHEIC, and eluded surveillance for another month. The delay in recognition limited mitigation efforts; by the time city- and statewide mandates were enacted, 16 and 22 days later, there was already widespread community transmission.
Sensitivity of Various Case Detection Algorithms for Community-based Tuberculosis Screening
Authors: Puma Daniela , Yuen Courtney M , Millones Ana K , Brooks Meredith B , Jimenez Judith , Calderon Roger I , Lecca Leonid , Becerra Mercedes C , Keshavjee Salmaan 
Published: June 2022

Abstract
Using data from 388 people diagnosed with tuberculosis through a community-based screening program in Lima, Peru, we estimated that cough screening followed by sputum smear microscopy would have detected only 23% of cases found using an algorithm of radiographic screening followed by rapid nucleic acid amplification testing and clinical evaluation.
Durability of Immune Responses After Boosting in Ad26.COV2.S-Primed Healthcare Workers
Authors: Sablerolles Roos S G , Rietdijk Wim J R , Goorhuis Abraham , Postma Douwe F , Visser Leo G , Schmitz Katharina S , Geers Daryl , Bogers Susanne , van Haren Eva , Koopmans Marion P G , Dalm Virgil A S H , Kootstra Neeltje A , Huckriede Anke L W , Akkerman Renate , Beukema Martin , Lafeber Melvin , van Baarle Debbie , de Vries Rory D , van der Kuy P Hugo M , GeurtsvanKessel Corine H ,   for the SWITCH Research Group
Published: June 2022

Abstract
The emergence of SARS-CoV-2 variants raised questions regarding the durability of immune responses after homologous or heterologous boosters after Ad26.COV2.S-priming. We found that SARS-CoV-2–specific binding antibodies, neutralizing antibodies, and T cells are detectable 5 months after boosting, although waning of antibodies and limited cross-reactivity with Omicron BA.1 was observed.
Virologic and Immunologic Characterization of Coronavirus Disease 2019 Recrudescence After Nirmatrelvir/Ritonavir Treatment
Authors: Carlin Aaron F , Clark Alex E , Chaillon Antoine , Garretson Aaron F , Bray William , Porrachia Magali , Santos AsherLev T , Rana Tariq M , Smith Davey M 
Published: June 2022

Abstract
We isolated a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) BA.2 variant from a person with coronavirus disease 2019 recrudescence after nirmatrelvir/ritonavir treatment. Antiviral sensitivity and neutralizing antibody testing were performed with both parental SARS-CoV-2 and multiple variants of concern. We found that neither nirmatrelvir resistance nor absence of neutralizing immunity was a likely cause of the recrudescence.
Hospitalized Patients With Severe Coronavirus Disease 2019 During the Omicron Wave in Israel: Benefits of a Fourth Vaccine Dose
Authors: Brosh-Nissimov Tal , Hussein Khetam , Wiener-Well Yonit , Orenbuch-Harroch Efrat , Elbaz Meital , Lipman-Arens Shelly , Maor Yasmin , Yagel Yael , Chazan Bibiana , Hershman-Sarafov Mirit , Rahav Galia , Zimhony Oren , Zaidman Shimshovitz Adi , Chowers Michal 
Published: June 2022

Abstract

Background
Waning immunity and an increased incidence of coronavirus disease 2019 (COVID-19) during the Omicron outbreak led the Israeli Ministry of Health to recommend a fourth vaccine dose for high-risk individuals. In this study, we assessed its effect for hospitalized patients with severe breakthrough COVID-19.

Methods
In this multicenter cohort study of hospitalized adults with severe COVID-19 in Israel, from 15 to 31 January 2022, cases were divided according to the number of vaccinations received. Poor outcome was defined as mechanical ventilation or in-hospital death and was compared between 3- and 4-dose vaccinees using logistic regression.

Results
Included were 1049 patients, median age 80 years. Among them, 394 were unvaccinated, 386 and 88 had received 3 or 4 doses, respectively. The 3-dose group was older, included more males, and immunosuppressed patients but with similar outcomes, 49% vs 51% compared with unvaccinated patients (P = .72). Patients who received 4 doses were similarly older and immunosuppressed but had better outcomes compared with unvaccinated patients, 34% vs 51% (P &lt; .01). We examined independent predictors for poor outcome in patients who received either 3 or 4 doses a median of 161 days or 14 days before diagnosis, respectively. Receipt of the fourth dose was associated with protection (odds ratio, 0.51; 95% confidence interval, .3–.87), as was remdesivir. Male sex, chronic renal failure, and dementia were associated with poor outcomes.

Conclusions
Among hospitalized patients with severe breakthrough COVID-19, a recent fourth dose was associated with significant protection against mechanical ventilation or death compared with 3 doses.
Optical coherence tomography-derived lipid core burden index and clinical outcomes: results from the CLIMA registry
Authors: Biccirè Flavio Giuseppe , Budassi Simone , Ozaki Yukio , Boi Alberto , Romagnoli Enrico , Di Pietro Riccardo , Bourantas Christos V , Marco Valeria , Paoletti Giulia , Debelak Caterina , Sammartini Emanuele , Versaci Francesco , Fabbiocchi Franco , Burzotta Francesco , Pastori Daniele , Crea Filippo , Arbustini Eloisa , Alfonso Fernando , Prati Francesco 
Published: June 2022

AbstractAimsThe aim of this study was to assess the morphological characteristics and prognostic implications of the optical coherence tomography (OCT)-derived lipid core burden index (LCBI).Methods and resultsOCT-LCBI was assessed in 1003 patients with 1-year follow-up from the CLIMA multicentre registry using a validated software able to automatically obtain a maximum OCT-LCBI in 4 mm (maxOCT-LCBI4mm). Primary composite clinical endpoint included cardiac death, myocardial infarction, and target-vessel revascularization. A secondary analysis using clinical outcomes of CLIMA study was performed. Patients with a maxOCT-LCBI4mm ≥ 400 showed higher prevalence of fibrous cap thickness (FCT) &lt;75 μm [odds ratio (OR) 1.43, 95% confidence interval (CI) 1.03–1.99; P = 0.034], lipid pool arc &gt;180° (OR 3.93, 95%CI 2.97–5.21; P &lt; 0.001), minimum lumen area &lt;3.5 mm2 (OR 1.5, 95%CI 1.16–1.94; P = 0.002), macrophage infiltration (OR 2.38, 95%CI 1.81–3.13; P &lt; 0.001), and intra-plaque intimal vasculature (OR 1.34, 95%CI 1.05–1.72; P = 0.021). A maxOCT-LCBI4mm ≥400 predicted the primary endpoint [adjusted hazard ratio (HR) 1.86, 95%CI 1.1–3.2; P = 0.019] as well as the CLIMA endpoint (HR 2.56, 95%CI 1.24–5.29; P = 0.011). Patients with high lipid content and thin FCT &lt; 75 µm were at higher risk for adverse events (HR 4.88, 95%CI 2.44–9.72; P &lt; 0.001).ConclusionsA high maxOCT-LCBI4mm was related to poor outcome and vulnerable plaque features. This study represents a step further in the automated assessment of the coronary plaque risk profile.
Cost-effectiveness of clopidogrel vs. ticagrelor in patients of 70 years or older with non-ST-elevation acute coronary syndrome
Authors: van den Broek Wout W A , van Paassen Jacqueline G , Gimbel Marieke E , Deneer Vera H M , ten Berg Jurriën M , Vreman Rick A 
Published: June 2022

Abstract

Objective
The POPular AGE trial showed that clopidogrel significantly reduced bleeding risk compared with ticagrelor without any signs of an increase in thrombotic events. The aim of this analysis was to estimate the long-term cost-effectiveness of clopidogrel compared with ticagrelor in these patients aged 70 years or older with non-ST-elevation acute coronary syndrome (NSTE-ACS).

Methods and results
A 1-year decision tree based on the POPular AGE trial in combination with a lifelong Markov model was developed to compare clopidogrel with ticagrelor in terms of clinical outcomes, costs, and quality-adjusted life years (QALYs) in elderly patients (above 70 year) with NSTE-ACS. Cost-effectiveness was assessed from a Dutch healthcare system perspective. Events rates and utility data observed in the POPular AGE trial were combined with lifetime projections to evaluate costs and effects for a fictional cohort of 1000 patients. Treatment with clopidogrel instead of ticagrelor led to a cost saving of €1484 575 (€1485 per patient) and a decrease of 10.96 QALYs (0.011 QALY per patient) in the fictional cohort. In an alternative base case with equal distribution over health states in the first year, treatment with clopidogrel led to an increase in QALYs. In all scenario analyses, treatment with clopidogrel was cost-saving.

Conclusion
Clopidogrel is a cost-saving alternative to ticagrelor in elderly patients after NSTE-ACS, though regarding overall cost-effectiveness clopidogrel was not superior to ticagrelor, as it resulted in a small negative effect on QALYs. However, based on the results of the alternative base case and clinical outcomes of the POPular AGE trial, clopidogrel could be a reasonable alternative to ticagrelor for elderly NSTE-ACS patients with a higher bleeding risk.
Are non-invasive estimations of plasma volume an accurate measure of congestion in patients with chronic heart failure?
Authors: Cuthbert J J , Pellicori P , Rigby A S , Abel A A I , Kalvickbacka-Bennet A , Shah P , Kearsley J W , Kazmi S , Cleland J G F , Clark A L 
Published: June 2022

Abstract

Aims
We report associations between different formulae for estimating plasma volume status (PVS) and clinical and ultrasound markers of congestion in patients with chronic heart failure (CHF) enrolled in the Hull Lifelab registry.

Methods and results
Cohort 1 comprised patients with data on signs and symptoms at initial evaluation (n = 3505). Cohort 2 included patients with ultrasound assessment of congestion [lung B-line count, inferior vena cava (IVC) diameter, jugular vein distensibility (JVD) ratio] (N = 341). Two formulae for PVS were used: (a) Hakim (HPVS) and (b) Duarte (DPVS). Results were compared with clinical and ultrasound markers of congestion. Outcomes assessed were mortality and the composite of heart failure (HF) hospitalisation and all-cause mortality. In cohort 1, HPVS was associated with mortality [hazard ratio (HR) per unitary increase = 1.02 (1.01–1.03); P &lt; 0.001]. In cohort 2, HPVS was associated with B-line count (HR) = 1.05 [95% confidence interval (CI) (1.01–1.08); P = 0.02] and DPVS with the composite outcome [HR = 1.26 (1.01–1.58); P = 0.04]. HPVS and DPVS were strongly related to haemoglobin concentration and HPVS to weight. After multivariable analysis, there were no strong or consistent associations between PVS and measures of congestion, severity of symptoms, or outcome. By contrast, log[NTproBNP] was strongly associated with all three.

Conclusion
Amongst patients with CHF, HPVS and DPVS are not strongly or consistently associated with clinical or ultrasound evidence of congestion, nor clinical outcomes after multivariable adjustment. They appear only to be surrogates of the variables from which they are calculated with no intrinsic clinical utility.
Trends in antibiotic prescribing in Dutch general practice and determinants of nonprudent antibiotic prescriptions
Authors: Janssen Manon W H , de Bont Eefje G P M , Hoebe Christian J P A , Cals Jochen W L , den Heijer Casper D J 
Published: June 2022

Abstract

Background
Antibiotic resistance is mainly driven by (incorrect) use of antibiotics. Most antibiotics are prescribed in family medicine. Therefore, regularly monitoring of antibiotic prescriptions and evaluation of their (non-) prudent use in primary care is warranted.

Objectives
The aim of this study was to determine time trends in antibiotic prescriptions by Dutch family physicians (FPs) and to identify determinants of nonprudent antibiotic prescriptions by Dutch FPs.

Methods
Retrospective study among 27 Dutch general practices from the Research Network Family Medicine Maastricht, from 2015 to 2019.

Results
In total 801,767 patient years were analysed. Antibiotic prescriptions mainly increased in patients aged 65+ while prescriptions mainly decreased in patients below 65 years. Nonprudent antibiotic prescriptions decreased from 2015 to 2019 with the highest percentage of decline found in skin infections (66.9% [2015] to 53.9% [2019]). Overall, higher likelihood of nonprudent antibiotic prescriptions was found among men (odds ratio [OR] 4.11, 95% confidence interval [CI]: 3.91–4.33), patients aged 80+ (OR 1.44, 95% CI: 1.03–2.01; reference category ≤17 years), patients with comedication (OR 1.24, 95% CI: 1.17–1.31), and patients in urban general practices (OR 1.47, 95% CI: 1.38–1.56).

Conclusions
Antibiotic prescriptions increased over time in the elderly aged categories. Although an overall decrease in nonprudent antibiotic prescriptions was established from 2015 to 2019, percentages of nonprudent prescriptions remained high for skin infections and respiratory tract infections. Additionally, men, elderly aged patients (80+), patients with comedication and patients in urban general practices were more likely to receive nonprudent antibiotic prescriptions. Our results will help FPs to prioritize optimalization of antibiotic prescriptions in family medicine.