bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating and implementing block jackknife resampling Mendelian randomization to mitigate bias induced by overlapping samples
Authors: Fang Si , Hemani Gibran , Richardson Tom G , Gaunt Tom R , Davey Smith George 
Published: August 2022

Abstract
Participant overlap can induce overfitting bias into Mendelian randomization (MR) and polygenic risk score (PRS) studies. Here, we evaluated a block jackknife resampling framework for genome-wide association studies (GWAS) and PRS construction to mitigate overfitting bias in MR analyses and implemented this study design in a causal inference setting using data from the UK Biobank. We simulated PRS and MR under three scenarios: (1) using weighted SNP estimates from an external GWAS, (2) using weighted SNP estimates from an overlapping GWAS sample and (3) using a block jackknife resampling framework. Based on a P-value threshold to derive genetic instruments for MR studies (P &lt; 5 × 10−8) and a 10% variance in the exposure explained by all SNPs, block-jackknifing PRS did not suffer from overfitting bias (mean R2 = 0.034) compared with the externally weighted PRS (mean R2 = 0.040). In contrast, genetic instruments derived from overlapping samples explained a higher variance (mean R2 = 0.048) compared with the externally derived score. Overfitting became considerably more severe when using a more liberal P-value threshold to construct PRS (e.g. P &lt; 0.05, overlapping sample PRS mean R2 = 0.103, externally weighted PRS mean R2 = 0.086), whereas estimates using jackknife score remained robust to overfitting (mean R2 = 0.084). Using block jackknife resampling MR in an applied analysis, we examined the effects of body mass index on circulating biomarkers which provided comparable estimates to an externally weighted instrument, whereas the overfitted scores typically provided narrower confidence intervals. Furthermore, we extended this framework into sex-stratified, multivariate and bidirectional settings to investigate the effect of childhood body size on adult testosterone levels.
Crohn’s Disease Patients Uniquely Contain Inflammatory Responses to Flagellin in a CD4 Effector Memory Subset
Authors: Morgan Nadine N , Duck Lennard W , Wu Jiongru , Rujani Mahmud , Thomes Paul G , Elson Charles O , Mannon Peter J 
Published: August 2022

Abstract

Background
Specific microbial antigens stimulate production of antibodies indicative of the aberrant immune response in Crohn’s disease (CD). We tested for T cell reactivity linkage to B cell responses and now report on the prevalence, functionality, and phenotypic differences of flagellin-specific T cells among CD patients, ulcerative colitis (UC) patients, and control subjects and association with clinical features and flagellin seropositivity within CD patients.

Methods
Sera from non–inflammatory bowel disease control subjects, CD patients, and UC patients were probed for antibody reactivity to gut bacterial recombinant flagellin antigens. Peripheral blood mononuclear cells were measured for flagellin antigen (CBir1, A4 Fla2, FlaX) or control (Candida albicans, and CytoStim) reactivity analyzed by flow cytometry for CD154 and cytokine expression on CD4+ T cells. Supernatants from post–flagellin-stimulated and unstimulated cells were used to measure effects on epithelial barrier function.

Results
CD patients had a significantly higher percentage of flagellin-specific CD154+ CD4+ cells that have an effector memory T helper 1 and T helper 17 phenotype compared with UC patients and healthy control subjects. There was a positive correlation between the frequency of flagellin-specific CD154+ CD4+ effector memory T cells and serum levels of anti-flagellin immunoglobulin G in the CD patients. In addition, A4 Fla2–reactive T cells from active CD patients produced cytokines that can decrease barrier function in a gut epithelium.

Conclusions
These findings demonstrate a Crohn’s-associated flagellin-reactive CD4 cell subset distinct from UC patients and control subjects. There is a link between these cells and flagellin seropositivity. This CD4 cell subset could reflect a particular endophenotype of CD, leading to novel insight into its pathology and treatment.
Evidence of Interventions and Strategies to Bridge the Quality Improvement Gap Led by HCW at the Frontline in SSA: A Scoping Review
Authors: Ng’ang’a Ruthpearl , Kimani Kellen N , Okutoyi Lydia , Adam Mary B 
Published: August 2022

Abstract

Introduction
Poor quality health care is a significant cause of preventable deaths, especially in low- and middle-income countries (LMICs). Quality improvement is multifaceted and includes strategies such as standard setting, quality assurance and clinic audits. In order to move quality improvement in health care into every day practice it is essential to fully engage the frontline where health care is delivered. The objective of this scoping review is to investigate front line health care worker line led quality improvement in Sub Saharan Africa (SSA).

Methods
We conducted a scoping review to identify, map and synthesize evidence on health care worker led quality improvement initiatives in Sub Sahara Africa using electronic databases PubMed, Cochrane, Embase, CINAHL, Scopus and Psychinfo to identify peer-reviewed literature published between January 2000 and January 2021. To identify grey literature, we used the same search terms in google search to a maximum of 10 pages or when there was no new information. All evidence was scored based on the 6 criteria described by Backhouse et al., which clearly distinguish quality improvement from clinical audit and research. Inclusion criteria were studies that involved frontline health care workers to test “change ideas” and used data systems to measure improvement in service delivery.

Results
A total of 75 records were identified and including 52 from the peer review search and 23 records from the grey literature search. Only 15 of 47 countries had publications (peer-review or grey literature) describing QI initiatives. Most quality improvement (QI) initiatives were multicomponent and included knowledge transfer, skills building, mentorship and learning visits. Most publications reported QI initiatives aimed at reproductive, maternal, neonatal and child health (n=23) and HIV (n=14) service delivery. Only 6 had experimental designs. No publications were identified prior to 2012 and a rapid escalation of published quality improvement initiatives from 2012 to 2020 was seen.

Conclusion
QI is in the very nascent stage in SSA. Most large-scale public health QI initiatives are sector specific, siloed, and donor driven. QI initiatives within sector specific programs have not moved horizontally and have had limited ability to change the broader system. Energy must be exerted to change the status quo. Making health care safer and more effective is not spontaneous.
Reassessing the Relationship between Equality and Vulnerability in relation to Refugees and Asylum Seekers in the ECtHR: The MSS Case 10 Years On
Authors: Yahyaoui Krivenko Ekaterina 
Published: August 2022

Abstract
This article reassesses the impact of the concept of vulnerability as it emerges from the MSS v Belgium and Greece case of the European Court of Human Rights, and subsequent developments relating to the rights of refugees and asylum seekers. This examination is performed in light of the human rights principle of equality. The choice of the principle of equality is justified by frequent claims that vulnerability allows more substantive equality outcomes. Examining the concrete functions and consequences of the recourse to vulnerability in relation to refugees and asylum seekers in post-MSS judgments, the article argues that, in the European setting at least, vulnerability produces a set of negative consequences. More specifically, the article demonstrates that the deployment of the language of vulnerability results in the positioning of refugees and asylum seekers as passive recipients of benevolence rather than as active rights claimants, the introduction of additional layers of subjectively constructed stratification, and the erasure of the specificity of refugees’ and asylum seekers’ experience. It is contended that these negative consequences of deploying the concept of vulnerability can be mitigated if recourse to vulnerability is accompanied by a highly skilled technical discussion of the principles of substantive equality as they are known in international human rights law, including such aspects of substantive equality as structural discrimination and intersectionality.
The Immunoglobulin M Response to Pneumococcal Polysaccharide Vaccine Is Sufficient for Conferring Immunity
Authors: Cravens Matthew P , Alugupalli Akhil S , Sandilya Vijay K , McGeady Stephen J , Alugupalli Kishore R 
Published: August 2022

Abstract
In mice, pneumococcal polysaccharide (PPS) vaccines generate antigen-specific immunoglobulin M (IgM) and immunoglobulins G1, G2, and G3. Antibody and complement-dependent opsonophagocytosis correlates with the protection induced by PPS vaccines in vivo. Since IgM is a very efficient immunoglobulin isotype in activating the complement system, we evaluated whether anti-PPS IgM alone is sufficient to confer protective immunity to Streptococcus pneumoniae. We found that immunization of wild-type and activation-induced cytidine deaminase–deficient mice capable of producing only IgM with Pneumovax 23 generated comparable anti-PPS IgM and resistance to lethal systemic challenge with S pneumoniae. These data suggest that an IgM response to PPS vaccines is sufficient for conferring immunity.
Analytics to monitor local impact of the Protecting Access to Medicare Act’s imaging clinical decision support requirements
Authors: Valtchinov Vladimir I , Murphy Shawn N , Lacson Ronilda , Ikonomov Nikolay , Zhai Bingxue K , Andriole Katherine , Rousseau Justin , Hanson Dick , Kohane Isaac S , Khorasani Ramin 
Published: August 2022

Abstract

Objective
This study aimed is to: (1) extend the Integrating the Biology and the Bedside (i2b2) data and application models to include medical imaging appropriate use criteria, enabling it to serve as a platform to monitor local impact of the Protecting Access to Medicare Act’s (PAMA) imaging clinical decision support (CDS) requirements, and (2) validate the i2b2 extension using data from the Medicare Imaging Demonstration (MID) CDS implementation.

Materials and Methods
This study provided a reference implementation and assessed its validity and reliability using data from the MID, the federal government’s predecessor to PAMA’s imaging CDS program. The Star Schema was extended to describe the interactions of imaging ordering providers with the CDS. New ontologies were added to enable mapping medical imaging appropriateness data to i2b2 schema. z-Ratio for testing the significance of the difference between 2 independent proportions was utilized.

Results
The reference implementation used 26 327 orders for imaging examinations which were persisted to the modified i2b2 schema. As an illustration of the analytical capabilities of the Web Client, we report that 331/1192 or 28.1% of imaging orders were deemed appropriate by the CDS system at the end of the intervention period (September 2013), an increase from 162/1223 or 13.2% for the first month of the baseline period, December 2011 (P = .0212), consistent with previous studies.

Conclusions
The i2b2 platform can be extended to monitor local impact of PAMA’s appropriateness of imaging ordering CDS requirements.
Comparison of Dried Blood Spot and Microtube Techniques for Trace Element Quantification by ICP-MS
Authors: Perrais Maïwenn , Thomas Aurélien , Augsburger Marc , Lenglet Sébastien 
Published: August 2022

AbstractMicrosampling techniques became more popular in the last decades, and their use for common analyses such as trace element quantification by inductively coupled plasma mass spectrometry (ICP-MS) has been investigated. We decided to compare two of these techniques (dried blood spots and microtubes) to evaluate their potential for the analysis of 12 trace elements in human whole blood: aluminum (Al), total arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), manganese (Mn), molybdenum (Mo), nickel (Ni), lead (Pb), selenium (Se) and zinc (Zn). Signal contributions from blank filter paper and instability at room temperature for several elements in the dried blood spot samples restrained our enthusiasm for the use of this technique. Conversely, microtube samples presented low background contamination and good stability under different temperature conditions. Therefore, our results demonstrate that the use of microtubes is more suitable than dried blood spots for trace element quantification in human blood, both in research and routine analysis.
MLNe: Simulating and estimating effective size and migration rate from temporal changes in allele frequencies
Authors: Wang Jinliang 
Published: August 2022

AbstractIn studies of molecular ecology, conservation biology, and evolutionary biology, the current or recent effective size (Ne) of a population is frequently estimated from the marker genotype data of two or more temporally spaced samples of individuals taken from the population. Despite the developments of numerous Bayesian, likelihood, and moment estimators, only a couple of them can use both temporally and spatially spaced samples of individuals to estimate jointly the effective size (Ne) of and the migration rate (m) into a population. In this note, I describe new implementations of these joint estimators of Ne and m in software MLNe which runs on multiple platforms (Windows, Mac, Linux) with or without a graphical user interface (GUI), and has an integrated simulation module to simulate genotype data for investigating the impacts of various factors (such as sample size and sampling interval) on estimation precision and accuracy, exploits both message passing interface (MPI) and openMP for parallel computations using multiple cores and nodes to speed up analysis. The program does not require data pre-processing and accepts multiple formats of a file of original genotype data and a file of parameters as input. The GUI facilitates data and parameter inputs and produces publication-quality output graphs, while the non-GUI version of software is convenient for batch analysis of multiple datasets as in simulations. MLNe will help advance the analysis of temporal genetic marker data for estimating Ne of and m between populations, which are important parameters that will help biologists for the conservation management of natural and managed populations. MLNe can be downloaded free from the website http://www.zsl.org/science/research/software/.
Recognizing a Mediastinal Mass: A Case of Primary Mediastinal Large B-Cell Lymphoma With Pruritus in a 23-Year-Old Adult Male Sailor
Authors: Kolberg Courtney , Doman Elizabeth , Mignano Salvatore , Mullikin Dolores , Vasta Lauren , Wadzinski William , Foster Brian 
Published: August 2022

ABSTRACT
Primary mediastinal large B-cell lymphoma (PMBCL) is a rare, non-Hodgkin, B-cell lymphoma thought to originate from thymic B cells, which occurs primarily in young adults such as in the active duty population. Primary mediastinal large B-cell lymphoma (PMBCL) presents as a large mediastinal mass, posing risks to the cardiopulmonary safety of patients and challenging the routine approach to diagnosis. We describe a case of a 23-year-old male sailor who presented to sick call on his ship while in port with shortness of breath, night sweats, 50-pound weight loss, and pruritic punched-out lesions on all extremities. An initial chest X-ray showed a large consolidation. After being seen in the pulmonary medicine clinic 5 weeks after his initial presentation, the patient was admitted to the intensive care unit after computed tomography of his chest revealed a mediastinal mass, causing compression of both the right bronchus and superior vena cava with a large pericardial effusion. Empiric high-dose dexamethasone was initiated before a formal diagnosis due to his significant risk for cardiopulmonary compromise. Following diagnosis and two cycles of chemotherapy, the patient was transferred to a medical oncology facility in the continental USA. This case demonstrates the need to educate all military providers to recognize the presentation of mediastinal masses in active duty service members and the importance of urgently escalating these patients to higher levels of care in order to avoid life-threatening complications.
The environments of the radio galaxy population in simba
Authors: Thomas Nicole , Davé Romeel 
Published: August 2022

ABSTRACT
We investigate the environmental properties of the z = 0 radio galaxy population using the simba cosmological hydrodynamic simulation. We identify centrals and satellites from a population of high and low excitation radio galaxies (HERGs and LERGs) in simba, and study their global properties. We find that $\sim 20{{\ \rm per\ cent}}$ of radio galaxies are satellites, and that there are insignificant differences in the global properties of LERGs based on their central/satellite classification. HERG satellites display lower values of star formation, 1.4 GHz radio luminosity, and Eddington fractions than HERG centrals. We further investigate the environments of radio galaxies and show that HERGs typically live in less dense environments, similar to star-forming galaxies. The environments of high-mass LERGs are similar to non-radio galaxies, but low-mass LERGs live in underdense environments similar to HERGs. LERGs with overmassive black holes reside in the most dense environments, while HERGs with overmassive black holes reside in underdense environments. The richness of a LERG’s environment decreases with increasing Eddington fraction, and the environments of all radio galaxies do not depend on radio luminosity for $\, P_{\rm 1.4~GHz}\lt 10^{24} \rm {~W~Hz}^{-1}$. Complementing these results, we find that LERGs cluster on the same scale as the total galaxy population, while multiple HERGs are not found within the same dark matter halo. Finally, we show that high density environments support the growth of HERGs rather than LERGs at z = 2. Simba predicts that with more sensitive surveys, we will find populations of radio galaxies in environments much similar to the total galaxy population.
The Zwicky Transient Facility phase I sample of hydrogen-rich superluminous supernovae without strong narrow emission lines
Authors: Kangas T , Yan Lin , Schulze S , Fransson C , Sollerman J , Lunnan R , Omand C M B , Andreoni I , Burruss R , Chen T-W , Drake A J , Fremling C , Gal-Yam A , Graham M J , Groom S L , Lezmy J , Mahabal A A , Masci F J , Perley D , Riddle R , Tartaglia L , Yao Y 
Published: August 2022

ABSTRACT
We present a sample of 14 hydrogen-rich superluminous supernovae (SLSNe II) from the Zwicky Transient Facility (ZTF) between 2018 and 2020. We include all classified SLSNe with peaks Mg &lt; −20 mag with observed broad but not narrow Balmer emission, corresponding to roughly 20 per cent of all hydrogen-rich SLSNe in ZTF phase I. We examine the light curves and spectra of SLSNe II and attempt to constrain their power source using light-curve models. The brightest events are photometrically and spectroscopically similar to the prototypical SN 2008es, while others are found spectroscopically more reminiscent of non-superluminous SNe II, especially SNe II-L. 56Ni decay as the primary power source is ruled out. Light-curve models generally cannot distinguish between circumstellar interaction (CSI) and a magnetar central engine, but an excess of ultraviolet (UV) emission signifying CSI is seen in most of the SNe with UV data, at a wide range of photometric properties. Simultaneously, the broad H α profiles of the brightest SLSNe II can be explained through electron scattering in a symmetric circumstellar medium (CSM). In other SLSNe II without narrow lines, the CSM may be confined and wholly overrun by the ejecta. CSI, possibly involving mass lost in recent eruptions, is implied to be the dominant power source in most SLSNe II, and the diversity in properties is likely the result of different mass loss histories. Based on their radiated energy, an additional power source may be required for the brightest SLSNe II, however – possibly a central engine combined with CSI.
Safety and effectiveness of baricitinib for rheumatoid arthritis in Japanese clinical practice: 24-week results of all-case post-marketing surveillance
Authors: Takagi Michiaki , Atsumi Tatsuya , Matsuno Hiroaki , Tamura Naoto , Fujii Takao , Okamoto Nami , Takahashi Nobunori , Nakajima Atsuo , Nakajima Ayako , Tsujimoto Naoto , Nishikawa Atsushi , Ishii Taeko , Takeuchi Tsutomu , Kuwana Masataka 
Published: August 2022

ABSTRACT

Objectives
To assess the safety and effectiveness of baricitinib treatment for rheumatoid arthritis (RA) in real-world clinical practice.

Methods
This ongoing all-case post-marketing surveillance study (starting September 2017) includes all patients with RA treated with baricitinib in Japan. Safety and effectiveness (disease activity) were assessed for 24 weeks.

Results
Safety analyses to February 2021 included 4731 patients (initial baricitinib dose: 4 mg/day, n = 3058; 2 mg/day, n = 1661; other, n = 12); 1059 (22.38%) were ≥75 years and 3362 (71.06%) previously received biologic therapy. The overall observational period was 1863.14 patient-years; 1174 (24.82%) patients discontinued baricitinib before Week 24, mostly for lack of effectiveness (n = 478; 10.10%). Adverse events occurred in 1271 (26.87%) patients [serious: 203 (4.29%); death: 18 (0.38%)]. The incidence of herpes zoster, hepatic function disorder, and serious infection was 3.09%, 2.77%, and 1.90%, respectively. Malignancy occurred in 17 patients (0.36%) and major adverse cardiovascular events in seven patients (0.15%). Among patients with effectiveness data, at least 26.57% (Boolean) achieved remission at Week 24.

Conclusions
This large nationwide surveillance study evaluated the safety and effectiveness of 24 weeks of baricitinib for RA in real-world clinical practice. Continued surveillance of long-term safety is ongoing.
Co-occurrence of pneumoconiosis with COPD, pneumonia and lung cancer
Authors: Rayens N T , Rayens E A , Tighe R M 
Published: August 2022

Abstract

Background
Pneumoconiosis is a well-documented occupational disease that is linked to conditions such as chronic obstructive pulmonary disease (COPD), pneumonia and congestive heart failure. Pneumoconiosis prevalence has decreased in the United States, but it remains implicated in tens of thousands of deaths worldwide per year.

Aims
To provide a recent update on associations of pneumoconiosis and smoking status with various pulmonary diseases in the United States.

Methods
The CDC’s National Vital Statistics System was analysed on the entity axis using ICD-10 codes for pulmonary disease and potential lung injury with a cohort of those aged 15 and older during the years 2010–2019. The cases of evaluated diseases were scaled to rates per 100 000 and compared through analysis of variance.

Results
Pneumoconiosis and smoking history were each associated with an increased rate of COPD, but combined, were associated with an even higher rate of COPD than either factor alone. Smoking history was associated with an increased rate of lung cancer, but pneumoconiosis status was only linked to increased lung cancer prevalence in non-smokers. Both pneumoconiosis and smoking were associated with an increased rate of pneumonia, but combined, had no deviation from the pneumonia rate in those with pneumoconiosis alone. Finally, pneumoconiosis status was associated with decreased rates of non-lung cancers and sepsis.

Conclusions
Although pneumoconiosis has become less common in the United States through regulatory and industrial shifts, it is still a significant risk factor for co-occurring pulmonary diseases and will likely remain relevant as international demands for mining, construction and manufacturing change.