bluuebunny/crossref_metadata_2025 huggingface dataset:
A pair of early- and late-forming galaxy cluster samples: A novel way of studying halo assembly bias assisted by a constrained simulation
Authors: Lin Yen-Ting , Miyatake Hironao , Guo Hong , Chiang Yi-Kuan , Chen Kai-Feng , Lan Ting-Wen , Chang Yu-Yen
Published: August 2022

The halo assembly bias, a phenomenon referring to dependencies of the large-scale bias of a dark matter halo other than its mass, is a fundamental property of the standard cosmological model. First discovered in 2005 from the Millennium Run simulation, it has been proven very difficult to be detected observationally, with only a few convincing claims of detection so far. The main obstacle lies in finding an accurate proxy of the halo formation time. In this study, by utilizing a constrained simulation that can faithfully reproduce the observed structures larger than 2 Mpc in the local universe, for a sample of 634 massive clusters at z ≤ 0.12, we found their counterpart halos in the simulation and used the mass growth history of the matched halos to estimate the formation time of the observed clusters. This allowed us to construct a pair of early- and late-forming clusters, with a similar mass as measured via weak gravitational lensing, and large-scale biases differing at the ≈3σ level, suggestive of the signature of assembly bias, which is further corroborated by the properties of cluster galaxies, including the brightest cluster galaxy and the spatial distribution and number of member galaxies. Our study paves a way to further detect assembly bias based on cluster samples constructed purely on observed quantities.
The impact of analyst forecast errors on fundamental indexation: the Australian evidence
Authors: Casavecchia Lorenzo , Hambusch Gerhard , Hitchen Justin
Published: August 2022

Evidence from many developed markets suggests that fundamental indices outperform capitalisation-weighted indices. Existing studies suspect a story of market mispricing, yet a mechanism has not been identified. Using Australian data, we study the relation between analyst forecast errors and the performance of various fundamental indices. We find that fundamental indices contain a relatively higher exposure to stocks with low analyst long-term growth forecasts. Valuations for these stocks are ex ante overly pessimistic and drive the statistical significance of alphas produced by fundamental indexation. We show how hedging against analyst forecast errors can generate additional alpha for investors using fundamental indexation.
Pattern selection for convective flow in a liquid bridge subjected to remote thermal action
Authors: Gaponenko Y. , Yano T. , Nishino K. , Matsumoto S. , Shevtsova V.
Published: August 2022

The stability of thermocapillary/buoyant flows is affected by a remote thermal source. We present a nonlinear two-phase computational study of convection in a liquid bridge that develops under the action of Marangoni and buoyancy forces as well as under the influence of distant thermal disturbances. The gas phase (air) occupies a typical annular container holding a liquid bridge (n-decane, Pr = 14), and the disturbances are locally imposed in the form of hot/cold spots on the outer wall of the container. The hydrothermal wave instability and pattern selection have been explored for two temperature differences ΔT by varying the intensity of thermal source Hf over a wide range. Not far from the critical point, in all the cases, the instability emerges in the form of a standing wave, but the azimuthal wavenumber depends on whether the external perturbation is caused by cooling (m = 2) or by heating (m = 1). Further into supercritical area, 45% above the threshold, in the region with thermal perturbations −200<Hf<50, the flow pattern comprises, but is not limited to, a hydrothermal traveling wave with the azimuthal wavenumber m = 2. For hotter perturbations, the instability develops either in the form of traveling or standing waves, depending on Hf, with the prevailing mode m = 1, but with a strong presence of other modes.
Recognition Awards in Pathology Specialty Societies: Gender Analysis Among Physician Recipients
Authors: Wobker Sara E , Ginter Paula S , Parra-Herran Carlos , Schwartz Lauren E , Booth Garrett S , Fitzhugh Valerie A , Silver Julie K , Khani Francesca
Published: August 2022

Objectives

Recognition awards build physician reputation and facilitate career advancement. We hypothesize women physicians are underrepresented as award recipients by pathology medical societies compared with representation in the specialty.

Methods

We analyzed publicly available online information about physician recipients (January 2015 to December 2021) from three general pathology society websites. Recipient gender was determined by pronoun use, first name, and photograph. Representation was compared with Association of American Medical Colleges (AAMC) specialty data from 2015 and 2019, which showed a minimum of 36.7% women pathologists in 2015 and up to 43.4% in 2019.

Results

Twenty-six awards and 230 physician recipients were included in the analysis. A total of 159 (69.1%) men physicians and 71 (30.9%) women physicians received awards. Overall, women physicians were underrepresented in recognition awards compared with AAMC benchmarks. Prestigious awards (defined as those that recognize a person’s body of work over time) showed a similar disparity with 22 (30.1%) of 73 recipients being women. Men physicians were more likely to receive multiple awards.

Conclusions

Women physicians are underrepresented overall for recognition awards by pathology medical societies. Disparities are greater for prestigious awards. Further research is needed to better understand the reasons for these findings and how they affect women physicians’ careers.
Dynamic regulation of lipid metabolism in the placenta of in vitro and in vivo models of gestational diabetes mellitus
Authors: Kim So Young , Lee Young Joo , An Sung-Min , Kim Min Jae , Jeong Jea Sic , Kim Da Som , Lim Yong , Jung Eui-Man , Kim Seung-Chul , An Beum-Soo
Published: August 2022

The purpose of this study was to investigate lipid metabolism in the placenta of gestational diabetes mellitus individuals and to evaluate its effect on the fetus. We examined the expression of lipogenesis- and lipolysis-related proteins in the in vitro and in vivo gestational diabetes mellitus placenta models. The levels of sterol regulatory element binding protein-1c were increased, and fat accumulated more during early hyperglycemia, indicating that lipogenesis was stimulated. When hyperglycemia was further extended, lipolysis was activated due to the phosphorylation of hormone-sensitive lipase and expression of adipose triglyceride lipase. In the animal model of gestational diabetes mellitus and in the placenta of gestational diabetes mellitus patients during the extended stage of gestational diabetes mellitus, the expression of sterol regulatory element binding protein-1c decreased and the deposition of fat increased. Similar to the results obtained in the in vitro study, lipolysis was enhanced in the animal and human placenta of extended gestational diabetes mellitus. These results suggest that fat synthesis may be stimulated by lipogenesis in the placenta when the blood glucose level is high. Subsequently, the accumulated fat can be degraded by lipolysis and more fat and its metabolites can be delivered to the fetus when the gestational diabetes mellitus condition is extended at the late stage of gestation. Imbalanced fat metabolism in the placenta and fetus of gestational diabetes mellitus patients can cause metabolic complications in the fetus, including fetal macrosomia, obesity, and type 2 diabetes mellitus.
Body and peripersonal space representations in chronic stroke patients with upper limb motor deficits
Authors: Bassolino Michela , Franza Matteo , Guanziroli Eleonora , Sorrentino Giuliana , Canzoneri Elisa , Colombo Maria , Crema Andrea , Bertoni Tommaso , Mastria Giulio , Vissani Matteo , Sokolov Arseny A , Micera Silvestro , Molteni Franco , Blanke Olaf , Serino Andrea
Published: August 2022

The continuous stream of multisensory information between the brain and the body during body–environment interactions is crucial to maintain the updated representation of the perceived dimensions of body parts (metric body representation) and the space around the body (the peripersonal space). Such flow of multisensory signals is often limited by upper limb sensorimotor deficits after stroke. This would suggest the presence of systematic distortions of metric body representation and peripersonal space in chronic patients with persistent sensorimotor deficits. We assessed metric body representation and peripersonal space representation in 60 chronic stroke patients with unilateral upper limb motor deficits, in comparison with age-matched healthy controls. We also administered a questionnaire capturing explicit feelings towards the affected limb. These novel measures were analysed with respect to patients’ clinical profiles and brain lesions to investigate the neural and functional origin of putative deficits. Stroke patients showed distortions in metric body representation of the affected limb, characterized by an underestimation of the arm length and an alteration of the arm global shape. A descriptive lesion analysis (subtraction analysis) suggests that these distortions may be more frequently associated with lesions involving the superior corona radiata and the superior frontal gyrus. Peripersonal space representation was also altered, with reduced multisensory facilitation for stimuli presented around the affected limb. These deficits were more common in patients reporting pain during motion. Explorative lesion analyses (subtraction analysis, disconnection maps) suggest that the peripersonal space distortions would be more frequently associated with lesions involving the parietal operculum and white matter frontoparietal connections. Moreover, patients reported altered feelings towards the affected limb, which were associated with right brain damage, proprioceptive deficits and a lower cognitive profile. These results reveal implicit and explicit distortions involving metric body representation, peripersonal space representation and the perception of the affected limb in chronic stroke patients. These findings might have important clinical implications for the longitudinal monitoring and the treatments of often-neglected deficits in body perception and representation.
The Conceptual and Methodological Characteristics of Ageism During COVID-19: A Scoping Review of Empirical Studies
Authors: Werner Perla , AboJabel Hanan
Published: August 2022

Background and Objectives

Printed and social media, as well as professional and scholarly platforms, have extensively discussed the proliferation of ageism during the coronavirus disease 2019 (COVID-19) pandemic. However, no study has systematically examined the body of knowledge on the topic. Framed around the characteristics of ageism in general, the aim of this review was to identify and characterize the conceptual and methodological underpinnings of the global, peer-reviewed, and empirical literature on ageism during COVID-19.

Research Design and Methods

We conducted a scoping review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, using PubMed, CINAHL, AgeLine, and PsycINFO. Quantitative and/or qualitative, English-language, and peer-reviewed articles were included. Data were tabulated and synthesized.

Results

Thirty six articles examining ageism during the COVID-19 pandemic met inclusion criteria. Most were quantitative (64%) and cross-sectional (81%). The level, correlates, and consequences of ageism during the pandemic were similar to the ones reported before it. Studies about ageism during COVID-19 had similar conceptualization and measurement problems to those before the pandemic.

Discussion and Implications

Empirical studies did not find ageism during COVID-19 to be a unique phenomenon, as suggested by the media. More theoretically sound and methodologically rigorous studies, using longitudinal designs and validated unique measures are needed to examine this unique phenomenon.
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

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 < 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 < 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

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

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

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

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

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

Microsampling 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

In 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/.
Management of cross-border mobilities during the SARS-CoV-2 pandemic in Europe and implications for public health provision to migrants
Authors: Kamenshchikova Alena , Hargreaves Sally , Chandler Clare I R
Published: August 2022

Although many countries introduced border-control measures to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), migrants on the move, like labour migrants and asylum seekers were trapped within the developing border politics. Here, we discuss how pre-existing gaps in international public health infrastructures have positioned migrants at a higher risk of SARS-CoV-2.
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

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

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

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 < −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

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

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.
Validation of the North Star Assessment for Limb-Girdle Type Muscular Dystrophies
Authors: James Meredith K , Alfano Lindsay N , Muni-Lofra Robert , Reash Natalie F , Sodhi Jassi , Iammarino Megan A , Moat Dionne , Shannon Kianna , McCallum Michelle , Richardson Mark , Eagle Michelle , Straub Volker , Marini-Bettolo Chiara , Lowes Linda P , Mayhew Anna G
Published: August 2022

Objective

The North Star Assessment for limb-girdle type muscular dystrophies (NSAD), a clinician-reported outcome measure (ClinRO) of motor performance, was initially developed and validated for use in dysferlinopathy, an autosomal recessive form of limb-girdle muscular dystrophy (LGMD R2/2B). Recent developments in treatments for limb-girdle muscular dystrophies (LGMD) have highlighted the urgent need for disease-specific ClinROs. The purpose of this study was to understand the ability of the NSAD to quantify motor function across the broad spectrum of LGMD phenotypes.

Methods

Assessments of 130 individuals with LGMD evaluated by the physical therapy teams at Nationwide Children’s Hospital and the John Walton Muscular Dystrophy Research Centre were included in the analysis. NSAD, 100-m timed test (100MTT), and Performance of Upper Limb 2.0 assessment data were collected. Psychometric analysis with Rasch measurement methods was used to examine the NSAD for suitability and robustness by determining the extent to which the observed data “fit” with predictions of those ratings from the Rasch model. The NSAD score was correlated with the 100MTT and Performance of Upper Limb 2.0 assessment scores for external construct validity.

Results

The NSAD demonstrated a good spread of items covering a continuum of abilities across both individuals who had LGMD and were ambulatory and individuals who had LGMD and were weaker and nonambulatory. Items fit well with the construct measured, validating a summed total score. The NSAD had excellent interrater reliability [intraclass correlation coefficient (ICC) = 0.986, 95% CI = 0.981–0.991] and was highly correlated with the 100MTT walk/run velocity (Spearman rho correlation coefficient of rs(134) = .92).

Conclusion

Although LGMD subtypes may differ in age of onset, rate of progression, and patterns of muscle weakness, the overall impact of progressive muscle weakness on motor function is similar. The NSAD is a reliable and valid ClinRO of motor performance for individuals with LGMD and is suitable for use in clinical practice and research settings.

Impact

Recent developments in potential pharmacological treatments for LGMD have highlighted the urgent need for disease-specific outcome measures. Validated and meaningful outcome measures are necessary to capture disease presentation, to inform expected rates of progression, and as endpoints for measuring the response to interventions in clinical trials. The NSAD, a scale of motor performance for both individuals who have LGMD and are ambulatory and those who are nonambulatory, is suitable for use in clinical and research settings.
Responding to a disease with resources from other diseases: Evidence from Zika vaccine research dynamics
Authors: Yaqub Ohid , Luna Javier A , Moore Duncan Aq , Yegros-Yegros Alfredo
Published: August 2022

Responding to health needs in one disease area might rely on being able to draw on research and funding oriented towards other disease areas. However, the tendency of medical research to cross-disease areas has received limited empirical consideration. An outbreak, in a disease area with little prior research or funding, means that any research response will necessarily be rich with cross-disease flows. This affords a setting that allows us to identify and examine the phenomenon over time. We estimate the extent to which the vaccine research community’s response to Zika virus drew on research and funding from other diseases. We find that a persistently low share of funding into Zika vaccine research was Zika-oriented. In contrast, a much higher share of knowledge inputs was oriented to Zika. The exercise serves to illustrate some general themes in priority setting for health research systems alongside some core features of vaccine innovation.
Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins
Authors: Liu Meifeng , Huang Liyu , Zhang Yan , Yan Zhaogui , Wang Nian
Published: August 2022

In previous studies, GA20 oxidase (GA20ox) has been identified to be an important enzyme in the biosynthesis of GA, and SHOOTMERISTEMLESS (STM) can repress the expression of GA20ox. In this study, the GATA transcription factor PdeGATA3 was identified in the poplar line NL895, and its overexpression (OE) transgenic lines showed a dwarf phenotype. RNA sequencing (RNA-Seq) analysis suggested that OE PdeGATA3 could promote the expression of PdeSTM and repress the expression of PdeGA20ox. Therefore, we hypothesized that PdeGATA3 would directly promote the expression of PdeSTM and that PdeSTM would repress the expression of PdeGA20ox. Four experiments, a dual-luciferase reporter assay, GUS transient coexpression assay, yeast one-hybrid assay and electrophoretic mobility shift assay, were conducted and verified that PdeGATA3 could promote the expression of PdeSTM by binding GATA-Boxes in its promoter. OE PdeSTM in poplar resulted in a dwarf phenotype and repressed the expression of PdeGA20ox. GA measurement of the OE PdeSTM and PdeGATA3 lines showed that GA3 and GA4 contents were significantly lower than those in the wild type (WT). Accordingly, we put forward a regulation model involving plant height regulation by PdeGATA3, PdeSTM and PdeGA20ox.
covSampler: A subsampling method with balanced genetic diversity for large-scale SARS-CoV-2 genome data sets
Authors: Cheng Yexiao , Ji Chengyang , Han Na , Li Jiaying , Xu Lin , Chen Ziyi , Yang Rong , Zhou Hang-Yu , Wu Aiping
Published: August 2022

Phylogenetic analysis has been widely used to describe, display, and infer the evolutionary patterns of viruses. The unprecedented accumulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes has provided valuable materials for the real-time study of SARS-CoV-2 evolution. However, the large number of SARS-CoV-2 genome sequences also poses great challenges for data analysis. Several methods for subsampling these large data sets have been introduced. However, current methods mainly focus on the spatiotemporal distribution of genomes without considering their genetic diversity, which might lead to post-subsampling bias. In this study, a subsampling method named covSampler was developed for the subsampling of SARS-CoV-2 genomes with consideration of both their spatiotemporal distribution and their genetic diversity. First, covSampler clusters all genomes according to their spatiotemporal distribution and genetic variation into groups that we call divergent pathways. Then, based on these divergent pathways, two kinds of subsampling strategies, representative subsampling and comprehensive subsampling, were provided with adjustable parameters to meet different users’ requirements. Our performance and validation tests indicate that covSampler is efficient and stable, with an abundance of options for user customization. Overall, our work has developed an easy-to-use tool and a webserver (https://www.covsampler.net) for the subsampling of SARS-CoV-2 genome sequences.
Activation of hTREK-1 by polyunsaturated fatty acids does not only involve membrane tension
Authors: Bechard Emilie , Arel Elodie , Bride Jamie , Louradour Julien , Bussy Xavier , Elloumi Anis , Vigor Claire , Soule Pierre , Oger Camille , Galano Jean-Marie , Durand Thierry , Le Guennec Jean-Yves , Moha-Ou-Maati Hamid , Demion Marie
Published: August 2022

TREK-1 is a mechanosensitive channel also activated by polyunsaturated fatty acids (PUFAs). In this study, we compared the effect of multiple fatty acids and ML402. First, we showed a variable TREK-1 activation by PUFAs related to the variable constitutive activity of TREK-1. Then, we observed no correlation between TREK-1 activation and acyl chain length or number of double bonds suggesting that the bilayer-couple hypothesis cannot explain by itself the activation of TREK-1 by PUFAs. The membrane fluidity measurement is not modified by PUFAs at 10 µM. The spectral shift analysis in TREK-1-enriched microsomes indicates a KD,TREK1at 44 µM of C22:6 n-3. PUFAs display the same activation and reversible kinetics than the direct activator ML402 and activate TREK-1 in both whole-cell and inside-out configurations of patch-clamp suggesting that the binding site of PUFAs is accessible from both sides of the membrane, as for ML402. Finally, we proposed a two steps mechanism for TREK-1 activation by PUFAs: first, insertion into the membrane, without fluidity or curvature modifications, and then interaction with TREK-1 channel to open it.
Resurrecting the Alternative Splicing Landscape of Archaic Hominins using Machine Learning
Authors: Brand Colin M. , Colbran Laura L. , Capra John A.
Published: August 2022

Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to many traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration, and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across Neanderthals, suggesting that older SAVs were more tolerated in modern human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.