bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mind the Gap: A Review of Disjunctions in Coastal Marine Species
Authors: Pagowski Veronica , Micheli Fiorenza 
Published: July 2024

Synopsis
Many coastal marine species have discontinuous distributions or genetic breakpoints throughout their geographical ranges. These spatial and genetic disjunctions occur in species that span limited to broad dispersal potential. Thus, the mechanisms that underlie these disjunctions remain speculative or incompletely known, particularly on small spatial scales where long-term historical processes are unlikely to be the only mechanism contributing to disjunction. Rather, ecological or oceanographic factors may be important. To identify key drivers of coastal disjunctions, we reviewed publications investigating spatial and genetic disjunctions in coastal marine species and visually summarized where and why they are thought to occur. The most frequently cited mechanisms implicated in causing disjunctions include historical processes, oceanographic features, heterogeneous habitat, species introductions, and limited larval dispersal capacities. However, the relative importance of each of these processes varies depending on the spatial scales investigated. Furthermore, locations associated with disjunctions for a suite of species are typically associated with multiple processes that maintain these disjunctions. This study provides a non-exhaustive synthesis of disjunctions in coastal marine species by visualizing where they occur, exploring underlying mechanisms, and investigating biases in how the scientific community studies this phenomenon.
Trajectories of Serum Hepatitis B Surface antigen (HBsAg) During Treatment and Association With HBsAg Loss in Children With Hepatitis B e Antigen–Positive Chronic Hepatitis B: A Latent Class Trajectory Analysis
Authors: Yao Zhenzhen , Gu Yingping , Lai Xin , Yang Meng , Xu Yi , Luo Jiayou , Peng Songxu 
Published: July 2024

Abstract

Background
Changes in serum hepatitis B surface antigen (HBsAg) during treatment are associated with HBsAg loss. However, little is known about the trajectory patterns of HBsAg in early treatment and their relationship to subsequent HBsAg loss.

Methods
A retrospective study was conducted on 166 treatment-naive children with hepatitis B e antigen (HBeAg)–positive chronic hepatitis B (CHB). Latent class trajectory analysis was used to identify trajectory groups of serum HBsAg. Cox proportional hazards models were used to assess the association between HBsAg trajectory groups and HBsAg loss.

Results
The median follow-up time was 20.70 (interquartile range, 12.54–34.17) months, and HBsAg loss occurred in 70 (42.17%) of all study participants. Using latent class trajectory analysis, HBeAg-positive patients with CHB were classified into 3 trajectory groups: trajectory 1 (sustained stability, 24.70%), trajectory 2 (slow decline, 38.55%), and trajectory 3 (rapid decline, 36.75%), respectively. The risk of achieving HBsAg loss was higher in both trajectory 2 (hazard ratio, 3.65 [95% confidence interval, 1.70–7.83]) and trajectory 3 (7.27 [3.01–17.61]), respectively.

Conclusions
Serum HBsAg levels during early treatment can be classified into distinct trajectory groups, which may serve as an additional predictive indicator for HBsAg loss in HBeAg-positive children with CHB.
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles
Authors: Nishikawa Yohei , Wagatsuma Ryota , Tsukada Yuko , Chia-ling Lin , Chijiiwa Rieka , Hosokawa Masahito , Takeyama Haruko 
Published: July 2024

Abstract
Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, whereas viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.
The Effect of Enhanced Rehabilitation Program on Upper Limb Function in Patients Undergoing Abdominal Pedicle Flap Surgery
Authors: Chen Zhiyu , Huang Ling , Yu Ran , Zhou Yaqin , Tan Jianglin 
Published: July 2024

Abstract
To investigate the effect of an enhanced rehabilitation program on upper limb function in patients with abdominal pedicle flap surgery, we retrospectively analyzed 70 patients who received abdominal pedicled flap surgery between 2017 and 2022. Patients were categorized into the traditional rehabilitation group (rehabilitation initiated after the stage II pedicle dissection of the abdominal pedicle flap) and the enhanced rehabilitation group (rehabilitation initiated on the first day following the stage II abdominal pedicle flap surgery). All the patients received identical rehabilitation protocols. Passive Range of Motion (PROM), activities of daily living (ADL), Functional Independence Measure (FIM), and Manual Muscle Testing (MMT) were assessed at 5 days and 1 month following the stage II surgery. The main causes of injury were electrical burns in both groups. The hospital stay of patients in the enhanced group was significantly shorter than the traditional group. One month assessment indicated both groups showed significant improvements in the PROM of shoulder flexion, abduction, and elbow extension compared to the 5 days assessment. Notably, at 5 days assessment, the enhanced group had significantly higher PROM in shoulder abduction and elbow extension compared to the traditional group. Furthermore, the enhanced group continued to exhibit higher PROM in shoulder flexion and abduction than the traditional group at one month assessment. At one month assessment, a significant increase was observed in the ADL, FIM, and MMT of both groups compared to the 5 days. The study indicated the enhanced rehabilitation program immediately following the stage I surgery can effectively improve the PROM of the shoulder and elbow and reduce the length of hospital stay for patients.
Epistemic Injustice at the ICC?
Authors: Evans Hayley N , Hazim Mahir 
Published: July 2024

Abstract
This article empirically assesses the role third-party evidence has played in the Office of the Prosecutor’s (OTP) initiation of an investigation into the Afghanistan Situation at the International Criminal Court (ICC). After finding that most of the evidence upon which the OTP relied in its request to initiate an investigation is from third parties, this article classifies and ranks the categories of third party upon which the OTP relied. Critically analysing the OTP’s use of third-party sources, this article uncovers the way potential biases towards dominant languages, affluent locations and prestigious institutions influence the choice of which information to use as evidence, possibly evincing an epistemic injustice at the OTP. Heeding Naz Modirzadeh’s call to use Third World Approaches to International Law (TWAIL) to empower Global South states, this article concludes with recommendations to the OTP and third parties on how they can maximize their collaboration while avoiding capitulation to the politics of exclusion. In addition, the article’s findings reveal opportunities for stakeholders to enhance evidence collection and use by particular third-party categories in Afghanistan and in similar situations.
Reducing exposure levels of immersion washing workers to ortho-phthalaldehyde by improving exhaust systems
Authors: Yamamoto Shinobu , Hachiya Yuriko , Goto Motohide , Takeuchi Akito , Ishidao Toru , Hori Hajime , Miyauchi Hiroyuki 
Published: July 2024

Abstract

Objectives
The American Conference of Governmental Industrial Hygienists recommends a threshold limit value-ceiling (TLV-C) of 0.1 ppb for occupational exposure to ortho-phthalaldehyde (OPA) used in washing endoscope probes. To adhere to this extremely low exposure limit, this case study aimed to reduce OPA exposure concentrations of workers during immersion washing of an endoscope probe body. This was achieved by attaching a new duct and hood to the existing ceiling exhaust system.

Methods
The type of hood was determined by calculating and comparing the capture velocity obtained by assuming either an exterior or an enclosing hood. Additionally, the effect on improving the working environment was tested before and after the installation of the hood by measuring the OPA vapor concentration.

Results
The calculated capture velocities of the exterior and enclosing hoods were 0.05 m/s and 0.19 m/s, respectively. Considering the operability, the exterior hood was more appropriate; however, the calculated capture velocity indicated potential inadequacy in meeting the TLV-C requirement, leading to the adoption of the enclosing hood. The OPA vapor concentration in ceiling value measurements taken after the enclosing hood was fitted was reduced to 0.2 ppb, that is, 1/10 of the original concentration.

Conclusions
Although the environmental concentration after the improvement still exceeded the TLV-C of 0.1 ppb, this study’s findings indicate that even substances with extremely low occupational exposure limits can be managed with appropriate local exhaust ventilation.
Employing Constrained Nonnegative Matrix Factorization for Microstructure Segmentation
Authors: Chauniyal Ashish , Thome Pascal , Stricker Markus 
Published: July 2024

Abstract
Materials characterization using electron backscatter diffraction (EBSD) requires indexing the orientation of the measured region from Kikuchi patterns. The quality of Kikuchi patterns can degrade due to pattern overlaps arising from two or more orientations, in the presence of defects or grain boundaries. In this work, we employ constrained nonnegative matrix factorization to segment a microstructure with small grain misorientations, (&lt;1∘), and predict the amount of pattern overlap. First, we implement the method on mixed simulated patterns—that replicates a pattern overlap scenario, and demonstrate the resolution limit of pattern mixing or factorization resolution using a weight metric. Subsequently, we segment a single-crystal dendritic microstructure and compare the results with high-resolution EBSD. By utilizing weight metrics across a low-angle grain boundary, we demonstrate how very small misorientations/low-angle grain boundaries can be resolved at a pixel level. Our approach constitutes a versatile and robust tool, complementing other fast indexing methods for microstructure characterization.
A catalogue of merging clusters of galaxies: cluster partners, merging subclusters, and post-collision clusters
Authors: Wen Z L , Han J L , Yuan Z S 
Published: July 2024

ABSTRACT
Clusters of galaxies are merging during the formation of large-scale structures in the Universe. Based on optical survey data, we identify a large sample of pre-mergers of galaxy clusters and merging subclusters in rich clusters. We find 39 382 partners within a velocity difference of 1500 km s$^{-1}$ and a projected separation of 5 $r_{500}$ around 33 126 main clusters, where $r_{500}$ is the radius of the main cluster. Based on the galaxy distribution inside rich clusters with more than 30 member galaxy candidates, we identify subclusters by modelling the smoothed optical distribution with a two-component profile, and a coupling factor is obtained for merging subclusters in 7845 clusters. In addition, we find 3446 post-collision mergers according to the deviations of brightest cluster galaxies from other member galaxies, most of which have been partially validated by using the Chandra and XMM–Newton X-ray images. Two new bullet-like clusters have been identified by using the optical and X-ray images. The large samples of merging clusters of galaxies presented here are important databases for studying the hierarchical structure formation, cluster evolution, and the physics of intergalactic medium.
AstroSat observations of the dipping low-mass X-ray binary XB 1254−690
Authors: Navale Nilam R , Pawar Devraj , Rao A R , Misra Ranjeev , Chakraborty Sudip , Bhattacharyya Sudip , Bambole Vaishali A 
Published: July 2024

ABSTRACT
XB 1254−690 is a neutron star low-mass X-ray binary with an orbital period of 3.88 h, and it exhibits energy-dependent intensity dips, thermonuclear bursts, and flares. We present the results of an analysis of a long observation of this source using the AstroSat satellite. The X-ray light curve gradually changed from a high-intensity flaring state to a low-intensity one with a few dips. The hardness–intensity diagram showed that the source is in a high-intensity banana state with a gradually changing flux. Based on this, we divide the observation into four flux levels for a flux-resolved spectral study. The X-ray spectra can be explained by a model consisting of absorption, thermal emission from the disc, and non-thermal emission from the corona. From our studies, we detect a correlation between the temperature of the thermal component and the flux and we examine the implications of our results for the accretion disc geometry of this source.
Applying the starquake model to study the formation of elastic mountains on spinning neutron stars
Authors: Gangwar Yashaswi , Jones David Ian 
Published: July 2024

ABSTRACT
When a neutron star is spun-up or spun-down, the changing strains in its solid elastic crust can give rise to sudden fractures known as starquakes. Early interest in starquakes focused on their possible connection to pulsar glitches. While modern glitch models rely on pinned superfluid vorticity rather than crustal fracture, starquakes may nevertheless play a role in the glitch mechanism. Recently, there has been interest in the issue of starquakes resulting in non-axisymmetric shape changes, potentially linking the quake phenomenon to the building of neutron star mountains, which would then produce continuous gravitational waves. Motivated by this issue, we present a simple model that extends the energy minimization-based calculations, originally developed to model axisymmetric glitches, to also include non-axisymmetric shape changes. We show that the creation of a mountain in a quake necessarily requires a change in the axisymmetric shape too. We apply our model to the specific problem of the spin-up of an initially non-rotating star, and estimate the maximum mountain that can be built in such a process, subject only to the constraints of energy and angular momentum conservation.
Immune Reconstitution Inflammatory Syndrome Related to Antiretroviral Therapy Initiation in People With HIV and Mpox: An Observational Retrospective Study
Authors: Rodríguez-Aldama Juan Carlos , Pérez-Barragán Edgar , Hernández-Silva Graciela , Lezama-Mora Jezer Ivan , Olin-López Ana Karen , González-Flores Berenice , Cruz-Flores Raul Adrián , Crabtree-Ramírez Brenda 
Published: July 2024

Abstract
The study aims to compare the outcomes of initiating antiretroviral therapy early vs late in people with HIV and mpox. No worse outcomes were found associated with mpox-related immune reconstitution inflammatory syndrome among those who started antiretroviral treatment early, suggesting initiation as soon as possible.
Extensively Antibiotic-Resistant Bacterial Infections in Trauma Cases Managed at the Médecins Sans Frontières Tertiary Orthopaedic Center in Mosul, Iraq: A Case Series
Authors: Abdulrahman Ahmed Hisham , Hasheem Mahmood Humam , Hosam Aldin Sami Haitham , Natiq Taher Abdullah , Garcia-Vello Pilar , Ali Engy , Repetto Ernestina , Williams Anita , Gordillo Gomez Fabiola , Moussally Krystel 
Published: July 2024

Abstract
The Médecins Sans Frontières Tertiary Orthopaedic Care center in Mosul, Iraq, provides reconstructive surgery, microbiological analysis, integrated infection prevention and control, and antibiotic stewardship services. Between May 2018 and February 2020, we recorded soft tissue and/or bone infections caused by gram-negative extensively drug-resistant (XDR) bacteria in 4.9% (13/266) of the admitted patients. The XDR bacteria identified among 12 patients in this case series were extended-spectrum β-lactamase–producing Klebsiella pneumoniae (n = 5, 41.7%) with intermediate sensitivity or resistance to imipenem and/or meropenem, Acinetobacter spp (n = 3, 25.0%; 2 Acinetobacter baumannii strains) resistant to imipenem and/or meropenem, Pseudomonas aeruginosa (n = 2, 16.7%) resistant to imipenem and meropenem, and extended-spectrum β-lactamase–producing Proteus mirabilis (n = 2, 16.7%) resistant to meropenem. Most XDR isolates were sensitive only to colistin or polymyxin B, neither of which is available in Iraq. Therefore, the only treatment option was multiple rounds of surgical debridement and wound care. The infection was deemed cured before discharge in 7 patients (58.3%). Meanwhile, 4 patients (33.3%) were discharged with unhealed wounds, and outpatient follow-up was planned. One patient died in the intensive care unit of a referral hospital after developing septicemia postsurgery. XDR bacteria pose substantial health risks in Iraq. Thus, improving antimicrobial stewardship and accessibility to essential antibiotics is critical to address this issue.
Donor-Derived Bartonella quintana Infection in Solid Organ Transplantation: An Emerging Public Health Issue With Diagnostic Challenges
Authors: Boodman Carl , Garcia Oscar Fernandez , Kabbani Dima , Villalobos Armelle Perez Cortes , Beeson Amy , Marx Grace E , van Griensven Johan , Doucette Karen 
Published: July 2024

Abstract
Bartonella quintana is a louse-borne intracellular bacterium that remains a neglected cause of bacteremia, bacillary angiomatosis, and infective endocarditis among individuals experiencing poverty. In October 2023, Health Canada notified Canadian organ transplantation programs of an outbreak of donor-derived B quintana infection. From March to August 2023, 5 cases of donor-derived B quintana disease were acquired in Alberta, Canada, from 3 deceased donors who had experienced homelessness. Similar cases recently occurred in the United States. In this article, we discuss strategies to screen organ donors and monitor transplant recipients for B quintana infection using epidemiologic risk factors, physical examination signs, and laboratory diagnostic tests. We review the limitations of existing diagnostic tests for B quintana and describe how these problems may be magnified in the organ transplantation context.
Adolescent sleep patterns, genetic predisposition, and risk of multiple sclerosis
Authors: Johansson Eva , Olsson Tomas , Strid Pernilla , Kockum Ingrid , Alfredsson Lars , Hedström Anna Karin 
Published: July 2024

Abstract

Study Objectives
Shift work, insufficient sleep, and poor sleep quality at young age have been associated with increased risk of multiple sclerosis (MS). This study aimed to investigate the potential interaction between aspects of inadequate sleep (short sleep, phase shift, and poor sleep quality) during adolescence and HLA-DRB1*15:01 in relation to MS risk.

Methods
We used a Swedish population-based case–control study (1253 cases and 1766 controls). Participants with different sleep patterns during adolescence and HLA-DRB1*15:01 status were compared regarding MS risk by calculating odds ratios with 95% confidence intervals (CI) using logistic regression models. Additive interaction between aspects of inadequate sleep and HLA-DRB1*15:01 status was assessed by calculating the attributable proportion due to interaction (AP) with 95% CI.

Results
Short sleep duration (&lt;7 hours/night) during adolescence acted synergistically with HLA-DRB1*15:01, increasing the risk of MS (AP 0.38, 95% CI: 0.01 to 0.75, p = .04). Similarly, subjective low sleep quality during adolescence interacted with HLA-DRB1*15:01 regarding risk of MS (AP 0.30, 95% CI: 0.06 to 0.56, p = .03), whereas phase shift did not significantly influence the risk of the disease, irrespective of HLA-DRB1*15:01 status.

Conclusions
Our findings underscore the importance of addressing inadequate sleep during adolescence, particularly in the context of the HLA-DRB1*15:01 allele, as it appears to amplify the risk of subsequently developing MS.
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model
Authors: Mai Uyen , Charvel Eduardo , Mirarab Siavash 
Published: July 2024

Abstract
Dating phylogenetic trees to obtain branch lengths in time units is essential for many downstream applications but has remained challenging. Dating requires inferring substitution rates that can change across the tree. While we can assume to have information about a small subset of nodes from the fossil record or sampling times (for fast-evolving organisms), inferring the ages of the other nodes essentially requires extrapolation and interpolation. Assuming a distribution of branch rates, we can formulate dating as a constrained maximum likelihood (ML) estimation problem. While ML dating methods exist, their accuracy degrades in the face of model misspecification, where the assumed parametric statistical distribution of branch rates vastly differs from the true distribution. Notably, most existing methods assume rigid, often unimodal, branch rate distributions. A second challenge is that the likelihood function involves an integral over the continuous domain of the rates, often leading to difficult non-convex optimization problems. To tackle both challenges, we propose a new method called Molecular Dating using Categorical-models (MD-Cat). MD-Cat uses a categorical model of rates inspired by non-parametric statistics and can approximate a large family of models by discretizing the rate distribution into k categories. Under this model, we can use the Expectation-Maximization algorithm to co-estimate rate categories and branch lengths in time units. Our model has fewer assumptions about the true distribution of branch rates than parametric models such as Gamma or LogNormal distribution. Our results on two simulated and real datasets of Angiosperms and HIV and a wide selection of rate distributions show that MD-Cat is often more accurate than the alternatives, especially on datasets with exponential or multimodal rate distributions.