bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing provides snapshots of the genetic variation within salmonid alphavirus-3 (SAV3) during an ongoing infection in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)
Authors: Roh HyeongJin , Skaftnesmo Kai Ove , Kannimuthu Dhamotharan , Madhun Abdullah , Patel Sonal , Kvamme Bjørn Olav , Morton H. Craig , Grove Søren 
Published: September 2024

AbstractFrequent RNA virus mutations raise concerns about evolving virulent variants. The purpose of this study was to investigate genetic variation in salmonid alphavirus-3 (SAV3) over the course of an experimental infection in Atlantic salmon and brown trout. Atlantic salmon and brown trout parr were infected using a cohabitation challenge, and heart samples were collected for analysis of the SAV3 genome at 2-, 4- and 8-weeks post-challenge. PCR was used to amplify eight overlapping amplicons covering 98.8% of the SAV3 genome. The amplicons were subsequently sequenced using the Nanopore platform. Nanopore sequencing identified a multitude of single nucleotide variants (SNVs) and deletions. The variation was widespread across the SAV3 genome in samples from both species. Mostly, specific SNVs were observed in single fish at some sampling time points, but two relatively frequent (i.e., major) SNVs were observed in two out of four fish within the same experimental group. Two other, less frequent (i.e., minor) SNVs only showed an increase in frequency in brown trout. Nanopore reads were de novo clustered using a 99% sequence identity threshold. For each amplicon, a number of variant clusters were observed that were defined by relatively large deletions. Nonmetric multidimensional scaling analysis integrating the cluster data for eight amplicons indicated that late in infection, SAV3 genomes isolated from brown trout had greater variation than those from Atlantic salmon. The sequencing methods and bioinformatics pipeline presented in this study provide an approach to investigate the composition of genetic diversity during viral infections.
The roles and mechanisms of endoplasmic reticulum stress-mediated autophagy in animal viral infections
Authors: Chen Lan , Wei Miaozhan , Zhou Bijun , Wang Kaigong , Zhu Erpeng , Cheng Zhentao 
Published: September 2024

AbstractThe endoplasmic reticulum (ER) is a unique organelle responsible for protein synthesis and processing, lipid synthesis in eukaryotic cells, and the replication of many animal viruses is closely related to ER. A considerable number of viral proteins are synthesised during viral infection, resulting in the accumulation of unfolded and misfolded proteins in ER, which in turn induces endoplasmic reticulum stress (ERS). ERS further drives three signalling pathways (PERK, IRE1, and ATF6) of the cellular unfolded protein response (UPR) to respond to the ERS. In numerous studies, ERS has been shown to mediate autophagy, a highly conserved cellular degradation mechanism to maintain cellular homeostasis in eukaryotic cells, through the UPR to restore ER homeostasis. ERS-mediated autophagy is closely linked to the occurrence and development of numerous viral diseases in animals. Host cells can inhibit viral replication by regulating ERS-mediated autophagy, restoring the ER's normal physiological process. Conversely, many viruses have evolved strategies to exploit ERS-mediated autophagy to achieve immune escape. These strategies include the regulation of PERK-eIF2α-Beclin1, PERK-eIF2α-ATF4-ATG12, IRE1α-JNK-Beclin1, and other signalling pathways, which provide favourable conditions for the replication of animal viruses in host cells. The ERS-mediated autophagy pathway has become a hot topic in animal virological research. This article reviews the most recent research regarding the regulatory functions of ERS-mediated autophagy pathways in animal viral infections, emphasising the underlying mechanisms in the context of different viral infections. Furthermore, it considers the future direction and challenges in the development of ERS-mediated autophagy targeting strategies for combating animal viral diseases, which will contribute to unveiling their pathogenic mechanism from a new perspective and provide a scientific reference for the discovery and development of new antiviral drugs and preventive strategies.
Metabolic reprogramming and immune evasion: the interplay in the tumor microenvironment
Authors: Zhang Haixia , Li Shizhen , Wang Dan , Liu Siyang , Xiao Tengfei , Gu Wangning , Yang Hongmin , Wang Hui , Yang Minghua , Chen Pan 
Published: September 2024

AbstractTumor cells possess complex immune evasion mechanisms to evade immune system attacks, primarily through metabolic reprogramming, which significantly alters the tumor microenvironment (TME) to modulate immune cell functions. When a tumor is sufficiently immunogenic, it can activate cytotoxic T-cells to target and destroy it. However, tumors adapt by manipulating their metabolic pathways, particularly glucose, amino acid, and lipid metabolism, to create an immunosuppressive TME that promotes immune escape. These metabolic alterations impact the function and differentiation of non-tumor cells within the TME, such as inhibiting effector T-cell activity while expanding regulatory T-cells and myeloid-derived suppressor cells. Additionally, these changes lead to an imbalance in cytokine and chemokine secretion, further enhancing the immunosuppressive landscape. Emerging research is increasingly focusing on the regulatory roles of non-tumor cells within the TME, evaluating how their reprogrammed glucose, amino acid, and lipid metabolism influence their functional changes and ultimately aid in tumor immune evasion. Despite our incomplete understanding of the intricate metabolic interactions between tumor and non-tumor cells, the connection between these elements presents significant challenges for cancer immunotherapy. This review highlights the impact of altered glucose, amino acid, and lipid metabolism in the TME on the metabolism and function of non-tumor cells, providing new insights that could facilitate the development of novel cancer immunotherapies.
Chemical and isotopic constraints on fluid origin and genesis of geothermal systems in the Tingri-Tangra Yumco rift, southern Tibetan Plateau
Authors: Liu Wei , Zhang Maoliang , Liu Yi , Cui Lifeng , Sano Yuji , Xu Sheng 
Published: September 2024

AbstractNumerous geothermal systems are hosted by extensional rifts that transect the Himalayas and Lhasa block in the Himalayan–Tibetan orogen. However, the relationships between hydrogeological processes and geothermal fluid circulation in different tectonic units remain unclear. Here, we report an integrated dataset of chemical and isotopic compositions (including major and trace elements, δD, δ18O, and 87Sr/86Sr) of thermal spring water from the Tingri-Tangra Yumco rift to assess their origins and circulation processes. δ18O (− 21.3 to − 17.0‰) and δD (− 166 to − 135‰) values of thermal springs indicate dominant recharge of meteoric waters from areas with elevation of > 6000 m and minor addition of magmatic fluids. Meteoric water could infiltrate to depths of about 1700–2900 m along the faults, whereby it is influenced by geothermal gradient and/or conductive heat transfer of magmatic fluids. The thermal spring waters are mainly Na-HCO3 type and are controlled by dissolution of silicate and carbonate minerals and mixing with deep fluids. The results of chemical and multicomponent geothermometers indicate reservoir temperatures of 115 − 195 ℃, corresponding to a convection heat flux of 3.96 × 105 J/s to 1.78 × 107 J/s from geothermal systems, which are comparable to that of the low-enthalpy geothermal systems in southern Italy. Geochemical modeling is conducted to assess the water–mineral equilibria in the reservoir. Trace elements and 87Sr/86Sr data suggest spatially variable controlling factors for the rift-related geothermal systems: (1) interaction with granitoid and carbonate in the Himalayas; (2) cold groundwater mixing with that leaching from granite and volcanic rocks in the Lhasa block; (3) the input of vapors from magmatic degassing. The geochemistry of thermal springs associated with extensional rift is largely induced by the interaction between fluid and different reservoir rocks in the Himalayas and Lhasa block. Based on these findings, a genetic model is proposed for exploration and development of geothermal resources in the Tingri-Tangra Yumco rift.
Regional distribution of mechanical strain and macrophage-associated lung inflammation after ventilator-induced lung injury: an experimental study
Authors: Liggieri Francesco , Chiodaroli Elena , Pellegrini Mariangela , Puuvuori Emmi , Sigfridsson Jonathan , Velikyan Irina , Chiumello Davide , Ball Lorenzo , Pelosi Paolo , Stramaglia Sebastiano , Antoni Gunnar , Eriksson Olof , Perchiazzi Gaetano 
Published: September 2024

Abstract
Background
Alveolar macrophages activation to the pro-inflammatory phenotype M1 is pivotal in the pathophysiology of Ventilator-Induced Lung Injury (VILI). Increased lung strain is a known determinant of VILI, but a direct correspondence between regional lung strain and macrophagic activation remains unestablished. [68Ga]Ga-DOTA-TATE is a Positron Emission Tomography (PET) radiopharmaceutical with a high affinity for somatostatin receptor subtype 2 (SSTR2), which is overexpressed by pro-inflammatory-activated macrophages. Aim of the study was to determine, in a porcine model of VILI, whether mechanical strain correlates topographically with distribution of activated macrophages detected by [68Ga]Ga-DOTA-TATE uptake.

Methods
Seven anesthetized pigs underwent VILI, while three served as control. Lung CT scans were acquired at incremental tidal volumes, simultaneously recording lung mechanics. [68Ga]Ga-DOTA-TATE was administered, followed by dynamic PET scans. Custom MatLab scripts generated voxel-by-voxel gas volume and strain maps from CT slices at para-diaphragmatic (Para-D) and mid-thoracic (Mid-T) levels. Analysis of regional Voxel-associated Normal Strain (VoStrain) and [68Ga]Ga-DOTA-TATE uptake was performed and a measure of the statistical correlation between these two variables was quantified using the linear mutual information (LMI) method.

Results
Compared to controls, the VILI group exhibited statistically significant higher VoStrain and Standardized Uptake Value Ratios (SUVR) both at Para-D and Mid-T levels. Both VoStrain and SUVR increased along the gravitational axis with an increment described by statistically different regression lines between VILI and healthy controls and reaching the peak in the dependent regions of the lung (for strain in VILI vs. control was at Para-D: 760 ± 210 vs. 449 ± 106; at Mid-T level 497 ± 373 vs. 193 ± 160; for SUVR, in VILI vs. control was at Para-D: 2.2 ± 1.3 vs. 1.3 ± 0.1; at Mid-T level 1.3 ± 1.0 vs. 0.6 ± 0.03). LMI in both Para-D and Mid-T was statistically significantly higher in VILI than in controls.

Conclusions
In this porcine model of VILI, we found a topographical correlation between lung strain and [68Ga]Ga-DOTA-TATE uptake at voxel level, suggesting that mechanical alteration and specific activation of inflammatory cells are strongly linked in VILI. This study represents the first voxel-by-voxel examination of this relationship in a multi-modal imaging analysis.
The validation and assessment of a curriculum based GAIT App used in teaching bachelor of physiotherapy students: a cross sectional study
Authors: Kalra Nidhi , Singh Pratibha , Parasher Raju K. 
Published: September 2024

Abstract
Introduction
There has been an advent in the use of Mobile Apps in the academic space. The pandemic hastened their usage, and forced us to rapidly innovate in order to meet the educational needs of our students. Also, Mobile Apps have been known to facilitate self-learning, make it enjoyable, and personalize the pace of learning of the individual. Given the level of skill-learning in Physiotherapy education, the use of Mobile Apps can pose a challenge, as well as offer an opportunity to explore its scope to enhance learning, and create innovative pedagogic strategies. There are a very few learning mobile apps that have been assessed in Physiotherapy education.

Aim
To develop, establish content validity and internal consistency of a curriculum based App on the kinesiology of normal Gait for bachelor of physiotherapy students, and to evaluate the App with regards to use, quality, engagement, and overall experience.

Materials & methods
In the first phase, a mobile app based on a bachelor of physiotherapy Gait curriculum was developed and validated using Delphi procedure, with 80% agreement criteria, by a group of experts. Subsequently, the App was rated by 200 users on: engagement, aesthetics, information, subjective quality.

Results
The content validity index following 2 rounds of Delphi was found to be 0.88. Also, therapists found the App easy to use, and 80% gave it a rating of > 3 stars.

Conclusion
Creating, designing, implementing, and evaluating the efficacy of a Gait App as a means to teaching the GAIT component to physiotherapy students was found to be appealing and beneficial.
On the computation of ray-velocity vectors for seismic body waves in viscoelastic anisotropic media
Authors: Zhou Bing , Darwis Muhammad Fadhil , Li Xingwang , Greenhalgh Stewart , Liu Xu 
Published: September 2024

Computation of the ray-velocity vector is crucial in seismic ray tracing for the three body waves (qP, qSV, qSH) in viscoelastic anisotropic media. The primary challenge is dealing with the likely cusps or triplications of the qSV wavefronts, which makes it theoretically difficult to track qSV raypaths and the reflection and transmission of these body waves in such media. We review three traditional methods, namely, g-Hamiltonian, p-Hamiltonian, and explicit c-derivative, and then present two new approaches called implicit c-derivative and g*-Hamiltonian to tackle the challenges of seismic ray tracing. We theoretically prove the equivalence of these five methods to calculate the group-velocity vector in a viscoelastic anisotropic medium, apply these methods to some rock samples, and investigate the applicability of each method. Our results indicate that if the body wave is homogeneous (i.e., its propagation and attenuation wavefronts are parallel to each other) or if the body wavefront has no cusps or triplications, then all the methods offer a consistent solution of the ray-velocity vector. If the body wave is inhomogeneous (its propagation and attenuation wavefronts are at different angles or cross each other) and cusps and triplications occur in the wavefronts, then all the methods but the g*-Hamiltonian one fail to give the proper solution of the ray-velocity vector. This work demonstrates that the innovative g*-Hamiltonian method is the only approach to overcome the theoretical difficulty of seismic ray tracing in viscoelastic anisotropic media.
Early detection of perinatal depression in couples: a single-center prospective study
Authors: Paria Anne , Atallah Anthony , Nourredine Mikail , Dubernard Gil , Joubert Fanny , Landel Verena , Viaux-Savelon Sylvie , De la Fournière Benoit 
Published: September 2024

Abstract

Objective
This prospective study aimed to assess couples’ psychological status during the perinatal period to identify those at risk for postpartum depression.

Methods
Conducted at Lyon University Hospital from March to July 2022, the study enrolled pregnant women without progressive psychiatric disorders or obstetric risk factors, and their partners. Participants completed the Edinburgh Postnatal Depression Scale (EPDS) at three points: during the 9th month of pregnancy, immediate postpartum, and 6–8 weeks after delivery. A score ≥10 on the EPDS indicated depression risk. A score ≥10 on the EPDS indicate depression risk. The primary endpoint was EPDS scores throughout the perinatal period.

Results
Ninety-five couples participated; 96% of patients and 68% of partners completed pre-delivery questionnaires, 81% and 71% during maternity stay, and 64% and 46% postpartum, respectively. Overall, 15% of patients and 1% of partners had EPDS scores >10 in the postpartum period. Psychiatric history and emergency cesarean sections were associated with higher immediate postpartum EPDS scores in patients [Beta 3.7 points, 95% CI 0.91; 6.4 and Beta 5.2 points, 2.2; 8.1, respectively]. Episiotomy was associated with higher EPDS scores in partners. No significant association between the different factors studied and the EPDS score was found at 6–8 weeks postpartum in patients nor their partners.

Conclusions
While specific risk factors for persistent perinatal depression in couples were not identified, a notable proportion of patients exhibited high EPDS scores. Screening all couples during prepartum and postpartum periods is crucial, regardless of identified risk factors.
Enhancing Precision in Detecting Severe Immune-Related Adverse Events: Comparative Analysis of Large Language Models and International Classification of Disease Codes in Patient Records
Authors: Sun Virginia H. , Heemelaar Julius C. , Hadzic Ibrahim , Raghu Vineet K. , Wu Chia-Yun , Zubiri Leyre , Ghamari Azin , LeBoeuf Nicole R. , Abu-Shawer Osama , Kehl Kenneth L. , Grover Shilpa , Singh Prabhsimranjot , Suero-Abreu Giselle A. , Wu Jessica , Falade Ayo S. , Grealish Kelley , Thomas Molly F. , Hathaway Nora , Medoff Benjamin D. , Gilman Hannah K. , Villani Alexandra-Chloe , Ho Jor Sam , Mooradian Meghan J. , Sise Meghan E. , Zlotoff Daniel A. , Blum Steven M. , Dougan Michael , Sullivan Ryan J. , Neilan Tomas G. , Reynolds Kerry L. 
Published: September 2024

PURPOSE
Current approaches to accurately identify immune-related adverse events (irAEs) in large retrospective studies are limited. Large language models (LLMs) offer a potential solution to this challenge, given their high performance in natural language comprehension tasks. Therefore, we investigated the use of an LLM to identify irAEs among hospitalized patients, comparing its performance with manual adjudication and International Classification of Disease (ICD) codes.

METHODS
Hospital admissions of patients receiving immune checkpoint inhibitor (ICI) therapy at a single institution from February 5, 2011, to September 5, 2023, were individually reviewed and adjudicated for the presence of irAEs. ICD codes and an LLM with retrieval-augmented generation were applied to detect frequent irAEs (ICI-induced colitis, hepatitis, and pneumonitis) and the most fatal irAE (ICI-myocarditis) from electronic health records. The performance between ICD codes and LLM was compared via sensitivity and specificity with an α = .05, relative to the gold standard of manual adjudication. External validation was performed using a data set of hospital admissions from June 1, 2018, to May 31, 2019, from a second institution.

RESULTS

Of the 7,555 admissions for patients on ICI therapy in the initial cohort, 2.0% were adjudicated to be due to ICI-colitis, 1.1% ICI-hepatitis, 0.7% ICI-pneumonitis, and 0.8% ICI-myocarditis. The LLM demonstrated higher sensitivity than ICD codes (94.7%
v
68.7%), achieving significance for ICI-hepatitis (
P
< .001), myocarditis (
P
< .001), and pneumonitis (
P
= .003) while yielding similar specificities (93.7%
v
92.4%). The LLM spent an average of 9.53 seconds/chart in comparison with an estimated 15 minutes for adjudication. In the validation cohort (N = 1,270), the mean LLM sensitivity and specificity were 98.1% and 95.7%, respectively.

CONCLUSION
LLMs are a useful tool for the detection of irAEs, outperforming ICD codes in sensitivity and adjudication in efficiency.
From a Tall Man to “Zhan the Chinese Giant”
Authors: Men Bozhou 
Published: September 2024

Abstract
Since the 1970s, institutionalized enfreakment as represented by the Victorian freak show has provided scholars with a lens through which to examine nineteenth-century Western societies. However, current scholarship sidesteps questions such as how people in colonized countries perceived their enfreaked compatriots and how they negotiated their positions in the new international order as symbolized by this globalized entertainment industry. This article addresses these questions through a case study of Zhan Wu, the celebrated “Chinese giant” in Euro-American freak shows from approximately 1865 to 1887 who was, at the time, a spectacle in Chinese print media. The article argues that the way the Chinese media represented Zhan's body, shifting from nonchalance to disdain and then to eventually viewing it as a symbol of China's recent suffering, epitomizes a history of cooperation and mutual influence among the global entertainment industry, print media, and their consumers worldwide. More important, it reveals that as China's mass media and reading public joined in a global imaginaire that enfreaked the Chinese as a race, they were not merely incorporated by this discourse; they also reshaped it to express their understandings about a new Chinese identity that was to emerge in the fin de siècle era.
Genomic analysis of Strongyloides stercoralis and Strongyloides fuelleborni in Bangladesh
Authors: de Ree Veroni , Nath Tilak Chandra , Barua Priyanka , Harbecke Dorothee , Lee Dongmin , Rödelsperger Christian , Streit Adrian 
Published: September 2024

Background
About 600 million people are estimated to be infected with Strongyloides stercoralis, the species that causes most of the human strongyloidiasis cases. S. stercoralis can also infect non-human primates (NHPs), dogs and cats, rendering these animals putative sources for zoonotic human S. stercoralis infection. S. fuelleborni is normally found in old world NHPs but occasionally also infects humans, mainly in Africa. Dogs in southeast Asia carry at least two types of Strongyloides, only one of which appears to be shared with humans ("dog only" and "human and dog" types). For S. stercoralis with molecular taxonomic information, there is a strong sampling bias towards southeast and east Asia and Australia.

Methodology/Principle findings
In order to extend the geographic range of sampling, we collected human and dog derived Strongyloides spp. and hookworms from two locations in Bangladesh and subjected them to molecular taxonomic and genomic analysis based on nuclear and mitochondrial sequences. All hookworms found were Necator americanus. Contrary to earlier studies in Asia, we noticed a rather high incidence of S. fuelleborni in humans. Also in this study, we found the two types of S. stercoralis and no indication for genetic isolation from the southeast Asian populations. However, we found one genomically "dog only" type S. stercoralis in a human sample and we found two worms in a dog sample that had a nuclear genome of the "dog only" but a mitochondrial genome of the "human and dog" type.

Conclusions/Significance
S. fuelleborni may play a more prominent role as a human parasite in certain places in Asia than previously thought. The introgression of a mitochondria haplotype into the "dog only" population suggests that rare interbreeding between the two S. stercoralis types does occur and that exchange of genetic properties, for example a drug resistance, between the two types is conceivable.