bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test of the minimum supero-inferior femoral neck diameter as a sex predictor in a contemporary documented osteological collection from Portugal
Authors: Luna Leandro H 
Published: August 2024

Abstract

Adult sex estimation is one of the first and most important steps in forensic examination. While dealing with disturbed burials, the most dimorphic anatomic areas of the skeleton (such as the coxae, the skull and the head of femur and humerus) may be deteriorated or fragmented. In contrast, the minimum supero-inferior femoral neck diameter (SID) is generally much better preserved. The aim of the present research is to identify the discriminatory potential of SID for sex estimation and to test different formulae and mathematical procedures currently available in the forensic literature, on a sample of 295 contemporary individuals from the 21st Century Identified Skeletal Collection (University of Coimbra, Portugal), in order to identify its relevance for application in Portuguese forensic cases. Results showed that SID is a dimorphic variable, with high frequencies and probabilities of cases correctly estimated (0.82 and 0.83, respectively); statistically significant differences between females and males, and a high association between the metrics and sex, were identified. Posterior probabilities allow reliable estimations for all the measurements, excepting those between 31.0 and 31.5 mm, and the procedures that show the highest accuracy are those proposed by Seidemann et al. (1998), Curate et al. (2016) and Luna et al. (2021), with frequencies and probabilities between 0.82 and 0.83 for both sexes. The validation procedures implemented in this study highlight both the need to test quantitative models generated from diverse contemporary human populations, and the value of SID for obtaining reliable adult sex estimates, as they improve the quality of the biological profiles obtained in forensic contexts.

Key points
Advances in the management of complications from cirrhosis
Authors: Singh Jasleen , Ebaid Mark , Saab Sammy 
Published: August 2024

Abstract
Cirrhosis with complications of liver decompensation and hepatocellular carcinoma (HCC) constitute a leading cause of morbidity and mortality worldwide. Portal hypertension is central to the progression of liver disease and decompensation. The most recent Baveno VII guidance included revision of the nomenclature for chronic liver disease, termed compensated advanced chronic liver disease, and leveraged the use of liver stiffness measurement to categorize the degree of portal hypertension. Additionally, non-selective beta blockers, especially carvedilol, can improve portal hypertension and may even have a survival benefit. Procedural techniques with interventional radiology have become more advanced in the management of refractory ascites and variceal bleeding, leading to improved prognosis in patients with decompensated liver disease. While lactulose and rifaximin are the preferred treatments for hepatic encephalopathy, many alternative treatment options may be used in refractory cases and even procedural interventions such as shunt embolization may be of benefit. The approval of terlipressin for the treatment of hepatorenal syndrome (HRS) in the USA has improved the way in which HRS is managed and will be discussed in detail. Malnutrition, frailty, and sarcopenia lead to poorer outcomes in patients with decompensated liver disease and should be addressed in this patient population. Palliative care interventions can lead to improved quality of life and clinical outcomes. Lastly, the investigation of systemic therapies, in particular immunotherapy, has revolutionized the management of HCC. These topics will be discussed in detail in this review.
A trade-off in evolution: the adaptive landscape of spiders without venom glands
Authors: Zhang Yiming , Shen Yunxiao , Jin Pengyu , Zhu Bingyue , Lin Yejie , Jiang Tongyao , Huang Xianting , Wang Yang , Zhao Zhe , Li Shuqiang 
Published: August 2024

Abstract

Background
Venom glands play a key role in the predation and defense strategies of almost all spider groups. However, the spider family Uloboridae lacks venom glands and has evolved an adaptive strategy: they excessively wrap their prey directly with spider silk instead of paralyzing it first with toxins. This shift in survival strategy is very fascinating, but the genetic underpinnings behind it are poorly understood.

Results
Spanning multiple spider groups, we conducted multiomics analyses on Octonoba sinensis and described the adaptive evolution of the Uloboridae family at the genome level. We observed the coding genes of myosin and twitchin in muscles are under positive selection, energy metabolism functions are enhanced, and gene families related to tracheal development and tissue mechanical strength are expanded or emerged, all of which are related to the unique anatomical structure and predatory behavior of spiders in the family Uloboridae. In addition, we also scanned the elements that are absent or under relaxed purifying selection, as well as toxin gene homologs in the genomes of 2 species in this family. The results show that the absence of regions and regions under relaxed selection in these spiders’ genomes are concentrated in areas related to development and neurosystem. The search for toxin homologs reveals possible gene function shift between toxins and nontoxins and confirms that there are no reliable toxin genes in the genome of this group.

Conclusions
This study demonstrates the trade-off between different predation strategies in spiders, using either chemical or physical strategy, and provides insights into the possible mechanism underlying this trade-off. Venomless spiders need to mobilize multiple developmental and metabolic pathways related to motor function and limb mechanical strength to cover the decline in adaptability caused by the absence of venom glands.
Intrinsic link between PGRN and Gba1 D409V mutation dosage in potentiating Gaucher disease
Authors: Lin Yi , Zhao Xiangli , Liou Benjamin , Fannin Venette , Zhang Wujuan , Setchell Kenneth D R , Wang Xiaohong , Pan Dao , Grabowski Gregory A , Liu Chuan-ju , Sun Ying 
Published: August 2024

Abstract
Gaucher disease (GD) is caused by biallelic GBA1/Gba1 mutations that encode defective glucocerebrosidase (GCase). Progranulin (PGRN, encoded by GRN/Grn) is a modifier of GCase, but the interplay between PGRN and GCase, specifically GBA1/Gba1 mutations, contributing to GD severity is unclear. Mouse models were developed with various dosages of Gba1 D409V mutation against the PGRN deficiency (Grn−/−) [Grn−/−;Gba1D409V/WT (PG9Vwt), Grn−/−;Gba1D409V/D409V (PG9V), Grn−/−;Gba1D409V/Null (PG9VN)]. Disease progression in those mouse models was characterized by biochemical, pathological, transcriptomic, and neurobehavioral analyses. Compared to PG9Vwt, Grn−/−;Gba1WT/Null and Grn−/− mice that had a higher level of GCase activity and undetectable pathologies, homozygous or hemizygous D409V in PG9V or PG9VN, respectively, resulted in profound inflammation and neurodegeneration. PG9VN mice exhibited much earlier onset, shorter life span, tissue fibrosis, and more severe phenotypes than PG9V mice. Glycosphingolipid accumulation, inflammatory responses, lysosomal-autophagy dysfunction, microgliosis, retinal gliosis, as well as α-Synuclein increases were much more pronounced in PG9VN mice. Neurodegeneration in PG9VN was characterized by activated microglial phagocytosis of impaired neurons and programmed cell death due to necrosis and, possibly, pyroptosis. Brain transcriptomic analyses revealed the intrinsic relationship between D409V dosage, and the degree of altered gene expression related to lysosome dysfunction, microgliosis, and neurodegeneration in GD, suggesting the disease severity is dependent on a GCase activity threshold related to Gba1 D409V dosage and loss of PGRN. These findings contribute to a deeper understanding of GD pathogenesis by elucidating additional underlying mechanisms of interplay between PGRN and Gba1 mutation dosage in modulating GCase function and disease severity in GD and GBA1-associated neurodegenerative diseases.
Lifestyle Intervention Modulates the CD4+ T Cell Profile in the Blood of Crohn’s Disease Patients
Authors: Mekes-Adamczyk Alexandra , Gausmann Nadine , Öznur Özlem , Pfuhlmann Katrin , Dziobaka Jan , Buer Jan , Langhorst Jost , Westendorf Astrid M 
Published: August 2024

Abstract

Background
Crohn’s disease (CD) significantly affects patients’ well-being and is influenced by stress and lifestyle factors, highlighting the importance of improving quality of life in CD management. An imbalance between pro- and anti-inflammatory CD4+ T cell responses is a key factor in CD, and stress has been shown to alter the function of CD4+ T cells. Therefore, this study aimed to evaluate the effect of a mind-body medicine stress management and lifestyle modification (MBM) program on the CD4+ T cell profile in CD patients.

Methods
Circulating CD4+ T cells from CD patients were analyzed by flow cytometry following the MBM program. Patients were randomly assigned to either a guided intervention group (IG) or a self-guided waitlist control group (CG) over a 9-month trial and compared with healthy blood donors.

Results
Lifestyle intervention reduced regulatory T cell (Treg) frequencies in the blood of CD patients. Notably, we observed a significant correlation between the quality of life improvement and Treg frequencies in the IG but not in the CG. Furthermore, differential activation and expression of the gut-homing molecules G protein–coupled receptor 15 and CCR9 on circulating Tregs and CD4+ effector T cells were detected in both the IG and CG.

Conclusions
The MBM program, whether guided or self-directed, has the potential to restore the CD4+ T cell profile of CD patients to levels comparable to healthy blood donors. Lifestyle interventions may benefit CD progression, symptoms, and immunological status, but further analysis is needed to substantiate these findings and to fully understand their clinical implications. (ClinicalTrials.gov: NCT05182645).
Habitat-specific response of fish assemblages in a small fully protected urban MPA
Authors: Ventura Patrícia , Gautier-Debernardi Jacqueline , Di Franco Eugenio , Francour Patrice , Di Franco Antonio , Pey Alexis 
Published: August 2024

Abstract
This study aims at assessing the reserve effect on fish assemblage in a small urban fully protected and highly enforced Marine Protected Area (MPA), Larvotto MPA (Monaco, Mediterranean Sea). The data about fish density, size, and biomass was collected by underwater visual census in the MPA and unprotected areas in two habitats, artificial rocky substrates and Posidonia oceanica meadows. On artificial rocky substrates, we recorded significantly higher fish biomass within the MPA compared to unprotected areas, while no significant difference was detected on Posidonia, with this suggesting the habitat-specific responses of fish assemblages to protection. Here we highlight the potential effectiveness of highly enforced small-sized urban MPAs, such as the Larvotto MPA, in generating ecological benefits, and speculate about their potential role in supporting networks of MPAs. This study supports increased attention to urban MPAs in conservation efforts, emphasizing the need for efficient management strategies in the face of ongoing coastal expansion.
Identification of Phosphodiesterase-7A (PDE7A) as a Novel Target for Reducing Ethanol Consumption in Mice
Authors: Wei Ran , Zong Fangjiao , Dong Jiahao , Zhao Wei , Zhang Fangfang , Wang Wei , Zhao Shuang , Wang Ziqi , Zhang Fang , Zhang Han-Ting 
Published: August 2024

Abstract

Background
Ethanol elicits a rapid stimulatory effect and a subsequent, prolonged sedative response, which are potential predictors of EtOH consumption by decreasing adenosine signaling; this phenomenon also reflects the obvious sex difference. cAMP (cyclic Adenosine Monophosphate)-PKA (Protein Kinase A) signaling pathway modulation can influence the stimulatory and sedative effects induced by EtOH in mice. This study’s objective is to clarify the role of phosphodiesterase (PDE) in mediating the observed sex differences in EtOH responsiveness between male and female animals.

Methods
EtOH was administered i.p. for 7 days to identify the changes in PDE isoforms in response to EtOH treatment. Additionally, EtOH consumption and preference of male and female C57BL/6J mice were assessed using the drinking-in-the-dark and 2-bottle choice tests. Further, pharmacological inhibition of PDE7A heterozygote knockout mice was performed to investigate its effects on EtOH-induced stimulation and sedation in both male and female mice. Finally, Western blotting analysis was performed to evaluate the alterations in cAMP-PKA/Epac2 pathways.

Results
EtOH administration resulted in an immediate upregulation in PDE7A expression in female mice, indicating a strong association between PDE7A and EtOH stimulation. Through the pharmacological inhibition of PDE7A KD mice, we have demonstrated for the first time, to our knowledge, that PDE7A selectively attenuates EtOH responsiveness and consumption exclusively in female mice, whichmay be associated with the cAMP-PKA/Epac2 pathway and downstream phosphorylation of CREB and ERK1/2.

Conclusions
Inhibition or knockdown of PDE7A attenuates EtOH responsivenessand consumption exclusively in female mice, which is associated with alterations in the cAMP-PKA/Epac2 signaling pathways, thereby highlighting its potential as a novel therapeutic target for alcohol use disorder.
On adversarial robustness and the use of Wasserstein ascent-descent dynamics to enforce it
Authors: García Trillos Camilo Andrés , García Trillos Nicolás 
Published: August 2024

Abstract
We propose iterative algorithms to solve adversarial training problems in a variety of supervised learning settings of interest. Our algorithms, which can be interpreted as suitable ascent-descent dynamics in Wasserstein spaces, take the form of a system of interacting particles. These interacting particle dynamics are shown to converge toward appropriate mean-field limit equations in certain large number of particles regimes. In turn, we prove that, under certain regularity assumptions, these mean-field equations converge, in the large time limit, toward approximate Nash equilibria of the original adversarial learning problems. We present results for non-convex non-concave settings, as well as for non-convex concave ones. Numerical experiments illustrate our results.
Biological invasions and epidemics with nonlocal diffusion along a line
Authors: Berestycki Henri , Roquejoffre Jean-Michel , Rossi Luca 
Published: August 2024

Abstract
To James D. Murray, with our admiration.
The goal of this work is to understand and quantify how a line with nonlocal diffusion given by an integral enhances a reaction-diffusion process occurring in the surrounding plane. This is part of a long-term programme where we aim at modelling, in a mathematically rigorous way, the effect of transportation networks on the speed of biological invasions or propagation of epidemics.
We prove the existence of a global propagation speed and characterize in terms of the parameters of the system the situations where such a speed is boosted by the presence of the line. In the course of the study we also uncover unexpected regularity properties of the model. On the quantitative side, the two main parameters are the intensity of the diffusion kernel and the characteristic size of its support. One outcome of this work is that the propagation speed will significantly be enhanced even if only one of the two is large, thus broadening the picture that we have already drawn in our previous works on the subject, with local diffusion modelled by a standard Laplacian.
We further investigate the role of the other parameters, enlightening some subtle effects due to the interplay between the diffusion in the half plane and that on the line. Lastly, in the context of propagation of epidemics, we also discuss the model where, instead of a diffusion, displacement on the line comes from a pure transport term.
Copy Number Variations of Plasmodium vivax DBP1, EBP/DBP2, and RBP2b in Ethiopians Who Are Duffy Positive and Duffy Negative
Authors: Pestana Kareen , Ford Anthony , Rama Rei , Abagero Beka , Kepple Daniel , Tomida Junya , Popovici Jean , Yewhalaw Delenasaw , Lo Eugenia 
Published: August 2024

Abstract
Recent evidence challenges the belief that individuals who are Duffy-negative are resistant to Plasmodium vivax due to lacking the Duffy antigen receptor for chemokines. Erythrocyte-binding protein (EBP/DBP2) has shown moderate binding to Duffy-negative erythrocytes in vitro. Reticulocyte-binding protein 2b (RBP2b) interactions with transferrin receptor 1 suggest involvement in Duffy-negative infections. Gene copy number variations in PvDBP1, PvEBP/DBP2, and PvRBP2b were investigated in Duffy-positive and Duffy-negative P vivax infections from Ethiopia. Among Duffy-positive samples, 34% displayed PvDBP1 duplications (Cambodian type). In Duffy-negative infections, 30% showed duplications, mostly Cambodian type. For PvEBP/DBP2 and PvRBP2b, Duffy-positive samples exhibited higher duplication rates (1–8 copies for PvEBP/DBP2, 46%; 1–5 copies for PvRBP2b, 43%) as compared with Duffy-negative samples (20.8% and 26%, respectively). The range of copy number variations was lower in Duffy-negative infections. Demographic and clinical factors associated with gene multiplications in both Duffy types were explored, enhancing understanding of P vivax evolution in Africans who are Duffy negative.
The active form of vitamin D (calcitriol) promotes CXCR5 expression during follicular helper T cell differentiation
Authors: Iwata Makoto , Takada Ayumi , Sakamoto Rei , Song Si-Young , Ito Etsuro 
Published: August 2024

Abstract
Follicular helper T (Tfh) cells promote B cell differentiation and antibody production in the B cell follicles of secondary lymphoid organs. Tfh cells express their signature transcription factor BCL6, interleukin (IL)-21, and surface molecules including inducible T cell costimulator (ICOS), programmed cell death-1 (PD-1), and C-X-C motif chemokine receptor 5 (CXCR5). Migration of Tfh cells to B cell follicles largely depends on the CXCR5 expression induced by interactions with antigen-presenting dendritic cells in the T cell area. How Tfh cells acquire sufficient levels of CXCR5 expression, however, has remained unclear. Using our in vitro culture system to generate CXCR5low Tfh-like cells from naive CD4+ T cells with IL-6 in the absence of other cell types, we found that the active form of vitamin D, calcitriol, markedly enhanced CXCR5 expression after the release from persistent T cell receptor (TCR) stimulation. CH-223191, an aryl hydrocarbon receptor antagonist, further enhanced CXCR5 expression. IL-12 but not IL-4, in place of IL-6, also supported calcitriol to enhance CXCR5 expression even before the release from TCR stimulation, whereas the cell viability sharply decreased after the release. The Tfh-like cells generated with IL-6 and calcitriol exhibited chemotaxis toward C-X-C motif chemokine ligand 13 (CXCL13), expressed IL-21, and helped B cells to produce IgG antibodies in vitro more efficiently than Tfh-like cells generated without added calcitriol. Calcitriol injections into antigen-primed mice increased the proportion of CXCR5+PD-1+CD4+ cells in their lymphoid organs, and enhanced T cell entry into B cell follicles. These results suggest that calcitriol promotes CXCR5 expression in developing Tfh cells and regulates their functional differentiation.
How far do forest container mosquitoes (Diptera: Culicidae) invade rural and urban areas in Japan? — Simple landscape ecology with comparison of the invasiveAedesecology between native and invasive ranges
Authors: Mogi Motoyoshi , Armbruster Peter A , Eritja Roger , Sunahara Toshihiko , Tuno Nobuko 
Published: August 2024

AbstractThe distribution of container mosquitoes in relation to distances from forests was studied in temperate Japan. Mosquito larvae were collected between May and September in 4 years from tree holes, bamboo stumps, riverine rock pools, and artificial containers; sampling ranged spatially from the mountain forest across the deforested plain developed as agriculture and urban areas to the seacoast. Although tree holes, bamboo stumps, and artificial containers existed throughout the deforested plain area, 10 container species of 6 genera were found virtually only within 5 km from the nearest forest edge. Worldwide invasive Aedes albopictus (Skuse) and Aedes japonicus (Theobald) of Asian origin showed unique occurrence patterns different from other container species and from each other. Ae. japonicus was dominant in artificial containers in and near the forest but minor in forest natural containers and only occurred within 5 km from the forest. Ae. albopictus was minor in the forest irrespective of container types but not bound to the forest and dominant in natural and artificial containers throughout rural and urban areas. The 5-km range was designated as the circum-forest zone for container mosquitoes (except Ae. albopictus) in Japan, and an expanded concept, circum-boundary zone, is proposed. The widths of these zones primarily depend on the dispersal traits of mosquitoes. Whether the relation of Ae. albopictus and Ae. japonicus to forests we observed are common in the native and invasive ranges is discussed. The study of across-ecosystem dispersal is important for mosquito management under anthropogenically changing environments due to either deforestation or green restoration.
Virtual Pooled Registry-Cancer Linkage System: an improved method for ascertaining cancer diagnoses
Authors: Deapen Dennis , Clerkin Castine , Howe William , Green Don , Johnson Christopher J , Kohler Betsy A , Landgren Annelie M , Preda Anca , Elena Joanne , Penberthy Lynne 
Published: August 2024

Abstract

Background
The National Cancer Institute funds many large cohort studies that rely on self-reported cancer data requiring medical record validation. This is labor intensive, costly, and prone to underreporting or misreporting of cancer and disparity-related differential response. US population-based central cancer registries identify incident cancer within their catchment area, yielding all malignant neoplasms and benign brain and central nervous system tumors with standardized data fields. This manuscript describes the development, implementation, and features of a system to facilitate linkage between cohort studies and cancer registries and the release of cancer registry data for matched cohort participants.

Methods
The Virtual Pooled Registry-Cancer Linkage System (VPR-CLS) provides an online system to link cohorts with multiple state cancer registries by 1) securely transmitting a study file to registries, 2) providing an optimized linkage algorithm to generate preliminary match counts, and 3) providing a streamlined process and templated forms for submitting and tracking data requests for cohort participants who matched with registries.

Results
In 2022, the VPR-CLS launched with 45 registries, covering 95% of the US state populations and Puerto Rico. Registries have linked with 15 studies having 14 273-10.9 million participants. Except in 1 study, linkage sensitivity ranged from 87.0% to 99.9%. Numerous registries have adopted the VPR-CLS templated institutional review board–registry application (n = 39), templated data use agreement (n = 25), and central institutional review board (n = 16).

Conclusions
The VPR-CLS markedly improves ascertainment of cancer outcomes and is the preferred approach for determination of outcomes from cohort studies, postmarketing surveillance, and clinical trials.