bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic architecture and sex chromosome systems of commercially important fish species in Asia – Current status, knowledge gaps and future prospects
Authors: Taslima Khanam , Kikuchi Kiyoshi , Hosoya Sho 
Published: June 2024

AbstractAquaculture is one of the fastest growing agro‐food industries in the world and Asia dominates the world's fish production (70% of total) with a high potential to ensure global food security. The leading aquaculture fish species in Asia show sexual dimorphism for traits such as growth, age at sexual maturity etc. in which one sex outperforms the other, increasing the need for controlling sex‐ratio in the farming system. Despite the huge contribution of Asian aquaculture to global fish production, the Asian aquaculture is facing a lot of challenges, for example, maintaining the genetic purity of the fish species and balancing the sex‐ratio in the culture system. Many of these difficulties arise due to a lack of deep understanding of fish genetics, or to the duplicated genome of cultured species, or to the unavailability of high‐quality reference genomes and information on sex determination mechanisms (crucial for monosex production and establishing appropriate breeding programme). This review has described the existing knowledge of the sex determination mechanisms in fish and genome architecture of four commercially important fish groups in Asia (carps, tilapias, catfishes and snakeheads). We also have outlined possible strategies for identifying sex‐determining gene/s using modern genome sequencing and computational technologies. Finally, we have highlighted the existing challenges and future prospects of Asian aquaculture. We anticipate that developments in genome sequencing technologies will help to address the biological complexities and challenges that exist in commercial aquaculture and will be of value for the future growth of the aquaculture industry in Asia.
A bed allocation model for pandemic situation considering general demand: A case study of Iran
Authors: Korzebor Mohammadreza , Nahavandi Nasim 
Published: June 2024

AbstractPandemics place a new type of demand from patients affected by the pandemic, imposing significant strain on hospital departments, particularly the intensive care unit. A crucial challenge during pandemics is the imbalance in addressing the needs of both pandemic patients and general patients. Often, the community's focus shifts toward the pandemic patients, causing an imbalance that can result in severe issues. Simultaneously considering both demands, pandemic‐related and general healthcare needs, has been largely overlooked. In this article, we propose a bi‐objective mathematical model for locating temporary hospitals and allocating patients to existing and temporary hospitals, considering both demand types during pandemics. Hospital departments, such as emergency beds, serve both demand types, but due to infection risks, accommodating a pandemic patient and a general patient in the same department is not feasible. The first objective function is to minimize the bed shortages considering both types of demands, whereas the second objective is cost minimization, which includes the fixed and variable costs of temporary facilities, the penalty cost of changing the allocation of existing facilities (between general and pandemic demand), the cost of adding expandable beds to existing facilities, and the service cost for different services and beds. To show the applicability of the model, a real case study has been conducted on the COVID‐19 pandemic in the city of Qom, Iran. Comparing the model results with real data reveals that using the proposed model can increase demand coverage by 16%.
“We Know What War Is”: Veterans, Soldiers, and Military Masculinity in the Soviet “Fight for Peace,” c. 1955–65
Authors: McCallum Claire E. 
Published: June 2024

AbstractThe aim of this article is to bring the issue of peace more definitively into the increasingly complex vision we have of the postwar era and to give particular thought to the place of the military man within a society that was now supposedly orientated toward peace. To do so, the discussion will range across both lived experience and cultural representations—predominantly of a visual nature—that broached the issue of peace, paying close attention to the ways in which the legacies of the Great Patriotic War shaped how serving soldiers and demobilized veterans articulated the need for peace and their role in ensuring its preservation. What will be repeatedly demonstrated in what follows is that the shadow of the Great Patriotic War loomed large over both cultural representations and personal conceptualizations of the ideal of peace, and as such the military man—both real and imagined, serving and demobilized—was integral to the discourse surrounding this most pressing social concern.
Revealing the impact of individual income inequality on different types of charitable giving in China through social interactions
Authors: Li Senlin , Zhang Le , Sun Yiying , Li Fulin 
Published: June 2024

AbstractObjectiveThis study delves into the correlation between individual income inequality as measured by the relative deprivation index and charitable giving, while also examining urban–rural heterogeneity. Additionally, it further explores the mechanisms by which online and offline forms of social interaction operate in this context.MethodsUtilizing data from the 2014–2020 China Family Panel Studies, we employed several methodologies including Probit regression models, cross‐model average marginal effects difference testing based on bootstrap method, instrumental variable method, and the Karlson–Holm–Breen (KHB) effect decomposition method.ResultsThe findings reveal that individual income inequality measured by the relative deprivation index significantly reduces charitable giving among Chinese households. The inhibitory effect of individual income inequality on social charitable giving is higher than that on charitable giving directed toward friends or colleagues. Furthermore, this impact exhibits some heterogeneity between urban and rural areas. Mechanism analysis indicates that the adverse effect of income inequality on charitable giving operates through reducing social interaction, including both online and offline forms.ConclusionOur results demonstrate that income inequality has distinct adverse effects on two types of charitable giving and explain the mechanisms underlying these effects through social interaction. A pattern of the differential mode of association similar to “ripples” in Chinese society is beneficial for understanding these differentiated impacts. We believe it is necessary to improve economic inequality conditions and enhance the enthusiasm of the Chinese public for participating in charitable donations by promoting various forms of social interaction.
Deep learning approaches for delineating wetlands on historical topographic maps
Authors: Vynikal Jakub , Müllerová Jana , Pacina Jan 
Published: June 2024

AbstractHistorical topographic maps are an important source of a visual record of the landscape, showing geographical elements such as terrain, elevation, rivers and water bodies, roads, buildings, and land use and land cover (LULC). Historical maps are scanned to their digital representation, a raster image. To quantify different classes of LULC, it is necessary to transform scanned maps to their vector equivalent. Traditionally, this has been done either manually, or by using (semi)automatic methods of clustering/segmentation. With the advent of deep neural networks, new horizons opened for more effective and accurate processing. This article attempts to use different deep‐learning approaches to detect and segment wetlands on historical Topographic Maps 1: 10000 (TM10), created during the 50s and 60s. Due to the specific symbology of wetlands, their processing can be challenging. It deals with two distinct approaches in the deep learning world, semantic segmentation and object detection, represented by the U‐Net and Single‐Shot Detector (SSD) neural networks, respectively. The suitability, speed, and accuracy of the two approaches in neural networks are analyzed. The results are satisfactory, with the U‐Net F1 score reaching 75.7% and the SSD object detection approach presenting an unconventional alternative.
Molecular and spatial evaluation of small rodents and Didelphimorphis infected with Mycobacterium leprae in the southern Amazon, Brazil
Authors: de Souza Valois Elderson Mariano , de Oliveira Nathan Guilherme , de Lázari Patrick Ricardo , da Silva David José Ferreira , Rotelli Raissa Campos , Batista Lavínia Cássia Ferreira , Sobral Marcos Henrique , Bortolomai Bruna Eduarda , Finardi Amanda Juliane , Levi Taal , Peres Carlos Augusto , de Morais Bronzoni Roberta Vieira , Baptista Ida Maria Foschiani Dias 
Published: June 2024

AbstractBackgroundThe high levels of recent transmission of leprosy worldwide demonstrate the necessity of epidemiologic surveillance to understand and control its dissemination. Brazil remains the second in number of cases around the world, indicating active transmission of Mycobacterium leprae (M. leprae) in the population. At this moment, there is a consensus that the bacillus is transmitted by inter‐human contact, however, different serologic, molecular, and histopathological approaches indicate the existence of non‐human transmission sources.Methods and ResultsThe qPCR assay was used to amplify the molecular targets 16S RNAr and RLEP, in samples of liver, spleen, and ear of wild animals belonging to Didelphimorphia and Rodentia orders, in highly endemic areas of Mato Grosso, Brazil. The RLEP repetitive sequence was positive in 202 (89.0%) samples, with 96 (42.3%) of these also being positive for the 16S gene. Regarding the collection sites, it was observed that the animals were found in areas profoundly deforested, close to urban areas.ConclusionsOur results suggest that wild animals can play an important role in the maintenance of M. leprae in endemic regions with major anthropic action in Brazil. Therefore, integrating human, animal, and environmental health care with the One Health initiative is highly efficient for the development of effective strategies to contain and control leprosy in Brazil.
Phylogeny and evolutionary timescales of the tribes Tagiadini and Celaenorrhinini (Hesperiidae, Pyrginae) inferred from mitochondrial genome and nuclear genes
Authors: Zhang Xuan , Liu Jiaqi , Chiba Hideyuki , Li Yiping , Yuan Xiangqun 
Published: June 2024

AbstractTagiadini and Celaenorrhinini, two closely related groups of skippers in the subfamily Pyrginae, are mainly distributed across the Oriental, Palaearctic and African regions. While some efforts have been made to explore the phylogenetic relationships within Tagiadini and Celaenorrhinini, several unresolved issues still persist. In this study, we sequenced 13 complete mitochondrial genomes from Tagiadini and Celaenorrhinini. Additionally, we extracted nuclear genes CAD, EF‐1α, IDH, MDH, RPS5 and Wingless from the public database. Through comparative analysis, we gained insights into the structure of these newly sequenced mitogenomes. Furthermore, we constructed a comprehensive phylogenetic tree for Tagiadini and Celaenorrhinini, integrating the newly obtained mitochondrial genomes and nuclear genes with previously published mitogenomes and data from the sequence read archive (SRA). The total length of the mitochondrial genomes of the 13 skipper species ranged from 15,228 bp (Seseria sambara indosinica) to 15,431 bp (Pseudocoladenia festa). The newly sequenced genomes featured the standard set of 13 protein‐coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a non‐coding A + T‐rich region implicated in replication initiation. The phylogenetic analysis encompassing all mitochondrial and nuclear gene data consistently upheld the monophyly of genera within the tribes Tagiadini and Celaenorrhinini. Most of the intergeneric relationships identified in our study agreed with recent genomic discoveries, showing enhanced nodal support values in some cases. Lastly, we estimated the divergence of the Tagiadini + Celaenorrhinini branch at approximately 44.06 million years ago (Ma) during the middle Eocene epoch. The crown ages of Tagiadini and Celaenorrhinini were estimated at approximately 41.69 Ma and 38.49 Ma, respectively.
Renal handling of albumin in rats with early stage diabetes: A theoretical analysis
Authors: Edwards Aurélie 
Published: June 2024

AbstractIn early diabetic nephropathy (DN), recent studies have shown that albuminuria stems mostly from alterations in tubular function rather than from glomerular damage. Several factors in DN, including hyperfiltration, hypertrophy and reduced abundance of the albumin receptors megalin and cubilin, affect albumin endocytosis in the proximal tubule (PT). To assess their respective contribution, we developed a model of albumin handling in the rat PT that couples the transport of albumin to that of water and solutes. Our simulations suggest that, under basal conditions, ∼75% of albumin is retrieved in the S1 segment. The model predicts negligible uptake in S3, as observed experimentally. It also accurately predicts the impact of acute hyperglycaemia on urinary albumin excretion. Simulations reproduce observed increases in albumin excretion in early DN by considering the combined effects of increased glomerular filtration rate (GFR), osmotic diuresis, hypertrophy, and megalin and cubilin downregulation, without stipulating changes in glomerular permselectivity. The results indicate that in isolation, glucose‐elicited osmotic diuresis and glucose transporter upregulation raise albumin excretion only slightly. Enlargement of PT diameter not only augments uptake via surface area expansion, but also reduces fluid velocity and thus shear stress‐induced stimulation of endocytosis. Overall, our model predicts that downregulation of megalin and cubilin and hyperfiltration both contribute significantly to increasing albumin excretion in rats with early‐stage diabetes. The results also suggest that acute sodium–glucose cotransporter 2 inhibition lowers albumin excretion only if GFR decreases sufficiently, and that angiotensin II receptor blockers mitigate urinary albumin loss in early DN in large part by upregulating albumin receptor abundance.
imageKey points
The urinary excretion of albumin is increased in early diabetic nephropathy (DN). It is difficult to experimentally disentangle the multiple factors that affect the renal handling of albumin in DN.
We developed a mathematical model of albumin transport in the rat proximal tubule (PT) to examine the impact of elevated plasma glucose, hyperfiltration, PT hypertrophy and reduced abundance of albumin receptors on albumin uptake and excretion in DN.
Our model predicts that glucose‐elicited osmotic diuresis per se raises albumin excretion only slightly. Conversely, increases in PT diameter and length favour reduced albumin excretion.
Our results suggest that downregulation of the receptors megalin and cubilin in PT cells and hyperfiltration both contribute significantly to increasing albumin excretion in DN.
The model helps to better understand the mechanisms underlying urinary loss of albumin in early‐stage diabetes, and the impact of specific treatments thereupon.
Ambiviricota
, a novel ribovirian phylum for viruses with viroid-like properties
Authors: Kuhn Jens H. , Botella Leticia , de la Peña Marcos , Vainio Eeva J. , Krupovic Mart , Lee Benjamin D. , Navarro Beatriz , Sabanadzovic Sead , Simmonds Peter , Turina Massimo 
Published: June 2024

ABSTRACT

Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as ‘ambiviruses,’ were described. ‘Ambiviruses’ have single-stranded RNA genomes of about 4–5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known ‘ambiviruses,’ and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom
Orthornavirae
. However, ‘ambivirus’ genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations—features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as ‘epsilonviruses,’ ‘zetaviruses,’ and some ‘obelisks’). As a first step toward the formal classification of ‘ambiviruses,’ the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum,
Ambiviricota
, to accommodate an initial set of 20 members with well-annotated genome sequences.
Application of the ESMO Magnitude of Clinical Benefit Scale to assess the clinical benefit of antibody drug conjugates in solid cancer: a systematic descriptive analysis of phase III and pivotal phase II trials
Authors: Ding Lieming , Yuan Xiaobin , Wang Yang , Shen Zhilin , Wu Pengxiang 
Published: June 2024

ObjectiveThe aim of this study was to assess the clinical benefit value of approved antibody drug conjugates (ADCs) for solid tumours using the European Society for Medical Oncology Magnitude of Clinical Benefit Scale (ESMO-MCBS) V.1.1.DesignSystematic descriptive analysis.Data sourcesPubMed was searched for publications from 1 January 2000 to 18 October 2023.Eligibility criteriaWe included the phase III randomised controlled trials or phase II pivotal trials leading to approval of ADCs in solid tumours.Data extraction and synthesisTwo independent reviewers extracted data and discrepancies were resolved by consensus in the presence of a third investigator.ResultsESMO-MCBS Scores were calculated for 16 positive clinical trials of eight ADCs, which were first approved by the US Food and Drug Administration (FDA), the European Medicines Agency (EMA), the China National Medical Products Administration and the Japanese Pharmaceuticals and Medical Devices Agency for solid cancers. Among 16 trials, 4 (25%) met the ESMO-MCBS benefit threshold grade, while 12 (75%) of the regimens did not meet the ESMO-MCBS benefit threshold grade. 5 (31%) of the 16 trials had no published scorecard on the ESMO website due to the approval by other jurisdictions but not by the FDA or EMA. Discrepancies between our results and the ESMO scorecard were observed in 4 (36%) of 11 trials, mostly owing to integration of more recent data.ConclusionsESMO-MCBS is an important tool for assessing the clinical benefit of cancer drugs, but not all drugs met the meaningful benefit threshold.
Supporting young women’s health through girl-friendly drug vendors in Lake Zone, Tanzania: protocol for the AmbassADDOrs for Health cluster-randomised controlled trial
Authors: Mnyippembe Agatha , Sheira Lila A , McCoy Sandra I , Njau Prosper F , Packel Laura J , Hassan Kassim , Solorzano-Barrera Camila , Maokola Werner , Kang Dufour Mi-Suk , Sabasaba Amon , Liu Jenny 
Published: June 2024

IntroductionAdverse sexual and reproductive health (SRH) outcomes, such as unplanned pregnancies and HIV infection, disproportionately affect adolescent girls and young women (AGYW; aged 15–24 years) in east Africa. Increasing uptake of preventive SRH services via innovative, youth-centred interventions is imperative to addressing disparities in SRH outcomes.Methods and analysisFrom 2018 to 2019, we used human-centred design to co-develop a theoretically driven HIV and pregnancy prevention intervention for AGYW at private drug shops called Accredited Drug Dispensing Outlets (ADDOs) in Tanzania. The result, Malkia Klabu (Queen Club), was a customer loyalty programme designed to strengthen ADDOs’ role as SRH providers while encouraging uptake of critical SRH prevention products among AGYW. Malkia Klabu members had access to free contraceptives and oral HIV self-test (HIVST) kits and earned punches on a loyalty card for other shop purchases; punches were redeemable for small prizes. Our pilot among 40 shops showed that intervention ADDOs had higher AGYW patronage and distributed more HIVST kits and contraceptives to AGYW relative to business-as-usual (ie, client purchasing) comparison shops. We will conduct a cluster-randomised controlled trial (c-RCT) among 120–140 ADDOs in 40 health catchment areas in Shinyanga and Mwanza Regions (Lake Zone), Tanzania. ADDO shop recruitment includes a 1-month run-in with a tablet-based electronic inventory management system for tracking shop transactions, followed by enrolment, randomisation and a 24-month trial period. Our c-RCT evaluating the human-centred design-derived intervention will assess population impact on the primary outcomes of HIV diagnoses and antenatal care registrations, measured with routine health facility data. We will also assess secondary outcomes focusing on mechanisms of action, evaluate programme exposure and AGYW behaviour change in interviews with AGYW, and assess shop-level implementation strategies and fidelity.Ethics and disseminationEthical approval was granted from both the University of California, San Francisco and the Tanzanian National Institute for Medical Research. Study progress and final outcomes will be posted annually to the National Clinical Trials website; study dissemination will occur at conferences, peer-reviewed manuscripts and local convenings of stakeholders.Trial registration numberNCT05357144.
Design, rationale and protocol for Glycemic Observation and Metabolic Outcomes in Mothers and Offspring (GO MOMs): an observational cohort study
Authors:   The GO MOMs Study Group
Published: June 2024

IntroductionGiven the increasing prevalence of both obesity and pre-diabetes in pregnant adults, there is growing interest in identifying hyperglycaemia in early pregnancy to optimise maternal and perinatal outcomes. Multiple organisations recommend first-trimester diabetes screening for individuals with risk factors; however, the benefits and drawbacks of detecting glucose abnormalities more mild than overt diabetes in early gestation and the best screening method to detect such abnormalities remain unclear.Methods and analysisThe goal of the Glycemic Observation and Metabolic Outcomes in Mothers and Offspring study (GO MOMs) is to evaluate how early pregnancy glycaemia, measured using continuous glucose monitoring and oral glucose tolerance testing, relates to the diagnosis of gestational diabetes (GDM) at 24–28 weeks’ gestation (maternal primary outcome) and large-for-gestational-age birth weight (newborn primary outcome). Secondary objectives include relating early pregnancy glycaemia to other adverse pregnancy outcomes and comprehensively detailing longitudinal changes in glucose over the course of pregnancy. GO MOMs enrolment began in April 2021 and will continue for 3.5 years with a target sample size of 2150 participants.Ethics and disseminationGO MOMs is centrally overseen by Vanderbilt University’s Institutional Review Board and an Observational Study Monitoring Board appointed by National Institute of Diabetes and Digestive and Kidney Diseases. GO MOMs has potential to yield data that will improve understanding of hyperglycaemia in pregnancy, elucidate better approaches for early pregnancy GDM screening, and inform future clinical trials of early GDM treatment.Trial registration numberNCT04860336.