bluuebunny/crossref_metadata_2025_split huggingface dataset:
MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning
Authors: Wang Tao , Li Zhen , Zhuo Linlin , Chen Yifan , Fu Xiangzheng , Zou Quan 
Published: March 2024

Abstract

Motivation
Accurately predicting molecular metabolic stability is of great significance to drug research and development, ensuring drug safety and effectiveness. Existing deep learning methods, especially graph neural networks, can reveal the molecular structure of drugs and thus efficiently predict the metabolic stability of molecules. However, most of these methods focus on the message passing between adjacent atoms in the molecular graph, ignoring the relationship between bonds. This makes it difficult for these methods to estimate accurate molecular representations, thereby being limited in molecular metabolic stability prediction tasks.

Results
We propose the MS-BACL model based on bond graph augmentation technology and contrastive learning strategy, which can efficiently and reliably predict the metabolic stability of molecules. To our knowledge, this is the first time that bond-to-bond relationships in molecular graph structures have been considered in the task of metabolic stability prediction. We build a bond graph based on ‘atom-bond-atom’, and the model can simultaneously capture the information of atoms and bonds during the message propagation process. This enhances the model’s ability to reveal the internal structure of the molecule, thereby improving the structural representation of the molecule. Furthermore, we perform contrastive learning training based on the molecular graph and its bond graph to learn the final molecular representation. Multiple sets of experimental results on public datasets show that the proposed MS-BACL model outperforms the state-of-the-art model.

Availability and Implementation
The code and data are publicly available at https://github.com/taowang11/MS.
Mice and minipigs with compromised expression of the Alzheimer’s disease gene SORL1 show cerebral metabolic disturbances on hyperpolarized [1-13C]pyruvate and sodium MRI
Authors: Bøgh Nikolaj , Sørensen Charlotte B , Alstrup Aage K O , Hansen Esben S S , Andersen Olav M , Laustsen Christoffer 
Published: March 2024

Abstract
The sortilin-related receptor 1 (SORL1) gene, encoding the cellular endosomal sorting-related receptor with A-type repeats (SORLA), is now established as a causal gene for Alzheimer’s disease. As the latest addition to the list of causal genes, the pathophysiological effects and biomarker potential of SORL1 variants remain relatively undiscovered. Metabolic dysfunction is, however, well described in patients with Alzheimer’s disease and is used as an imaging biomarker in clinical diagnosis settings. To understand the metabolic consequences of loss-of-function SORL1 mutations, we applied two metabolic MRI technologies, sodium (23Na) MRI and MRI with hyperpolarized [1-13C]pyruvate, in minipigs and mice with compromised expression of SORL1. At the age analysed here, both animal models display no conventional imaging evidence of neurodegeneration but show biochemical signs of elevated amyloid production, thus representing the early preclinical disease. With hyperpolarized MRI, the exchange from [1-13C]pyruvate to [1-13C]lactate and 13C-bicarbonate was decreased by 32 and 23%, respectively, in the cerebrum of SORL1-haploinsufficient minipigs. A robust 11% decrease in the sodium content was observed with 23Na-MRI in the same minipigs. Comparably, the brain sodium concentration gradually decreased from control to SORL1 haploinsufficient (−11%) to SORL1 knockout mice (−23%), suggesting a gene dose dependence in the metabolic dysfunction. The present study highlights that metabolic MRI technologies are sensitive to the functional, metabolic consequences of Alzheimer’s disease and Alzheimer’s disease–linked genotypes. Further, the study suggests a potential avenue of research into the mechanisms of metabolic alterations by SORL1 mutations and their potential role in neurodegeneration.
‘It’s nice that we can do that too’: investigating transgender persons' negotiations with identity and community questions in Indian science institutions
Authors: Datta Sayantan 
Published: March 2024

Abstract
In 2014, the Indian Supreme Court passed the landmark NALSA v. Union of India judgment that not only granted transgender persons the right to self-identify their gender but also recognized their right to equitable and accessible education. Further, in 2018, the apex court passed another landmark judgment in the case of Navtej Singh Johar & Ors. v. Union of India, reading down Section 377 of the Indian Penal Code, and, therefore, decriminalizing consensual adult homosexual sex acts. In the backdrop of these landmark judgments – i.e. in post-NALSA and post-377 India – identity and community questions pertaining to transgender, gender non-conforming, and non-binary persons’ access to and presence in educational institutions in India have intensified. Focusing on science institutions, this paper attempts to delineate the ways in which proximal and distal networks of caste-class and gender shape transgender, gender non-conforming, and non-binary persons’ exclusion from and belonging in science collectivities. Further, this paper also investigates how transgender persons’ sense of belonging to certain communities speaks to their shifting epistemic dispositions. Finally, contextualizing transpersons’ negotiations in science communities and individual and collective scales as ‘unstable and hybrid assemblages’, this paper demonstrates the ways in which trans collectives in science institutions radicalize community building and development in these institutional spaces by interrupting dominant institutional cultures and practices.
Precarious life in a heartless world: COVID-19 and the gender transgressive Shivashaktis in Southern India
Authors: Mukherjee Debomita , Rao Archana , Kumar Pushpesh 
Published: March 2024

Abstract
This paper attempts to understand and narrate the experiences of Shivashaktis, a gender transgressive community from Southern India, during the COVID-19 pandemic. The Shivashaktis’ gender transgressions and embodied ritual power allow them to intercede between the human and the divine. This secures them religious sanction and legitimacy and offers a source of income for them. They are engaged in several livelihood practices that are associated with ritual practices such as performing oracles, laggams (deity marriages), joggu, etc. Their embeddedness in heterosexual family structures, however, hinder their access to benefits that are allocated for the transgender community through the state and non-state policy programmes. During the pandemic, with the state-announced lockdown across the nation, and particularly in Telangana, Shivashaktis were pushed further into precarity, burdened by economic, psychological and community disruptions. Within this context, the paper critically engages with the impact of COVID-19 that brought the entire relational world of the gender transgressive Shivashaktis to collapse rigorously, affecting their livelihood and sense of being and belonging in the world.
National Unified Renal Translational Research Enterprise: Idiopathic Nephrotic Syndrome (NURTuRE-INS) study
Authors: Colby Elizabeth , Hayward Samantha , Benavente Melissa , Robertson Fiona , Bierzynska Agnieszka , Osborne Amy , Parmesar Kevon , Afzal Maryam , Chapman Tracey , Ullah Fatima , Davies Elaine , Nation Michael , Cook Wendy , Johnson Tim , Andag Uwe , Radresa Olivier , Skroblin Philipp , Bayerlova Michaela , Unwin Robert , Vuilleumier Nicolas , Banks Rosamonde E , Braddon Fiona , Koziell Ania , Taal Maarten W , Welsh Gavin I , Saleem Moin A 
Published: March 2024

ABSTRACT

Background
Idiopathic nephrotic syndrome (INS) is a heterogenous disease and current classification is based on observational responses to therapies or kidney histology. The National Unified Renal Translational Research Enterprise (NURTuRE)-INS cohort aims to facilitate novel ways of stratifying INS patients to improve disease understanding, therapeutics and design of clinical trials.

Methods
NURTuRE-INS is a prospective cohort study of children and adults with INS in a linked biorepository. All recruits had at least one sampling visit collecting serum, plasma, urine and blood for RNA and DNA extraction, frozen within 2 hours of collection. Clinical histology slides and biopsy tissue blocks were also collected.

Results
A total of 739 participants were recruited from 23 centres to NURTuRE-INS, half of whom were diagnosed in childhood [n = 365 (49%)]. The majority were white [n = 525 (71%)] and the median age at recruitment was 32 years (interquartile range 12–54). Steroid-sensitive nephrotic syndrome (SSNS) was the most common clinical diagnosis [n = 518 (70%)]. Of patients diagnosed in childhood who underwent a kidney biopsy, for SSNS (n =103), 76 demonstrated minimal change disease (MCD), whereas for steroid-resistant nephrotic syndrome (n =80), 21 had MCD. Almost all patients diagnosed in adulthood had a kidney biopsy [n = 352 (94%)]; 187 had MCD and 162 had focal segmental glomerulosclerosis.

Conclusions
NURTuRE-INS is a prospective cohort study with high-quality biosamples and longitudinal data that will assist research into the mechanistic stratification of INS. Samples and data will be available through a Strategic Access and Oversight Committee.
Seasonal impacts on gut microbial composition of the Eastern subterranean termite (Blattodea: Rhinotermitidae)
Authors: Sapkota Rajani , Nakatsu Cindy H , Scharf Michael E 
Published: March 2024

Abstract
Termite hindguts are inhabited by symbionts that help with numerous processes, but changes in the gut microbiome due to season can potentially impact the physiology of termites. This study investigated the impact of seasonal changes on the composition of bacteria and protozoa in the termite gut. Termites were obtained monthly from May to October 2020 at a location in the central United States that typically experiences seasonal air temperatures ranging from &lt; 0 to &gt; 30 °C. The guts of 10 termites per biological replication were dissected and frozen within 1 day after collections. DNA was extracted from the frozen gut tissues and used for termite 16S rRNA mitochondrial gene analysis and bacterial 16S rRNA gene sequence surveys. Phylogenetic analysis of termite 16S rRNA gene sequences verified that the same colony was sampled across all time points. On processing bacterial 16S sequences, we observed alpha (observed features, Pielou’s evenness, and Shannon diversity) and beta diversity (unweighted Unifrac, Bray-Curtis, and Jaccard) metrics to vary significantly across months. Based on the analysis of the composition of microbiomes with bias correction (ANCOM-BC) at the genus level, we found several significant bacterial taxa over collection months. In addition, Spearman correlation analysis demonstrated that 41 bacterial taxa were significantly correlated (positively and negatively) with average soil temperature. These results from a single termite colony suggest termite microbial communities go through seasonal changes in relative abundance related to temperature, although other seasonal effects cannot be excluded. Further investigations are required to conclusively define the consistency of microbial variation among different colonies with season.
Noncontiguous operon atlas for the Staphylococcus aureus genome
Authors: Iturbe Pablo , Martín Alvaro San , Hamamoto Hiroshi , Marcet-Houben Marina , Galbaldón Toni , Solano Cristina , Lasa Iñigo 
Published: March 2024

Abstract
Bacteria synchronize the expression of genes with related functions by organizing genes into operons so that they are cotranscribed together in a single polycistronic messenger RNA. However, some cellular processes may benefit if the simultaneous production of the operon proteins coincides with the inhibition of the expression of an antagonist gene. To coordinate such situations, bacteria have evolved noncontiguous operons (NcOs), a subtype of operons that contain one or more genes that are transcribed in the opposite direction to the other operon genes. This structure results in overlapping transcripts whose expression is mutually repressed. The presence of NcOs cannot be predicted computationally and their identification requires a detailed knowledge of the bacterial transcriptome. In this study, we used direct RNA sequencing methodology to determine the NcOs map in the Staphylococcus aureus genome. We detected the presence of 18 NcOs in the genome of S. aureus and four in the genome of the lysogenic prophage 80α. The identified NcOs comprise genes involved in energy metabolism, metal acquisition and transport, toxin–antitoxin systems, and control of the phage life cycle. Using the menaquinone operon as a proof of concept, we show that disarrangement of the NcO architecture results in a reduction of bacterial fitness due to an increase in menaquinone levels and a decrease in the rate of oxygen consumption. Our study demonstrates the significance of NcO structures in bacterial physiology and emphasizes the importance of combining operon maps with transcriptomic data to uncover previously unnoticed functional relationships between neighbouring genes.
Interplay between gut microbiota and the master iron regulator, hepcidin, in the pathogenesis of liver fibrosis
Authors: Ahmadi Badi Sara , Bereimipour Ahmad , Rohani Pejman , Khatami Shohreh , Siadat Seyed Davar 
Published: March 2024

Abstract
Introduction: There is a proven role for hepcidin and the composition of gut microbiota and its derivatives in the pathophysiology of liver fibrosis. Area covered: This review focuses on the literature search regarding the effect of hepcidin and gut microbiota on regulating liver physiology. We presented the regulating mechanisms of hepcidin expression and discussed the possible interaction between gut microbiota and hepcidin regulation. Furthermore, we investigated the importance of the hepcidin gene in biological processes and bacterial interactions using bioinformatics analysis. Expert Opinion: One of the main features of liver fibrosis is iron accumulation in hepatic cells, including hepatocytes. This accumulation can induce an oxidative stress response, inflammation, and activation of hepatic stellate cells. Hepcidin is a crucial regulator of iron by targeting ferroportin expressed on hepatocytes, macrophages, and enterocytes. Various stimuli, such as iron load and inflammatory signals, control hepcidin regulation. Furthermore, a bidirectional relationship exists between iron and the composition and metabolic activity of gut microbiota. We explored the potential of gut microbiota to influence hepcidin expression and potentially manage liver fibrosis, as the regulation of iron metabolism plays a crucial role in this context.
Lipidomic Profiling of Kidney Cortical Tubule Segments Identifies Lipotypes with Physiological Implications
Authors: Cheval Lydie , Poindessous Virginie , Sampaio Julio L , Crambert Gilles , Pallet Nicolas 
Published: March 2024

Abstract
A detailed knowledge of the lipid composition of components of nephrons is crucial for understanding physiological processes and the development of kidney diseases. However, the lipidomic composition of kidney tubular segments is unknown. We manually isolated the proximal convoluted tubule (PCT), the cortical thick ascending limb of Henle’s loop, and the cortical collecting duct from 5 lean and obese mice and subjected the samples to shotgun lipidomics analysis by high-resolution mass spectrometry acquisition. Across all samples, more than 500 lipid species were identified, quantified, and compared. We observed significant compositional differences among the 3 tubular segments, which serve as true signatures. These intrinsic lipidomic features are associated with a distinct proteomic program that regulates highly specific physiological functions. The distinctive lipidomic features of each of the 3 segments are mostly based on the relative composition of neutral lipids, long-chain polyunsaturated fatty acids, sphingolipids, and ether phospholipids. These features support the hypothesis of a lipotype assigned to specific tubular segments. Obesity profoundly impacts the lipotype of PCT. In conclusion, we present a comprehensive lipidomic analysis of 3 cortical segments of mouse kidney tubules. This valuable resource provides unparalleled detail that enhances our understanding of tubular physiology and the potential impact of pathological conditions.
Application of insecticide dusts for the management of Indian meal moth (Lepidoptera: Pyralidae) wandering larvae under laboratory conditions
Authors: Pan Xiaodan , Wang Changlu 
Published: March 2024

Abstract
The Indian meal moth, Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae), is a very common stored-product pest. The mature larvae wander around searching for suitable places to pupate, offering an opportunity to control this pest. We evaluated the efficacy of 5 insecticide dusts: Alpine (0.25% dinotefuran, 95% diatomaceous earth [DE]), CimeXa (92.1% amorphous silica gel), DX13 (100% DE), Tempo (1% cyfluthrin), and Tri-Die (1% pyrethrin, 10% piperonyl butoxide, 40% amorphous silica) against P. interpunctella wandering larvae by allowing larvae to pass 1-inch treated band, expose to treated vinyl tiles for 5 min, and expose to treated harborage (with or without the presence of an untreated harborage). A commercially treated harborage product (Nattaro band) served as a positive control in the exposure to the treated harborage test. Tempo was significantly more effective than other insecticide dusts in the 1-inch band and forced exposure tests but caused only 44% and 54% larvae mortality in the 2 tests. In contrast, CimeXa, Tri-Die, and Tempo caused 84%–89% mortality when the larvae were provided with treated harborages. When both treated and untreated harborages were present, Tempo caused a significantly higher mortality and a lower percentage of emerged adults from larvae than Tri-Die, but not significantly more than CimeXa. Deploying Tempo or CimeXa-treated harborages and/or applying insecticide dust directly into the wall crevices, perimeters of the floor, shipping pallets, and other areas where P. interpunctella larvae hide could be an effective method for the management of the wandering stage of P. interpunctella larvae in storage facilities.
Effects of deploying ethanol lures in tandem with generic pheromone lures for attraction of cerambycid beetles in field bioassays
Authors: Rice Marlin E , Zou Yunfan , Millar Jocelyn G , Hanks Lawrence M 
Published: March 2024

Abstract
Male cerambycid beetles of the large subfamilies Cerambycinae and Lamiinae produce aggregation-sex pheromones that attract both sexes. The pheromones of many species are conserved among both closely related species (e.g., congeners) and more distantly related species (e.g., different subfamilies), including those endemic to different continents. This parsimony in pheromone structures suggests that multiple species may be attracted to traps baited with blends of pheromones, and such blends are finding use in delineating geographic ranges of native species and in surveillance programs for incursions of exotic species. Here, we present the results of a field experiment conducted at multiple sites in Iowa that tested the effects of deploying ethanol lures in tandem with a 6-component blend of common pheromone components for cerambycine and lamiine species and a 5-component blend that specifically targeted lamiines. Eight cerambycine species showed significant treatment effects, most of which were attracted to the 6-component blend, and ethanol increased attraction for half of these species. Two cerambycine species were attracted only by ethanol. Seven lamiine species were attracted by the lamiine-specific blend, alone or when combined with ethanol, and 3 of these species also were attracted to the 6-component blend. Taken together, these findings provide further evidence that carefully crafted blends of pheromones can be used to monitor the presence or abundance of multiple cerambycid species. Ethanol either increased the number of beetles attracted by pheromones or had no effect, so there is no apparent downside to deploying ethanol lures in combination with pheromones.
Epithelioid hemangioendothelioma—its history, clinical features, molecular biology and current therapy
Authors: Tsuchihashi Kenji , Baba Eishi 
Published: March 2024

Abstract
Epithelioid hemangioendothelioma (EHE) is a remarkably rare tumor arising from endothelial cells that is classified as a vascular tumor in the WHO classification. The tumor is predominantly characterized by the presence of fusion genes, such as WWTR1-CAMTA1 or YAP1-TFE3, with a minority of cases exhibiting other rare fusion genes. EHE exhibits a broad age of onset, typically presenting at ~50 years, but it is not uncommon in pediatric populations. It manifests in a variety of organs, including the liver, lung, soft tissue and bone. Initial multiple-organ involvement is also observed. The tumor’s biological behavior and prognosis vary substantially based on the primary site of manifestation. From a therapeutic perspective, initial active surveillance might be considered in selected cases, although surgical intervention remains the mainstay of treatment, especially for localized single-organ involvement. Chemotherapy is administered to patients with progressive unresectable tumors. Recent advances in the biological analysis of EHE fusion genes have elucidated their diverse functions. Additionally, next-generation sequencing has facilitated the identification of other mutations beyond the fusion genes. These continuous efforts to understand the biology of the fusion genes themselves and/or the dysregulated signaling by fusion genes are expected to lead to the development of novel therapeutic strategies for EHE. This article aims to provide a comprehensive review of EHE, encompassing its historical context, clinical manifestations, molecular biology and the current state of treatment.