bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic insights into the terrestrial snails Helicoidei (Gastropoda: Stylommatophora) with special emphasis on the Camaenidae
Authors: Zhang Guoyi , Naggs Fred , Andrus Peter S , Wade Christopher M 
Published: March 2024

Abstract
The superfamily Helicoidei are a widely distributed and diverse infraorder of land snails and slugs. Here, we constructed a phylogenetic tree based on sequences of the large subunit ribosomal RNA gene to investigate the relationships within the Helicoidei. Based on our phylogenetic tree, the family Camaenidae, as currently recognized, is not monophyletic, with the Polygyridae falling within the group. Likewise, the family Hygromiidae as currently defined is not monophyletic and incorporates the Geomitridae. The family Xanthoncyhidae form a monophyletic group that is sister to the Pleurodontidae. Likewise, the family Helicidae form a monophyletic group; it is sister to the branch incorporating Hygromiidae, Geomitridae, Pleurodontidae, Helicodontidae, and Xanthonychidae. The Solaropsidae are the sister group to a clade comprising other Sagdoidea. Our findings suggest that the Hygromiidae s.l. families should be restored to their previous name, Hygromiidae. A new genus of Bradybaeninae, Jiaoliaous Zhang gen. nov., is described here, with a simple genital system, single dart sac with multi-branched mucous glands, and a penis with a penial sheath.
Automating Academic Document Analysis with ChatGPT: A Mendeley Case
Authors: Abuella Mohamed 
Published: March 2024

AbstractThe management and organization of a large collection of academic documents is an important part of scientific research. This study explores the use of ChatGPT, a large language model from OpenAI, to extract insights from a large collection of academic documents stored in Mendeley. The study found that ChatGPT can be used to generate insightful graphs, concise summaries, and other tasks tailored to user needs. The study also demonstrated that ChatGPT can be used to analyze a large number of publications in PDF format. This suggests that ChatGPT could be a valuable tool for researchers who want to save time and effort by automating the analysis of their data. The GitHub repository for the source code and the output of this study is available at:https://github.com/MohamedAbuella/Analysis_Mendeley.
Phospholipase C β4 promotes RANKL-dependent osteoclastogenesis by interacting with MKK3 and p38 MAPK
Authors: Lee Dong-Kyo , Jin Xian , Choi Poo-Reum , Cui Ying , Che Xiangguo , Lee Sihoon , Hur Keun , Kim Hyun-Ju , Choi Je-Yong 
Published: March 2024

AbstractPhospholipase C beta (PLCβ) exerts diverse biological processes, including inflammatory responses and neurogenesis; however, its role in bone cell function is largely unknown. Among the PLCβ isoforms (β1–β4), we found that PLCβ4 was most highly upregulated during osteoclastogenesis. In this study, we used global knockout and osteoclast lineage-specific PLCβ4 conditional knockout (LysM-PLCβ4−/−) mice and demonstrated that PLCβ4 is a crucial regulator of receptor activator of nuclear factor κB ligand (RANKL)-induced osteoclast differentiation. Deletion of PLCβ4, both globally and in the osteoclast lineage, resulted in a significant reduction in osteoclast formation and the downregulation of osteoclast marker genes. Importantly,LysM-PLCβ4−/−male mice exhibited greater bone mass and a lower number of osteoclastsin vivothan their wild-type littermates, without altering osteoblast function. Mechanistically, we found that PLCβ4 forms a complex with p38 mitogen-activated protein kinase (MAPK) and MAPK kinase 3 (MKK3) in response to RANKL, thereby modulating p38 activation. An immunofluorescence assay further confirmed the colocalization of PLCβ4 with p38 after RANKL exposure. Moreover, p38 activation rescued the impaired osteoclast formation and restored the reduced p38 phosphorylation due toPLCβ4deficiency. Thus, our findings reveal that PLCβ4 controls osteoclastogenesis via the RANKL-dependent MKK3-p38 MAPK pathway, and PLCβ4 may be a potential therapeutic candidate for bone diseases such as osteoporosis.
Stand structure as the proximate driver of endemic biodiversity and ecosystem functions in tropical mosaic landscapes
Authors: Rajaonarimalala Rindrasoa , Korol Yevgeniya , Andrianarimisa Aristide , Dröge Saskia , Fulgence Thio Rosin , Grass Ingo , Kreft Holger , Osen Kristina , Rakotomalala Anjaharinony A. N. A. , Rakouth Bakolimalala , Ranarijaona Hery Lisy Tiana , Randriamanantena Romual , Ratsoavina Fanomezana Mihaja , Ravaomanarivo Lala Harivelo Raveloson , Raveloaritiana Estelle , Schwab Dominik , Soazafy Marie Rolande , Tscharntke Teja , Wurz Annemarie , Hölscher Dirk , Martin Dominic Andreas 
Published: March 2024

AbstractTransformation of forests into agricultural lands threatens biodiversity and ecosystem functions globally. In the biodiversity hotspot Madagascar, key ecosystem functions along with highly endemic flora and fauna are under threat. Comprehensive studies identifying proximate drivers are lacking, with no studies accounting for endemic species richness across multiple taxa. We assess how plot-scale stand structural attributes (basal area, leaf area index, diameter diversity, and tree species richness) and landscape-scale forest cover affect biodiversity (species richness of butterflies, ants, birds, amphibians, reptiles, herbaceous plants, and multidiversity) and ecosystem functions (soil organic carbon, predation rate, acoustic diversity index, and multifunctionality) in the tropical mosaic landscape of northeastern Madagascar. Across a prevalent land-use gradient in the region, we sampled five woody land-use types: old-growth forest, forest fragment, woody fallow, forest-derived and fallow-derived vanilla agroforests. Complexly structured stands with a larger basal area and higher tree species richness promoted greater endemic multidiversity and certain ecosystem functions. Landscape-scale forest cover significantly favored, particularly, endemic bird species richness. Our models explained 70% of the variance in endemic multidiversity, 26% in multidiversity, and 43% in multifunctionality. Significant effects directions of our predictors differed between taxa but were univocally positive for endemic species richness. Our findings highlight that a simplified stand structure, resulting from land-use change, substantially reduces endemic biodiversity and ecosystem functions in this historically forested region. Conservation actions should aim at maintaining complex stand structure in forests and agroforests, while restoration interventions should focus on re-building such structures.
The seminal vesicle is a juvenile hormone-responsive tissue in adult maleDrosophila melanogaster
Authors: Kurogi Yoshitomo , Mizuno Yosuke , Okamoto Naoki , Barton Lacy , Niwa Ryusuke 
Published: March 2024

AbstractJuvenile hormone (JH) is one of the most essential hormones controlling insect metamorphosis and physiology. While it is well known that JH affects many tissues throughout the insects life cycle, the difference in JH responsiveness and the repertoire of JH-inducible genes among different tissues has not been fully investigated. In this study, we monitored JH responsivenessin vivousing transgenicDrosophila melanogasterflies carrying aJH response element-GFP(JHRE-GFP) construct. Our data highlight the high responsiveness of the epithelial cells within the seminal vesicle, a component of the male reproductive tract, to JH. Specifically, we observe an elevation in the JHRE-GFP signal within the seminal vesicle epithelium upon JH analog administration, while suppression occurs upon knockdown of genes encoding the intracellular JH receptors,Methoprene-tolerantandgerm cell-expressed. Starting from published transcriptomic and proteomics datasets, we next identifiedLactate dehydrogenaseas a JH-response gene expressed in the seminal vesicle epithelium, suggesting insect seminal vesicles undergo metabolic regulation by JH. Together, this study sheds new light on biology of the insect reproductive regulatory system.
Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors
Authors: Brennan Reid S. , deMayo James A. , Finiguerra Michael , Baumann Hannes , Dam Hans G. , Pespeni Melissa H. 
Published: March 2024

AbstractTo persist in the geologically unprecedented rates of global change, populations can adapt or acclimate. However, how these mechanisms of resilience interact, particularly the role of epigenetic variation in long-term adaptation, is unknown. To address this gap, we experimentally evolved the foundational marine copepodAcartia tonsafor 25 generations under ocean acidification, warming, their combination, and control conditions then measured epigenomic, genomic, and transcriptomic responses. We observed clear and consistent epigenomic and genomic divergence between treatments, with epigenomic divergence concentrated in genes related to stress response and the regulation of transposable elements. However, epigenetic and genetic changes occurred in different regions of the genome such that regions with significant methylation divergence had 2-2.5 fold lower FSTthan regions without methylation divergence. This negative relationship between epigenetic and genetic divergence could be driven by local inhibition of one another or distinct functional targets of selection. In contrast, epigenetic divergence was positively linked to gene expression divergence, indicating that epigenetic changes may facilitate phenotypic change. Taken together, these results suggest that unique, complementary genetic and epigenetic mechanisms promote resilience to global change.Significance StatementOrganisms must adapt or acclimate to survive global change, but how these processes interact and the role of epigenetic variation is unknown. To address these gaps, we experimentally evolved the marine copepodAcartia tonsafor 25 generations in global change conditions and measured their genomic, epigenomic, and gene expression responses. We found that both genetic and epigenetic changes contributed to resilience and were inversely related, acting in different regions of the genome. Epigenetic changes were functionally linked to the regulation of stress and transposable elements and correlated with shifts in gene expression. Therefore, the resilience of populations to ongoing global change is driven by the complementary contribution of both genetic and epigenetic mechanisms.
SUC2 sucrose transporter is required for leaf apoplasmic sucrose levels. Consequences for phloem loading strategies
Authors: Vilaine Françoise , Bill Laurence , Hir Rozenn Le , Bellini Catherine , Dinant Sylvie 
Published: March 2024

Summary• The SUC/SUT sucrose transporters belong to a family of active H+/sucrose symporters, with a role of SUC2 in active apoplasmic phloem loading to drive long-distance phloem transport of sucrose in Arabidopsis. However, the cooperation with the symplasmic pathway for phloem loading remains unclear.• In this study, we explored the consequences of reducing either apoplasmic or symplasmic pathways of phloem loading. We compared a series of lines with modified expression ofSUC2gene, and we analyzed the effects on plant growth, sugar accumulation in source and sink organs, phloem transport, and gene expression.• Our data revealed that a modified expression ofSUC2impacted apoplasmic sucrose levels in source leaves but did not impact phloem transport, as might be expected, while increasing foliar storage of carbohydrates. This response differed from lines in which symplasmic communications between phloem cells was disrupted by the over-expression of a plasmodesmata-associated protein, NHL26.• Altogether, our studies indicate an unexpected effect of SUC2 for apoplasmic sucrose levels in source leaves, together with SUC1, and suggest a feedback regulation on foliar storage. This data sheds new light on the interplay between symplasmic and apoplasmic pathways for sugar loading and the consequences on leaf water flows.Summary statementThe mechanisms that coordinate apoplasmic and symplasmic loading pathways, and their effects on foliar carbon storage, remain largely unexplored. Surprisingly, the sucrose transporter SUC2 plays a significant role in maintaining sucrose levels in the apoplasm, shedding light on how apoplasmic sugar levels and water flows can interact for phloem loading.
First evaluation and detection of ivermectin resistance in gastrointestinal nematodes of sheep and goats in South Darfur, Sudan
Authors: Mohammedsalih Khalid M. , Ibrahim Abdoelnaim I. Y. , Juma Fathel-Rahman , Abdalmalaik Abdalhakaim A. H. , Bashar Ahmed , Coles Gerald , von Samson-Himmelstjerna Georg , Krücken Jürgen 
Published: March 2024

AbstractIn Sudan, resistance to benzimidazoles has been reported recently in cattle and goats from South Darfur. Herein, ivermectin efficacy against gastrointestinal nematodes (GINs) was evaluated in sheep and goats in three study areas in South Darfur. The faecal egg count reduction test (FECRT) was used to evaluate the efficacy of ivermectin in sheep and goats naturally infected with GINs in the region of Bulbul (goats:n=106), Kass (goats:n=40) and Nyala (Domaia (sheep:n=47, goats:n=77) and the University farm (goats:n=52)), using different treatment plans, and the efficacy was evaluated 12 days after treatment. Ivermectin efficacy was also evaluated in goats experimentally infected using localHaemonchus contortusisolates from Kass and Nyala. Nematodes surviving ivermectin treatment in goats in Bulbul and Nyala were harvested and larvae used to infect worm-free male sheep (n=6, ≤6 months old). Infected sheep were dosed subcutaneously with ivermectin every eight days with increasing doses from 0.2 mg/kg to 1.6 mg/kg bodyweight (bw). Reduced ivermectin efficacy was identified in sheep and goats in the four study locations. Using a paired statistic, the efficacy of a therapeutic dose in sheep was 75.6% (90% upper credible limit (UCrL): 77.5%), while twice the recommended dose led to a reduction of 92.6% (90% UCrL: 93.3%). In goats, the FECRs of a therapeutic dose were 72.9 – 95.3% (90% UCrL range: 73.6 – 95.7%) in Bulbul, Nyala Domaia, Nyala University farm and Kass. Twice the dose recommended for goats in Bulbul revealed a 90% UCrL of 87.6%. All post-treatment faecal cultures contained onlyHaemonchusspp. larvae. The experimental infection trials in sheep and goats supported our findings from field trials and calculated upper 90% CrL of below 98.9%. For the first time highly ivermectin resistantH. contortuspopulations have been identified in sheep and goats in Sudan, and resistance was experimentally confirmed.
How does perception of zoo animal welfare influence public attitudes, experiences, and behavioural intentions? A mixed-methods systematic review
Authors: Phillips Nicki , Maréchal Laëtitia , Ventura Beth , Cooper Jonathan 
Published: March 2024

AbstractThe public expects zoos to provide high standards of animal care. Failing to meet public expectations can have detrimental impacts on public experiences and behaviour, which in turn can compromise zoos’ organisational goals relative to conservation and public education. Despite increased research interest in understanding how the public perceives animal welfare in zoo settings, to date the factors that influence such perceptions are still unclear. To address this gap in knowledge, we conducted a mixed methods systematic review using a PRISMA approach to identify the factors that influence public perceptions of zoo animal welfare and the potential ramifications of these perceptions on public attitudes, experiences, and behaviours. A total of 115 peer reviewed journal articles were analysed: 43 provided qualitative data for thematic synthesis and 85 reported quantitative data for content analysis. Three main groupings were identified that impacted public perception of animal welfare in zoos: human, animal, and environmental factors. Within the human factors, ethical justifications, direct interactions, and inappropriate visitor behaviours were important. For the animal factors, animals’ behaviour, apparent health status, and the suitability of certain taxa for captivity were found to be key. Finally, several aspects of the environment -- conditions of the facility, the exhibit, and welfare-related educational material --were influential. Overall, negative perceptions of animal welfare resulted in negative visitor attitudes towards zoos, detrimentally impacted experiences, and lowered likelihood to visit zoos and engagement in conservation efforts. The articles in this review provided valuable insights into the factors affecting public perception of zoo animal welfare; however, future research may benefit from a more structured approach to increase comparability and validity of results across studies. We conclude by proposing seven recommendations to increase the robustness and validity of future research in this area.
Molecular events accompanying aggregation-induced energy quenching in Fucoxanthin-Chlorophyll Proteins
Authors: Alexandre Maxime T. A. , Krüger Tjaart P.J. , Pascal Andrew A. , Veremeienko Vasyl , Llansola-Portoles Manuel , Gundermann Kathi , van Grondelle Rienk , Büchel Claudia , Robert Bruno 
Published: March 2024

AbstractIn high light, the antenna system in oxygenic photosynthetic organisms switches to a photoprotective mode, dissipating excess energy in a process called non-photochemical quenching (NPQ). Diatoms exhibit very efficient NPQ, accompanied by a xanthophyll cycle in which diadinoxanthin is de-epoxidized into diatoxanthin. Diatoms accumulate pigments from this cycle in high light, and exhibit faster and more pronounced NPQ. The mechanisms underlying NPQ in diatoms remain unclear, but it can be mimicked by aggregation of their isolated light-harvesting complexes, FCP (fucoxanthin chlorophyll-a/c protein). We assess this model system by resonance Raman measurements of two peripheral FCPs, trimeric FCPa and nonameric FCPb, isolated from high- and low-light-adapted cells (LL, HL). Quenching is associated with a reorganisation of these proteins, affecting the conformation of their bound carotenoids, and in a manner which is highly dependent on the protein considered. FCPa from LL diatoms exhibits significant changes in diadinoxanthin structure, together with a smaller conformational change of at least one fucoxanthin. For these LL-FCPa, quenching is associated with consecutive events, displaying distinct spectral signatures, and its amplitude correlates with the planarity of the diadinoxanthin structure. HL-FCPa aggregation is associated with a change in planarity of a 515-nm-absorbing fucoxanthin, and, to a lesser extent, of diadinoxanthin. Finally, in FCPb, a blue-absorbing fucoxanthin is primarily affected. FCPs thus possess a plastic structure, undergoing several conformational changes upon aggregation, dependent upon their precise composition and structure. NPQ in diatoms may therefore arise from a combination of structural changes, dependent on the environment the cells are adapted to.
Attention-based approach to predict drug-target interactions across seven target superfamilies
Authors: Schulman Aron , Rousu Juho , Aittokallio Tero , Tanoli Ziaurrehman 
Published: March 2024

ABSTRACTMotivationDrug-target interactions (DTIs) hold pivotal role in drug repurposing and elucidation of drug mechanisms of action. While single-targeted drugs have demonstrated clinical success, they often exhibit limited efficacy against complex diseases, such as cancers, whose development and treatment is dependent on several biological processes. Therefore, a comprehensive understanding of primary, secondary, and even inactive targets becomes essential in the quest for effective and safe treatments for cancer and other indications. The human proteome offers over a thousand druggable targets. Yet, most FDA-approved drugs bind with only a small fraction of disease targets.ResultsThis study introduces an attention-based method to predict drug-target bioactivities for all human proteins across seven superfamilies. Nine different descriptor sets were meticulously examined to identify optimal signature descriptors for predicting novel DTIs. Our testing results demonstrated Spearman correlations exceeding 0.72 (P<0.001) for six out of seven superfamilies. The proposed method outperformed nine state-of-the-art deep learning and graph-based methods, and importantly, maintained relatively high performance for most target superfamilies when tested in independent sources of bioactivity data. We computationally validated 185,676 drug-target pairs from ChEMBL-V33, that were not available in model training, with a reasonable performance of Spearman correlation > 0.57 (P<0.001) for most superfamilies. This justifies the robustness of the proposed method for predicting novel DTIs. Finally, we applied our method to predict missing activities among 3,492 approved molecules in ChEMBL-V33, offering a valuable tool for advancing drug mechanism discovery and repurposing existing drugs for new indications.Availability and implementationThe codes and training datasets to reproduce and extend the results are available athttps://github.com/AronSchulman/MMAtt-DTA.
Uncovering organizing principles of protein-protein interaction networks
Authors: Ojha Anju K. , Dhar Pawan K. 
Published: March 2024

AbstractThis study explores the intricate world of protein-protein interaction (PPI) networks and the critical role of hub proteins within them. PPIs, mediated by various biomolecular forces, orchestrate diverse cellular processes through transient or stable interactions. The study delves into the unique ability of hubs to connect with numerous partners within the network. This research investigates the network properties and focuses on hub-centric questions. This study explores information-carrying capacity, power laws in protein circuits, connectivity profiles of hub proteins, and network expansion or shrinkage during evolution. The study validates the power law for connectivity, identifies a marginal network compression in evolution, unveils hub connectivity patterns, and encourages the exploration of the correlation between protein structure, connectivity, and function. These findings offer valuable insights into network design principles and the critical role of hub proteins in cellular function and evolution.