bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insecticide resistance inAedes aegyptifrom the National Capital Region, Philippines
Authors: Angeles Jason R. , Malijan Richard Paul B. , Apilado Ariza Minelle A. , Ammugauan Mary Ann T. , Salazar Ferdinand V. 
Published: September 2023

AbstractBackgroundHuman arboviral diseases such as dengue, chikungunya and Zika can be transmitted by the mosquitoAedes aegypti. The insecticide-based vector control strategy is critical in reducing the transmission of theseAedes-borne diseases but is threatened mainly by the emergence of insecticide resistance.Methodology/Principal FindingsAdultAedes aegyptifrom National Capital Region, Philippines were subjected to bioassay to determine their susceptibility to the diagnostic doses of pyrethroid, organochlorine and organophosphate insecticides following the standard World Health Organization insecticide susceptibility test. This study reports for the first time the existence of insecticide resistance inAe. aegyptifrom the Philippines to pyrethroids and organochlorine. Results from this study showed that most of theAe. aegyptipopulations exhibited phenotypic resistance to the pyrethroids (permethrin and etofenprox) and an organochlorine (DDT) while all populations tested to malathion were still susceptible to this organophosphate. Varying resistance levels to deltamethrin, cyfluthrin and lambdacyhalothrin were also observed in the different mosquito populations.ConclusionsInsecticide resistance exists in local populations ofAe. aegyptifrom the National Capital Region. This finding should alert public health authorities to consider modifying the existing vector management package for greater control efficacy. Best practices that are proven to prevent and/or delay the development of insecticide resistance such as insecticide rotation should be implemented. Alternative toxicants and chemicals with a different mode of action, such as repellents, should be explored to ensure continuing efficacy of program interventions.Author summaryThe National Capital Region (NCR), Philippines reports the country’s highest dengue incidence. Apart from being populous and the center of economic activity, the local government authorities of this region have undertaken significant vector control efforts devoted to dengue. The use of insecticides to reduce mosquito vector density remains the handiest control method. This scenario necessitated the documentation of the resistance levels, particularly of the most important vectorAedes aegypti. An insect is said to be resistant when the known effective dose of an insecticide can no longer sufficiently kills the same insect population. This study showed thatAe. aegyptipopulation from cities in NCR had developed resistance to commonly used pyrethroids (permethrin, etofenprox) and to an organochlorine (DDT). Highly localized variations of resistance and susceptibility within cities at NCR were recorded against deltamethrin, cyfluthrin and lambdacyhalothrin. This finding should alert public health authorities to consider modifying the existing vector management package for greater control efficacy.
An AI Agent for Fully Automated Multi-omic Analyses
Authors: Zhou Juexiao , Zhang Bin , Chen Xiuying , Li Haoyang , Xu Xiaopeng , Chen Siyuan , He Wenjia , Xu Chencheng , Gao Xin 
Published: September 2023

AbstractWith the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the bioinformatics analysis continues to grow. In response to this need, we introduce Automated Bioinformatics Analysis (AutoBA), an autonomous AI agent designed explicitly for fully automated multi-omic analyses based on large language models. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA’s robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome/exome sequencing (WGS/WES), chromatin immunoprecipitation assays with sequencing (ChIP-seq), RNA sequencing (RNA-seq), single-cell RNA-seq, spatial transcriptomics and so on. AutoBA’s unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA offers multiple LLM backends, with options for both online and local usage, prioritizing data security and user privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents an advanced and convenient tool, offering robustness and adaptability for conventional multi-omic analyses.
Postnatal intestinal epithelial maturation by LSD1 controls the small intestinal immune cell composition independently from the microbiota
Authors: Díez-Sánchez Alberto , Lindholm Håvard T. , Vornewald Pia M , Ostrop Jenny , Parmar Naveen , Shaw Tovah N. , Martín-Alonso Mara , Oudhoff Menno J. 
Published: September 2023

ABSTRACTPostnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, maturation of the intestinal epithelium, and the acquisition of immune tolerance via a balanced immune cell composition. While studies have uncovered an interplay between the commensal microbiota and immune system development, less is known about the role of the maturing epithelium. Here, we comprehensively show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium as well as maintaining this developed epithelial state in adulthood. Although the stool microbiome was altered in animals with an intestinal-epithelial specific deletion ofLsd1, by depleting the microbial component using antibiotics, we found that the cellular state and number of certain immune cell types were dependent on maturation of the epithelium. We found plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to be depending on epithelial LSD1 expression. We propose that LSD1 controls the expression of epithelial-derived chemokines, such asCxcl16, and this is a mode of action for this epithelial-immune cell interplay. For example, we show that LSD1-mediated epithelial-intrinsic CXCL16 controls the number of local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.
Sex-specific central regulation of reproductive activity revealed by the use of deslorelin in the grey mouse lemur,Microcebus murinus
Authors: Noiret Aude , Aujard Fabienne , Terrien Jeremy 
Published: September 2023

AbstractDeslorelin is a GnRH agonist used in veterinary medicine to temporarily inhibit reproduction in domestic animals and is sometimes tested in captive species in zoo to control population or tame aggressive behaviours in males. However, some studies have revealed the inefficacy of deslorelin specifically in males, contrary to females that follow a classic long-term inhibition of the reproductive hypothalamic-pituitary axis through sexual steroid negative feedback. We implanted 5 males and 6 females grey mouse lemurs (Microcebus murinus), long-day breeders that display a complete inhibition of the reproductive system during winter, at the end of the short-day period, a few weeks before the breeding season. Contrary to females, which exhibited a classic inhibitory response to deslorelin, males testosterone levels increased as well as their testis size, which suggests a sex-specific sensitivity to the negative feedback of sexual steroids before the mating period. We propose that this sex-imbalance is related to the different life-history of males as opposed to females concerning reproductive tasks and behaviour.
Challenging age-structured and first order transition cell cycle models of cell proliferation
Authors: Ubezio Paolo 
Published: September 2023

AbstractUncontrolled cell proliferation is the key feature of tumours. Because experimental measures provide only a partial view to the underlying proliferative processes, such as cell cycling, cell quiescence and cell death, mathematical modelling aims to provide a unifying view of the data with a quantitative description of the contributing basic processes. Modelling approaches to proliferation of cell populations can be divided in two main categories: those based on first order transitions between successive compartments and those including a structure of the cells’ life cycle. Here we challenge basic models belonging to the two categories to fit time course data sets, from our laboratory experience, obtained observing the proliferative phenomenon with different experimental techniques in a cancer cell line. We disclose the limitations of too simple models. At the minimal complexity level accounting for all available data the two approaches converge and suggest similar scenarios for the underlying proliferation process, in both untreated conditions and after treatment.
The rural urban divide, insights from immuno-genetic profiles and implications for health
Authors: Hamad Reem , Eid Nahid A , Aboswar Safa A.E , Saeed Azza , Hussein Ayman A , Elhassan Ibrahim M , Rockett Kirk A , Kwiatkowski Dominic P , Ibrahim Muntaser E , Elhassan Ahmed M 
Published: September 2023

AbstractPopulation disparities in health and disease, has been observed, and amply documented. While often attributable to genetic underpinnings, such disparities, extends beyond population genetic predisposition to include environmental and geographic determinants most pronouncedly the division between rural and urban lifestyles. Under such influences, genes and gene products may become affected by epigenetic factors, microbial modifiers including infections and the body microbiome that ultimately shapes the outcome of complex milieu of protein networks. Retrospective, demographic, genotype, and expression data of two rural populations from eastern Sudan were analysed for genotype, allele frequency distribution, Hardy Weinberg Equilibrium and expression profiles using an array panel of Th1, Th2 and Th3 genes in a subset of rural population sample against matched urban control.Differences between urban and rural samples were observed in the departure from HWE with excess of heterozygosity in the rural sample. In the Th1, Th2 and Th3 array, cytokines were consistently overexpressed in the rural as compared to urban cohort and was replicated in 7 selected genes that are associated with chronic diseases amongst urban dwellers in contrast to rural village inhabitants. IgE levels as feature of parasitic infections is one other difference to include in that dichotomy.Gene expression appears to be more exposing to an overall outcome of genetic variations, including the interaction with environmental influences within and outside the body. Here, it may be gathered from the contrast in the expression patterns between the rural and urban samples. The presence of signals of natural selection in genes that are key to certain biological functions as CD40L and FasL, and the sharp contrast between urban and rural populations in gene variants distribution and expression patterns may provide important clues towards understanding the disparity between human communities in non-communicable diseases of lifestyle as well as some of the emerging infectious diseases.
Moonless night sky increasesIsistiusspecies and live human contact
Authors: Minaglia Steven , Liegl Melodee 
Published: September 2023

AbstractThe nocturnal feeding behavior and zoogeographical habitat of cookiecutter sharksIsistius brasiliensisandIsistius plutodus(Isistius spp.) greatly reduces interaction of this species with live humans. Attacks on live humans are exceedingly rare with 7 cases reported worldwide, 6 of them in Hawai‘i, and 5 of these occuring among channel swimmers. Published research suggests that periods of bright moonlight may increaseIsistius spp. contact with live humans and does not otherwise identify significant trends or risk factors. Yet 5 of the 6Isistius spp. bites on live humans in Hawai‘ian waters occurred with the moon set and after nautical twilight end and before nautical twilight start. From 1961-2023 in Hawai‘i, 129 successful solo channel crosses and 5Isistius spp. related injuries in the habitat of cookiecutter sharks were analyzed across two groups: one where both the moon and sun were set (dark group) and one where the moon and/or sun was in the sky (light group). There was a significant difference for swimmers bitten byIsistius spp. in the dark 4 (12%) versus light groups 1 (1%), p=0.012, RR 12.6 (95% confidence interval: 1.5-108.9). Swim start time and year was also significant (Pearson correlation 0.566, p <0.001). Swimmer gender and use of shark deterrent devices and artificial illumination were not significant. The growing popularity of channel swimming in Hawai‘i and swim start times have contributed to an increasing likelihood of live human andIsistius spp. contact and a moonless night sky is a significant risk factor for this interaction.
Phylogenetic diversity and regionalization of root nodule symbiosis
Authors: Folk R.A , Belitz M.W. , Siniscalchi C.M. , Kates H.R. , Soltis D.E. , Soltis P.S. , Guralnick R.P. , Borges L.M. 
Published: September 2023

ABSTRACTAimHere we determine centers of species richness (SR), relative phylogenetic diversity (RPD) and centers of paleo- and neo-endemism, and regionalizations of phylogenetic diversity in the mimosoid clade of the legumes to understand the distribution and environmental associates of mimosoids lacking RNS (root nodule symbiosis).LocationGlobal.Time periodPresent.Major taxa studiedMimosoid legumes.MethodsWe built a phylogenetic tree of 1313 species and high-quality species distribution models for 1128 species representing the phylogenetic breadth of the mimosoid clade to identify the geographic distribution of RNS. Centers of significant RPD and endemism were identified using a randomization approach, the latter using CANAPE. Phylogenetic regionalization used a distance-based phylogenetic beta-diversity approach.ResultsWe recognized nine areas of contiguous high SR as distinct SR hotspots. Non-RNS species occur mainly outside hotspots but are closely correlated with high RPD. Absence of RNS was best predicted by high precipitation, and represents multiple independent phylogenetic assemblages in different biogeographic areas.Main conclusionsSR hotspots are partly incongruent with centers of RPD and phylogenetic endemism. Lineages lacking RNS are distributed in SR hotspots in Africa and the Americas, belong to biogeographically separate species assemblages, and are, in most cases, associated with relatively moist tropical environments with low temperature seasonality and high available soil nitrogen.
Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks
Authors: Airas Justin , Ding Xinqiang , Zhang Bin 
Published: September 2023

AbstractCoarse-grained (CG) force fields are essential for molecular dynamics simulations of biomolecules, striking a balance between computational efficiency and biological realism. These simulations employ simplified models grouping atoms into interaction sites, enabling the study of complex biomolecular systems over biologically relevant timescales. Efforts are underway to develop accurate and transferable CG force fields, guided by a bottom-up approach that matches the CG energy function with the potential of mean force (PMF) defined by the finer system. However, practical challenges arise due to many-body effects, lack of analytical expressions for the PMF, and limitations in parameterizing CG force fields. To address these challenges, a machine learning-based approach is proposed, utilizing graph neural networks (GNNs) to represent CG force fields and potential contrasting for parameterization from atomistic simulation data. We demonstrate the effectiveness of the approach by deriving a transferable GNN implicit solvent model using 600,000 atomistic configurations of six proteins obtained from explicit solvent simulations. The GNN model provides solvation free energy estimations much more accurately than state-of-the-art implicit solvent models, reproducing configurational distributions of explicit solvent simulations. We also demonstrate the reasonable transferability of the GNN model outside the training data. Our study offers valuable insights for building accurate coarse-grained models bottom-up.
Dietary burden of phosphorus and aluminum in ready-to-eat wheat flour tortillas exceed that of corn tortillas: Implications for patients with renal or cardiovascular disease
Authors: Chiang Kate C. , Yokel Robert A. , Unrine Jason M. , Kalantar-Zadeh Kamyar , Gupta Ajay 
Published: September 2023

AbstractReady-to-eat, shelf-stable tortillas contain several phosphorus- and aluminum-containing additives that may increase the risk of adverse events in patients with chronic kidney disease (CKD). The present study analyzes and compares the elemental content of wheat flour and corn tortillas with special reference to dietary aluminum and phosphorus burden. Twenty-one elements were quantified by ICP-MS and ICP-OES in 14 corn and 13 wheat flour tortilla brands purchased from local supermarkets in Southern California. The aluminum and phosphorus concentrations of many ready-to-eat tortilla brands can present a daily dietary load of up to approximately 100 mg aluminum and 700 mg phosphorus based on an average daily tortilla intake of 330 grams. Ready-to-eat wheat flour tortillas generally had more phosphorus than corn tortillas. Tortillas with aluminum listed as a food additive contained a higher aluminum content than those without such listing, exceeding the tolerable weekly intake. Despite conventional wisdom that CKD patients should avoid phosphorus-rich corn tortillas, ready-to-eat wheat flour tortillas consistently had a higher aluminum and phosphorus content due to additives. CKD patients and healthcare providers should pay attention to food labels, and regulatory authorities should monitor the use of approved food additives and mandate food label warnings for patients at risk.
In Silico Analysis of Drug Off-Target Effects on Diverse Isoforms of Cervical Cancer for Enhanced Therapeutic Strategies
Authors: Iqbal Azhar , Ali Faisal , Aziz Moawaz , Shakil Asad Ullah , Choudhary Shanza , Qayyum Adiba , Arshad Fiza , Ashraf Sarah , Sehgal Sheikh Arslan , Hussain Momina , Sajid Muhammad 
Published: September 2023

AbstractCervical cancer is a severe medical issue as 500,000 new cases of cervical cancer are identified in the world every year. The selection and analysis of the suitable gene target are the most crucial in the early phases of drug design. The emphasis at one protein while ignoring its several isoforms or splice variations may have unexpected therapeutic or harmful side effects. In this work, we provide a computational analysis of interactions between cervical cancer drugs and their targets that are influenced by alternative splicing. By using open-accessible databases, we targeted 45 FDA-approved cervical cancer drugs targeting various genes having more than two distinct protein-coding isoforms. Binding pocket interactions revealed that many drugs do not have possible targets at the isoform level. In terms of size, shape, electrostatic characteristics, and structural analysis have shown that various isoforms of the same gene with distinct ligand-binding pocket configurations. Our results emphasized the risks of ignoring possibly significant interactions at the isoform level by concentrating just on the canonical isoform and promoting consideration of the impacts of cervical cancer drugs on- and off-target at the isoform level to further research.
Genetic Variants That Modify the Neuroendocrine Regulation of Foraging Behavior inC. elegans
Authors: Lee Harksun , Boor Sonia A. , Hilbert Zoë A. , Meisel Joshua D. , Park Jaeseok , Wang Ye , McKeown Ryan , Fischer Sylvia E. J. , Andersen Erik C. , Kim Dennis H. 
Published: September 2023

AbstractThe molecular mechanisms underlying diversity in animal behavior are not well understood. A major experimental challenge is determining the contribution of genetic variants that affect neuronal gene expression to differences in behavioral traits. The neuroendocrine TGF-beta ligand, DAF-7, regulates diverse behavioral responses ofCaenorhabditis elegansto bacterial food and pathogens. The dynamic neuron-specific expression ofdaf-7is modulated by environmental and endogenous bacteria-derived cues. Here, we investigated natural variation in the expression ofdaf-7from the ASJ pair of chemosensory neurons and identified common variants ingap-2, encoding a GTPase-Activating Protein homologous to mammalian SynGAP proteins, which modifydaf-7expression cell-non-autonomously and promote exploratory foraging behavior in a DAF-7-dependent manner. Our data connect natural variation in neuron-specific gene expression to differences in behavior and suggest that genetic variation in neuroendocrine signaling pathways mediating host-microbe interactions may give rise to diversity in animal behavior.
Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests
Authors: Hatfield Jack H. , Banks-Leite Cristina , Barlow Jos , Lees Alexander C. , Tobias Joseph A. 
Published: September 2023

Abstract1. Seed dispersal – one of the many services supplied by biodiversity – is a critical process underpinning the resilience of tropical forests. Forest loss or degradation typically leads to defaunation, altering seed transfer dynamics and impairing the ability of forested habitats to regenerate or recover from perturbation. However, the extent of defaunation, and its likely impacts on the seed dispersers needed to restore highly degraded or clear-felled areas, remains poorly understood, particularly in human-modified tropical forest landscapes.2. To quantify defaunation of seed-dispersing birds, we used field survey data from more than 400 transects in three regions of Brazil, first comparing the recorded assemblages with those predicted by geographic range maps, and then assessing frugivore habitat associations across gradients of land cover modification at local scales.3. We found that current bird assemblages have lower functional trait diversity than predicted by species range maps in Amazonia (4–6%), with a greater reduction (28%) for the Atlantic Forest region, which has been more heavily deforested for a longer period. These reductions are probably caused by local extinctions of forest-dependent bird species following land-use change.4. Direct measures of seed dispersal are difficult to obtain, so we instead focused on the potential for seed transfer inferred from shared species occurrence between land cover types. Of 83 predominantly frugivorous bird species recorded in relatively intact forests, we show that 10% were absent from degraded forest, and 57% absent from the surrounding matrix of agricultural land covers, including many of the large-beaked species. Of 112 frugivorous species using degraded forest, 47% were absent from matrix habitats.5. Our findings suggest that degraded forest can supply seed dispersal services to adjacent cleared lands, and that direct transfer of seeds from intact forest to cleared areas may be limited, particularly for large-seeded trees. We conclude that resilience of tropical forest landscapes is best achieved by protecting a mosaic of forest types, including sufficient core areas of intact forest surrounded by buffer zones of degraded forest.