bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the appropriateness of pesticide administration-concentrations to honey beeApis melliferacolony in long-term field experiments and modest proposal
Authors: Yamada Toshiro 
Published: August 2023

AbstractFor investigating the effects of pesticides on bee colonies in actual apiaries, field experiments in an open environment are effective. It is natural to assume that the total food or pesticide intake taken by a honey bee colony includes their intakes from nature in addition to each administered in the field experiment. Therefore, in field experiments, setting the administration-concentration of pesticides for honey bee colonies is one of the most difficult tasks.The validity of pesticide concentrations administered to bee colonies was evaluated by various intakes of pesticides and foods obtained from five long-term field experiments conducted in Midwest Japan with distinct changes of four seasons and Maui, U.S.A. without cold winter.The author found a relationship, logPBD=logCP–2.4, between pesticide concentration (CP) and the average daily intake of pesticide ingested by one bee (PBD), and found that their ratioPBD/CPwas about 1/250, which was significantly lower than theLD50value.This fact supports that the concentration of pesticide administration in long-term field experiments conducted so far was not too high, but rather reasonable.In addition, the average daily intakes of sugar syrup and pollen paste ingested by one bee was found to be 3.1 mg/bee/day and 0.8 mg/bee/day, respectively, and notwithstanding their wide variation, be roughly constant regardless of the concentration of pesticides.I believe that this paper will help provide new guidelines for setting pesticide dosing concentrations, which have not been clear so far, in field experiments on the administration of pesticides to bee colonies.
Contributions of individual satellite cells to muscle regeneration assessed using a confetti mouse model
Authors: Heemskerk Hans , Jagannathan N. Suhas , Nasir N. Jannah M. , Nguyen Binh P. , Sacadevan Keshmarathy , Matsudaira Paul T. , So Peter T.C. , Tucker-Kellogg Lisa 
Published: August 2023

SummaryInsufficient regeneration is implicated in muscle pathologies, but much remains unknown about the regenerative output of individual muscle stem cells, called satellite cells (SCs). Prior work showed that individual SCs contribute to regeneration of more than one muscle fiber (“fiber-crossing”) after full-muscle damage. We investigated whether fiber-crossing also occurred in peripheral regions of a localized muscle injury. To assess fiber-crossing with a minimum number of mice, we used lineage tracing with confetti fluorescence, and developed a novel stochastic modeling method to interpret the ambiguity of multi-color fluorescent lineage tags. Microscopy of the regenerated muscle showed that adjacent fibers often expressed the same-colored tags. Computational analysis concluded that the observed color patches would be extremely unlikely to occur by chance unless SCs contributed myonuclei to multiple adjacent fibers (26-33% of SCs contributing to at most 1-2 additional fibers). Interestingly, these results were similar across the different regions studied, suggesting that severe destruction is not required for fiber-crossing. Our method to assess fiber-crossing may be useful for future study of gene and cell therapies that use fiber-crossing to aid muscle regeneration.
The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR
Authors: Westmann Cauã Antunes , Goldbach Leander , Wagner Andreas 
Published: August 2023

AbstractTranscription factor binding sites (TFBSs) are important sources of evolutionary innovations. Understanding how evolution navigates the sequence space of such sites can be achieved by mapping TFBS adaptive landscapes. In such a landscape, an individual location corresponds to a TFBS bound by a transcription factor. The elevation at that location corresponds to the strength of transcriptional regulation conveyed by the sequence. We developed anin vivomassively parallel reporter assay to map the landscape of bacterial TFBSs. We applied this assay to the TetR repressor, for which few TFBSs are known. We quantify the strength of transcriptional repression for 17,765 TFBSs and show that the resulting landscape is highly rugged, with 2,092 peaks. Only a few peaks convey stronger repression than the wild type. Non-additive (epistatic) interactions between mutations are frequent. Despite these hallmarks of ruggedness, most high peaks are evolutionarily accessible. They have large basins of attraction and are reached by around 20% of populations evolving on the landscape. Which high peak is reached during evolution is unpredictable and contingent on the mutational path taken. This first in-depth analysis of a prokaryotic gene regulator reveals a landscape that is navigable but much more rugged than the landscapes of eukaryotic regulators.SignificanceUnderstanding how evolution explores the vast space of genotypic possibilities is a fundamental question in evolutionary biology. The mapping of genotypes to quantitative traits (such as phenotypes and fitness) allows us to delineate adaptive landscapes and their topological properties, shedding light on how evolution can navigate such vast spaces. In this study, we focused on mapping a transcription factor binding site (TFBS) landscape to gene expression levels, as changes in gene expression patterns play a crucial role in biological innovation. We developed a massively parallel reporter assay and mapped the first comprehensive in vivo gene regulatory landscape for a bacterial transcriptional regulator, TetR. Surprisingly, this landscape is way more rugged than those observed in eukaryotic regulators. Despite its ruggedness, the landscape remains highly navigable through adaptive evolution. Our study presents the first high-resolution landscape for a bacterial TFBS, offering valuable insights into the evolution of TFBS in vivo. Moreover, it holds promise as a framework for discovering new genetic components for synthetic biological systems.
The genetic basis of apple shape and size unraveled by digital phenotyping
Authors: Keller Beat , Jung Michaela , Bühlmann-Schütz Simone , Hodel Marius , Studer Bruno , Broggini Giovanni AL , Patocchi Andrea 
Published: August 2023

AbstractGreat diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the fruit FruitPhenoBox to digitally phenotype 506 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, nine and four principal components (PCs) as well as 16 and eight uncorrelated features were chosen to carry out genome-wide association studies for fruit shape, size, and fruit skin color, respectively. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and uncorrelated features related to red over color as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.
iSanXoT: a Standalone Application for the Integrative Analysis of Mass Spectrometry-Based Quantitative Proteomics Data
Authors: Rodríguez Jose Manuel , Jorge Inmaculada , Barrero-Rodríguez Rafael , Magni Ricardo , Núñez Estefanía , Laguillo Andrea , Devesa Cristina A. , López Juan A. , Camafeita Emilio , Vázquez Jesús 
Published: August 2023

AbstractNumerous bioinformatics tools currently exist to perform quantitative analysis of proteomics experiments. The majority of these tools apply diverse statistical models to assign a quantitative protein value from the mass-spectrometry information. Here we present iSanXoT, a standalone application that allows integrative analysis of quantitative proteomics data. iSanXoT processes relative abundances between MS signals and integrates them sequentially to upper levels using our previously published Generic Integration Algorithm (GIA). iSanXoT offers unique capabilities that complement conventional quantitative softwares, including statistical weighting and independent modeling of error distributions in each integration, aggregation of technical or biological replicates, quantification of posttranslational modifications or analysis of coordinated protein behavior. iSanXoT is a standalone, user-friendly application which accepts output from widespread proteomics pipelines and enables free construction of quantification workflows and fully customizable reports than can be reused across different projects or shared among users. Diverse integrative workflows constructed using GIA for the analysis of high-throughput quantitative proteomics experiments have been successfully applied in numerous publications. iSanXoT has been tested with the main operating systems. Download links for the corresponding distributions are available athttps://github.com/CNIC-Proteomics/iSanXoT/releases.
In silico spatial transcriptomic editing at single-cell resolution
Authors: Wu Jiqing , Koelzer Viktor H. 
Published: August 2023

AbstractMotivationGenerative artificial intelligence (AI) has enabled fundamental breakthroughs in visual content creation by text-guided editing. However, the utility of such generative models remains largely understudied for processing increasingly complex bioimage data.ResultsWe propose to algorithmically edit gene expression data to drive cell-level morphological transitions using Generative Adversarial Networks (GAN) and GAN Inversion models. Leveraging cutting-edge spatial transcriptomic datasets with subcellular in-situ resolution and matched high-content imaging data, we propose an in-silico approach to quantify, model and imitate pathological processes in real-life clinical tissue samples.Availability and implementationThe code and video demo is accessible viahttps://github.com/CTPLab/In-silico-editing
Beyond Lux: Methods for Species and Photoreceptor-Specific Quantification of Ambient Light for Mammals
Authors: McDowell Richard J , Didikoglu Altug , Woelders Tom , Gatt Mazie J , Hut Roelof A , Brown Timothy M , Lucas Robert J 
Published: August 2023

AbstractBackgroundLight is a key environmental regulator of physiology and behaviour. Mistimed or insufficient light disrupts circadian rhythms and is associated with impaired health and well-being across mammals. Appropriate lighting is therefore crucial for indoor housed mammals. The most commonly used measurement for lighting is lux. However, this employs a spectral weighting function based on human perceived brightness and is not suitable for ‘non-visual’ effects of light or use across species. In humans, a photoreceptor-specific (α-opic) metrology system has been proposed as a more appropriate way of measuring light.ResultsHere we establish technology to allow this α-opic measurement approach to be readily extended to any mammalian species, accounting for differences in photoreceptor types, photopigment spectral sensitivities, and eye anatomy. Since measuring photopigment spectral sensitivity can be hard to derive for novel animals and photoreceptors, we developed a high-throughput, easy-to-use, method to derive spectral sensitivities for recombinantly expressed melanopsins and use it to establish the spectral sensitivity of melanopsin from 12 non-human mammals. We further address the need for simple measurement strategies for species-specific α-opic measures by developing an accessible online toolbox for calculating these units and validating an open hardware, low-cost, multichannel light sensor for ‘point and click’ measurement. We finally demonstrate that species-specific α-opic measurements are superior to photopic lux as predictors of physiological responses to light in mice and allow ecologically relevant comparisons of photosensitivity between species.ConclusionOur study demonstrates that measuring light more accurately using species-specific α-opic units is superior to the existing unit of photopic lux and holds the promise of improvements to the health and welfare of animals, scientific research reproducibility, agricultural productivity, and energy usage.
Examining dynamics of three-dimensional genome organization with multi-task matrix factorization
Authors: Lee Da-Inn , Roy Sushmita 
Published: August 2023

AbstractThree-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation datasets, such as Hi-C, have become available across multiple conditions and timepoints, offering a unique opportunity to examine changes in 3D genome organization and link them to phenotypic changes in normal and diseases processes. However, systematic detection of higher-order structural changes across multiple Hi-C datasets remains a major challenge. Existing computational methods either do not model higher-order structural units or cannot model dynamics across more than two conditions of interest. We address these limitations with Tree-Guided Integrated Factorization (TGIF), a generalizable multi-task Non-negative Matrix Factorization (NMF) approach that can be applied to time series or hierarchically related biological conditions. TGIF can identify large-scale changes at compartment or subcompartment levels, as well as local changes at boundaries of topologically associated domains (TADs). Compared to existing methods, TGIF boundaries are more enriched in CTCF and reproducible across biological replicates, normalization methods, depths, and resolutions. Application to three multi-sample mammalian datasets shows TGIF can detect differential regions at compartment, subcompartment, and boundary levels that are associated with significant changes in regulatory signals and gene expression enriched in tissue-specific processes. Finally, we leverage TGIF boundaries to prioritize sequence variants for multiple phenotypes from the NHGRI GWAS catalog. Taken together, TGIF is a flexible tool to examine 3D genome organization dynamics across disease and developmental processes.
NRF2 Regulates Contractile Vascular Smooth Muscle Cells Phenotypic Switching In Abdominal Aortic Aneurysm
Authors: Xiao Xiaoyong , Huang Xiaoran , Song Feier , Chen Guona , Zhang Yuelin , Liu Xincheng , Zhou Xueke , Hong Yimei , He Haiwei , Meng Jinxiu , Huang Xiaojia , Zhong Lintao , Li Xin 
Published: August 2023

OBJECTIVEEvidence from previous studies has demonstrated that NRF2 can protect cardiovascular progression,which prompted us to study if NRF2 is involved in AAA development.APPROACH AND RESULTSThe difference and function of NRF2 in AAA were verified on human aortic tissues combined with scRNA-seq samples.We then used angiotensin II (Ang II) infusion mouse model with VSMCs-specific knockout to study the role of NRF2 in AAA formation.Primary cultured VSMCs were used to study how NRF2 regulates contractile VSMCs phenotype.Patient specimens were obtained to investigate the relevance of NRF2 expression to human AAA disease. NRF2 was induced in abdominal aortic VSMCs in both mouse and human AAA tissues. VSMCs-specific NRF2 knockout increased experimental AAA formation. Mechanistically, NRF2 regulates the contractile VSMCs phenotypic through miRNA145, leading to increased classic contractile protein level to prevent the development of AAA.CONCLUSIONSNRF2 is a negative regulator of AAA development, and thus may represent a potentially new therapeutic target to inhibit AAA growth and rupture.
ANOTHER PERSPECTIVE ON THE RELATIONSHIP BETWEEN BREASTFEEDING, NEWBORN CARE AND MATERNAL PERINATAL DEPRESSION IN A RURAL AFRICAN SETTING
Authors: Ogah Adenike Oluwakemi , Ogah James Aaron Ogbole Oluwasegun 
Published: August 2023

AbstractBackgroundMaternal postpartum depression (PPD) is still one of the major health challenges across the globe with detrimental consequences on newborn bonding, growth and feeding. However, the bidirectional pathways between breastfeeding and PPD have not been sufficiently characterized. This study investigated the risk factors of poor maternal mental health and its relationship with breastfeeding initiation, in a remote community in East Africa.Subject and methodsThis was a cross-sectional secondary analysis of the baseline data collected for a 2019 prospective cohort study on infant growth in a rural community in East Africa. Healthy, 529 mother-singleton infant pairs were recruited consecutively from Gitwe district hospital. Maternal peri-partum depression score was obtained using the Edinburgh post-partum depression scale. The cut-off point on the depression scale, used in this study was 6.5.ResultsThe burden of maternal perinatal depression was 59.7%. Elderly mothers >35years of age (75.9%; p<0.001), poor antenatal visits of less than 4 (74.4%; p<0.001), vaginal delivery (74.7%; p<0.001; OR 5.26; 95% CI 3.57, 7.69), did not give prelacteal feeds (62.4%; p<0.001; OR 7.14; 95% CI 2.94, 16.7), primary education (69.5%, p<0.001), engaged in semi-skilled or skilled jobs (71.8%, p<0.001), poor socioeconomic class (74.8%, p<0.001), Christians (60.9%; p<0.001; OR 8.33; 95% CI 1.89, 33.3), HIV negative (61.6%; p<0.001; OR 4.57; 95% CI 1.90, 11.02), lack of water (82.0%; p<0.001; OR 27.1; 95% CI 16.39, 44.80) and toilet facilities (81.9%; p<0.001; OR 5.68; 95% CI 3.76, 8.58) in their home yard, not being exposed to potentially harmful social habits such as tobacco, alcohol (63.3%; p<0.001; OR 3.22; 95% CI 1.89, 5.56) significantly characterized mothers with high depression score. Peripartum depression was more common among mothers with small for gestational age babies (p=0.004; OR 3.12; 95%CI 1.44, 6.73) and those who initiated breastfeeding early (p<0.001; OR 9.17; 95%CI 5.21, 16.13).Conclusion and RecommendationsThe burden of maternal peripartum depression was high in this community and is still on the increase. Therefore, PPD and its risk factors require early recognition, intervention and follow up during the antenatal period up till at least 12 months postpartum, in order to prevent lactation failure and decline in exclusive breastfeeding and continued breastfeeding rates and duration. The poor WASH situation and difficult road access to health facilities in the community requires urgent attention.
Functionally annotated electrophysiological neuromarkers of healthy ageing and memory function
Authors: Auer Tibor , Goldthorpe Robin , Peach Robert , Hebron Henry , Violante Ines R. 
Published: August 2023

AbstractThe unprecedented increase in life expectancy presents a unique opportunity and the necessity to explore both healthy and pathological aspects of ageing. Electroencephalography (EEG) has been widely used to identify neuromarkers of cognitive ageing due to its affordability and richness in information. However, despite the growing volume of data and methodological advancements, the abundance of contradictory and non-reproducible findings has hindered clinical translation. To address these challenges, our study introduces a comprehensive workflow expanding on previous EEG studies and investigates various static and dynamic power and connectivity estimates as potential neuromarkers of cognitive ageing in a large dataset. We also assess the robustness of our findings by testing their susceptibility to band specification. Finally, we characterise our findings using functionally annotated brain networks to improve their interpretability and multi-modal integration.Our analysis demonstrates the effect of methodological choices on findings and that dynamic rather than static neuromarkers are not only more sensitive but also more robust. Consequently, they emerge as strong candidates for cognitive ageing neuromarkers. Moreover, we were able to replicate the most established EEG findings in cognitive ageing, such as alpha oscillation slowing, increased beta power, reduced reactivity across multiple bands, and decreased delta connectivity. Additionally, when considering individual variations in alpha band, we clarified that alpha power is characteristic of memory performance rather than ageing, highlighting its potential as a neuromarker for cognitive ageing. Finally, our approach using functionally annotated source reconstruction allowed us to provide insights into domain-specific electrophysiological mechanisms underlying memory performance and ageing.
Ploidy inference from single-cell data: application to human and mouse cell atlases
Authors: Takeuchi Fumihiko , Kato Norihiro 
Published: August 2023

AbstractPloidy is relevant to numerous biological phenomena, including development, metabolism, and tissue regeneration. Single-cell RNA-seq and other omics studies are revolutionizing our understanding of biology, yet they have largely overlooked ploidy. This is likely due to the additional assay step required for ploidy measurement. Here, we developed a statistical method to infer ploidy from single-cell ATAC-seq data. When applied to the data from human and mouse cell atlases, our method enabled systematic detection of polyploidy across a range of cell types. This method allows for the integration of ploidy analysis into single-cell studies.Article summaryPloidy plays a crucial role in many biological processes. Though modern studies offer deep insights into biology, they often neglect ploidy because it’s challenging to measure. In this research, we have created a new method to detect ploidy using single-cell data. This technique helps identify polyploid cells across various cell types, bridging a gap in our understanding.