bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome assembly of the Little Millet (Panicum sumatrense) genome: A climate resilient crop species
Authors: Das Rasmita Rani , Kumar Ashish , Baghel Dushyant Singh , Mahato Ajay K , Dey Nrisingha , Mukherjee Pulok K , Pradhan Seema 
Published: February 2024

AbstractLittle millet (Panicum sumatrense) belongs to one of the largest genera,Panicumcomprising of 500 species that are distributed especially in tropical and sub-tropical Asia as well as Africa. This is a climate resilient crop that has the ability to adapt to adverse growing conditions, especially drought. Added to this is the better nutritional profile of little millet, which has higher iron and fibre contents as compared with rice. These characteristics make it an important crop species that would be pivotal for ensuring food security. Generating genomic resources for the species is significant and will have implications in crop improvement. Therefore, in the present study we report thede novowhole genome sequence ofP. sumatrense. Long read sequencing and Hi-C based scaffolding resulted in a total of 279 scaffolds with N50 of 7.8Mb. The genome was annotated to predict protein coding genes and orthologous groups were analysed after comparison with various plant genomes. This high-quality genome assembly can be a valuable resource as future reference for genomic studies in this crop and related crop species.
A new interesting and unidentified Schmidtea species in Romania (Platyhelminthes, Tricladida, Dugesiidae)
Authors: Babalean Anda Felicia 
Published: February 2024

AbstractThis paper presents the characters (morphology and aspects of reproductive biology) of a population belonging to the genusSchmidtea, in Romania. This population shows similarities with the other Schmidtea species: withS. polychroa, the presence of cephalic sensory fossae; withS. mediterranea, the asexual reproduction by fission; withS. nova, the presence of a diaphragm of the ejaculatory duct to the secondary seminal vesicle. Set of characters make the population distinct and thus, candidate for a new species: the disposition / arrangement of the genital atria; a wide and straight / narrow and convoluted ejaculatory duct within the penis papilla; in some specimens the penis papilla has two lobes, each with own duct.
Stress Granule-Related Genes during Embryogenesis of an Invertebrate Chordate
Authors: Drago Laura , Pennati Alessandro , Rothbächer Ute , Ashita Ryuji , Hashimoto Seika , Saito Ryota , Fujiwara Shigeki , Ballarin Loriano 
Published: February 2024

ABSTRACTControl of global protein synthesis through the assembly of stress granules (SGs) represents a strategy adopted by eukaryotic cells to face various stress conditions. TIAR, TTP and G3BP are key components of SGs, allowing the regulation of mRNA stability and thus controlling not only stress responses but also cell proliferation and differentiation. In the present work we aimed to investigate the role oftiar,ttpandg3bpduring embryogenesis of the solitary ascidianCiona robusta, both in physiological and stress conditions. We carried out CRISPR/Cas9 knockout to evaluate the effects on normal embryonic development, and gene reporter assays to study time and tissue specificity of gene expression, together with whole mount ISH and qRT-PCR. To induce acute stress conditions, we used iron and cadmium as “essential” and “non-essential” metals, respectively. Our results highlight, for the first time, the importance oftiar, ttpandg3bpin the control of development of mesendodermal tissue derivatives during embryogenesis of an invertebrate chordate.HIGHLIGHTS- Mesenchyme, nervous cells, and endoderm are the embryonic regions mainly transcribingcr-tiarx1,cr-ttpandcr-g3bp2during metal stress conditions.- Onlycr-ttptranscription is regulated at mid gastrula stage.- The highest transcription levels are reached in hatching larvae after iron exposure.-cr-tiarx1,cr-ttpandcr-g3bp2knockouts resulted in impaired embryogenesis.
“Long-Term Quarantine is Associated with High Cortisol and Low DNA Methylation in New World monkeys”
Authors: Seenayah Shayna , Sanchez Nofre , Paredes Ursula M 
Published: February 2024

ABSTRACTQuarantines prevent infectious disease spread during primate transport, fostering acclimatisation. Environmental stress can lead to altered physiology, health risks, and epigenetic changes in other primates. We analysed PeruvianSaguinus fuscicollisandSaimiri macrodon, immobilised for 10 months in quarantine during the COVID-19 crisis, and compared them to wild counterparts to determine effects of quarantine as a stressor in New World monkeys.MethodsBoth quarantine and wild samples were collected from two riverine islands near the city of Iquitos, situated in the Peruvian Amazon (Island Muyuy and Padre Island). Cortisol levels in hair were quantified using ELISA (n=37; quarantine n=16; wild=21), and global DNA methylation levels were assessed for epigenetic comparison in dried blood spots (n=45; Quarantine: n=23; Wild: n=22), also utilising ELISA. Two-way ANOVA was employed to explore the effect of quarantine on cortisol and DNA methylation, considering the effect of species, and sex differences on these measurements.ResultsCortisol analysis revealed a significant association between quarantine and elevated cortisol secretion when testing both species together and independently, with a greater difference between quarantine and wild forSaguinus fuscicollis. Quarantine was associated with global DNA hypomethylation when testing both species together, however, independent ANOVAs show there was no effect of quarantine onSaguinus fuscicollis, and a marginal significant effect of quarantine onSaimiri macrodon.DiscussionNew World monkey species displayed hormonal and epigenetic dysregulation 10-months after starting quarantine period, suggesting long-term physiological and genomic stress as a response to captivity. Species specific differences in stress adaptability might mediate observed effects.
Individual corticosterone response to intermittent swim stress predicts a shift in economic demand for ethanol from pre- stress to post-stress in male rats
Authors: Robison Christopher L. , Madore Victoria , Cova Nicole , Drugan Robert C. , Charntikov Sergios 
Published: February 2024

AbstractThis study investigated the relationship between stress exposure and subsequent ethanol use, focusing on individual differences among male rats. We combined operant self-administration with behavioral economics to assess how intermittent swim stress affects ethanol consumption. This approach allowed for a nuanced analysis of the transition from regular ethanol intake to stress-induced escalation in economic demand. Results showed a consistent rise in ethanol demand post-stress among subjects, irrespective of exposure to actual swim stress or a sham procedure. This increase may result from a two-week abstinence or an inherent rise in demand over time. Significantly, we identified a direct link between post-stress corticosterone levels and the demand for ethanol, considering baseline levels. This correlation was particularly pronounced when examining the shifts in both corticosterone levels and demand for ethanol post-stress. However, neither post-stress corticosterone levels nor their change over time correlated significantly with changes in ethanol demand following a forced swim test that was administered 24 hours after the intermittent swim stress test. This suggests potential context-specific or stressor-specific effects. Importantly, pre-stress ethanol demand did not significantly predict the corticosterone response to stress, indicating that high ethanol-demand rats do not inherently exhibit heightened stress sensitivity. Our research brings to light the complex interplay between stress and ethanol consumption, highlighting the critical role of individual differences in this relationship. This research introduces a nuanced perspective, underscoring the need for future studies in the realm of stress and substance use to give greater consideration to individual variability.
CryoVesNet: A Dedicated Framework for Synaptic Vesicle Segmentation in Cryo Electron Tomograms
Authors: Khosrozadeh Amin , Seeger Raphaela , Witz Guillaume , Radecke Julika , Sørensen Jakob B. , Zuber Benoît 
Published: February 2024

AbstractCryo-electron Tomography (Cryo-ET) has the potential to reveal cell structure down to atomic resolution. Nevertheless, cellular cryo-ET data is often highly complex, and visualization, as well as quantification, of subcellular structures require image segmentation. Due to a relatively high level of noise and anisotropic resolution in cryo-ET data, automatic segmentation based on classical computer vision approaches usually does not perform satisfactorily. For this reason, cryo-ET researchers have mostly performed manual segmentation.Communication between neurons relies on neurotransmitter-filled synaptic vesicle (SV) exocytosis. Recruitment of SVs to the plasma membrane is an important means of regulating exocytosis and is influenced by interactions between SVs. Cryo-ET study of the spatial organization of SVs and of their interconnections allows a better understanding of the mechanisms of exocytosis regulation.Extremely accurate SV segmentation is a prerequisite to obtaining a faithful representation of SVs state of connectivity. Hundreds to thousands of SVs are present in a typical synapse, and their time-consuming manual segmentation is a bottleneck in this analysis.Several attempts to automate vesicle segmentation by classical computer vision or machine learning algorithms have not yielded robust results. We addressed this problem by designing a workflow consisting of a U-Net convolutional segmentation network followed by post-processing steps. This combination yields highly accurate results. Furthermore, we provide an interactive tool for accurately segmenting spherical vesicles in a fraction of the time required by available manual segmentation methods. This tool can be used to segment vesicles that were missed by the fully automatic procedure or to quickly segment a handful of vesicles while bypassing the fully automatic procedure. Our pipeline can in principle be used to segment any spherical vesicle in any cell type as well as extracellular vesicles.
Biomechanical Costs Influence Decisions Made During Ongoing Actions
Authors: Canaveral Cesar Augusto , Lata William , Green Andrea M , Cisek Paul 
Published: February 2024

ABSTRACTAccurate interaction with the environment relies on the integration of external information about the spatial layout of potential actions and knowledge of their costs and benefits. Previous studies have shown that when given a choice between voluntary reaching movements, humans tend to prefer actions with lower biomechanical costs. However, these studies primarily focused on decisions made before the onset of movement (“decide-then-act” scenarios), and it is not known to what extent their conclusions generalize to many real-life situations, in which decisions occur during ongoing actions (“decide-while-acting”). For example, one recent study found that biomechanical costs did not influence decisions to switch from a continuous manual tracking movement to a point-to-point movement, suggesting that biomechanical costs may be disregarded in decide-while-acting scenarios. To better understand this surprising result, we designed an experiment in which participants were faced with the decision between continuing to track a target moving along a straight path or changing paths to track a new target that gradually moved along a direction that deviated from the initial one. We manipulated tracking direction, angular deviation rate, and side of deviation, allowing us to compare scenarios where biomechanical costs favored either continuing or changing the path. Crucially, here the choice was always between two continuous tracking actions. Our results show that in this situation, decisions clearly took biomechanical costs into account. Thus, we conclude that biomechanics are not disregarded during decide-while-acting scenarios, but rather, that cost comparisons can only be made between similar types of actions.NEW & NOTEWORTHYIn this study, we aim to shed light on how biomechanical factors influence decisions made during ongoing actions. Previous work suggested that decisions made during actions disregard biomechanical costs, in contrast to decisions made prior to movement. Our results challenge that proposal and suggest instead that the effect of biomechanical factors is dependent on the types of actions being compared (e.g., continuous tracking vs. point-to-point reaching). These findings contribute to our understanding of the dynamic interplay between biomechanical considerations and action choices during ongoing interactions with the environment.
Interim 2023/24 season influenza vaccine effectiveness in primary and secondary care in the United Kingdom
Authors: Whitaker Heather , Findlay Beth , Zitha Jana , Goudie Rosalind , Hassell Katie , Evans Josie , Kalapotharakou Panoraia , Agrawal Utkarsh , Kele Beatrix , Hamilton Mark , Moore Catherine , Byford Rachel , Stowe Julia , Robertson Chris , Couzens Anastazia , Jamie Gavin , Hoschler Katja , Pheasant Kathleen , Button Elizabeth , Quinot Catherine , Jones Tim , Anand Sneha , Watson Conall , Andrews Nick , de Lusignan Simon , Zambon Maria , Williams Christopher , Cottrell Simon , Marsh Kimberly , McMenamin Jim , Bernal Jamie Lopez 
Published: February 2024

AbstractWe report 2023/24 season interim influenza vaccine effectiveness for three studies, including primary care in Great Britain, hospital settings in Scotland and hospital settings in England. Adjusted vaccine effectiveness against all influenzas ranged from 63% (46 to 75%) to 65% (41 to 79%) among children aged 2-17, from 36% (20 to 49%) to 55% (43 to 65%) among adults 18-64 and from 40% (29 to 50%) to 55% (32 to 70%) among adults aged 65 and over.
Food insecurity prevalence among tertiary students in Ghana
Authors: Agbetsise Evelyn , Letsa Crystal Bubune , Esime Ofori Charlotte Abra , Asalu Geoffrey Adebayo 
Published: February 2024

AbstractBackgroundFood insecurity (FI) is a collective term for inadequate access to available, affordable, and safe nutritious food. FI could affect students’ health and academic performance adversely. Currently, there is a paucity of research on food insecurity among tertiary students in Ghana. This study determined the prevalence of food insecurity among tertiary students in an Eastern city of Ghana.Materials and methodsA descriptive cross-sectional study design was employed. A multistage sampling technique was used to select 411 respondents from four tertiary institutions. The United States Department of Agriculture Adult Household Food Security Survey (HFSS) Module tool was used to collect information on students’ food insecurity status. Data were entered with Epi-data version 3.0 software and then exported into Stata/MP version 16.0 for analysis. For all statistical tests, a p-value < 0.05 was considered significant.ResultsThe prevalence of food insecurity was 61.0 %. Of these, 40.4 % had very low food security and 20.2% had low food security. Multiple logistic regression showed that the odds of food insecurity were significantly higher for students who did not have family support [AOR=2.56 (95% CI:1.17 - 5.63), p= 0.019] as compared to those who had family support and students whose fathers were farmers compared to fathers who were employed [AOR=2.71 (95% CI:1.49 - 4.92), p= 0.001].ConclusionThe study found high levels of food insecurity among tertiary students in Hohoe. An insight into food insecurity among this at-risk population group requires further investigation and action. There is an urgent need for research to better understand the severity and persistence of food insecurity among higher education students in Ghana.
Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals
Authors: Frédérick Pierre-Marc , Jannot Guillaume , Banville Isabelle , Simard Martin J. 
Published: February 2024

ABSTRACTMicroRNAs (miRNAs) are essential regulators of several biological processes. They are loaded onto Argonaute (AGO) proteins to achieve their repressive function, forming the microRNA-Induced Silencing Complex (miRISC). While several AGO proteins are expressed in plants and animals, it is still unclear why specific AGOs are strictly binding miRNAs. Here, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs inCaenorhabditis elegans. DNJ-12 does not interact with ALG-2, the other major miRNA-specific AGO, and PRG-1 and RDE-1, two AGOs involved in other small RNA pathways, making it a specific actor in ALG-1-dependent miRNA-mediated gene silencing. The loss of DNJ-12 causes developmental defects associated with defective miRNA function. Using the Auxin Inducible Degron (AID) system, a powerful tool to acutely degrade proteins in specific tissues, we show that DNJ-12 depletion hampers ALG-1 interaction with HSP70, a chaperone required for miRISC loadingin vitro. Moreover, DNJ-12 depletion leads to the decrease of several miRNAs and prevents their loading onto ALG-1. This study uncovers the importance of a co-chaperone for the miRNA functionin vivoand provides insights to explain how different small RNAs associate with specific AGO in animals.
ILLUSORY LIGHT DRIVES PUPIL RESPONSES IN PRIMATES
Authors: Durand Jean-Baptiste , Marchand Sarah , Nasres Ilyas , Laeng Bruno , De Castro Vanessa 
Published: February 2024

ABSTRACTIn humans, the eye pupils respond to both physical light sensed by the retina and mental representations of light produced by the brain. Notably, our pupils constrict when a visual stimulus is illusorily perceived brighter, even if retinal illumination is constant. Yet, it remains unclear whether such perceptual penetrability of pupil responses is an epiphenomenon unique to humans or whether it represents an adaptive mechanism shared with other animals to anticipate variations in retinal illumination between successive eye fixations. To address this issue, we measured the pupil responses of both humans and macaque monkeys exposed to three chromatic versions (cyan, magenta, and yellow) of the Asahi brightness illusion. We found that the stimuli illusorily perceived brighter or darker trigger differential pupil responses that are very similar in macaques and human participants. Additionally, we show that this phenomenon exhibits an analogous cyan bias in both primate species. Beyond evincing the macaque monkey as a relevant model to study the perceptual penetrability of pupil responses, our results suggest that this phenomenon is tuned to ecological conditions since the exposure to a “bright cyan-bluish sky” may be associated with increased risks of dazzle and retinal damages.
Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation
Authors: Laso Pérez Rafael , Santisteban Juan Rivas , Fernandez-Gonzalez Nuria , Mundy Christopher J. , Tamames Javier , Pedrós-Alió Carlos 
Published: February 2024

AbstractIn the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Besides, bloom dynamics is affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community during a phytoplankton bloom with a special focus on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of genomic abundance in early spring, whenNitrososphaeriaarchaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amoA, nirK). The resulting nitrite was presumably further oxidized to nitrate by aNitrospinotabacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyllaindicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidetes,AlphaproteobacteriaandGammaproteobacteria). These bacterial taxa showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter, reduced their relative abundance and the expression of their catabolic genes. Based on the functional analysis of our data, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role, to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups specialize in different nitrogen sources.
Altruistic disease signalling in ant colonies
Authors: Dawson Erika H. , Kampleitner Niklas , Robb Jennifer , Strahodinsky Florian , Grasse Anna V. , Cremer Sylvia 
Published: February 2024

AbstractSick individuals often conceal their disease status to group members, thereby preventing social exclusion or aggression. Here, we show that infected ant pupae, on the contrary, actively emit a chemical signal that triggers their own destruction by colony members. In our experiments, this altruistic disease-signalling was performed only by worker but not queen pupae, reflecting differences in their immune capabilities, as worker pupae suffered from extensive pathogen replication whereas queen pupae were able to restrain infection. Inducing others to sacrifice oneself, only if one’s own immunity fails, suggests a fine-tuned interplay between individual and social immunity, efficiently achieving whole-colony health.
Villification of the intestinal epithelium is driven by Foxl1
Authors: Zhu Guoli , Lahori Deeksha , Schug Jonathan , Kaestner Klaus H 
Published: February 2024

AbstractThe primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRα as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed-forward loop with Foxo3.
Discovery of an anti-virulence compound that targets theStaphylococcus aureusSaeRS two-component system to inhibit toxic shock syndrome toxin 1 (TSST-1) production
Authors: Dufresne Karine , DiMaggio Dennis A. , Maduta Carla S. , Brinsmade Shaun R. , McCormick John K. 
Published: February 2024

AbstractMenstrual toxic shock syndrome (mTSS) is a rare but severe disorder associated with the use of menstrual products such as high-absorbency tampons and is caused byStaphylococcus aureusstrains that produce the toxic shock syndrome toxin-1 (TSST-1) superantigen. Herein, we screened a library of 3920 small bioactive molecules for the ability to inhibit transcription of the TSST-1 gene without inhibiting growth ofS. aureus. The dominant positive regulator of TSST-1 is the SaeRS two-component system (TCS), and we identified phenazopyridine hydrochloride (PP-HCl) that repressed production of TSST-1 by inhibiting the kinase function of SaeS. PP-HCl competed with ATP for binding of the kinase SaeS leading to decreased phosphorylation of SaeR and reduced expression of TSST-1 as well as several other secreted virulence factors known to be regulated by SaeRS. PP-HCl targets virulence ofS. aureus, but it also decreases the impact of TSST-1 on human lymphocytes without affecting the healthy vaginal microbiota. Our findings demonstrate the promising potential of PP-HCl as a therapeutic strategy against mTSS.