bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ultra-short-acting benzodiazepine in thalamic nucleus reuniens undermines fear extinction via intermediation of hippocamposeptal circuits
Authors: Cheung Hoiyin , Yu Tong-Zhou , Yi Xin , Wu Yan-Jiao , Wang Qi , Gu Xue , Xu Miao , Cai Meihua , Wen Wen , Li Xin-Ni , Liu Ying-Xiao , Sun Ying , Zheng Jijian , Xu Tian-Le , Luo Yan , Zhang Mazhong , Li Wei-Guang 
Published: May 2024

AbstractBenzodiazepines, commonly used for anxiolytics, hinder conditioned fear extinction, and the underlying circuit mechanisms are unclear. Utilizing remimazolam, an ultra-short-acting benzodiazepine, we reveal its impact on the thalamic nucleus reuniens (RE) and interconnected hippocamposeptal circuits during fear extinction. Systemic or RE-specific administration of remimazolam impedes fear extinction by reducing RE activation through A type GABA receptors. Remimazolam enhances long-range GABAergic inhibition from lateral septum (LS) to RE, underlying the compromised fear extinction. RE projects to ventral hippocampus (vHPC), which in turn sends projections characterized by feed-forward inhibition to the GABAergic neurons of the LS. This is coupled with long-range GABAergic projections from the LS to RE, collectively constituting an overall positive feedback circuit construct that promotes fear extinction. RE-specific remimazolam negates the facilitation of fear extinction by disrupting this circuit. Thus, remimazolam in RE disrupts fear extinction caused by hippocamposeptal intermediation, offering mechanistic insights for the dilemma of combining anxiolytics with extinction-based exposure therapy.
Assessing sprint technique with shoe-mounted inertial sensors
Authors: Pla Gerard Aristizábal , Martini Douglas N. , Potter Michael V. , Hoogkamer Wouter , Cain Stephen M. 
Published: May 2024

AbstractNegative foot speed (i.e., the speed of the backward and downward motion of the foot relative to the body at ground contact) is a strong predictor of sprinting performance. Inertial measurement units (IMUs) are becoming a popular approach for assessing sports performance. The primary aim of this study was to use IMUs to investigate the relationship between negative foot speed and top running speed attained during a sprint on an outdoor track. Seventeen participants performed 80-meter track sprints while wearing a shoe-mounted IMU. Anteroposterior and vertical components of negative foot speed were extracted from the IMU. For the mean peak stride speed of 7.98±0.78m/s, the adjusted R2values were 0.27 and 0.42 versus the anteroposterior and vertical components of negative foot speed, respectively. In conclusion, our findings support the common coaching tip of increasing negative foot speed to improve sprint speed. In addition, the results of this study support the use of IMUs for quantifying sprinting technique with actionable metrics.
The crystal structure of Nictaba reveals its carbohydrate-binding properties and a new lectin dimerization mode
Authors: Bloch Yehudi , Osterne Vinicius J.S. , Savvides Savvas N. , Van Damme Els J.M. 
Published: May 2024

ABSTRACTNictaba is a (GlcNAc)n-binding, stress-inducible lectin from Nicotiana tabacum that serves as a representative for the family of Nictaba-related lectins, a group of proteins that play pivotal roles in plant defense mechanisms and stress response pathways. Despite extensive research into the biological activities and physiological role(s) of the lectin, the three-dimensional structure of Nictaba remained largely unknown. Here, we report crystal structures for Nictaba in the apo form and bound to chitotriose. The structures reveal a jelly-roll fold for the Nictaba protomer similar to the cucumber Cus17 lectin, but show an unprecedented dimerization mode among all structurally characterized lectins to date. The chitotriose binding mode, similar to Cus17, centers around the central GlcNAc residue, providing insights into the determinants of specificity of Nictaba towards carbohydrate structures. By integrating these structural insights with inputs from glycan arrays, molecular docking, and molecular dynamics simulations, we propose that Nictaba employs a single carbohydrate-recognition domain within each of the two subunits in the dimer to display pronounced specificity towards GlcNAc-containing carbohydrates. Furthermore, we identified amino acid residues involved in the extended binding site capable of accommodating structurally diverse high-mannose and complex N-glycans. Glycan array and in silico analyses revealed interactions centered around the conserved Man3GlcNAc2 core, explaining the broad recognition of N-glycan structures. Collectively, the structural and biochemical insights presented here fill a hitherto substantial void into the atlas of lectin structure-function relationships and pave the way for future developments in plant stress biology and lectin-based applications.
Maroon rice genomic diversity reflects 350 years of colonial history
Authors: van de Loosdrecht Marieke S. , Pinas Nicholaas M. , Tjoe Awie Jerry R. , Becker Frank F.M. , Maat Harro , van Velzen Robin , van Andel Tinde , Schranz M. Eric 
Published: May 2024

AbstractMaroons in Suriname and French Guiana descend from enslaved Africans who escaped the plantations during colonial times. Maroon farmers still cultivate a large rice diversity, their oldest staple crop. Maroon oral history and written records by colonial authorities provide contrasting perspectives on the origins of Maroon rice. Here, we integrated genomic ancestry analyses of 136 newly sequenced Maroon rice varieties with ethnobotanical and archival research to reconstruct the historical contexts associated with the introduction of rice varieties to the Guianas. We found that a large subset traces to West Africa, linked to the transatlantic slave trade (c.1530-1825). Maroons obtained other varieties from indentured laborers from Java (1890 onwards), USA rice breeders (1932 onwards), and Hmong refugees from the Vietnam War (1991). Furthermore, we found rice types never documented before, indicating Maroon farmers selected from crosses. Overall, our results demonstrate that the Maroon farming system prioritizes maintenance of a high stock diversity, which we posit reflects the expertise they inherited from their (African) ancestors. Ignored by agricultural modernization initiatives, Maroon farmers today are important custodians of a unique cultural heritage. Moreover, the genomic findings underline many Maroon stories about their past. This study hence demonstrates the power of cross-disciplinary crop research to reconstruct aspects of the human past for which historical records may be biased or incomplete. We anticipate that a similar study approach can be applied to other heirloom crops of (Indigenous) communities that may have preserved their history on their farms to reconstruct, acknowledge and honor the past.
Productivity of the eelgrass biotope and the resilience of fisher-hunter-gatherers in prehistoric Denmark
Authors: Meadows John , Fischer Anders 
Published: May 2024

AbstractIn the shallow coastal waters of the Danish archipelago, eelgrass (Zostera marina) forms extensive and extremely productive stands, which support food webs that are isotopically distinct from those based on the primary productivity of marine phytoplankton. The isotopic signatures of eelgrass and phytoplankton food webs explain much of the variation in δ13C, δ15N and δ34S values in marine vertebrate remains recovered from prehistoric coastal sites in Denmark. Isotope data from human and dog remains reflect the overwhelming importance of the eelgrass biotope to the fisher-hunter-gatherer (FHG) subsistence during the Late Mesolithic Ertebølle epoch (∼7400-5800 cal BP). By recognising eelgrass and pelagic resources as isotopically distinct, we obtain more accurate diet reconstructions and dietary14C reservoir effect corrections for Ertebølle individuals. Longstanding research issues, including technology, palaeodemography, and the resilience and sustainability of the FHG economy need to be reassessed in view of the isotopic signature and productivity of the eelgrass biotope in Danish waters. Eelgrass productivity is also pertinent to comparisons between Ertebølle and Neolithic economies in Denmark, and between FHG adaptations in Denmark and neighbouring regions, and may be key to understanding the much-discussed delay in the transition to farming.
Genome-wide screen ofMycobacterium tuberculosis-infected macrophages identified the GID/CTLH complex as a determinant of intracellular bacterial growth
Authors: Simwela Nelson V. , Johnston Luana , Pavinski Bitar Paulina , Jaecklein Eleni , Altier Craig , Sassetti Christopher M. , Russell David G. 
Published: May 2024

SummaryThe eukaryotic GID/CTLH complex is a highly conserved E3 ubiquitin ligase involved in a broad range of biological processes. However, a role of this complex in host antimicrobial defenses has not been described. We exploitedMycobacterium tuberculosis(Mtb) induced cytotoxicity in macrophages in a FACS based CRISPR genetic screen to identify host determinants of intracellularMtbgrowth restriction. Our screen identified 5 (GID8,YPEL5,WDR26,UBE2H,MAEA) of the 10 predicted members of the GID/CTLH complex as determinants of intracellular growth of bothMtbandSalmonellaserovar Typhimurium. We show that the antimicrobial properties of the GID/CTLH complex knockdown macrophages are mediated by enhanced GABAergic signaling, activated AMPK, increased autophagic flux and resistance to cell death. Meanwhile,Mtbisolated from GID/CTLH knockdown macrophages are nutritionally starved and oxidatively stressed. Our study identifies the GID/CTLH complex activity as broadly suppressive of host antimicrobial responses against intracellular bacterial infections.Graphical abstract
Fast and reliable ancestral reconstruction on ancient genotype data with non-negative Least square and Principal Component Analysis
Authors: de Gennaro Luciana , Molinaro Ludovica , Raveane Alessandro , Santonastaso Federica , Saponetti Sandro Sublimi , Massi Michela Carlotta , Pagani Luca , Metspalu Mait , Hellenthal Garrett , Kivisild Toomas , Ventura Mario , Montinaro Francesco 
Published: May 2024

AbstractThe history of human populations has been strongly shaped by admixture events, contributing to the patterns of observed genetic diversity across populations. Given its significance for evolutionary and medical studies, many algorithms focusing on the inference of the genetic composition of admixed populations have been developed. In particular, the recent development of new ancestry estimation methods that consider the fragmentary nature of ancient genotype data, such as the f-statistics family and its derivations, have radically changed our understanding of the past. F-statistics capture similar genetic similarity information as Principal Component Analysis (PCA), which is widely used in population genetics to quantify genetic affinity between populations or individuals. In this study, we introduce ASAP (ASsessing ancestry proportions through Principal component Analysis) method that leverages PCA and Non-Negative Least Square (NNLS) to assess the ancestral compositions of admixed individuals given a large set of populations. We tested ASAP on different simulated models, incorporating high levels of missingness. Our results show its ability to reliably estimate ancestry across numerous scenarios, even those with a significant proportion of missing genotypes, in a fraction of the time required when using other tools. When harnessed on Eurasia’s genotype data, ASAP helped replicate and extend findings from previous studies proving to be a fast, efficient, and straightforward new ancestry estimation tool.
Episodic memory supports the acquisition of structured task representations
Authors: Lu Qihong , Hummos Ali , Norman Kenneth A. 
Published: May 2024

AbstractGeneralization to new tasks requires learning of task representations that accurately reflect the similarity structure of the task space. Here, we argue that episodic memory (EM) plays an essential role in this process by stabilizing task representations, thereby supporting the accumulation of structured knowledge. We demonstrate this using a neural network model that infers task representations that minimize the current task’s objective function; crucially, the model can retrieve previously encoded task representations from EM and use these to initialize the task inference process. With EM, the model succeeds in learning the underlying task structure; without EM, task representations drift and the network fails to learn the structure. We further show that EM errors can support structure learning by promoting the activation of similar task representations in tasks with similar sensory inputs. Overall, this model provides a novel account of how EM supports the acquisition of structured task representations.
Intraspecies warfare restricts strain coexistence in human skin microbiomes
Authors: Mancuso Christopher P. , Baker Jacob S. , Qu Evan , Tripp A. Delphine , Balogun Ishaq O. , Lieberman Tami D. 
Published: May 2024

AbstractDetermining why only a fraction of encountered or applied bacterial strains engraft in a given person’s microbiome is crucial for understanding and engineering these communities1. Previous work has established that metabolism can determine colonization successin vivo2–4, but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions betweenStaphylococcus epidermidiscultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-personS. epidermidiscommunity. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.
The visuomotor transformations underlying target-directed behavior
Authors: Zhao Peixiong , Tong Yuxin , Lazarte Ivan P. , Khan Biswadeep , Tian Guangnan , Chen Kenny K. Y. , Lam Thomas K. C. , Hu Yu , Semmelhack Julie L. 
Published: May 2024

SummaryThe visual system can process diverse stimuli and make the decision to execute appropriate behaviors, but it remains unclear where and how this transformation takes place. We imaged the zebrafish visual system while larvae responded with hunting, freezing, and escape behaviors, and systematically identified visually driven neurons and behaviorally correlated sensorimotor neurons. Our analyses indicate within the optic tectum, broadly tuned sensory neurons are functionally connected to sensorimotor neurons that respond specifically during one behavior, transforming visual information into motor output. We also identified sensorimotor neurons in four other areas downstream of the tectum, and these neurons are also specific for one behavior, indicating that once the decision to behave has been made, the segregation of the pathways continues in later areas. Our findings suggest that the tectum receives visual sensory information and is responsible for selecting a single behavioral outcome, which is then relayed to downstream areas.Significance statementHere, we developed a novel visually-evoked freezing paradigm in zebrafish, and combined this with escape and hunting behaviors to ask how visual stimuli are identified and converted into different behavioral outcomes. We found that the optic tectum contains neurons that detect all three stimuli, as well as sensorimotor neurons for the three behaviors, suggesting that it is a site of sensorimotor transformation, which was supported by our analysis of correlations between the populations. The sensorimotor neurons in the tectum are highly specific for one behavior, and this segregation is maintained in the three downstream areas where we also identified sensorimotor neurons, indicating that the tectum flexibly transforms visual information into a single behavioral output.
Mechanisms of RecA filament nucleation on ssDNA by the DprA protein
Authors: Bakhlanova Irina , Alekseev Aleksandr , Yakunina Maria , Morozova Natalia , Khodorkovskii Mikhail , Petukhov Michael , Baitin Dmitry 
Published: May 2024

AbstractThe DprA protein has been implicated in the protecton of incoming DNA. However, the presence of dprA gene family members, also known as smf, across diverse bacterial species suggests a broader functonality for their gene products. We eaamined the role of the Escherichia coli DprA/Smf homologue in conjugaton. Remarkably, Bacillus subtilis dprA/smf can complement an E. coli dprA mutant, indicatng interchangeability of dprA/smf genes between competent and non-competent species in conjugatonal processes. The DprA protein forms a complex with DNA, facilitatng the nucleaton of RecA protein flaments onto circular single-stranded DNA coated with SSB protein. To focus on RecA nucleaton, we employed short DNA oligonucleotdes that restrict RecA-DNA binding but allow for DprA-RecA-DNA binding. Analysis of dATPase actvity revealed that RecA-DNA complexes were readily formed only with olig50, while DprA-RecA-DNA complexes were also feasible with olig21. Combining eaperimental data with a full-atomic model of the RecA-DprA-ssDNA complex’s spatal structure, we proposed a molecular mechanism for DprA-mediated loading of RecA proteins onto ssDNA. Our fndings suggest that only one DprA-ssDNA interacton can occur sterically, occupying one strand of ssDNA in the complex.
Modulation of host signalling pathways reveal a major role for Wnt signalling in the maturation ofPlasmodium falciparumliver schizonts
Authors: Kanyal Abhishek , van Gemert Geert-Jan , Wu Haoyu , van der Starre Alex , de Wilt Johannes HW , Bousema Teun , Sauerwein Robert W. , Bartfai Richard , Yang Annie SP 
Published: May 2024

AbstractAfter infection of the human host, the initial stage of thePlasmodium falciparum(Pf) lifecycle takes place in the liver. However, understanding of the host-parasite interaction has been limited by the rapid loss of functionality in cultured primary human hepatocytes (PHHs). Here, we link loss of hepatic functionality to drastic loss in Pf permissiveness, which we effectively prevent by using a novel medium containing serum-replacement and signal transduction inhibitors. Integrating transcriptomic analysis and phenotypic assessment of infection outcome, we identified several host signalling pathways that influence Pf liver stage development. Inhibition of the Wnt pathway in particular plays a major role in determining the size and maturity of Pf-liver schizonts, via retaining metabolic activity and epithelial nature of hepatocytes. Host signalling pathways determining Pf liver stage permissiveness provide insight into the complex host-parasite interaction and may accelerate development of novel therapeutic strategies for Pf-liver stages. (145)
Identification and Characterization of Novel Metagenome Assembled Uncultivated Virus Genomes from Human Gut
Authors: Bhardwaj Kanchan , Niharika  , Garg Anjali , Jain Aakriti , Kumar Manish , Datt Manish , Singh Vijay , Vrati Sudhanshu 
Published: May 2024

ABSTRACTMetagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains to be characterized. In this study, we mined a collection of 1090 metagenome assembled “high quality” genomes of human gut viruses. Sequence analysis has revealed eight new species from seven genera of the class,Caudoviricetesand nineteen new species from fourteen genera of the ssDNA virus family,Microviridae.In addition, four “high quality” genomes were identified, which do not show similarity to sequences present in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation of the “high-quality” genomes and KEGG pathway analysis has identifiedantB,dnaB,DNMT1,DUT,xlyAB,xtmBandxtmAas the most widespread viral and Auxiliary Metabolic Genes (AMGs). Genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also found. Bacterial hosts are predicted for around 40% of the analyzed genomes. Overall, we report identification of new viral genomes and genome analyses of human gut viruses, which will be useful for biological characterization to establish their significance in physiology.IMPORTANCEMultiple studies have found that dysbiosis of gut virome is associated with conditions such as metabolic syndromes, autoimmune disorders and infectious diseases. In the interest of its therapeutic and diagnostic potential, intestinal virome warrants detailed investigation. However, limited ability to culture gut viruses becomes one of the challenges for their biological characterization and fully understanding their role in physiology. Sequence analysis and host prediction methods provide opportunities to understand gut viruses, their functional potential and devise ways for further characterization.
The impact of biophilic design in university study areas on students' productivity
Authors: Terblanche Rolien , Khumalo Dorcas 
Published: May 2024

PurposeThe objective of this study is to determine how biophilic designs in study areas affect the productivity of students at the University of the Witwatersrand. The study also seeks to evaluate study areas at Wits in terms of biophilic design, determine whether biophilic design contributes to the preference of students and their study productivity.Design/methodology/approachThis is a cross sectional study that used a mixed methodology. Five study areas were identified and evaluated in terms of biophilic design. At each study area, nine students participated in an open- and close-ended questionnaire regarding their perceptions on study areas and productivity.FindingsThe five study areas scored the following results according to the biophilic test: 29.09%, 34.55%, 36.36%, 80.00% and 85.45%, respectively. The students prefer to study in biophilic study areas as it prompts positive emotions and make them feel rejuvenated and energized. However, there are still students studying in the non-biophilic areas due to convenience or due to the biophilic areas that are noisy and lacks monitoring.Research limitations/implicationsWith the small sample size, the generalizability of the findings are limited, but does create a foundation for further research.Practical implicationsUniversities can learn from the findings and benefit greatly from many biophilic study areas. This could also encourage architects and interior designers to include biophilic design more so in general buildings/rooms.Originality/valueStudy areas at the University of the Witwatersrand was evaluated in terms of biophilic design, while determining whether biophilic design contributes to the preference of students and study productivity.