bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial chromosome organization and adaptation ofEscherichia coliunder heat stress
Authors: Wang Xu-Ting , Ma Bin-Guang 
Published: June 2024

AbstractThe spatial organization of bacterial chromosomes is crucial for cellular functions. It remains unclear how bacterial chromosomes adapt to high temperature stress. This study delves into the 3D genome architecture and transcriptomic responses ofEscherichia coliunder heat stress condition to unravel the intricate interplay between chromosome structure and environmental cues. By examining the role of macrodomains, chromosome interaction domains (CIDs), and nucleoid-associated proteins (NAPs), this work unveils the dynamic changes in chromosome conformation and gene expression patterns induced by high temperature stress. It was observed that under heat stress, short-range interaction frequency of chromosome decreased, while the long-range interaction frequency of the Ter macrodomain increased. Furthermore, two metrics, namely, Global Compactness (GC) and Local Compactness (LC), were devised to measure and compare the compactness of chromosomes based on their 3D structure models. The findings in this work shed light on the molecular mechanisms underlying thermal adaptation and chromosomal organization in bacterial cells, offering valuable insights into the complex interrelationships between environmental stimuli and genomic responses.
Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT
Authors: Huynh Khoa L. A. , Tyc Katarzyna M. , Matuck Bruno F. , Easter Quinn T. , Pratapa Aditya , Kumar Nikhil V. , Pérez Paola , Kulchar Rachel , Pranzatelli Thomas , de Souza Deiziane , Weaver Theresa M. , Qu Xufeng , Alberto Valente Soares Junior Luiz , Dolhnokoff Marisa , Kleiner David E. , Hewitt Stephen M. , Fernando Ferraz da Silva Luiz , Rocha Vanderson Geraldo , Warner Blake M. , Byrd Kevin M. , Liu Jinze 
Published: June 2024

ABSTRACTIdentifying cell types and states remains a time-consuming and error-prone challenge for spatial biology. While deep learning is increasingly used, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in health and disease. To address this, we developed TACIT, an unsupervised algorithm for cell annotation using predefined signatures that operates without training data, using unbiased thresholding to distinguish positive cells from background, focusing on relevant markers to identify ambiguous cells in multiomic assays. Using five datasets (5,000,000-cells; 51-cell types) from three niches (brain, intestine, gland), TACIT outperformed existing unsupervised methods in accuracy and scalability. Integration of TACIT-identified cell with a novel Shiny app revealed new phenotypes in two inflammatory gland diseases. Finally, using combined spatial transcriptomics and proteomics, we discover under- and overrepresented immune cell types and states in regions of interest, suggesting multimodality is essential for translating spatial biology to clinical applications.
An Unbiased Proteomic Platform for Activity-based Arginylation Profiling
Authors: Lin Zongtao , Xie Yixuan , Gongora Joanna , Liu Xingyu , Zahn Emily , Palai Bibhuti Bhusana , Ramirez Daniel , Searfoss Rick M. , Vitorino Francisca N. , Dann Geoffrey P. , Zhao Chenfeng , Han Xian , MacTaggart Brittany , Lan Xin , Fu Dechen , Greenberg Lina , Zhang Yi , Lavine Kory J. , Greenberg Michael J. , Lv Dongwen , Kashina Anna , Garcia Benjamin A. 
Published: June 2024

AbstractProtein arginylation is an essential posttranslational modification (PTM) catalyzed by arginyl-tRNA-protein transferase 1 (ATE1) in mammalian systems. Arginylation features a post-translational conjugation of an arginyl to a protein, making it extremely challenging to differentiate from translational arginine residues with the same mass in a protein sequence. Here we present a general activity-based arginylation profiling (ABAP) platform for the unbiased discovery of arginylation substrates and their precise modification sites. This method integrates isotopic arginine labeling into an ATE1 assay utilizing biological lysates (ex vivo) rather than live cells, thus eliminating translational bias derived from the ribosomal activity and enablingbona fidearginylation identification using isotopic features. ABAP has been successfully applied to an array of peptide, protein, cell, patient, and animal tissue samples using 20 µg sample input, with 229 unique arginylation sites revealed from human proteomes. Representative sites were validated and followed up for their biological functions. The developed platform is globally applicable to the aforementioned sample types and therefore paves the way for functional studies of this difficult-to-characterize protein modification.
Differences in phenotype between long-lived memory B cells againstPlasmodium falciparummerozoite antigens and variant surface antigens
Authors: Reyes Raphael A. , Turner Louise , Ssewanyana Isaac , Jagannathan Prasanna , Feeney Margaret E. , Lavstsen Thomas , Greenhouse Bryan , Bol Sebastiaan , Bunnik Evelien M. 
Published: June 2024

ABSTRACTPlasmodium falciparuminfections elicit strong humoral immune responses to two main groups of antigens expressed by blood-stage parasites: merozoite antigens that are involved in the erythrocyte invasion process and variant surface antigens that mediate endothelial sequestration of infected erythrocytes. Long-lived B cells against both antigen classes can be detected in the circulation for years after exposure, but have not been directly compared. Here, we studied the phenotype of long-lived memory and atypical B cells to merozoite antigens (MSP1 and AMA1) and variant surface antigens (the CIDRα1 domain of PfEMP1) in Ugandan adults before and after local reduction ofP. falciparumtransmission. After a median of 1.7 years withoutP. falciparuminfections, the percentage of antigen-specific activated B cells declined, but long-lived antigen-specific B cells were still detectable in all individuals. The majority of MSP1/AMA1-specific B cells were CD95+CD11c+memory B cells, which are primed for rapid differentiation into antibody-secreting cells, and FcRL5-T-bet-atypical B cells. On the other hand, most CIDRα1-specific B cells were CD95-CD11c-memory B cells. CIDRα1-specific B cells were also enriched among a subset of atypical B cells that seem poised for antigen presentation. These results point to differences in how these antigens are recognized or processed by the immune system and howP. falciparum-specific B cells will respond upon re-infection.
Temporal-spatial transcriptomics reveals key gene regulation for grain yield and quality in wheat
Authors: Li Xiaohui , Wan Yiman , Wang Dongzhi , Li Xingguo , Wu Jiajie , Chen Kunming , Han Xue , Chen Yuan 
Published: June 2024

AbstractCereal grain size and quality are important agronomic traits in crop production. The development of wheat grains is underpinned by complex regulatory networks. The precise spatial and temporal coordination of diverse cell types is essential for the formation of functional compartments. To provide comprehensive spatiotemporal information about biological processes in developing wheat grain, we performed a spatial transcriptomics study during the early grain development stage from 4 to 12 days after pollination. We defined a set of tissue-specific marker genes and discovered that certain genes or gene families exhibit specific spatial expression patterns over time. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes potentially regulating wheat grain development. The embryo and surrounding endosperm specifically expressed transcription factorTaABI3-3Bnegatively regulates embryo and grain size. In Chinese breeding programs, a haplotype associated with higher grain weight was identified, linked to altered expression levels ofTaABI3-3B. Data and knowledge obtained from the proposed study will provide pivotal insights into yield improvement and serve as important genetic information for future wheat breeding.
Reliability of structural brain change in cognitively healthy adult samples
Authors: Vidal-Piñeiro Didac , Sørensen Øystein , Strømstad Marie , Amlien Inge K. , Anderson Micael , Baaré William F.C. , Bartrés-Faz David , Brandmaier Andreas M. , Bråthen Anne Cecilie , Garrido Pablo , Ghisletta Paolo , Grydeland Håkon , Henson Richard N. , Kievit Rogier A. , Kormacher Max , Kühn Simone , Lindenberger Ulman , Mowinckel Athanasia M. , Nyberg Lars , Roe James M. , Sneve Markus H. , Sole-Padulles Cristina , Watne Leiv-Otto , Walhovd Kristine B. , Fjell Anders M. 
Published: June 2024

AbstractIn neuroimaging research, tracking individuals over time is key to understanding the interplay between brain changes and genetic, environmental, or cognitive factors across the lifespan. Yet, the extent to which we can estimate the individual trajectories of brain change over time with precision remains uncertain. In this study, we estimated the reliability of structural brain change in cognitively healthy adults from multiple samples and assessed the influence of follow-up time and number of observations. Estimates of cross-sectional measurement error and brain change variance were obtained using the longitudinal FreeSurfer processing stream. Our findings showed, on average, modest longitudinal reliability with two years of follow-up. Increasing the follow-up time was associated with a substantial increase in longitudinal reliability while the impact of increasing the number of observations was comparatively minor. On average, 2-year follow-up studies require ≈2.7 and ≈4.0 times more individuals than designs with follow-ups of 4 and 6 years to achieve comparable statistical power. Subcortical volume exhibited higher longitudinal reliability compared to cortical area, thickness, and volume. The reliability estimates were comparable to those estimated from empirical data. The reliability estimates were affected by both the cohort’s age where younger adults had lower reliability of change, and the preprocessing pipeline where the FreeSurfer’s longitudinal stream was notably superior than the cross-sectional. Suboptimal reliability inflated sample size requirements and compromised the ability to distinguish individual trajectories of brain aging. This study underscores the importance of long-term follow-ups and the need to consider reliability in longitudinal neuroimaging research.
Crystallographic fragment screening of CDK2-cyclin A: FragLites map sites of protein-protein interaction
Authors: Hope Ian , Noble Martin E. M. , Waring Michael J. , Noble E. M. Martin , Endicott Jane A. , Tatum Natalie J. 
Published: June 2024

AbstractProtein-protein interaction sites (PPIs) are potentially more selective therapeutic binding sites than protein substrate binding sites. PPIs include distinct regions frequently called “hotspots,” sites of key amino acid interactions. Prospective identification of these hotspots through X-ray crystallographic screening could assist in the identification of separation of function mutants for experimental validation, enhance confidence in AI-generated multiprotein complex predictions and accelerate development of selective chemical probes. To explore these applications, we utilize the FragLite library to examine the binding surfaces of CDK2-cyclin A. The many protein- and peptide-CDK2-cyclin A complexes that have been structurally characterised make this complex an appropriate test case. We show that FragLites comprehensively map both known sites of protein-protein interaction on CDK2-cyclin A and identify a possible uncharacterised site, providing a structural method toward directing mechanistic studies and providing starting points for chemical probe design.
Dissolved organic matter fluxes and fatty acid composition from shallow-water and deep-water demo- and hexactinellid sponges from New Zealand
Authors: Stratmann Tanja , Miranda Mario L. M. , de Kluijver Anna , Busch Kathrin , Kelly Michelle , Mills Sadie , Schupp Peter J. 
Published: June 2024

AbstractSponges are an important component of shallow- and deep-water ecosystems enhancing eukaryotic biodiversity via diverse endo- and epibiota and by providing three dimensional habitats for benthic invertebrates and fishes. Sponge biodiversity is particularly high in the waters around New Zealand (Southwest Pacific), where we collected two shallow- and two deep-water sponge species (Tedaniasp.,Suberea meandrina,Farrea raoulensis,Artemisinasp.) forex-situincubation experiments to detect whether these sponges may process dissolved organic matter.We assessed the biochemical and phospholipid-derived fatty acids (PLFAs) and measured dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) fluxes. Changes in fluorescent dissolved organic matter (FDOM) over time were analyzed and the results were linked to the bacterial communities of the sponge holobiont.Dried sponge tissue consisted of 17.5 ± 3.75% organic (org.) C and of 4.34 ± 1.02% total nitrogen (TN) with a natural stable isotope composition of -19.0 ±0.25‰ for δ13org. C and of 10.2 ±2.43‰ for δ15TN. None of the DOC fluxes was significant and only the release of TDN byTedaniasp. was significantly different from 0 μmol TDN g org. C-1d-1. We detected the presence of four fluorophores in the FDOM pool: 2 tryptophan- and protein-like fluorophores (C1, C2), 1 humic-like fluorophore (C3), and 1 tyrosine-like fluorophore (C4). The maximum fluorescence intensity Fmaxof C1 decreased significantly inS. meandrinaincubations, whereas Fmaxof C2 grew in the same incubations. Fmaxof C3 increased inTedaniasp. incubations, in which Fmaxof C4 decreased. In comparison, Fmaxof C4 inS. meandrinarose.The PLFA composition of sponge tissue was dominated by long-chain fatty acids, saturated fatty acids, and monosaturated fatty acids and most PLFAs were sponge- and bacteria-specific. The bacterial community of the demospongesArtemisinasp.,S. meandrinaandTedaniasp. consisted mostly of Proteobacteria and Chloroflexota, whereas the dominating bacteria phylum of the hexactinellidF. raoulensiswas Proteobacteria.We proposed that the holobionts ofS. meandrinaandTedaniasp. contain bacteria that are involved in the transformation and degradation of DOM. InS. meandrina, Chloroflexota and Poribacteria may degrade tryptophan-like fluorophores to a chemically modified tryptophan-like and protein-like fluorophore, while producing a tyrosine-like fluorophore. InTedaniasp., Chloroflexota may contribute to the release of significant amounts of TDN by producing humic-like fluorophores, while degrading tyrosine-like fluorophores.Farrea raoulensismay not take up DOM due to a lack of Poribacteria and Chloroflexota or may use colloidal instead of truly dissolved DOC.
Chemogenetic activation of astrocytes modulates sleep/wakefulness states in a brain region-dependent manner
Authors: Kurogi Yuta , Sanagi Tomomi , Ono Daisuke , Tsunematsu Tomomi 
Published: June 2024

AbstractStudy objectivesAstrocytes change their intracellular calcium (Ca2+) concentration during sleep/wakefulness states in mice. Furthermore, the Ca2+dynamics in astrocytes vary depending on the brain region. However, whether alterations in intracellular Ca2+concentration in astrocytes can affect sleep/wakefulness states and cortical oscillations in a brain region-dependent manner remain unclear.MethodsThe Ca2+concentration in astrocytes was artificially increased using chemogenetics in mice. Astrocytes in the hippocampus and pons, which are 2 brain regions previously classified into different clusters based on their Ca2+dynamics during sleep/wakefulness, were focused on to compare whether there are differences in the effects of astrocytes from different brain regions.ResultsThe activation of astrocytes in the hippocampus significantly decreased the total time of wakefulness and increased the total time of sleep. This had minimal effects on cortical oscillations in all sleep/wakefulness states. On the other hand, the activation of astrocytes in the pons substantially suppressed rapid eye movement (REM) sleep in association with a decreased number of REM episodes, indicating strong inhibition of REM onset. Regarding cortical oscillations, the delta wave component during non-REM sleep was significantly enhanced.ConclusionsThese results suggest that astrocytes modulate sleep/wakefulness states and cortical oscillations. Furthermore, the role of astrocytes in sleep/wakefulness states appears to vary among brain regions.Statement of SignificanceSleep is an instinctive behavior for many organisms. Recently, it has been reported that not only neurons, but also astrocytes, a type of glial cell, contribute to sleep/wakefulness states. Intracellular Ca2+concentration, an indicator of astrocyte activity, fluctuates during sleep/wakefulness states. However, it is still unclear whether changes in Ca2+concentration in astrocytes can affect sleep/wakefulness states. In this study, we utilized chemogenetics to activate astrocytes in mice. Our results showed that activation of astrocytes in the hippocampus causes decreased wakefulness, and that in the pons causes decreased REM sleep. Therefore, our findings demonstrate that the activation of astrocytes modulates sleep/wakefulness states in a brain region-dependent manner.Graphical Abstract
Stochastic optimal tuning for flight control system of morphing arm octorotor
Authors: Kose Oguz 
Published: June 2024

Purpose
This study aims to discuss the simultaneous longitudinal and lateral flight control of the octorotor, a rotary wing unmanned aerial vehicle (UAV), for the first time under the effect of morphing and to improve autonomous flight performance.

Design/methodology/approach
This study aims to design and control the octorotor flight control system with stochastic optimal tuning under morphnig effect. For this purpose, models of different arm lengths of the octorotor were drawn in the Solidworks program. The morphing was carried out by simultaneously lengthening or shortening the arm lengths of the octorotor. The morphing rate was estimated by using simultaneous perturbation stochastic approximation (SPSA). The stochastic gradient descent algorithm, which is frequently used in machine learning, was used to estimate the changing moments of inertia with the change of arm lengths. The proportional integral derivative (PID) controller has been preferred as an octorotor control algorithm because of its simplicity of structure. The PID gains required to control both longitudinal and lateral flight were also estimated with SPSA.

Findings
With SPSA, three longitudinal flight PID gains, three lateral flight PID gains and one morphing ratio were estimated. PID gains remained within the limits set for SPSA, giving satisfactory results. In addition, the cost index created was 93% successful. The gradient descent algorithm used for the moment of inertia estimation achieved the optimum result in 1,570 iterations. However, in the simulations made with the obtained data, longitudinal and lateral flight was successfully carried out.

Originality/value
Octorotor longitudinal and lateral flight control was performed quickly and effectively with the proposed method. In addition, the desired parameters were obtained with the optimization methods used, and the longitudinal and lateral flight of the octorotor was successfully carried out in the desired trajectory.
The market reaction of energy companies to the announcement of the Russian–Ukrainian invasion
Authors: Yudaruddin Rizky , Lesmana Dadang 
Published: June 2024

PurposeThis study aims to empirically analyze the market response of energy companies to the Russian-Ukrainian invasion. Additionally, it examines the comparison of market reactions between companies in NATO member countries and non-member countries.Design/methodology/approachThis study utilizes a sample of 1,511 energy sector companies. To achieve the research objectives, two methods are employed. First, an event study is used to analyze the market reaction using Cumulative Abnormal Return (CAR) to the announcement of Russia's invasion of Ukraine on February 24, 2022 (event day) within an event window of (−30, +30). Second, a cross-sectional analysis is conducted to compare the responses of companies in NATO member countries with those in non-member countries.FindingsThe findings of this study reveal that energy companies worldwide reacted positively both before and after the announcement of the invasion, with significant reactions observed in companies from the Americas, Europe, and Asia & Pacific regions. However, the Middle East and Africa markets did not show significant reactions. Furthermore, the study indicates that most developed and emerging markets responded positively, likely due to the increase in energy commodity prices during the war. Moreover, the market reaction of companies in NATO member countries was stronger compared to other markets.Originality/valueThis study contributes to the existing literature by being the first to examine the impact of the Russian invasion of Ukraine on the energy sector, while categorizing markets as developed, emerging, and frontier. It also specifically explores the market reaction of energy companies in NATO member countries, providing unique insights into the differential responses within the energy sector.
For Da Brothas: a call for fat, black male and masculine folx literature
Authors: Jackson Jarvais , Taste Allen D. , Prosser Robert 
Published: June 2024

Purpose
This study rigorously explores the intersectional challenges faced by black fat males, emphasizing the amalgamation of anti-fat bias, gender and sexuality and racial discrimination within educational contexts. The purpose of this study is to dissect the complex dynamics of this intersection, shedding light on the nuanced experiences of black men. Central to this exploration is the advocacy for creating inclusive educational sanctuaries, providing a safe space for these individuals to thrive, learn and engage in holistic personal development.

Design/methodology/approach
To accomplish our objectives, this paper reviewed existing literature on anti-fatness, intersecting with issues of race, gender and sexuality. Drawing upon qualitative data, this study incorporated personal narratives and experiences to offer a comprehensive perspective. Our research methodology also involved an analysis of metrics like body mass index (BMI) and its impact on health-care practices and policies, particularly concerning the black community.

Findings
The research discerns that black fat males encounter multifaceted challenges in educational settings, often rooted in societal prejudices and systemic biases. It highlights the inadequacy of conventional metrics like BMI in capturing the complexity of these experiences. The study identifies the urgent need for safe school spaces, emphasizing the importance of inclusive language, varied seating arrangements and tailored educational content. These findings underscore the imperative for proactive measures in dismantling anti-fatness within academic institutions.

Originality/value
This research contributes significantly to the academic discourse by pioneering an in-depth exploration of the intersectional challenges black fat males face in education. This study offers a novel perspective by focusing on the unique amalgamation of anti-fat bias and racial discrimination. The proposal for educational sanctuaries tailored to the needs of this demographic represents an innovative solution, bridging gaps in the existing literature. Through its nuanced approach and advocacy for inclusivity, this study stands as an original and pioneering contribution to the field, urging educators and policymakers to reevaluate their practices and create equitable learning environments.