bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systemic CD8+ T cell effector signature predicts prognosis of lung cancer immunotherapy
Authors: Sim Hyungtai , Park Geun-Ho , Park Woong-Yang , Lee Se-Hoon , Choi Murim 
Published: September 2024

AbstractBackgroundWhile immune checkpoint inhibitors (ICIs) are adopted as standard therapy in non-small cell lung cancer (NSCLC) patients, factors that influence variable prognosis still remain elusive. Therefore, a deeper understanding is needed of how germline variants regulate the transcriptomes of circulating immune cells in metastasis, and ultimately influence immunotherapy outcomes.MethodsWe collected peripheral blood mononuclear cells (PBMCs) from 73 ICI-treated NSCLC patients, conducted single-cell RNA sequencing, and called germline variants via SNP microarray. Determination of expression quantitative trait loci (eQTL) allows elucidating genetic interactions between germline variants and gene expression. Utilizing aggregation-based eQTL mapping and network analysis across eight blood cell types, we sought cell-type-specific and ICI-prognosis-dependent gene regulatory signatures.ResultsOur sc-eQTL analysis identified 3,616 blood- and 702 lung-cancer-specific eGenes across eight major clusters and treatment conditions, highlighting involvement of immune-related pathways. Network analysis revealed TBX21-EOMES regulons activity in CD8+ T cells and the enrichment of eQTLs in higher-centrality genes as predictive factors of ICI response.ConclusionsOur findings suggest that in the circulating immune cells of NSCLC patients, transcriptomic regulation differs in a cell type- and treatment-specific manner. They further highlight the role of eQTL loci as broad controllers of ICI-prognosis-predicting gene networks. The predictive networks and identification of eQTL contributions can lead to deeper understanding and personalized ICI therapy response prediction based on germline variants.
PANOMIQ: A Unified Approach to Whole-Genome, Exome, and Microbiome Data Analysis
Authors: Srivastava Shivani , Ehsaan Saba , Chowdhury Linkon , Faruk Muhammad Omar , Singh Abhishek , Kapoor Anmol , Bhinder Sidharth , Singh M. P. , Mishra Divya 
Published: September 2024

AbstractThe integration of whole-genome sequencing (WGS), whole-exome sequencing (WES), and microbiome analysis has become essential for advancing our understanding of complex biological systems. However, the fragmented nature of current analytical tools often complicates the process, leading to inefficiencies and potential data loss. To address this challenge, we present PANOMIQ, a comprehensive software solution that unifies the analysis of WGS, WES, and microbiome data into a single, streamlined pipeline. PANOMIQ is designed to facilitate the entire analysis process from raw data to interpretable results. It is the fastest algorithm that can achieve results much more quickly compared to traditional pipeline approaches of WGS and WES analysis. It incorporates advanced algorithms for high-accuracy variant calling in both WGS and WES, along with robust tools for characterizing microbial communities. The software’s modular architecture allows for seamless integration of these diverse data types, enabling researchers to uncover complex interactions between host genomics and microbiomes. In this study, we demonstrate the capabilities of PANOMIQ by applying it to a series of datasets encompassing a wide range of applications, including disease association studies and environmental microbiome profiling. Our results highlight PANOMIQ’s ability to deliver comprehensive insights, significantly reducing the time and computational resources required for multi-omic analysis. By providing a unified platform for WGS, WES, and microbiome analysis, PANOMIQ offers a powerful tool for researchers aiming to explore the full spectrum of genomic and microbial diversity. This software not only simplifies the analytical workflow but also enhances the depth of biological interpretation, paving the way for more integrated and holistic studies in genomics and microbiology.
A Combined Approach to Extract Rotational Dynamics of Globular Proteins undergoing Liquid- Liquid Phase Separation
Authors: Gendreizig Dominik , Kalarikkal Abhishek , Holtbrügge Simon L. , Mukherjee Saumyak , Galazzo Laura , Kucher Svetlana , Rosspeintner Arnulf , Schäfer Lars V. , Bordignon Enrica 
Published: September 2024

AbstractThe formation of protein condensates (droplets) via liquid-liquid phase separation (LLPS) is a commonly observed phenomenon in vitro. Changing the environmental properties with cosolutes, molecular crowders, protein partners, temperature, pressure, etc. was shown to favour or disfavour the formation of protein droplets by fine-tuning the water-water, water-protein and protein-protein interactions. Therefore, these environmental properties and their spatiotemporal fine-tuning are likely to be important also in a cellular context at the existing protein expression levels. One of the key physicochemical properties of biomolecules impacted by molecular crowding is diffusion, which determines the viscoelastic behaviour of the condensates. Here we investigate the change in the rotational diffusion of γD-crystallin, undergoing LLPS in vitro in aqueous solutions in absence and presence of cosolutes. We studied its rotational dynamics using molecular dynamics simulations (MD), electron paramagnetic resonance (EPR) spectroscopy and fluorescence spectroscopy. MD simulations performed under dilute and crowded conditions show that the rotational diffusion of crystallin in water is retarded by one to two orders of magnitude in the condensed phase. To obtain the rotational dynamics in the dilute phase we used fluorescence anisotropy and to extract the retardation factor in the condensed phase we used spin-labeled γD-crystallin proteins as EPR viscosity nanoprobes. Aided by a viscosity nanoruler calibrated with solutions at increasing sucrose concentrations, we validate the rotational diffusion retardation predicted by MD simulations. This study underlines the predictive power of MD simulations and showcases the use of a sensitive EPR nanoprobe to extract the viscosity of biomolecular condensates.
A chronic murine model of pulmonaryAcinetobacter baumanniiinfection enabling the investigation of late virulence factors, long-term antibiotic treatments, and polymicrobial infections
Authors: Jackson-Litteken Clay D. , Di Venanzio Gisela , Janet-Maitre Manon , Castro Ítalo A. , Mackel Joseph J. , Rosen David A. , López Carolina B. , Feldman Mario F. 
Published: September 2024

AbstractAcinetobacter baumanniican cause prolonged infections that disproportionately affect immunocompromised populations. Our understanding ofA. baumanniirespiratory pathogenesis relies on an acute murine infection model with limited clinical relevance that employs an unnaturally high number of bacteria and requires the assessment of bacterial load at 24-36 hours post-infection. Here, we demonstrate that low intranasal inoculums in immunocompromised mice with atlr4mutation leads to reduced inflammation, allowing for persistent infections lasting at least 3 weeks. Using this “chronic infection model,” we determined the adhesin InvL is an imperative virulence factor required during later stages of infection, despite being dispensable in the early phase. We also demonstrate that the chronic model enables the distinction between antibiotics that, although initially reduce bacterial burden, either lead to complete clearance or result in the formation of bacterial persisters. To illustrate how our model can be applied to study polymicrobial infections, we inoculated mice with an activeA. baumanniiinfection withStaphylococcus aureusorKlebsiella pneumoniae. We found thatS. aureusexacerbates the infection, whileK. pneumoniaeenhancesA. baumanniiclearance. In all, the chronic model overcomes some limitations of the acute pulmonary model, expanding our capabilities to study ofA. baumanniipathogenesis and lays the groundwork for the development of similar models for other important opportunistic pathogens.
Neuroimaging model of visceral manipulation in awake rat
Authors: Cramer Samuel R. , Han Xu , Chan Dennis C.Y. , Neuberger Thomas , Zhang Nanyin 
Published: September 2024

AbstractReciprocal neuronal connections exist between the internal organs of the body and the nervous system. These projections to and from the viscera play an essential role in maintaining and finetuning organ responses in order to sustain homeostasis and allostasis. Functional maps of brain regions participating in this bidirectional communication have been previously studied in awake humans and anesthetized rodents. To further refine the mechanistic understanding of visceral influence on brain states, however, new paradigms that allow for more invasive, and ultimately more informative, measurements and perturbations must be explored. Further, such paradigms should prioritize human translatability. In the current paper, we address these issues by demonstrating the feasibility of non-anesthetized animal imaging during visceral manipulation. More specifically, we used a barostat interfaced with an implanted gastric balloon to cyclically induce distension of a non-anesthetized rat’s stomach during simultaneous BOLD fMRI. General linear modeling and spatial independent component analysis revealed several regions with BOLD activation temporally coincident with the gastric distension stimulus. The ON-OFF (20 mmHg - 0 mmHg) barostat-balloon pressure cycle resulted in widespread BOLD activation of the inferior colliculus, cerebellum, ventral midbrain, and a variety of hippocampal structures. These results suggest that neuroimaging models of gastric manipulation in the non-anesthetized rat are achievable and provide an avenue for more comprehensive studies involving the integration of other neuroscience techniques like electrophysiology.Significance StatementIt is unclear to what extent measurements of brain activity are affected by background, and experimentally unrelated, interoceptive processes. To advance our understanding of ongoing visceral activity’s influence on brain states, here we provide a proof of concept, anesthesia-free animal model of visceral manipulation during simultaneous BOLD fMRI. We successfully demonstrated BOLD activation during gastric distension of the unanesthetized rat in both classically reported (cerebellum, hippocampus) and novel (inferior colliculus) regions. This paradigm establishes an important foundation for further interrogation of viscera-brain interactions.
Notch/Hairless Pathway Modulation ofsogTranscriptional Bursting in Prelude to Gastrulation
Authors: Fenelon Kelli D. , Borad Priyanshi , Rout Biraaj , Boodaghimalidarreh Parisa , Nasr Mohammad S. , Luber Jacob , Koromila Theodora 
Published: September 2024

AbstractTranscriptional regulation, orchestrated by the interplay between transcription factors (TFs) and enhancers, governs gene expression dynamics crucial for cellular processes. While gross, qualitative fluctuations in transcription factor-dependent gene expression patterning have a long history of characterization, the roles of these factors in the nuclei retaining expression in the presence or absence of these factors are now observable using modern techniques. Our study investigates the impact of Suppressor of Hairless (Su(H)), a broadly expressed transcription factor, on enhancer-driven transcriptional modulation usingDrosophilaearly embryos as a model system. Building upon previous findings, we employ super-resolution microscopy to dissect Su(H)’s influence onsogDistal (sogD) enhancer activity specifically in nuclei with preservedsogD-driven expression in the absence of Su(H) binding. We demonstrate that Su(H) occupancy perturbations alter expression levels and bursting dynamics. Notably, Su(H) absence during embryonic development exhibits region-specific effects, inhibiting expression dorsally and enhancing expression ventrally, implying a nuanced role in enhancer regulation. Our findings shed light on the intricate mechanisms that govern transcriptional dynamics and suggest a patterning role for Notch/Hairless signaling insogexpression during the transition to gastrulation.
Reducing oxidative stress improves ex vivo polymer-based human haematopoietic stem and progenitor cell culture and gene editing
Authors: Bozhilov Yavor , Brown Elizabeth , Hsu Ian , Singh Indranil , Rodriguez-Fraticelli Alejo , Roy Anindita , Yamazaki Satoshi , Wilkinson Adam C. 
Published: September 2024

AbstractSelf-renewing multipotent haematopoietic stem cells (HSCs) have the unique capacity to stably regenerate the entire blood and immune systems following transplantation. HSCs are used clinically to reconstitute a healthy blood system in patients suffering from a range of haematological diseases. However, HSCs are very rare and have been challenging to grow ex vivo, which has hampered efforts to collect large numbers of HSCs for both basic research and clinical therapies. Polymer-based culture conditions have recently been developed to support expansion of mouse and human haematopoietic stem and progenitor cells (HSPCs). While mouse HSPCs expanded rapidly in polymer-based cultures, growth speeds for human HSPCs in polymer-based cultures was limited to ∼70-fold over 4-weeks. Here we have found that reducing oxidative stress improves human HSPC growth in these conditions. We describe an optimised culture condition that improves growth to 250-1400-fold over 4-weeks through reducing oxygen tension and the addition of antioxidants. These conditions also enable efficient gene editing in these polymer-based cultures. We envision these improved culture conditions will support a range of research into human HSPC biology and provide a platform for clinical-scale HSPC expansion and gene editing.
Mid-infrared chemical imaging of living cells enabled by plasmonic metasurfaces
Authors: Huang Steven H. , Shen Po-Ting , Mahalanabish Aditya , Sartorello Giovanni , Shvets Gennady 
Published: September 2024

AbstractMid-Infrared (MIR) chemical imaging provides rich chemical information of biological samples in a label-free and non-destructive manner. Yet, its adoption to live-cell analysis is limited by the strong attenuation of MIR light in water, often necessitating cell culture geometries that are incompatible with the prolonged viability of cells and with standard high-throughput workflow. Here, we introduce a new approach to MIR microscopy, where cells are imaged through their localized near-field interaction with a plasmonic metasurface. Chemical contrast of distinct molecular groups provided sub-cellular resolution images of the proteins, lipids, and nucleic acids in the cells that were collected using an inverted MIR microscope. Time-lapse imaging of living cells demonstrated that their behaviors, including motility, viability, and substrate adhesion, can be monitored over extended periods of time using low-power MIR light. The presented approach provides a method for the non-perturbative MIR imaging of living cells, which is well-suited for integration with modern high-throughput screening technologies for the label-free, high-content chemical imaging of living cells.
Effects of the chirp rate on single-shot coherent Rayleigh-Brillouin scattering
Authors: Suzuki S. , Gerakis A. , Hara K. 
Published: September 2024

Single-shot coherent Rayleigh-Brillouin scattering (CRBS) is modeled using direct simulation Monte Carlo (DSMC). In CRBS, an optical lattice generated by the interference of two pump lasers traps the neutral particles via the dipole force. The gradient of refractive index due to the trapped particles of the gaseous media leads to coherent scattering of a probe beam, resulting in the CRBS signal. Additionally, using a chirped laser beam, CRBS signals can be obtained in a single laser shot, shortening the measurement time of the gas flow (on the order of 100 ns). The DSMC results of single-shot CRBS assuming Maxwellian velocity distribution functions (VDFs) show good agreement with experimental data, including argon, carbon dioxide, and xenon, for different gas pressures. One of the key observations obtained from the present simulations is that the CRBS signals become asymmetric when using a fast chirp rate due to finite time for collisionless trapping and collisional thermalization.

Published by the American Physical Society
2024
Estimating the uncertainty of cosmological first order phase transitions with numerical simulations of bubble nucleation
Authors: Guo Huai-Ke , Li Song , Xiao Yang , Yang Jin Min , Zhang Yang 
Published: September 2024

In order to study the validity of analytical formulas used in the calculation of characteristic physical quantities related to vacuum bubbles, we conduct several numerical simulations of bubble kinematics in the context of cosmological first-order phase transitions to determine potentially existing systematic uncertainties. By comparing with the analytical results, we obtain the following observations: (1) The simulated false vacuum fraction will approach the theoretical one with increasing simulated volume. When the side length of the cubic simulation volume becomes larger than 14.5βth−1, the simulated results do not change significantly. (2) The theoretical expected total number of bubbles do not agree with the simulated ones, which may be caused by the inconsistent use of the false vacuum fraction formula. (3) The different nucleation rate prefactors do not affect the bubble kinetics much. (4) The lifetime distribution in the sound shell model does not obey an exponential distribution, in such a way as to cause a suppression in the gravitational wave spectra.

Published by the American Physical Society
2024
Unscrambling the preference puzzle: an in-depth exploration of why Indian international students shy away from home institutions for Master’s programs
Authors: Chanda Ruby S. , Pawar Sanjay Krishnapratap 
Published: September 2024

PurposeIn 2021, more than half a million Indian students traveled abroad to pursue Master’s programs. Against this background, we explore why Indian students do not enroll in Master’s programs in Indian higher education (IHE) institutions.Design/methodology/approachSemi-structured, in-depth online interviews of 30 Indian international students pursuing post-graduation studies in four major host countries were conducted to elicit the required information. The interviews were recorded, transcribed and analyzed using a thematic approach. The attribution theory was used as a theoretical lens to discuss the findings.FindingsThe results indicate that the primary reasons for students not choosing Indian institutions are wide-ranging. The need to study abroad, decision influencers and why they did not consider IHE institutes were three significant categories encompassing nine themes. The study revealed that besides other factors, the rigor of admission in premier Indian universities is much higher when compared with other international universities. Also, the perceived rate of return in investing in those developed countries' universities is better when compared with those of premier Indian universities.Practical implicationsThe insights will act as marketing intelligence for supporting the business and university administrators of Indian universities in formulating effective tactics to admit more students from this in-demand Indian subgroup.Originality/valueMost of the existing research papers discuss the motivation and challenges of Indian international students for studying abroad, There is negligible research on their demotivation to join IHE institutions. The present study tries to focus on the aspects that most of them considered but did not join IHE. Also, the attribution theory is a new perspective for understanding their behavior in selecting higher education institutions.
ESG performance and financial distress during COVID-19: the moderating effects of innovation and capital intensity
Authors: Binesh Fatemeh (Nasim) , E-Vahdati Sahar , Ozdemir Ozgur 
Published: September 2024

PurposeThis study examines the relationship between Environmental, Social and Governance (ESG) practices and financial distress in times of uncertainty.Design/methodology/approachThomson Reuters ESG database, Compustat and Center for Research in Security Prices (CRSP) were used to derive a final sample size of 1,572 firms and 11,618 firm-year observations from 2003 to 2022. Fixed-effects regression was used to analyze the data.FindingsIt was found that increasing ESG involvement leads to an increase in Z score (i.e. lower financial distress), and this impact was more profound during the COVID-19 period and also when firms' innovativeness increased. However, during the COVID-19 period, increases in capital expenditures weaken the positive effect of ESG on financial distress.Research limitations/implicationsThis study contributes to the growing body of literature on the impact of ESG performance on financial distress and the nature of this relationship during times of uncertainty such as COVID-19.Practical implicationsThis study offers insights to managers and practitioners when developing their corporate financial strategies, particularly financial distress management, showing the potential benefits of innovativeness and capital intensity during turbulent times similar to COVID-19.Originality/valueLittle knowledge exists on how ESG engagement helps weather financial distress during periods of uncertainty due to external shocks (e.g. COVID-19). This paper looks at the effect of ESG engagement on financial distress and how capital intensity and innovativeness could influence this relationship while giving fresh insights into the impact of COVID-19.
Fast payment, credit and bank diversification: the impact of Pix adoption on the local credit market structure
Authors: Gomes Adriana , Silva Thiago Christiano 
Published: September 2024

PurposeIn this article, the research objective is to empirically investigate the effect of the adoption of the Brazilian instant payment system, Pix, on the local credit market structure and the diversification of the banking system in Brazilian municipalities.Design/methodology/approachBy analyzing the data, in this study, we compile and align data from supervisory and public sources, covering the period from 2019 to 2022 in Brazil. As of 2014, Brazil was comprised of 5568 municipalities distributed across five regions: North (450 municipalities), Northeast (1792), Midwest (467), Southeast (1668) and South (1191), according to the Brazilian Institute of Geography and Statistics (IBGE). Our analysis relies on the volume and quantity of Pix to the outstanding credit operations in Brazil.FindingsThis article provides evidence that the widespread adoption of Pix has impacted the financial structure of municipalities. This analysis of banking concentration in the country and municipalities, based on banking relationships, helped us assess whether the adoption of Pix had any correlation with the increase in credit lines. Overall, the results from the statistical tables suggest that the adoption of Pix may be having a positive impact on the local credit market structure.Originality/valueThe originality contribution of the study is to initiate an investigation into the impact of this instant payment system, Pix, on the Brazilian reality. Pix was launched in 2020, amid the COVID-19 pandemic, and had significant numbers, such as over 61% of the adult population having at least one Pix key registered in a little over a year; about 100 million people made at least one payment with Pix; and more than 1.4 billion transactions per month, with 72% between individuals, as presented by the REB 2021.