bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sphingobacterium tenebrionis sp. nov., isolated from intestine of mealworm
Authors: Zhang Chengsong , Zhang Guoqiang , Chen Yuexing , Zheng Shanmin , Du Jieke , Zhao Zhiyi , Zhao Yushuo , Wang Ning , Chen Cheng , Gao Zhengquan , Li Shengying , Liu Kun 
Published: July 2024

A bacterial strain designated PU5-4T was isolated from the mealworm (the larvae of Tenebrio molitor) intestines. It was identified to be Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Strain PU5-4T was observed to grow at 10–40 °C, at pH 7.0–10.0, and in the presence of 0–3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PU5-4T should be assigned to the genus Sphingobacterium. The 16S rRNA gene sequence similarity analysis showed that strain PU5-4T was closely related to the type strains of Sphingobacterium lactis DSM 22361T (98.49 %), Sphingobacterium endophyticum NYYP31T (98.11 %), Sphingobacterium soli NCCP 698T (97.69 %) and Sphingobacterium olei HAL-9T (95.73 %). The predominant isoprenoid quinone is MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 03-OH and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 9 (iso-C17 : 0
ω9c). The polar lipids are phosphatidylethanolamine, one unidentified phospholipid, and six unidentified lipids. The genomic DNA G+C content of strain PU5-4T is 40.24 mol%. The average nucleotide identity of strain PU5-4T exhibited respective values of 73.88, 73.37, 73.36 and 70.84 % comparing to the type strains of S. lactis DSM 22361T, S. soli NCCP 698T, S. endophyticum NYYP31T and S. olei HAL-9T, which are below the cut-off level (95–96 %) for species delineation. Based on the above results, strain PU5-4T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium temoinsis sp. nov. is proposed. The type strain is PU5-4T (=CGMCC 1.61908T=JCM 36663T).
Enhancing sleep via rocking ameliorates motor behavior and reduces beta-amyloid levels in a mouse model of Alzheimer’s disease
Authors: Zhang Luyan , Santoni Letizia , Ngo Nam Anh , Simayi Reyila , Ficiará Eleonora , de Vivo Luisa , Bellesi Michele 
Published: July 2024

AbstractAlzheimer’s disease (AD) is a progressive neurodegenerative disorder associated with cognitive decline and characterized by beta-amyloid plaque and tau tangle pathology. Recent research indicates a bidirectional relationship between AD pathology and sleep disturbances, with disrupted sleep exacerbating AD progression through increased beta-amyloid and tau accumulation. This strongly indicates that improving sleep may exert a direct protective effect on preventing the accumulation and spreading of AD pathology, and possibly slow the cognitive decline.Here we investigated the effects of enhancing sleep via vestibular stimulation (rocking) on AD progression in a 3xTg mouse model. Over a four-month period starting in early adulthood (p60), we monitored sleep patterns, motor function, memory, and AD pathology. Twelve-hour rocking during the light period significantly increased non-rapid eye movement (NREM) sleep duration in mice, although this effect diminished over time due to habituation. Despite this, rocking attenuated motor function decline and reduced beta-amyloid levels in the cerebral cortex of treated mice. No noticeable changes in tau levels were observed following sleep enhancement.In conclusion, our findings highlight the potential of non-pharmacological methods to enhance NREM sleep and modify disease trajectory in AD models, emphasizing the critical role of sleep in neuroprotection.
CompactTree: A lightweight header-only C++ library for ultra-large phylogenetics
Authors: Moshiri Niema 
Published: July 2024

AbstractMotivationThe study of viral and bacterial species requires the ability to load and traverse ultra-large phylogenies with tens of millions of tips, but existing tree libraries struggle to scale to these sizes.ResultsWe introduce CompactTree, a lightweight header-only C++ library for traversing ultra-large trees that can be easily incorporated into other tools, and we show that it is orders of magnitude faster and requires orders of magnitude less memory than existing tree packages.AvailabilityCompactTree can be accessed at:https://github.com/niemasd/CompactTreeContactniema@ucsd.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Butyrate as a growth factor ofClostridium acetobutylicum
Authors: Seo Hyeongmin , Capece Sofia H. , Hill John D. , Otten Jonathan K. , Papoutsakis Eleftherios T. 
Published: July 2024

AbstractThe butyrate biosynthetic pathway not only contributes to electron management and energy generation in butyrate forming bacteria, but also confers evolutionary advantages to the host by inhibiting the growth of surrounding butyrate-sensitive microbes. Proteomic data suggest that butyrate may lead to lysine butyrylation, a lesser-known post-translational modification, which might affect enzyme catalysis and thus cellular metabolism. Although high levels of butyrate induce toxic stress responses, it is not known if butyrate at non-toxic levels influences cellular processes such as growth, health, metabolism, and sporulation. Here, we show that butyrate stimulates cellular processes ofClostridium acetobutylicum, a model butyrate forming Firmicute. First, we deleted the 3-hydroxybutyryl-CoA dehydrogenase gene (hbd) from theC. acetobutylicumchromosome in order to eliminate the butyrate synthetic pathway and thus butyrate formation. For rapid genome engineering, a xylose inducible Cas9 cassette was chromosomally integrated and utilized for the one-step markerless gene deletions. The addition of non-toxic levels of butyrate revealed that butyrate has a profound effect on the growth, health, and sporulation ofC. acetobutylicum. By further deletingspo0A, the gene of the master regulator of sporulation, and followed by butyrate addition experiments, we conclude that butyrate affects cellular metabolism through both Spo0A dependent and independent mechanisms. We also deleted thehbdgene from the chromosome of the asporogenousC. acetobutylicumM5 strain lacking the pSOL1 plasmid to examine the potential involvement of pSOL1 genes on the observed butyrate effects. Addition of the precursor of butyrate biosynthesis crotonate to thehbddeficient M5 strain was used to probe the role of butyrate biosynthesis pathway in electron and metabolic fluxes. Finally, we found that butyrate addition can enhance the growth of the non-butyrate formingClostridium saccharolyticum. Our data suggest that butyrate functions as a stimulator of cellular processes, like a growth factor, inC. acetobutylicumand otherClostridiumorganisms, and may thus be as a modulator of microbial population dynamics.HighlightsDeployed chromosomally integrated spCas9 for markerless one-stepClostridium acetobutylicumgenome engineering.Deleted 3-hydroxybutyryl-CoA dehydrogenase gene (hbd) fromClostridium acetobutylicumto elucidate the roles of butyrate in cellular processes.Demonstrated butyrate as a growth factor stimulating cellular processes inClostridium acetobutylicumand potentially otherClostridiumspecies.Suggested butyrate as a potential modulator of microbial population based on different responses of microbes against butyrate.
Peptide Coated Polycaprolactone-Benzalkonium Chloride Nanocapsules for Targeted Drug Delivery to the Pancreatic β-Cell
Authors: Collins Jillian , Barra Jessie M. , Holcomb Kiefer , Ocampo Andres , Fremin Ashton , Akolade Jubril , Kratz Austin , Hays Julianna K. , Shilleh Ali , Hodson David J. , Broichhagen Johannes , Russ Holger A. , Farnsworth Nikki L. 
Published: July 2024

ABSTRACTTargeting of current therapies to treat or prevent loss of pancreatic islet β-cells in Type 1 Diabetes (T1D) may provide improved efficacy and reduce off target effects. Current efforts to target the β-cell are limited by a lack of β-cell specific targets and the inability to test multiple targeting moieties with the same delivery vehicle. Here we fabricate a novel tailorable polycaprolactone nanocapsule (NC) where multiple different targeting peptides can be interchangeably attached for β-cell specific delivery. Incorporation of a cationic surfactant in the NC shell allows for the attachment of Exendin-4 and an antibody for ectonucleoside triphosphate diphosphohydrolase 3 (ENTPD3) for β-cell specific targeting. The average NC size ranges from 250-300nm with a polydispersity index under 0.2. The NCs are non-toxic, stable in media culture, and can be lyophilized and reconstituted. NCs coated with targeting peptide were taken up by human cadaveric islet β-cells and human stem cell-derived β-like cells (sBC)in vitrowith a high level of specificity. Furthermore, NCs successfully delivered both hydrophobic and hydrophilic cargo to human β-cells. Finally, Exendin-4 coated NCs were stable and targeted the mouse pancreatic islet β-cellin vivo. Our unique NC design allows for the interchangeable coating of targeting peptides for future screening of targets with improved cell specificity. The ability to target and deliver thera-peutics to human pancreatic β-cells opens avenues for improved therapies and treatments to help the delay onset, prevent, or reverse T1D.
Visual field asymmetries in responses to ON and OFF pathway biasing stimuli
Authors: Scott Martin T.W. , Yakovleva Alexandra , Norcia Anthony Matthew 
Published: July 2024

AbstractRecent reports suggest the ON and OFF pathways are differentially susceptible to selective vision loss in glaucoma. Thus, perimetric assessment of ON- and OFF-pathway function may serve as a useful diagnostic. However, this necessitates a developed understanding of normal ON/OFF pathway function around the visual field and as a function of input intensity. Here, using electroencephalography, we measured ON- and OFF-pathway biased contrast response functions in the upper and lower visual fields. Using the steady-state visually evoked potential paradigm, we flickered achromatic luminance probes according to a saw-tooth waveform, the fast-phase of which biased responses towards the ON or OFF pathways. Neural responses from the upper and lower visual fields were simultaneously measured using frequency tagging - probes in the upper visual field modulated at 3.75Hz, while those in the lower visual field modulated at 3Hz. We find that responses to OFF/decrements are larger than ON/increments, especially in the lower visual field. In the lower visual field, both ON and OFF responses were well described by a sigmoidal non-linearity. In the upper visual field, the ON pathway function was very similar to that of the lower, but the OFF pathway function showed reduced saturation and more cross-subject variability. Overall, this demonstrates that the relationship between the ON and OFF pathways depends on the visual field location and contrast level, potentially reflective of natural scene statistics.
TheBordetellaeffector protein BteA induces host cell death by disruption of calcium homeostasis
Authors: Zmuda Martin , Sedlackova Eliska , Pravdova Barbora , Cizkova Monika , Cerny Ondrej , Allsop Tania Romero , Grousl Tomas , Malcova Ivana , Kamanova Jana 
Published: July 2024

AbstractBordetella pertussisis the causative agent of whooping cough in humans, a disease that has recently experienced a resurgence. In contrast,Bordetella bronchisepticainfects the respiratory tract of various mammalian species, causing a range of symptoms from asymptomatic chronic carriage to acute illness. Both pathogens utilize type III secretion system (T3SS) to deliver the effector protein BteA into host cells. Once injected, BteA triggers a cascade of events leading to caspase 1-independent necrosis through a mechanism that remains incompletely understood. We demonstrate that BteA-induced cell death is characterized by the fragmentation of the cellular endoplasmic reticulum and mitochondria, the formation of necrotic balloon-like protrusions, and plasma membrane permeabilization. Importantly, genome-wide CRISPR-Cas9 screen targeting 19,050 genes failed to identify any host factors required for BteA cytotoxicity, suggesting that BteA does not require a single nonessential host factor for its cytotoxicity. We further reveal that BteA triggers rapid and sustained influx of calcium ions, which is associated with organelle fragmentation and plasma membrane permeabilization. The sustained elevation of cytosolic Ca2+levels results in mitochondrial calcium overload, mitochondrial swelling, cristolysis, and loss of mitochondrial membrane potential. Inhibition of calcium channels with 2-APB delays both the Ca2+influx and BteA-induced cell death. Our findings indicate that BteA exploits essential host processes and/or redundant pathways to disrupt calcium homeostasis and mitochondrial function, ultimately leading to host cell death.ImportanceThe respiratory pathogens,Bordetella pertussisandBordetella bronchiseptica, exhibit cytotoxicity towards a variety of mammalian cells, which depends on the type III secretion effector BteA. Moreover, the increased virulence ofB. bronchisepticais associated with enhanced expression of T3SS and BteA effector. However, the molecular mechanism underlying BteA cytotoxicity is elusive. In this study, we performed a CRISPR-Cas9 screen, revealing that BteA-induced cell death depends on essential or redundant host processes. Additionally, we demonstrate that BteA disrupts calcium homeostasis, which leads to mitochondrial dysfunction and cell death. These findings contribute to closing the gap in our understanding of the signaling cascades targeted by BteA.
Prevalence of bias attributable to composite outcome in clinical trials: a systematic review
Authors: Silva José Mário Nunes da , Conceição Juliana Ferreira Souza , Ramírez Paula C. , Diaz-León Christian Leonardo , Diaz-Quijano Fredi Alexander 
Published: July 2024

AbstractObjectiveTo investigate the prevalence of bias attributable to composite outcome (BACO) in clinical trials.Study design and settingWe searched PubMed for randomized clinical trials where the primary outcome was a binary composite that included all-cause mortality among its components from January 1, 2019, to December 31, 2020. For each trial, the BACO index was calculated to assess the correspondence between effects on the composite outcome and that on mortality. This systematic review was registered in PROSPERO (CRD42021229554).ResultsAfter screening 1,076 citations and 171 full-text articles, 91 studies were included from 13 different medical areas. The prevalence of significant or suggestive BACO among the 91 included articles was 25.2% (n=23), including 12 with p<0.005 and 11 with p between 0.005 and <0.05. We observed that in 17 (73.9%) of these 23 studies, the BACO index value was between zero and <1, indicating an underestimation of the effect. The other six studies showed negative values (26.1%), indicating an inversion of the association with mortality. None of the studies showed significant overestimation of the association attributable to the composite outcome.ConclusionThese findings highlight the need to predefine guidelines for interpreting effects on composite endpoints based on objective criteria such as the BACO index.What is new?Key FindingsThe study found that 25.2% of the included clinical trials exhibited significant or suggestive bias attributable to composite outcomes (BACO).In 73.9% of these cases, the BACO index was less than 1, indicating an underestimation of the effect. 26.1% of the studies showed an inversion of the association with mortality.No significant overestimation of the association due to composite outcomes was observed.What This Adds to What Was Known?This study contributes to the existing knowledge by quantifying the prevalence of bias attributable to composite outcomes in clinical trials.It highlights that a significant proportion of trials may underestimate the effect or even show an inversion of the association with mortality when composite outcomes are used.This finding emphasizes the need for careful consideration and objective criteria, like the BACO index, in the design and interpretation of clinical trials involving composite outcomes.What Is the Implication and What Should Change Now?Researchers and clinicians should be cautious about relying solely on composite outcomes without assessing the potential biases they introduce.The study suggests a need for predefined guidelines and objective criteria, such as the BACO index, for interpreting the effects of composite outcomes.
Branched actin networks in innate immune cells mediate host microbiota homeostasis
Authors: Vasconcellos Luiz Ricardo C. , Huang Shaina Chor Mei , Suarez-Bonnet Alejandro , Priestnall Simon , Varsani-Brown Sunita , Winder Matthew L. , Shah Kathleen , Kogata Naoko , Stockinger Brigitta , Way Michael 
Published: July 2024

AbstractAssembly of branched actin networks, driven by the Arp2/3 complex are essential for the function and integrity of the immune system. Patients with loss-of-function mutations in the ARPC5 subunit of the Arp2/3 complex develop inflammation and immunodeficiency after birth, leading to early mortality. However, the mechanistic basis for these phenotypes remains obscure. Here we demonstrate that loss of Arpc5 in the murine hematopoietic system, but not the corresponding Arpc5l isoform causes early-onset intestinal inflammation. This condition is initiated by microbiota breaching the ileal mucosa, leading to local and systemic inflammation. Macrophage and neutrophils infiltrate into the ileum, but in the absence of Arpc5 fail to restrict microbial invasion. Loss of Arpc5 compromises the ability of macrophages to phagocytose and kill intra-cellular bacteria. Our results underscore the indispensable role of Arpc5, but not Arpc5l containing Arp2/3 complexes in mononuclear phagocytes function and host-microbiota homeostasis.One-Sentence SummaryArpc5 containing Arp2/3 complexes are essential for host-microbiota homeostasis
Longitudinal analysis of production process variability: an organizational information processing theory perspective
Authors: Karbasi Ata , Mahdikhani Maryam , Gerschberger Melanie , Aghaie Sina 
Published: July 2024

PurposeThis study applies organizational information processing theory (OIPT) to investigate managing production process variability in uncertain environments using information technology (IT) capabilities.Design/methodology/approachWe conduct an empirical analysis using the three-stage least squares (3SLS) technique on 1,612 manufacturing firms over ten years.FindingsThe findings show that IT capability plays a dual role: it reduces the positive impact of environmental uncertainty on production process variability and mitigates the negative relationship between production process variability and operational performance.Practical implicationsOur findings suggest that managers should focus on reducing production process variability by strengthening their firms' IT capabilities. This is particularly crucial in volatile environments where external uncertainties can significantly impact operational processes.Originality/valueVariability in the production process is a significant source of inefficiency and disruption within business processes. Using OIPT, our study contributes to the field by empirically analyzing the role of IT capabilities in reducing production process variability under environmental uncertainty.
The influence of brands’ internationalization degree on consumers’ attitudes toward cross-border philanthropy: based on theory of legitimacy
Authors: Tong Zelin , Liu Huilin , Liu Diyi , Zhou Ling 
Published: July 2024

Purpose
This study aims to explore how brands’ degree of internationalization influences consumers’ attitudes toward brands’ engagement in cross-border philanthropy by taking legitimacy as a mediating mechanism. The authors further investigate the moderating role of cause acuteness in this effect to identify practical strategies for managers.

Design/methodology/approach
The hypotheses are tested via laboratory experiments. In brief, Study 1 investigates the relationship between a brand’s degree of internationalization and perceived legitimacy for corporate cross-border philanthropy and the impact of internationalization on consumers’ brand evaluations of such philanthropy. Study 2 addresses the moderating role of cause acuteness.

Findings
The authors discover that companies with a high (vs low) degree of internationalization gained more legitimacy, and thus better brand evaluations, upon engaging in corporate cross-border philanthropy. This effect reverses when the causes are related to sudden disasters rather than ongoing tragedies.

Practical implications
This study provides valuable guidance for marketers seeking to leverage cross-border philanthropy to enhance consumers’ brand attitudes. Specifically, brands’ degree of internationalization should be consistent when performing cross-border philanthropy. Otherwise, brands will struggle to gain legitimacy and will earn less favorable consumer evaluations.

Originality/value
This work enriches the literature on corporate social responsibility in the domain of cross-border philanthropy and elucidates consumers’ attitudes toward this type of philanthropy in a corporate context. This study also meaningfully contributes to research on brands’ internationalization and legitimacy.
Disaster risk reduction in the wicked problems framework
Authors: Kasdan David Oliver 
Published: July 2024

PurposeApplying the wicked problems framework to disaster risk reduction makes for a more appropriate understanding of the modern challenges of mitigation that may inform better strategies and communications.Design/methodology/approachThis research employs a literature review of wicked problems to posit a theoretical application of the concept to disaster risk reduction in the format of a reflective examination and argument with reasoned lessons for policy and governance.FindingsThere is a broad body of research that informs the application of the wicked problems framework to improve disaster risk reduction. Understanding the value of rationality, complexity, clumsy solutions, and inter-disciplinary approaches for risk scenarios helps to frame and communicate a realistic perspective of disaster risk reduction objectives.Practical implicationsRecognizing the various modes of response to the wicked problem of disaster risk reduction can help construct more comprehensive, inclusive, and effective approaches for continuous improvement.Social implicationsUnderstanding disaster risk as a wicked problem broadens the base for mitigation efforts by promoting more inclusion and perspectives from all segments of society.Originality/valueWicked problems have been loosely referenced in disaster management research, but there is a lack of theoretical foundation for the concept applied to disaster risk reduction and extension into practical policy.