bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maximum vertical height during wing flapping of laying hens captured with a depth camera
Authors: Grebey Tessa , Bongiorno Valentina , Han Junjie , Steibel Juan , Siegford Janice M. 
Published: October 2024

AbstractCage-free housing systems for laying hens, and their accompanying guidelines, legislation, and audits, are becoming more common around the world. Cage-free regulations often specify requirements for floor space and cage height, but the availability of three-dimensional space can vary depending on system configurations. Little research has looked at how much vertical space a hen occupies while flapping her wings, which is arguably her most space-intensive behavior. Therefore, the objective of this study was to use a depth sensing camera to measure the maximum vertical height hens reach when wing flapping without physical obstructions. Twenty-eight individually caged Hy-line W36 hens at 45 weeks of age were evaluated. A ceiling-mounted depth camera was centered above a test pen and calibrated prior to collecting data. During testing, one hen at a time was placed in the test pen and recorded flapping her wings. From depth footage, the minimum distance between pixels was obtained for each frame, and we computed the maximum vertical height reached by each hen. Results for vertical space used during a wing flapping event showed that hens reached a maximum height of 51.0 ± 4.7 cm. No physical measures correlated with maximum height obtained from the depth camera (P>0.05). Hens in this study were from a single strain, were old enough to have keel damage, and were cage-reared and housed, preventing us from generalizing the results too far. However, depth cameras provide a useful approach to measure how much space laying hens of varying strains, ages, and rearing/housing methods need to perform dynamic behaviors.
A noncanonical glycoprotein H complex enhances cytomegalovirus entry
Authors: Norris Michael J. , Henderson Lauren A. , Siddiquey Mohammed N.A. , Yin Jieyun , Yoo Kwangsun , Brunel Simon , Saphire Erica Ollmann , Benedict Chris A. , Kamil Jeremy P. 
Published: October 2024

SUMMARYHuman cytomegalovirus (HCMV) causes severe birth defects, lifelong health complications, and $4 billion in annual costs in the United States alone. A major challenge in vaccine design is the incomplete understanding of the diverse protein complexes the virus uses to infect cells. InHerpesviridae, the gH/gL glycoprotein heterodimer is expected to be a basal element of virion cell entry machinery. For HCMV, gH/gL forms a “trimer” with gO and a “pentamer” with UL128, UL130, and UL131A, with each complex binding distinct receptors to enter varied cell types. Here, we reveal a third glycoprotein complex, abundant in HCMV virions, which significantly enhances infection of endothelial cells. In this “3-mer” complex, gH, without gL, associates with UL116 and UL141, an immunoevasin previously known to function in an intracellular role. Cryo-EM reveals the virion-surface 3-mer is structurally unique amongHerpesviridaegH complexes, with gH-only scaffolding, UL141-mediated dimerization and a heavily glycosylated UL116 cap. Given that antibodies directed at gH and UL141 each can restrict HCMV replication, our work highlights this virion surface complex as a new target for vaccines and antiviral therapies.
The food grade bacteriumLactobacillus helveticus VEL12193promotes autophagy by releasing membrane vesicles
Authors: Bringer Marie-Agnès , Al Azzaz Jana , Buteau Bénédicte , Proukhnitzky Lil , Aumeunier Amaury , Manceau Simon , Bermúdez-Humarán Luis G. , Florian Chain F , Daniel Catherine , Jacquin Elise , Acar Niyazi , Rieu Aurélie , Lapaquette Pierre 
Published: October 2024

AbstractAutophagy-related processes, including canonical macroautophagy, are crucial for maintaining cellular homeostasis in eukaryotic organisms. Alterations or reduced activity of these processes have been strongly linked to a broad range of human diseases including inflammatory bowel disease (IBD) and age-related diseases such as age-related macular degeneration - a disease that affect the central area of the retina. In contrast, long-term autophagy stimulation appears to be safe and to extend lifespan in model organisms such as mice. Thus, enhancing autophagy represents a promising strategy for promoting healthy aging. Several studies indicate that the gut microbiota can influence host autophagy at the gut mucosa but also in peripheral organs, and some microbial metabolites have been identified as autophagy modulators. In this study, we studied the capacity of bacterial species commonly used in food fermentation (ferments) or health (probiotics) to modulate host autophagy byin vitroandin vivoapproaches.In vitroscreening of a library of 11 bacterial strains revealed a strain-dependent ability of lactobacilli and bifidobacteria to stimulate autophagy in human epithelial cells. TheLactobacillus helveticusstrain VEL12193, isolated from cheese, emerged as the most effective inducer of autophagy.In vivoexperiment using mice showed that long-term dietary supplementation withL. helveticusVEL12193 was associated with stimulation of autophagy in the gut mucosa and retina. We identifiedL. helveticus-derived membrane vesicles (MVs) as a bacterial component involved in bacterial-induced autophagy in epithelial and immune cells. Moreover,in vitro, we demonstrated thatL. helveticusVEL12193 possesses immunomodulatory properties in macrophages, as well as in the gut mucosa of a preclinical mouse model of IBD. With this study we provide robust proof of concept that ferments/probiotics can stimulate autophagy at the organism scale and that this phenotype involved MVs. In addition, we identifyL. helveticusVEL12193 as a candidate strain of interest for the design of healthy-aging strategies.
In vitroactivity of hydroxychloroquine in combination with antibiotics against intracellular uropathogenicEscherichia coli
Authors: Pargny V. , Vautrin N. , Ribet D. , Minlong O. , Caron F. , Pestel-Caron M. , Alexandre K. 
Published: October 2024

AbstractBackgroundTwo pathophysiological concepts may explain recurrent UTI: a reinfection by a bacterial strain from the digestive microbiota or a relapse fromEscherichia colipersisting within the superficial urothelial cells as intracellular bacterial communities (IBC). Hydroxychloroquine (HCQ)-antibiotic combination is effective against intracellular adherent-invasiveE. coliisolated from patients with Crohn’s disease. We hypothesized that HCQ may enhanced antibiotic efficacy againstE. coliIBC.MethodsUTI89 reference strain and two clinicalE. colistrains forming IBCs (VITALE#2157, VITALE#2206) were used in this study. MIC, MBC and time killing curves (4xMIC) were performed for AZYTHROMYCIN (AZT), CIPROFLOXACIN (CIP), DOXYCYCLINE (DC), FOSFMOMYCIN (FF) and HCQ.In vitroactivity of antibiotics alone and combined with HCQ was evaluated on intracellular bacterial survival assay using a model of urothelium cells (HTB-9).ResultsTime-killing curves showed that CIP has a bactericidal activity at H6 (-4.6 log10CFU/mL) with regrowth at H24 against 2157, and a bactericidal activity at H6 without regrowth at H24 against 2206 (-3.3 log10CFU/mL) and UTI89 (-3.4 log10CFU/mL); DC, AZT and FF demonstrated bacteriostatic activity at H24 regardless of the strain. We observed a significant decrease in the number of intracellular bacteria at H42 with CIP (-1.83 log10/ 106cells). DC, FF, and AZT exposure did not reduce IBC formation at H42 (P>0.05). IBC formation after HCQ-antibiotic combination exposure was not significantly different (P>0.05) from antibiotic exposure alone, regardless of the antibiotic or strain studied.ConclusionsIn conclusion, HCQ exposure does not enhance antibiotics activity against intracellular uropathogenicE. coli.HighlightsUsing anin vitromodel of superficial urothelium monolayer, we observed a significant decrease in intracellular uropathogenicEscherichia coliin response to ciprofloxacin exposure.Hydroxychloroquine exposure does not enhance antibiotics activity against intracellular uropathogenicEscherichia coli.
A family of Tn7-like transposons evolved to target CRISPR repeats
Authors: Chacon Machado Laura , Peters Joseph E. 
Published: October 2024

AbstractTn7 family transposons are mobile genetic elements known for precise target site selection, with some co-opting CRISPR-Cas systems for RNA-guided transposition. We identified a novel group of Tn7-like transposons in Cyanobacteria that preferentially target CRISPR arrays, suggesting a new functional interaction between these elements and CRISPR-Cas systems. Using bioinformatics tools, we characterized their phylogeny, target specificity, and sub-specialization. The array-targeting elements are phylogenetically close to tRNA-targeting elements. The distinct target preference coincides with loss of a C-terminal region in the TnsD protein which is responsible for recognizing target sites when compared to closely related elements. Notably, elements are found integrated into a fixed position within CRISPR spacer regions, a behavior that might minimize negative impacts on the host defense system. These transposons were identified in both plasmid and genomic CRISPR arrays, indicating that their preferred target provides a means for both safe insertion in the host chromosome and a mechanism for dissemination. Attempts to reconstitute these elements inE. coliwere unsuccessful, indicating possible dependence on native host factors. Our findings expand the diversity of interactions between Tn7-like transposons and CRISPR systems.
Surfactin acceleratesBacillus subtilispellicle biofilm development
Authors: Stannius Rune Overlund , Fusco Sarah , Cowled Michael , Kovács Ákos T. 
Published: October 2024

AbstractSurfactin is a biosurfactant produced by manyB. subtilisstrains with a wide variety of functions from lowering surface tension to allowing motility of bacterial swarms, acting as a signaling molecule, and even exhibiting antimicrobial activities. However, the impact of surfactin during biofilm formation has been debated with variable findings between studies depending on the experimental conditions.B. subtilisis known to form biofilms at the solid-air, the solid-medium, and the liquid-air interfaces, the latter of which is known as a pellicle biofilm. Pellicle formation is a complex process requiring coordinated movement to the liquid-air interface and subsequent cooperative production of biofilm matrix components to allow robust pellicle biofilm formation. This makes pellicle formation a promising model system for assaying factors in biofilm formation and regulation.Here, we assayed the influence of surfactin and additional metabolites on the timing of pellicle biofilm formation. Using of time-lapse imaging, we assayed pellicle formation timing in 12B. subtilisisolates and found that one, MB9_B4, was significantly delayed in pellicle formation by approximately 10 hours. MB9_B4 was previously noted to lack robust surfactin production. Indeed, deletion of surfactin synthesis in the other isolates delayed pellicle formation. Further, pellicle delay was rescued by addition of exogeneous surfactin and spent media from mature pellicles. Testing reporters of biofilm-related gene expression revealed that induction of pellicle formation was caused by a combination of increased gene expression of one of the biofilm components and promotion of growth. Intriguingly, spent media of surfactin mutant strains were also able to stimulate pellicle formation, indicating possible additional metabolites also influence the timing of pellicle development.
Independent control of neurogenesis and dorsoventral patterning by NKX2-2
Authors: Jang Sumin , Abarinov Elena , Dobkin Julie , Wichterle Hynek 
Published: October 2024

SUMMARYHuman neurogenesis is disproportionately protracted, lasting >10 times longer than in mouse, allowing neural progenitors to undergo more rounds of self-renewing cell divisions and generate larger neuronal populations. In the human spinal cord, expansion of the motor neuron lineage is achieved through a newly evolved progenitor domain called vpMN (ventral motor neuron progenitor) that uniquely extends and expands motor neurogenesis. This behavior of vpMNs is controlled by transcription factor NKX2-2, which in vpMNs is co-expressed with classical motor neuron progenitor (pMN) marker OLIG2. In this study, we sought to determine the molecular basis of NKX2-2-mediated extension and expansion of motor neurogenesis. We found that NKX2-2 represses proneural geneNEUROG2by two distinct, Notch-independent mechanisms that are respectively apparent in rodent and human spinal progenitors: in rodents (and chick), NKX2-2 repressesOlig2and the motor neuron lineage through its tinman domain, leading to loss ofNeurog2expression. In human vpMNs, however, NKX2-2 repressesNEUROG2but notOLIG2, thereby allowing motor neurogenesis to proceed, albeit in a delayed and protracted manner. Interestingly, we found that ectopic expression of tinman-mutantNkx2-2in mouse pMNs phenocopies human vpMNs, repressingNeurog2but notOlig2, and leading to delayed and protracted motor neurogenesis. Our studies identify a Notch- and tinman-independent mode ofNkx2-2-mediatedNeurog2repression that is observed in human spinal progenitors, but is normally masked in rodents and chicks due toNkx2-2’s tinman-dependent repression ofOlig2.
Robust quantification of cellular mechanics using optical tweezers
Authors: Rodenburg Wessel S. , Ebben Sven F.A. , Eeftens Jorine M. 
Published: October 2024

AbstractMechanical properties of cells are closely related to function and play a crucial role in many cellular processes, including migration, differentiation, and cell fate determination. Numerous methods have been developed to assess cell mechanics under various conditions, but they often lack accuracy on biologically relevant piconewton-range forces, or have limited control over the applied force. Here, we use optically-trapped polystyrene beads to accurately apply piconewton-range forces to adherent and suspended cells. We precisely apply a constant force to cells by means of a force-feedback system, allowing for quantification of deformation, cell stiffness and creep response from a single measurement. Using drug-induced perturbations of the cytoskeleton, we show that this approach is sensitive to detecting changes in cellular mechanical properties. Collectively, we provide a framework for using optical tweezers to apply highly accurate forces to adherent and suspended cells, and describe straightforward metrics to quantify cellular mechanical properties.
From data silos to seamless integration and coordination: a data-asset centric approach to smart hospital facility management
Authors: Li Lingzhi , Jiang Shilong , Yuan Jingfeng , Zhang Lei , Xu Xiaoxiao , Wang Jing , Zhou Yilun , Li Yunlong , Xu Jin 
Published: October 2024

PurposeExisting hospital building operations involve numerous information technology applications and complex building systems; therefore, an intelligent facility management (FM) platform is required to ensure their continuous operation. To address the persistent issues of data silos, inefficient data interoperability, and workflow incoordination that have been identified in the current body of FM practice and literature, the present study develops a data-asset (DA) centric FM platform specifically designed for hospital buildings.Design/methodology/approachThis study proposes a semi-customized approach to develop the DA-centric FM platform for hospital buildings. To elucidate the precise function requirements of the hospital FM platform, focus group interviews are employed. By seamlessly integrating the as-built BIM model, IoT sensor data and FM workflow data, the BIM-based DA model with a data transfer mechanism is developed. The development of the FM platform with function modules in a case study is guided by a five-tier architecture and the coordination theory (CT). The case study provides an in-depth introduction to the applications of DA management, space management and maintenance management modules.FindingsThe capabilities of the developed DA-centric hospital FM platform are validated through the case application and user satisfaction survey, which assess data quality, automation level, operation efficiency, flexibility and functionality. For hospital FM activities, this DA-centric FM platform realizes data integration and seamless transformation, optimizes workflow coordination and enhances operation performance.Originality/valueThe initial scholarly contribution is the establishment of the BIM-based DA model, which serves as the data middle platform for continuous data integration, transmission and sharing within the FM platform. Subsequently, under the guidance of the CT, the business process of function modules is designed, improving the intra-module and inter-module workflow coordination. The developed DA-centric FM system along with its performance benchmarking application, assists facility managers and decision-makers in implementing smart operations for hospital buildings and achieving the management goals of safety, efficiency, energy savings and convenience.
Relational antecedents of sharing and not sharing knowledge: a configurational approach
Authors: Rudawska Aleksandra , Sławik Anna 
Published: October 2024

PurposeKnowledge sharing within organizations has significant benefits for group and organizational performance. This study aims to identify the combinations of individual and relational factors that influence high- and low-intensity knowledge sharing among workers using the ability-motivation-opportunities (AMO) framework.Design/methodology/approachThis research adopts a qualitative, set-theoretic approach, using fuzzy set qualitative comparative analysis (fsQCA) to analyse data collected from knowledge workers in an international corporation.FindingsOur findings show that knowledge sharing is fundamentally relational, meaning that the quality and history of interaction with co-workers affect the intensity of knowledge-sharing behaviour. All AMO dimensions prove important for sharing, although some of them can substitute one another. However, if there is a lack of ability and opportunity, employees will not share knowledge even if they are motivated by reciprocity.Practical implicationsThe results offer human resources and project management practice alternative combinations of individual and relational factors that can be used to streamline knowledge sharing, emphasizing the need to invest in building relationships among co-workers.Originality/valueThis study contributes to the literature by identifying configurations of core and peripheral conditions pertaining to abilities, motivation and opportunities that can facilitate or constrain knowledge-giving.
Do firms submit fewer tender bids with high inflation? An analysis of firms’ participation in public procurement in the EU
Authors: Klimavičiūtė Luka , Schito Marco , Barcevičius Egidijus 
Published: October 2024

Purpose
This paper aims to explore the effect of sustained high inflation on public procurement participation in the European Union, both in terms of the average number of bids submitted and in the proportion of bids by small- and medium-sized enterprises (SMEs) out of all submitted bids.

Design/methodology/approach
Regression modelling, using contract award notices in the Tender Electronics Daily database between 2018 and 2022, at quarterly intervals.

Findings
Each inflation point increase is associated with a decline in the average number of offers received per tender by 0.43%. A more marked reduction of 8.6% in the average number of offers and a decrease in 3.4 percentage points in the SME participation rate are observed for firms operating in sectors that experienced very high levels of inflation (>20% year-on-year rate of change), compared with a situation of low inflation (0–5%).

Social implications
Claims about difficulties in delivering public contracts for the set price should be taken with a grain of salt, unless businesses operate in sectors experiencing very high inflation levels. Measures to foster competition could also reduce price pressures.

Originality/value
To the best of the authors’ knowledge, this is the first study to quantitatively assess the association between high inflation and public procurement participation. Two methodological novelties are introduced: the operationalisation of sectoral-level inflation down to two-digit NACE codes, based mainly on producer prices; and a matching between two-digit NACE codes for inflation and the common procurement vocabulary codes to classify calls to bid for public contracts by economic activity.
The impact of a brief and immersive use-of-force training exercise on citizens’ attitudes toward police
Authors: Exum M. Lyn , Kuhns Joseph B. , Johnson Shelley L. , DeWitt Samuel E. 
Published: October 2024

Purpose Citizens’ attitudes toward police (ATP) have declined dramatically in recent years, prompting many agencies to implement police–community relations programs designed to build back the community’s trust. Such programs are often time-intensive, requiring many hours to complete. The current study examined the impact of a brief (approximately 15 minutes) community relations intervention on citizens’ ATP and police use of force (UoF).Design/methodology/approach A sample of 104 citizens completed three UoF training exercises (i.e., the intervention) inside a video simulator at a municipal police department. Immediately before and after the intervention, citizens’ ATP and police UoF were recorded.Findings Despite having relatively favorable impressions of police at baseline, many attitudes grew to be more favorable following the intervention, including perceptions of job difficulty and the belief that police are treated too harshly by the media. While global impressions of the police did not change, citizens came to believe that greater UoF levels were warranted in specific types of encounters, such as when a suspect tries to strike an officer.Originality/value These findings suggest that providing citizens with an opportunity to experience UoF decision-making first-hand can positively impact certain ATP and police work. Law enforcement agencies may find that such brief, immersive interventions are useful tools for improving police–community relations.
Attention mechanism‐assisted recurrent neural network for well log lithology classification
Authors: Gao Yining , Tian Miao , Grana Dario , Xu Zhaohui , Xu Huaimin 
Published: October 2024

AbstractLithology classification is a fundamental aspect of reservoir classification. Due to the limited availability of core samples, computational modelling methods for lithology classification based on indirect measurements are required. The main challenge for standard clustering methods is the complex vertical dependency of sedimentological sequences as well as the spatial coupling of well logs. Machine learning methods, such as recurrent neural networks, long short‐term memory and bidirectional long short‐term memory, can account for the spatial correlation of the measured data and the predicted model. Based on these developments, we propose a novel approach using two distinct models: a self‐attention‐assisted bidirectional long short‐term memory model and a multi‐head attention‐based bidirectional long short‐term memory model. These models consider spatial continuity and adaptively adjust the weight in each step to improve the classification using the attention mechanism. The proposed method is tested on a set of real well logs with limited training data obtained from core samples. The prediction results from the proposed models and the benchmark one are compared in terms of the accuracy of lithology classification. Additionally, the weight matrices from both attention mechanisms are visualized to elucidate the correlations between depth steps and to help analyse how these mechanisms contribute to improved prediction accuracy. The study shows that the proposed multi‐head attention‐based bidirectional long short‐term memory model improves classification, especially for thin layers.