bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans
Authors: Jurado Mariano Ruz , Tombor Lukas S , Arsalan Mani , Holubec Tomas , Emrich Fabian , Walther Thomas , Abplanalp Wesley , Fischer Ariane , Zeiher Andreas M , Schulz Marcel H , Dimmeler Stefanie , John David 
Published: April 2024

Abstract

Background
Cardiovascular research heavily relies on mouse (Mus musculus) models to study disease mechanisms and to test novel biomarkers and medications. Yet, applying these results to patients remains a major challenge and often results in noneffective drugs. Therefore, it is an open challenge of translational science to develop models with high similarities and predictive value. This requires a comparison of disease models in mice with diseased tissue derived from humans.

Results
To compare the transcriptional signatures at single-cell resolution, we implemented an integration pipeline called OrthoIntegrate, which uniquely assigns orthologs and therewith merges single-cell RNA sequencing (scRNA-seq) RNA of different species. The pipeline has been designed to be as easy to use and is fully integrable in the standard Seurat workflow.
We applied OrthoIntegrate on scRNA-seq from cardiac tissue of heart failure patients with reduced ejection fraction (HFrEF) and scRNA-seq from the mice after chronic infarction, which is a commonly used mouse model to mimic HFrEF. We discovered shared and distinct regulatory pathways between human HFrEF patients and the corresponding mouse model. Overall, 54% of genes were commonly regulated, including major changes in cardiomyocyte energy metabolism. However, several regulatory pathways (e.g., angiogenesis) were specifically regulated in humans.

Conclusions
The demonstration of unique pathways occurring in humans indicates limitations on the comparability between mice models and human HFrEF and shows that results from the mice model should be validated carefully. OrthoIntegrate is publicly accessible (https://github.com/MarianoRuzJurado/OrthoIntegrate) and can be used to integrate other large datasets to provide a general comparison of models with patient data.
The social science side of marine biodiversity monitoring
Authors: Vadrot Alice B M , Wanneau Krystel 
Published: April 2024

Abstract
Marine biodiversity monitoring is a complex task given the vast ocean areas to be covered, the types of data to be integrated, and the large number of possible parameters to consider when measuring biodiversity change. International agreements, such as the Convention on Biological Diversity (CBD) or the recently adopted ‘BBNJ treaty’protecting biodiversity beyond national jurisdiction (BBNJ), encourage states to monitor marine life both within and beyond their national waters to foster marine biodiversity conservation and sustainable use. While oceanographers in general, and marine biologists in particular, are aware of the challenges and complexities of measuring biodiversity in the ocean, the politics of marine biodiversity monitoring and the added value of social science perspectives tend to be neglected. This story from the frontline describes our experiences with turning marine biodiversity monitoring into an object of social science inquiry. The MARIPOLDATA project developed an innovative multi-sited approach to capture both the politics and practices of monitoring marine life. During our research, we were confronted with a diversity of perspectives and expectations of what monitoring is, how it works, why it should be done, and whom it should serve. By adopting a mixed-method approach and collecting data at different epistemic sites (negotiation rooms, scientific fields, laboratories, and conferences), we tried to cut through some of the observed ambiguities and trends. We conclude that studying monitoring necessitates a multidisciplinary approach and a sensitivity for the regional, institutional, and cultural specificities and inequalities that shape how we know and govern the ocean.
Left atrial function of patients with atrial fibrillation undergoing thoracoscopic hybrid ablation
Authors: van der Heijden Claudia A J , Adriaans Bouke P , van Kuijk Sander M J , Luermans Justin G L M , Chaldoupi Sevasti-Marisevi , Maessen Jos G , Bidar Elham , Maesen Bart 
Published: April 2024

Abstract

OBJECTIVES
Thoracoscopic hybrid ablation is an effective and safe rhythm control strategy for patients with complex forms of atrial fibrillation. Its effect on left atrial function has not yet been studied.

METHODS
In a retrospective single-centre analysis of patients undergoing thoracoscopic hybrid ablation, the left atrial emptying fraction was calculated using the biplane modified Simpson method in the apical 2- and 4-chamber views on transthoracic echocardiography. Left atrial strain (reservoir, conduction and contractility) was quantified using dedicated software.

RESULTS
Sixty-seven patients were included (mean age 64 years, long-standing persistent atrial fibrillation in 69%, median atrial fibrillation history duration 64 months). At baseline, left atrial function and contractility were poor. The reservoir and contractile strain improved postprocedure compared to baseline [15 (standard deviation (SD): 8) and 17 (SD: 6); P = 0.013; 3 (SD: 5) and 4 (SD: 4), P = 0.008], whereas the left atrial volume indexed to the body surface area was reduced [51 ml/m2 (SD: 14) and 47 ml/m2 (SD: 18), P = 0.0024]. In patients with preoperative (long-standing) persistent atrial fibrillation and in patients with rhythm restoration, improvements in the emptying fraction, (reservoir and contractile) strain and the left ventricular ejection fraction were observed, whereas the left atrial volume decreased (P &lt; 0.05).

CONCLUSIONS
In this cohort of patients with severely diseased left atria, improvement in left atrial contractility and in the emptying fraction after thoracoscopic hybrid ablation for atrial fibrillation in patients with persistent atrial fibrillation is mainly due to rhythm restoration. Interestingly, the procedure itself also results in improved left atrial reservoir strain and reversed left atrial remodelling by reducing left atrial volume.
Wrap-around loop pulsating heat-pipe heat exchanger for enhancing the energy efficiency of high-tech cleanroom HVAC systems
Authors: Zheng Jia-Wei , Lin Hong-Yi , Hsieh Chia-Hsing , Wu Yu-Lieh , Yang Kai-Shing 
Published: April 2024

Abstract
To maintain strict temperature, humidity, and cleanliness requirements, the cleanrooms of high-tech semiconductor fabrication plants have heating, ventilation, and air conditioning (HVAC) systems, which require substantial amounts of energy. To reduce energy consumption, this study proposes using a wrap-around loop pulsating heat pipe (WLPHP) heat exchanger comprising a pulsating heat pipe for precooling high-temperature outdoor air to reduce relative humidity. The heat absorbed by the heat-pipe evaporator is then transferred to the condenser and released, reducing the energy required to subsequently reheat the air with an HVAC system. The experimental results reveal that the system reduces the required reheating energy and increased the moisture removal rate per unit energy consumption by an average of 24.8% and 33% compared with a typical heat exchanger. Hence, using the WLPHP heat exchanger in HVAC systems could provide large energy savings.
Prevotella timonensis Bacteria Associated With Vaginal Dysbiosis Enhance Human Immunodeficiency Virus Type 1 Susceptibility Of Vaginal CD4+ T Cells
Authors: van Teijlingen Nienke H , van Smoorenburg Marleen Y , Sarrami-Forooshani Ramin , Zijlstra-Willems Esther M , van Hamme John L , Borgdorff Hanneke , van de Wijgert Janneke H H M , van Leeuwen Elisabeth , van der Post Joris A M , Strijbis Karin , Ribeiro Carla M S , Geijtenbeek Teunis B H 
Published: April 2024

Abstract
Dysbiosis of the vaginal microbiome poses a serious risk for sexual human immunodeficiency virus type 1 (HIV-1) transmission. Prevotella spp are abundant during vaginal dysbiosis and associated with enhanced HIV-1 susceptibility; however, underlying mechanisms remain unclear. Here, we investigated the direct effect of vaginal bacteria on HIV-1 susceptibility of vaginal CD4+ T cells. Notably, pre-exposure to Prevotella timonensis enhanced HIV-1 uptake by vaginal T cells, leading to increased viral fusion and enhanced virus production. Pre-exposure to antiretroviral inhibitors abolished P timonensis–enhanced infection. Our study shows that the vaginal microbiome directly affects mucosal CD4+ T-cell susceptibility, emphasizing importance of vaginal dysbiosis diagnosis and treatment.
Reviewing the evidence of antimicrobial activity of glycols
Authors: Duggan Katrina , Ijaz M Khalid , McKinney Julie , Maillard Jean-Yves 
Published: April 2024

Abstract
In the 1940s and 1950s, researchers seeking safe and novel ways to eliminate airborne pathogens from enclosed spaces, investigated glycol vapours as a method of disinfection. More recently, the COVID-19 pandemic highlighted the need for a non-toxic aerial disinfectant that can be used in the presence of people. This scoping review is intended to analyse the early and more recent literature on glycol disinfection, scrutinizing the methodologies used, and to determine if the use of glycols as modern-day disinfectants is justified
PRISMA-ScR guidelines were used to assess the 749 articles retrieved from the Web of Science platform, with 46 articles retained after the search strategy was applied. Early studies generally demonstrated good disinfection capabilities against airborne bacteria and viruses, particularly with propylene glycol (PG) vapour. Vapour pressure, relative humidity, and glycol concentration were found to be important factors affecting the efficacy of glycol vapours. Contact times depended mainly on the glycol application method (i.e. aerosolization or liquid formulation), although information on how glycol efficacy is impacted by contact time is limited. Triethylene glycol (TEG) is deemed to have low toxicity, carcinogenicity, and mutagenicity and is registered for use in air sanitization and deodorization by the US Environmental Protection Agency. Glycols are also used in liquid formulations for their antimicrobial activity against a wide range of microorganisms, although when used as a non-active excipient in products, their contribution to antimicrobial efficacy is rarely assessed. The appropriate use of liquid glycol-containing formulations was found to positively impact the antimicrobial capabilities of disinfectants when used at temperatures &lt;0, food preservatives, and dental medicaments. Providing modern delivery technology can accurately control environmental conditions, the use of aerosolized glycol formulations should lead to successful disinfection, aiding infection prevention, and control regimens.
A novel method to build knowledge graph models for the configuration and operation design of smart and connected industrial products
Authors: Yang Yuqian , Yang Maolin , Shangguan Siwei , Cao Yifan , Jiang Pingyu 
Published: April 2024

Abstract
Smart and connected industrial products (SCIPs), characterized by their capabilities of self-monitoring, environment awareness, machine–machine/machine–human communication and collaboration, intelligent decision-making, etc., have become the fundamental elements for cyber-physical systems, digital twin, industrial internet of things, etc. Configuring the components in SCIPs and modeling their interaction and operation mechanisms are important during SCIPs design. However, existing product design methods were originally developed for none smart and connected products. This could limit the accuracy of SCIP modeling during the design stage and consequently, it may cause more reworks during the implementation stage of the designed SCIPs. In this regard, a SCIP configuration and operation design method is established, including (i) meta knowledge graph (KG)-based configuration of the components in the physical system and status monitoring system of a required SCIP, (ii) event-state swimlane flowchart-based analysis of the dynamic interaction, operation, and data monitoring mechanisms among the components, and (iii) event-state KG based modeling of the overall workflow, monitoring data self-updating and intelligent operation mechanisms of the SCIP. Compared with existing SCIP design methods, the work provides a specific method for not only the configuration of the static components in customized SCIPs, but also the dynamic interaction, data acquisition/storing/transmitting, and intelligent function implementation mechanisms of the configured SCIP using a kind of event-state KG. The event-state KG is both human-readable and computer-programmable, and it can self-update according to predefined reasoning algorithms during the operation of the SCIP. The configuration and operation design modeling of a robot-based grinding processing line is used as a case study.
Harnessing regulatory networks in Actinobacteria for natural product discovery
Authors: Augustijn Hannah E , Roseboom Anna M , Medema Marnix H , van Wezel Gilles P 
Published: April 2024

Abstract

Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches.

One-Sentence Summary
This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
Hadronotus pennsylvanicus (Hymenoptera: Scelionidae): a biological control agent for pestiferous leaffooted bugs (Hemiptera: Coreidae)
Authors: Boyle Sean M , Cornelius Mary , Talamas Elijah J , Straser Robert K , Wilson Houston , Daane Kent M , Weber Donald C , Kuhar Thomas P 
Published: April 2024

Abstract
In recent decades, the egg parasitoid Hadronotus pennsylvanicus (Ashmead) has gained substantial attention as an important natural enemy of pestiferous leaffooted bug species in the genera Anasa Amyot and Serville and Leptoglossus Guérin-Méneville. Throughout its native range of North America, H. pennsylvanicus parasitizes Anasa and Leptoglossus eggs in various vegetable and orchard systems. The overreliance on broad-spectrum insecticides in these systems and the demand for effective and sustainable coreid pest management strategies have motivated researchers to consider H. pennsylvanicus as an augmentative biological control agent. The potential use of H. pennsylvanicus as a classical biological control agent has also been studied in Europe in response to the rapid spread of Leptoglossus occidentalis Heidemann, an invasive pest causing significant economic losses to the European pine nut industry. Improved understanding of H. pennsylvanicus taxonomy, life history, host range, parasitoid–host ecology, laboratory rearing, and field deployment techniques have created a robust scaffold on which to build future biological control programs. This natural enemy profile reviews the current advances in the aforementioned areas of H. pennsylvanicus research and outlines the parasitoid’s prospects as a biological control agent.
“Give Me Five”: The Case for 5 Days of Antibiotics as the Default Duration for Acute Respiratory Tract Infections
Authors: El Feghaly Rana E , Jaggi Preeti , Katz Sophie E , Poole Nicole M 
Published: April 2024

Abstract
Acute respiratory tract infections (ARTIs) account for most antibiotic prescriptions in pediatrics. Although US guidelines continue to recommend ≥10 days antibiotics for common ARTIs, evidence suggests that 5-day courses can be safe and effective. Academic imprinting seems to play a major role in the continued use of prolonged antibiotic durations. In this report, we discuss the evidence supporting short antibiotic courses for group A streptococcal pharyngitis, acute otitis media, and acute bacterial rhinosinusitis. We discuss the basis for prolonged antibiotic course recommendations and recent literature investigating shorter courses. Prescribers in the United States should overcome academic imprinting and follow international trends to reduce antibiotic durations for common ARTIs, where 5 days is a safe and efficacious course when antibiotics are prescribed.
How free-ranging Indian Flying Fox (Pteropus medius) forage in urban areas? A study from Kolkata, India
Authors: Roy Kanad , Saha Goutam Kumar , Mazumdar Subhendu 
Published: April 2024

Abstract
Foraging behaviour plays a significant role in the fitness of animals and is influenced by habitat quality. Habitat change due to rapid urbanization often results in altered behaviour and resource use patterns in animals thriving in such changed habitats. Bats play a crucial role as tree pollinators, seed dispersers and forest regenerators. Particularly in urban areas they are among the few pollinators that help regenerating the urban green spaces. Therefore, it is crucial to understand their foraging patterns in these human-dominated landscapes. Loss and degradation of roost and foraging resources threatens the survival of many bat species, including Indian Flying Foxes (IFF). Still, very few studies have been carried out on their feeding behaviour and ecology. Hence, we carried out this study to (i) identify the foraging sites of IFF, (ii) find out the urban land cover features influencing their foraging site selection and (iii) to identify the foraging trees used by them in urban areas. IFFs were observed to forage on 16 species of trees belonging to 10 families in four different sites in urban areas, of which Ficus species are most important. Amongst various urban land covers, the area of tree cover in the foraging sites were found to significantly influence the number of foraging IFFs. Our findings strongly advocate for the protection of the trees preferred by IFFs along with overall urban tree canopy covers, as these are essential resources for the survival of bats, as well as many other species in urban areas.
Transient fading X-ray emission detected during the optical rise of a tidal disruption event
Authors: Malyali A , Rau A , Bonnerot C , Goodwin A J , Liu Z , Anderson G E , Brink J , Buckley D A H , Merloni A , Miller-Jones J C A , Grotova I , Kawka A 
Published: April 2024

ABSTRACT
We report on the SRG/eROSITA detection of ultra-soft ($kT=47^{+5}_{-5}$ eV) X-ray emission (LX =$2.5^{+0.6}_{-0.5} \times 10^{43}$ erg s−1) from the tidal disruption event (TDE) candidate AT 2022dsb ∼14 d before peak optical brightness. As the optical luminosity increases after the eROSITA detection, then the 0.2–2 keV observed flux decays, decreasing by a factor of ∼39 over the 19 d after the initial X-ray detection. Multi-epoch optical spectroscopic follow-up observations reveal transient broad Balmer emission lines and a broad He ii 4686 Å emission complex with respect to the pre-outburst spectrum. Despite the early drop in the observed X-ray flux, the He ii 4686  Å complex is still detected for ∼40 d after the optical peak, suggesting the persistence of an obscured hard ionizing source in the system. Three outflow signatures are also detected at early times: (i) blueshifted H α emission lines in a pre-peak optical spectrum, (ii) transient radio emission, and (iii) blueshifted Ly α absorption lines. The joint evolution of this early-time X-ray emission, the He ii 4686 Å complex, and these outflow signatures suggests that the X-ray emitting disc (formed promptly in this TDE) is still present after optical peak, but may have been enshrouded by optically thick debris, leading to the X-ray faintness in the months after the disruption. If the observed early-time properties in this TDE are not unique to this system, then other TDEs may also be X-ray bright at early times and become X-ray faint upon being veiled by debris launched shortly after the onset of circularization.
Synchro-curvature description of γ-ray light curves and spectra of pulsars: global properties
Authors: Íñiguez-Pascual Daniel , Torres Diego F , Viganò Daniele 
Published: April 2024

ABSTRACT
This work presents a methodological approach to generate realistic γ-ray light curves of pulsars, resembling reasonably well the observational ones observed by the Fermi-Large Area Telescope (Fermi-LAT) instrument, fitting at the same time their high-energy spectra. The theoretical light curves are obtained from a spectral and geometrical model of the synchro-curvature emission. Despite our model relying on a few effective physical parameters, the synthetic light curves present the same main features observed in the observational γ-ray light-curve zoo, such as the different shapes, variety in the number of peaks, and a diversity of peak widths. The morphological features of the light curves allow us to statistically compare the observed properties. In particular, we find that the proportion of the number of peaks found in our synthetic light curves is in agreement with the observational one provided by the third Fermi-LAT pulsar catalogue. We also found that the detection probability due to beaming is much higher for orthogonal rotators (approaching 100 per cent) than for small inclination angles (less than 20 per cent). The small variation in the synthetic skymaps generated for different pulsars indicates that the geometry dominates over timing and spectral properties in shaping the γ-ray light curves. This means that geometrical parameters such as the inclination angle can be in principle constrained by γ-ray data alone independently of the specific properties of a pulsar. At the same time, we find that γ-ray spectra seen by different observers can slightly differ, opening the door to constraining the viewing angle of a particular pulsar.