bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung injury-induced activated endothelial cell states persist in aging-associated progressive fibrosis
Authors: Raslan Ahmed A. , Pham Tho X. , Lee Jisu , Kontodimas Konstantinos , Tilston-Lunel Andrew , Schmottlach Jillian , Hong Jeongmin , Dinc Taha , Bujor Andreea M. , Caporarello Nunzia , Thiriot Aude , von Andrian Ulrich H. , Huang Steven K. , Nicosia Roberto F. , Trojanowska Maria , Varelas Xaralabos , Ligresti Giovanni 
Published: June 2024

AbstractProgressive lung fibrosis is associated with poorly understood aging-related endothelial cell dysfunction. To gain insight into endothelial cell alterations in lung fibrosis we performed single cell RNA-sequencing of bleomycin-injured lungs from young and aged mice. Analysis reveals activated cell states enriched for hypoxia, glycolysis and YAP/TAZ activity in ACKR1+ venous and TrkB+ capillary endothelial cells. Endothelial cell activation is prevalent in lungs of aged mice and can also be detected in human fibrotic lungs. Longitudinal single cell RNA-sequencing combined with lineage tracing demonstrate that endothelial activation resolves in young mouse lungs but persists in aged ones, indicating a failure of the aged vasculature to return to quiescence. Genes associated with activated lung endothelial cells states in vivo can be induced in vitro by activating YAP/TAZ. YAP/TAZ also cooperate with BDNF, a TrkB ligand that is reduced in fibrotic lungs, to promote capillary morphogenesis. These findings offer insights into aging-related lung endothelial cell dysfunction that may contribute to defective lung injury repair and persistent fibrosis.
CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems
Authors: Kern Nathan R. , Lee Jumin , Choi Yeol Kyo , Im Wonpil 
Published: June 2024

AbstractAtomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.
Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation
Authors: Huh Hyun , Shen Jiayu , Ajjugal Yogeeshwar , Ramachandran Aparna , Patel Smita S. , Lee Sang-Hyuk 
Published: June 2024

AbstractMitochondrial transcription factor A (TFAM) employs DNA bending to package mitochondrial DNA (mtDNA) into nucleoids and recruit mitochondrial RNA polymerase (POLRMT) at specific promoter sites, light strand promoter (LSP) and heavy strand promoter (HSP). Herein, we characterize the conformational dynamics of TFAM on promoter and non-promoter sequences using single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule protein-induced fluorescence enhancement (smPIFE) methods. The DNA-TFAM complexes dynamically transition between partially and fully bent DNA conformational states. The bending/unbending transition rates and bending stability are DNA sequence-dependent—LSP forms the most stable fully bent complex and the non-specific sequence the least, which correlates with the lifetimes and affinities of TFAM with these DNA sequences. By quantifying the dynamic nature of the DNA-TFAM complexes, our study provides insights into how TFAM acts as a multifunctional protein through the DNA bending states to achieve sequence specificity and fidelity in mitochondrial transcription while performing mtDNA packaging.
Observation of heat pumping effect by radiative shuttling
Authors: Li Yuxuan , Dang Yongdi , Zhang Sen , Li Xinran , Chen Tianle , Choudhury Pankaj K. , Jin Yi , Xu Jianbin , Ben-Abdallah Philippe , Ju Bing-Feng , Ma Yungui 
Published: June 2024

AbstractHeat shuttling phenomenon is characterized by the presence of a non-zero heat flow between two bodies without net thermal bias on average. It was initially predicted in the context of nonlinear heat conduction within atomic lattices coupled to two time-oscillating thermostats. Recent theoretical works revealed an analog of this effect for heat exchanges mediated by thermal photons between two solids having a temperature dependent emissivity. In this paper, we present the experimental proof of this effect using systems made with composite materials based on phase change materials. By periodically modulating the temperature of one of two solids we report that the system akin to heat pumping with a controllable heat flow direction. Additionally, we demonstrate the effectiveness of a simultaneous modulation of two temperatures to control both the strength and direction of heat shuttling by exploiting the phase delay between these temperatures. These results show that this effect is promising for an active thermal management of solid-state technology, to cool down solids, to insulate them from their background or to amplify heat exchanges.
Substantial contribution of slush to meltwater area across Antarctic ice shelves
Authors: Dell Rebecca L. , Willis Ian C. , Arnold Neil S. , Banwell Alison F. , de Roda Husman Sophie 
Published: June 2024

AbstractSurface melting occurs across many of Antarctica’s ice shelves, mainly during the austral summer. The onset, duration, area and fate of surface melting varies spatially and temporally, and the resultant surface meltwater is stored as ponded water (lakes) or as slush (saturated firn or snow), with implications for ice-shelf hydrofracture, firn air content reduction, surface energy balance and thermal evolution. This study applies a machine-learning method to the entire Landsat 8 image catalogue to derive monthly records of slush and ponded water area across 57 ice shelves between 2013 and 2021. We find that slush and ponded water occupy roughly equal areas of Antarctica’s ice shelves in January, with inter-regional variations in partitioning. This suggests that studies that neglect slush may substantially underestimate the area of ice shelves covered by surface meltwater. Furthermore, we found that adjusting the surface albedo in a regional climate model to account for the lower albedo of surface meltwater resulted in 2.8 times greater snowmelt across five representative ice shelves. This extra melt is currently unaccounted for in regional climate models, which may lead to underestimates in projections of ice-sheet melting and ice-shelf stability.
A large-scale and PCR-referenced vocal audio dataset for COVID-19
Authors: Budd Jobie , Baker Kieran , Karoune Emma , Coppock Harry , Patel Selina , Payne Richard , Tendero Cañadas Ana , Titcomb Alexander , Hurley David , Egglestone Sabrina , Butler Lorraine , Mellor Jonathon , Nicholson George , Kiskin Ivan , Koutra Vasiliki , Jersakova Radka , McKendry Rachel A. , Diggle Peter , Richardson Sylvia , Schuller Björn W. , Gilmour Steven , Pigoli Davide , Roberts Stephen , Packham Josef , Thornley Tracey , Holmes Chris 
Published: June 2024

AbstractThe UK COVID-19 Vocal Audio Dataset is designed for the training and evaluation of machine learning models that classify SARS-CoV-2 infection status or associated respiratory symptoms using vocal audio. The UK Health Security Agency recruited voluntary participants through the national Test and Trace programme and the REACT-1 survey in England from March 2021 to March 2022, during dominant transmission of the Alpha and Delta SARS-CoV-2 variants and some Omicron variant sublineages. Audio recordings of volitional coughs, exhalations, and speech were collected in the ‘Speak up and help beat coronavirus’ digital survey alongside demographic, symptom and self-reported respiratory condition data. Digital survey submissions were linked to SARS-CoV-2 test results. The UK COVID-19 Vocal Audio Dataset represents the largest collection of SARS-CoV-2 PCR-referenced audio recordings to date. PCR results were linked to 70,565 of 72,999 participants and 24,105 of 25,706 positive cases. Respiratory symptoms were reported by 45.6% of participants. This dataset has additional potential uses for bioacoustics research, with 11.3% participants self-reporting asthma, and 27.2% with linked influenza PCR test results.
Unraveling the therapeutic potential of quercetin and quercetin-3-O-glucuronide in Alzheimer's disease through network pharmacology, molecular docking, and dynamic simulations
Authors: Sabarathinam Sarvesh 
Published: June 2024

AbstractQuercetin is a flavonoid with notable pharmacological effects and promising therapeutic potential. Quercetin plays a significant role in neuroinflammation, which helps reduce Alzheimer's disease (AD) severity. Quercetin (Q) and quercetin 3-O-glucuronide (Q3OG) are some of the most potent antioxidants available from natural sources. However, the natural form of quercetin converted into Q3OG when reacted with intestinal microbes. The study aims to ensure the therapeutic potential of Q and Q3OG. In this study, potential molecular targets of Q and Q3OG were first identified using the Swiss Target Prediction platform and pathogenic targets of AD were identified using the DisGeNET database. Followed by compound and disease target overlapping, 77 targets were placed in that AKT1, EGFR, MMP9, TNF, PTGS2, MMP2, IGF1R, MCL1, MET and PARP1 was the top-ranked target, which was estimated by CytoHubba plug-in. The Molecular docking was performed for Q and Q3OG towards the PDB:1UNQ target. The binding score of Q and Q3OG was − 6.2 kcal/mol and − 6.58 kcal/mol respectively. Molecular dynamics simulation was conducted for Q and Q3OG towards the PDB:1UNQ target at 200 ns. This study's results help identify the multiple target sites for the bioactive compounds. Thus, synthesizing new chemical entity-based quercetin on structural modification may aid in eradicating AD complications.
Micromachined needle-like calorimetric flow sensor for sap flux density measurement in the xylem of plants
Authors: Kim Gigyu , Lee Junghoon 
Published: June 2024

AbstractMiniaturized silicon thermal probes for plant’s sap flow measurement, or micro sap flow sensors, have advantages in minimum invasiveness, low power consumption, and fast responses. Practical applications in sap flow measurement has been demonstrated with the single-probe silicon micro sensors. However, the sensors could not detect flow directions and require estimating zero sap flow output that leads to significant source of uncertainty. Furthermore, silicon-needles would break easily during the insertion into plants. We present the first three-element micro thermal sap flow sensor packaged on a durable printed circuit board needle that can measure bidirectional flows with improved dynamics and precision. The performance of the newly designed calorimetric flow sensor was confirmed through precision calibration and field test on tomato stems. A calibration curve for a tomato stem was obtained with a sensitivity of 0.299 K/(µL mm−2 s−1) under the maximum temperature increase of 4.61 K. Results from the field test for one month revealed a correlation between the measured sap flux density and related conditions such as solar radiation, vapor pressure deficit, sunshade and irrigation. The developed sensor will contribute to practical long-term sap flow monitoring for small and delicate plants with minimal physical invasion.
Construction of warfarin population pharmacokinetics and pharmacodynamics model in Han population based on Bayesian method
Authors: Xia Xiaotong , Cai Xiaofang , Chen Jiana , Jiang Shaojun , Zhang Jinhua 
Published: June 2024

AbstractThe purpose of this paper is to study the genetic polymorphisms of related gene loci (CYP2C9*3, VKORC1-1639G > A) based on demographic and clinical factors, and use the maximum a posterior Bayesian method to construct a warfarin individualized dose prediction model in line with the Chinese Han population. Finally, the built model is compared and analyzed with the widely used models at home and abroad. In this study, a total of 5467 INR measurements are collected from 646 eligible subjects in our hospital, and the maximum a posterior Bayesian method is used to construct a warfarin dose prediction that conforms to the Chinese Han population on the basis of the Hamberg model. The model is verified and compared with foreign models. This study finds that body weight and concomitant use of amiodarone have a significant effect on the anticoagulant effect of warfarin. The model can provide an effective basis for individualized and rational dosing of warfarin in Han population more accurately. In the performance of comparison with different warfarin dose prediction models, the new model has the highest prediction accuracy, and the prediction percentage is as high as 72.56%. The dose predicted by the Huang model is the closest to the actual dose of warfarin. The population pharmacokinetics and pharmacodynamics model established in this study can better reflect the distribution characteristics of INR values after warfarin administration in the Han population, and performs better than the models reported in the literature.
Nudging against consent is effective but lowers welfare
Authors: Gerver Mollie , Banerjee Sanchayan , John Peter 
Published: June 2024

AbstractBehavioural nudges are often criticised because they “work best in the dark”. However, recent experimental evidence suggests that the effectiveness of nudges is not reduced when they are delivered transparently. Most people also endorse transparent nudges. Yet, transparent nudging may undermine human autonomy—a minority may oppose to being nudged and feel manipulated, even if they know what is happening. We propose an alternative way of maintaining autonomy that is not reducible to transparency: individuals can be asked if they consent in advance to being nudged. To assess whether consensual nudges are effective, we ask consent from 1518 UK citizens to be nudged. Subsequently, we default all participants into donating to a charity of their choice, irrespective of self-reported consent. We find that the default nudge is equally effective for both consenting and non-consenting individuals, with negligible difference in average donations. However, non-consenting individuals report higher levels of resentment and regret and lower levels of happiness and support compared to the consenting group. Based on these findings, we argue that ignoring consent can have serious ethical ramifications for policy-making with nudges.
Impact of helminth infections during pregnancy on maternal and newborn Vitamin D and on birth outcomes
Authors: Berry Sèyigbéna P. Déo-Gracias , Honkpèhedji Yabo Josiane , Ludwig Esther , Mahmoudou Saïdou , Prodjinotho Ulrich Fabien , Adamou Rafiou , Nouatin Odilon P. , Adégbitè Bayode R. , Dejon-Agobe Jean Claude , Mba Romuald Beh , Maloum Moustapha , Nkoma Anne Marie Mouima , Zinsou Jeannot Fréjus , Luty Adrian J. F. , Esen Meral , Adégnika Ayôla Akim , Prazeres da Costa Clarissa 
Published: June 2024

AbstractPoor birth outcomes in low- and middle income countries are associated with maternal vitamin D deficiency and chronic helminth infections. Here, we investigated whether maternal Schistosoma haematobium affects maternal or cord vitamin D status as well as birth outcomes. In a prospective cross-sectional study of pregnant women conducted in Lambaréné, Gabon, we diagnosed maternal parasitic infections in blood, urine and stool. At delivery we measured vitamin D in maternal and cord blood. S. haematobium, soil-transmitted helminths, and microfilariae were found at prevalences of 30.2%, 13.0%, and 8.8%, respectively. Insufficient vitamin D and calcium levels were found in 28% and 15% of mothers, and in 11.5% and 1.5% of newborns. Mothers with adequate vitamin D had lower risk of low birthweight babies (aOR = 0.11, 95% CI 0.02–0.52, p = 0.01), whilst offspring of primipars had low cord vitamin D levels, and low vitamin D levels increased the risk of maternal inflammation. Maternal filariasis was associated with low calcium levels, but other helminth infections affected neither vitamin D nor calcium levels in either mothers or newborns. Healthy birth outcomes require maintenance of adequate vitamin D and calcium levels. Chronic maternal helminth infections do not disrupt those levels in a semi-rural setting in sub-Saharan Africa.
The effect of including a mobile arch, toe joint, and joint coupling on predictive neuromuscular simulations of human walking
Authors: Buchmann Alexandra , Wenzler Simon , Welte Lauren , Renjewski Daniel 
Published: June 2024

AbstractPredictive neuromuscular simulations are a powerful tool for studying the biomechanics of human walking, and deriving design criteria for technical devices like prostheses or biorobots. Good agreement between simulation and human data is essential for transferability to the real world. The human foot is often modeled with a single rigid element, but knowledge of how the foot model affects gait prediction is limited. Standardized procedures for selecting appropriate foot models are lacking. We performed 2D predictive neuromuscular simulations with six different foot models of increasing complexity to answer two questions: What is the effect of a mobile arch, a toe joint, and the coupling of toe and arch motion through the plantar fascia on gait prediction? and How much of the foot’s anatomy do we need to model to predict sagittal plane walking kinematics and kinetics in good agreement with human data? We found that the foot model had a significant impact on ankle kinematics during terminal stance, push-off, and toe and arch kinematics. When focusing only on hip and knee kinematics, rigid foot models are sufficient. We hope our findings will help guide the community in modeling the human foot according to specific research goals and improve neuromuscular simulation accuracy.
Exploring the potential biological significance of KDELR family genes in lung adenocarcinoma
Authors: Li Peitong , Cui Pengfei , Yue Qing , Xu Zijun , Liu Ziling 
Published: June 2024

AbstractThe Lys-Asp-Glu-Leu receptor (KDELR) family genes play critical roles in a variety of biological processes in different tumors. Our study aimed to provide a comprehensive analysis of the potential roles of KDELRs in lung adenocarcinoma (LUAD). Utilizing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, as well as clinical samples, we conducted a series of analyses and validations using R software tools and various online resources. The results showed that KDELR family genes and proteins were highly expressed and associated with a poor prognosis of LUAD. Promoter hypomethylation and the competing endogenous RNA (ceRNA) network of PCAT6/hsa-miR-326/KDELR1 might be potential causes of aberrant KDELR1 overexpression in LUAD. Three key Transcription factors (TFs) (SPI1, EP300, and MAZ) and a TFs-miRNAs-KDELRs network (involving 11 TFs) might be involved in modulating KDELRs expression abnormalities. Gene Set Enrichment Analysis (GSEA) indicated enrichment of genes highly expressing KDELR1, KDELR2, and KDELR3 in MTORC1_SIGNALING, P53_PATHWAY, and ANGIOGENESIS. Negative correlations between KDELRs expression and CD8 + T cell infiltration, as well as CTLA-4 expression. Our multiple analyses suggested that the KDELRs are important signaling molecules in LUAD. These results provided novel insights for developing prognostic markers and novel therapies of LUAD.
Identifying plasma proteomic signatures from health to heart failure, across the ejection fraction spectrum
Authors: Andrzejczyk Karolina , Abou Kamar Sabrina , van Ommen Anne-Mar , Canto Elisa Dal , Petersen Teun B. , Valstar Gideon , Akkerhuis K. Martijn , Cramer Maarten Jan , Umans Victor , Rutten Frans H. , Teske Arco , Boersma Eric , Menken Roxana , van Dalen Bas M. , Hofstra Leonard , Verhaar Marianne , Brugts Jasper , Asselbergs Folkert , den Ruijter Hester , Kardys Isabella 
Published: June 2024

AbstractCirculating proteins may provide insights into the varying biological mechanisms involved in heart failure (HF) with preserved ejection fraction (HFpEF) and reduced ejection fraction (HFrEF). We aimed to identify specific proteomic patterns for HF, by comparing proteomic profiles across the ejection fraction spectrum. We investigated 4210 circulating proteins in 739 patients with normal (Stage A/Healthy) or elevated (Stage B) filling pressures, HFpEF, or ischemic HFrEF (iHFrEF). We found 2122 differentially expressed proteins between iHFrEF-Stage A/Healthy, 1462 between iHFrEF–HFpEF and 52 between HFpEF-Stage A/Healthy. Of these 52 proteins, 50 were also found in iHFrEF vs. Stage A/Healthy, leaving SLITRK6 and NELL2 expressed in lower levels only in HFpEF. Moreover, 108 proteins, linked to regulation of cell fate commitment, differed only between iHFrEF–HFpEF. Proteomics across the HF spectrum reveals overlap in differentially expressed proteins compared to stage A/Healthy. Multiple proteins are unique for distinguishing iHFrEF from HFpEF, supporting the capacity of proteomics to discern between these conditions.
Analyzing post-COVID-19 demographic and mobility changes in Andalusia using mobile phone data
Authors: Osorio Arjona Joaquín 
Published: June 2024

AbstractThis work studies changes in the demographics of the different spatial units that make up the Andalusia region in Spain throughout the year 2021, with the aim of seeing the progressive recovery of the population after the COVID-19 pandemic. Mobile phone data from Origin–Destination matrices has been used, due to the ease of obtaining updated information quickly and constantly. A methodology has been developed to transform the number of travelers into an estimated population without biases, and an interpolation function has been used to take into account all the data available in the year 2021. Results show a direct link between the demographic changes in Andalusia and the removal of the mobility restrictions caused by the COVID-19 pandemic, with an increase of non-related work mobility and a decrease of static population. Travel distances between home and work places are also affected, with an increase of long trips after the end of the mobility restrictions. In addition, different patterns have been visualized, such as the concentration of commuting in the metropolitan areas of the region during working days, the population growth in rural areas during weekends, or the population displacement to coastal areas in summer.