bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexible modeling of regulatory networks improves transcription factor activity estimation
Authors: Chen Chen , Padi Megha 
Published: May 2024

AbstractTranscriptional regulation plays a crucial role in determining cell fate and disease, yet inferring the key regulators from gene expression data remains a significant challenge. Existing methods for estimating transcription factor (TF) activity often rely on static TF-gene interaction databases and cannot adapt to changes in regulatory mechanisms across different cell types and disease conditions. Here, we present a new algorithm - Transcriptional Inference using Gene Expression and Regulatory data (TIGER) - that overcomes these limitations by flexibly modeling activation and inhibition events, up-weighting essential edges, shrinking irrelevant edges towards zero through a sparse Bayesian prior, and simultaneously estimating both TF activity levels and changes in the underlying regulatory network. When applied to yeast and cancer TF knock-out datasets, TIGER outperforms comparable methods in terms of prediction accuracy. Moreover, our application of TIGER to tissue- and cell-type-specific RNA-seq data demonstrates its ability to uncover differences in regulatory mechanisms. Collectively, our findings highlight the utility of modeling context-specific regulation when inferring transcription factor activities.
Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells
Authors: Grimes Karen , Jeong Hyobin , Amoah Amanda , Xu Nuo , Niemann Julian , Raeder Benjamin , Hasenfeld Patrick , Stober Catherine , Rausch Tobias , Benito Eva , Jann Johann-Christoph , Nowak Daniel , Emini Ramiz , Hoenicka Markus , Liebold Andreas , Ho Anthony , Shuai Shimin , Geiger Hartmut , Sanders Ashley D. , Korbel Jan O. 
Published: May 2024

AbstractThe functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the heterogeneous mSV landscapes of hematopoietic stem and progenitor cells. While mSVs are continuously acquired throughout life, expanded subclones in our cohort are confined to individuals >60. Cells already harboring mSVs are more likely to acquire additional somatic structural variants, including megabase-scale segmental aneuploidies. Capitalizing on comprehensive single-cell micrococcal nuclease digestion with sequencing reference data, we conducted high-resolution cell-typing for eight hematopoietic stem and progenitor cells. Clonally expanded mSVs disrupt normal cellular function by dysregulating diverse cellular pathways, and enriching for myeloid progenitors. Our findings underscore the contribution of mSVs to the cellular and molecular phenotypes associated with the aging hematopoietic system, and establish a foundation for deciphering the molecular links between mSVs, aging and disease susceptibility in normal tissues.
Cellular mechanisms mediating the anti-cancer effects of carnosol on gingiva carcinoma
Authors: Gassib Nassima , Issa Hawraa , Loubaki Lionel , Behaz Sarah , Almutairi Mikhlid H. , Rouabhia Mahmoud , Semlali Abdelhabib 
Published: May 2024

AbstractCarnosol, a rosemary polyphenol, displays anticancer properties and is suggested as a safer alternative to conventional surgery, radiotherapy, and chemotherapy. Given that its effects on gingiva carcinoma have not yet been investigated, the aim of this study was to explore its anti-tumor selectivity and to unravel its underlying mechanisms of action. Hence, oral tongue and gingiva carcinoma cell lines exposed to carnosol were analyzed to estimate cytotoxicity, cell viability, cell proliferation, and colony formation potential as compared with those of normal cells. Key cell cycle and apoptotic markers were also measured. Finally, cell migration, oxidative stress, and crucial cell signaling pathways were assessed. Selective anti-gingiva carcinoma activity was disclosed. Overall, carnosol mediated colony formation and proliferation suppression in addition to cytotoxicity induction. Cell cycle arrest was highlighted by the disruption of the c-myc oncogene/p53 tumor suppressor balance. Carnosol also increased apoptosis, oxidative stress, and antioxidant activity. On a larger scale, the alteration of cell cycle and apoptotic profiles was also demonstrated by QPCR array. This was most likely achieved by controlling the STAT5, ERK1/2, p38, and NF-ĸB signaling pathways. Lastly, carnosol reduced inflammation and invasion ability by modulating IL-6 and MMP9/TIMP-1 axes. This study establishes a robust foundation, urging extensive inquiry both in vivo and in clinical settings, to substantiate the efficacy of carnosol in managing gingiva carcinoma.
Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility
Authors: Chander Atul Munish , de Melo Teixeira Marcus , Singh Nitin K. , Williams Michael P. , Parker Ceth W. , Leo Patrick , Stajich Jason E. , Torok Tamas , Tighe Scott , Mason Christopher E. , Venkateswaran Kasthuri 
Published: May 2024

AbstractMembers of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genus Knufia encompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain of Knufia obscura (CBS 148926T) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926T) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed as K. obscura. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments.
PMMA dialyzers modulate both humoral and cell-mediate immune response to anti-COVID-19 vaccine (BNT162b2) in a cohort of chronic hemodialyzed patients
Authors: Castellano Giuseppe , Netti Giuseppe Stefano , Cantaluppi Vincenzo , Losappio Vincenzo , Spadaccino Federica , Ranieri Elena , Marengo Marita , Borzumati Maurizio , Alfieri Carlo , Stallone Giovanni 
Published: May 2024

AbstractPatients on hemodialysis (HD) have a high risk of death from COVID-19. We evaluated the humoral and cell-mediated immune response to BNT162b2 (Pfizer-BioNTech) vaccine in HD patients, comparing HD with Poly-methyl-methacrylate (PMMA) and HD with Polysulphone (PS). Samples were collected before vaccination (T0) and 14-days after the 2ndvaccine (T2) in a TG (TG, n = 16-Foggia) and in a VG (CG, n = 36-Novara). Anti-SARS-CoV-2-Ig were titrated in the cohort 2-weeks after the 2nddose of vaccine. In the Testing-Group, serum neutralizing antibodies (NAb) were assayed and PBMCs isolated from patients were thawed, counted and stimulated with SARS-CoV-2 IGRA stimulation tube set. All patients had a positive ab-response, except in a case. PMMA-patients had higher levels of anti-SARS-CoV-2 IgG (p = 0.031); VG data confirmed these findings (p < 0.05). NAb evaluation: PMMA patients passed the positive cut-off value, while in PS group only only 1/8 patient did not respond. PMMA patients showed higher percentages of anti-SARS-CoV-2 S1/RBD-Ig after a complete vaccine schedule (p = 0.028). Interferon-gamma release: PMMA patients showed significantly higher release of IFNγ (p = 0.014). The full vaccination course provided sufficient protection against SARS-CoV-2 across the entire cohort, regardless of dialyzer type. After vaccination, PMMA patients show a better immune response, both humoral and cellular, at the end of the vaccination course than PS patients.
Fractal fractional model for tuberculosis: existence and numerical solutions
Authors: Khan Aziz , Shah Kamal , Abdeljawad Thabet , Amacha Inas 
Published: May 2024

AbstractThis paper deals with the mathematical analysis of Tuberculosis by using fractal fractional operator. Mycobacterium TB is the bacteria that causes tuberculosis. This airborne illness mostly impacts the lungs but may extend to other body organs. When the infected individual coughs, sneezes or speaks, the bacterium gets released into the air and travels from one person to another. Five classes have been formulated to study the dynamics of this disease: susceptible class, infected of DS, infected of MDR, isolated class, and recovered class. To study the suggested fractal fractional model’s wellposedness associated with existence results, and boundedness of solutions. Further, the invariant region of the considered model, positive solutions, equilibrium point, and reproduction number. One would typically employ a fractional calculus approach to obtain numerical solutions for the fractional order Tuberculosis model using the Adams-Bashforth-Moulton method. The fractional order derivatives in the model can be approximated using appropriate numerical schemes designed for fractional order differential equations.
Experimental investigation of influence of amide polymer on loess for subgrade
Authors: Yue Jianwei , Zhang Haonan , Zhang Yage , Xu Shaopeng 
Published: May 2024

AbstractThe effects of moisture and drying shrinkage can lead to uneven settlement, cracking, and other diseases in loess subgrade. The objective of this study was to investigate the effects of amide polymer (AP) on the permeability, mechanical properties and crack resistance of loess by orthogonal experiments. The basic properties of AP and the permeability, mechanical properties, and dry–wet variation properties of polymer-modified loess were tested, and a scale model verification and simulation analysis were conducted. In this paper, water migration in subgrade is regulated by improving the water sensitivity of loess. By reducing the variation range of subgrade water content, the stress accumulation in subgrade caused by water is weakened. The results show that the curing time and mechanical properties of AP are directly affected by the oxidant and reducing agent, and the mechanical properties of AP are compatible with the characteristics of loess. AP filled the grain gap and reduced the permeability of loess by 34.05–280.83%. The ductility of polymer-modified loess is significantly increased, and the strain of peak strength is increased by 17.21–126.36%. AP can regulate moisture change, reduce the surface tension between particles, and reduce stress concentration. The strength loss rate was reduced by 19.98–51.21% by enhancing the cracking resistance and weakening the strength loss caused by dry and wet cycling. The increase of upper layer moisture content in the scale model of polymer-modified loess subgrade is reduced by 31.38–36.11%.
The impact of dose rate on responses of human lens epithelial cells to ionizing irradiation
Authors: Matsuya Yusuke , Sato Tatsuhiko , Yachi Yoshie , Date Hiroyuki , Hamada Nobuyuki 
Published: May 2024

AbstractThe knowledge on responses of human lens epithelial cells (HLECs) to ionizing radiation exposure is important to understand mechanisms of radiation cataracts that are of concern in the field of radiation protection and radiation therapy. However, biological effects in HLECs following protracted exposure have not yet fully been explored. Here, we investigated the temporal kinetics of γ-H2AX foci as a marker for DNA double-strand breaks (DSBs) and cell survival in HLECs after exposure to photon beams at various dose rates (i.e., 150 kVp X-rays at 1.82, 0.1, and 0.033 Gy/min, and 137Cs γ-rays at 0.00461 Gy/min (27.7 cGy/h) and 0.00081 Gy/min (4.9 cGy/h)), compared to those in human lung fibroblasts (WI-38). In parallel, we quantified the recovery for DSBs and cell survival using a biophysical model. The study revealed that HLECs have a lower DSB repair rate than WI-38 cells. There is no significant impact of dose rate on cell survival in both cell lines in the dose-rate range of 0.033–1.82 Gy/min. In contrast, the experimental residual γ-H2AX foci showed inverse dose rate effects (IDREs) compared to the model prediction, highlighting the importance of the IDREs in evaluating radiation effects on the ocular lens.
Hydrostatic bearing groove multi-objective optimization of the gear ring housing interface in a straight-line conjugate internal meshing gear pump
Authors: Zhang Tiangui , Yan Guishan , Liu Xianhang , Ding Beichen , Feng Guodong , Ai Chao 
Published: May 2024

AbstractThe lubrication performance of a straight-line conjugate internal meshing gear pump is poor under the low-speed, high-pressure operating conditions of the volumetric servo speed control system, and it is difficult to establish a full fluid lubricating oil film between the gear ring and the housing. This leads to significant wear and severe heating between the gear ring and the housing. The lubrication performance of the interface moving pair of the electro-hydraulic actuator pump gear ring housing can be improved by designing a reasonable lubrication bearing structure for the gear ring housing. In this study, a multi-field coupling multi-objective optimization model was established to improve lubrication performance and volumetric efficiency. The whole model consists of the dynamic model of the gear ring components, the fluid lubrication model of the gear ring housing interface, the oil film formation and sealing model considering the influence of temperature, and the multi-objective optimization model. The comprehensive performance of the straight-line conjugate internal meshing gear pump was verified experimentally using a test bench. The results show that the lubrication performance is improved, the mechanical loss is reduced by 31.52%, and the volumetric efficiency is increased by 4.91%.
The effect of socioeconomic status, depression, and diabetes symptoms severity on diabetes patient’s life satisfaction in India
Authors: Ranjan Shubham , Thakur Ramna 
Published: May 2024

AbstractEvidence suggests that diabetes is on the rise in India, affecting many people’s life satisfaction. Comprehensive estimation of life satisfaction among diabetes patients does not exist in the country. This study examined the effects of socioeconomic status, depression, and diabetes symptoms severity on the life satisfaction of diabetes patients by controlling various demographic variables. It was a cross-sectional study comprising 583 diabetes patients from Punjab, India. Patients were interviewed using a multi-stage purposeful random sampling method. Descriptive analysis and partial least squares structural equation modelling were used in the study to test the hypotheses. Results revealed that socioeconomic status, depression and diabetes symptoms severity significantly influence the life satisfaction of diabetes patients. A 1% drop in diabetes symptoms severity corresponds to a 0.849% increase in life satisfaction, whereas a 1% decrease in depression results in a 0.898% increase in life satisfaction. Patients with higher diabetes symptoms severity were coping with common mental disorders. Women reported higher diabetes symptoms severity and depression than men, resulting in lower life satisfaction. An experimental evaluation of the effects of socioeconomic status, depression and diabetes symptoms severity, and numerous demographic factors on life satisfaction was reported. The findings will help policymakers understand the problem associated with life satisfaction among diabetes patients in the country.
Scheduling optimisation of alcohol test sites
Authors: Yu Hongjun , Moylan Emily , Bambach Mike , Levinson David , Ramezani Mohsen 
Published: May 2024

AbstractDrink driving is an infamous factor in road crashes and fatalities. Alcohol testing is a major countermeasure, and random breath tests (RBTs) deter tested drivers and passersby (observers who are not tested). We propose a genetic algorithm (GA)-based RBT scheduling optimisation method to achieve maximal deterrence of drink driving. The RBT schedule denotes the daily plan of where, when, and for how long tests should occur in the road network. The test results (positive and negative) and observing drivers are considered in the fitness function. The limited testing resource capacity is modeled by a number of constraints that consider the total duration of tests, the minimum and maximum duration of a single test site, and the total number of test sites during the day. Clustering of the alcohol-related crash data is used to estimate the matrix for drink driving on the scheduled day. The crash data and traffic flow data from Victoria, Australia are analysed and used to describe sober/drink driving. A detailed synthetic example is developed and a significant improvement with 150% more positive results and 59% more overall tests is observed using the proposed scheduling optimisation method.
Effects of overwintering on the transcriptome and fitness traits in a damselfly with variable voltinism across two latitudes
Authors: Wos Guillaume , Palomar Gemma , Golab Maria J. , Marszałek Marzena , Sniegula Szymon 
Published: May 2024

AbstractWinter diapause consists of cessation of development that allows individuals to survive unfavourable conditions. Winter diapause may bear various costs and questions have been raised about the evolutionary mechanisms maintaining facultative diapause. Here, we explored to what extent a facultative winter diapause affects life-history traits and the transcriptome in the damselfly Ischnura elegans, and whether these effects were latitude-specific. We collected adult females at central and high latitudes and raised their larvae in growth chambers. Larvae were split into a non-diapausing and post-winter (diapausing) cohort, were phenotyped and collected for a gene expression analysis. At the phenotypic level, we found no difference in survival between the two cohorts, and the post-winter cohort was larger and heavier than the non-winter cohort. These effects were mostly independent of the latitude of origin. At the transcriptomic level, wintering affected gene expression with a small fraction of genes significantly overlapping across latitudes, especially those related to morphogenesis. In conclusion, we found clear effects of diapause on the phenotype but little evidence for latitudinal-specific effects of diapause. Our results showed a shared transcriptomic basis underpinning diapause demonstrated, here, at the intraspecific level and supported the idea of evolutionary convergence of the response to diapause across organisms.
Increased stability of short femoral stem through customized distribution of coefficient of friction in porous coating
Authors: Solou Konstantina , Solou Anna Vasiliki , Tatani Irini , Lakoumentas John , Tserpes Konstantinos , Megas Panagiotis 
Published: May 2024

AbstractStress shielding and aseptic loosening are complications of short stem total hip arthroplasty, which may lead to hardware failure. Stems with increased porosity toward the distal end were discovered to be effective in reducing stress shielding, however, there is a lack of research on optimized porous distribution in stem’s coating. This study aimed to optimize the distribution of the coefficient of friction of a metaphyseal femoral stem, aiming for reducing stress shielding in the proximal area. A finite element analysis model of an implanted, titanium alloy short-tapered wedge stem featuring a porous coating made of titanium was designed to simulate a static structural analysis of the femoral stem's behavior under axial loading in Analysis System Mechanical Software. For computational feasibility, 500 combinations of coefficients of friction were randomly sampled. Increased strains in proximal femur were found in 8.4% of the models, which had decreased coefficients of friction in middle medial areas of porous coating and increased in lateral proximal and lateral and medial distal areas. This study reported the importance of the interface between bone and middle medial and distal lateral areas of the porous coating in influencing the biomechanical behavior of the proximal femur, and potentially reducing stress shielding.
Crystal structure, stability, and transport properties of Li2BeAl and Li2BeGa Heusler alloys: a DFT study
Authors: Mahmoudi Sima , Golzan Mir Maqsood , Nemati-Kande Ebrahim 
Published: May 2024

AbstractIn this study, the structural, elastic, electronic, and thermoelectric properties of full Li2BeAl and Li2BeGa Heusler alloys were explored using density functional and the Boltzmann transport theories. The GGA and HSE approximations have been used for the exchange–correlation potential. Results indicated that these two compounds are more energetically stable in the inverse Heusler structure. Additionally, both Li2BeAl and Li2BeGa Heusler alloys were found to be mechanically stable due to the positive values of the elastic constants. Also, the high values of the Young's modulus indicate that these compounds are stiff and exhibit a semi-metallic nature. The band gaps were determined to be 0.13 eV and − 0.22 eV for Li2BeAl and Li2BeGa alloys, respectively, using the GGA approximation. By employing the HSE hybrid functional, however, the band gap for Li2BeAl increased to 0.26 eV, and for Li2BeGa, it decreased to − 0.16 eV. Regarding thermoelectric properties, Seebeck coefficient, electrical conductivity, electronic and lattice thermal conductivities, power factor, and the figure of merit have been calculated for both Li2BeAl and Li2BeGa Heusler alloys at different temperatures. Seebeck coefficient in both alloys decreases with increasing the temperature and has the highest value at 300 K. Thermal conductivity and electrical conductivity increase with increasing the temperature, which confirms the intermetallic behavior of the Heusler alloys. The results obtained for both alloys show that n-type doping has better thermoelectric properties than p-type doping. The maximum value of the figure of merit (ZT) was obtained for n-type doping, which was 1.43 at 660 K for Li2BeAl and 0.39 at 1000 K for Li2BeGa alloy. The high values of ZT especially for electron-dopped Li2BeAl suggest the great potential of this material for use in thermoelectric devices. This study suggests that the proposed materials have potential applications in spintronic devices and thermoelectric materials due to their intermetallic character and effective thermoelectric coefficients.