bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of genes with oscillatory expression in glioblastoma: the paradigm of SOX2
Authors: Fu Richard Zhiming , Cottrell Oliver , Cutillo Luisa , Rowntree Andrew , Zador Zsolt , Wurdak Heiko , Papalopulu Nancy , Marinopoulou Elli 
Published: January 2024

AbstractQuiescence, a reversible state of cell-cycle arrest, is an important state during both normal development and cancer progression. For example, in glioblastoma (GBM) quiescent glioblastoma stem cells (GSCs) play an important role in re-establishing the tumour, leading to relapse. While most studies have focused on identifying differentially expressed genes between proliferative and quiescent cells as potential drivers of this transition, recent studies have shown the importance of protein oscillations in controlling the exit from quiescence of neural stem cells. Here, we have undertaken a genome-wide bioinformatic inference approach to identify genes whose expression oscillates and which may be good candidates for controlling the transition to and from the quiescent cell state in GBM. Our analysis identified, among others, a list of important transcription regulators as potential oscillators, including the stemness gene SOX2, which we verified to oscillate in quiescent GSCs. These findings expand on the way we think about gene regulation and introduce new candidate genes as key regulators of quiescence.
GAILS: an effective multi-object job shop scheduler based on genetic algorithm and iterative local search
Authors: Shao Xiaorui , Kshitij Fuladi Shubhendu , Kim Chang Soo 
Published: January 2024

AbstractThe job shop scheduling problem (JSSP) is critical for building one smart factory regarding resource management, effective production, and intelligent supply. However, it is still very challenging due to the complex production environment. Besides, most current research only focuses on classical JSSP, while flexible JSSP (FJSSP) is more usual. This article proposes an effective method, GAILS, to deal with JSSP and FJSSP based on genetic algorithm (GA) and iterative local search (ILS). GA is used to find the approximate global solution for the JSSP instance. Each instance was encoded into machine and subtask sequences. The corresponding machine and subtasks chromosome could be obtained through serval-time gene selection, crossover, and mutation. Moreover, multi-objects, including makespan, average utilization ratio, and maximum loading, are used to choose the best chromosome to guide ILS to explore the best local path. Therefore, the proposed method has an excellent search capacity and could balance globality and diversity. To verify the proposed method's effectiveness, the authors compared it with some state-of-the-art methods on sixty-six public JSSP and FJSSP instances. The comparative analysis confirmed the proposed method's effectiveness for classical JSSP and FJSSP in makespan, average utilization ratio, and maximum loading. Primarily, it obtains optimal-like solutions for several instances and outperforms others in most instances.
Analyzing urban influence on extreme winter precipitation through observations and numerical simulation of two South China case studies
Authors: Hu Chenxi , Tam Chi-Yung , Yang Zong-liang , Wang Ziqian 
Published: January 2024

AbstractThis study investigates the impact of urbanization on extreme winter rainfall in the South China Greater Bay Area (GBA) through the analysis of hourly station observations and simulations using the Weather Research and Forecasting Model with the Single Layer Urban Canopy Model (WRF-SLUCM). Data from 2008 to 2017 reveal that urban areas in the GBA experience lower 99th percentile hourly winter rainfall intensity compared to surrounding rural regions. However, urban locations exhibit higher annual maximum hourly rainfall (Rmax) and very extreme rainfall events (99.99th percentile) in winter, suggesting a positive influence of urbanization on extreme winter precipitation. A case study further underscores the role of the Urban Heat Island (UHI) effect in enhancing extreme rainfall intensity and probability in the GBA urban areas. Additionally, two extreme cases were dynamically downscaled using WRF-SLUCM, involving four parallel experiments: replacing urban land use with cropland (Nourban), using historical urban land use data from 1999 (99LS), projecting near-future urban land use for 2030 (30LS), and considering 2030 urban land use without anthropogenic heat (AH) (30LS-AH0). Synoptic analysis demonstrates that cold air intrusion suppresses the GBA UHI in Case 2013 but not in Case 2015. Reduced evaporation and humidity induced by urban surfaces significantly decrease urban precipitation in Case 2013. In contrast, the persistent UHI in Case 2015 enhances local convection and land–ocean circulation, leading to increased moisture flux convergence and amplified urban precipitation intensity and probability in 30LS compared to Nourban. This amplification is primarily attributed to AH, while the change in 99LS remains insignificant. These findings suggest that urban influences on extreme precipitation in the GBA persist during winter, particularly when the UHI effect is maintained.
Experimental study on the damage performance and forced response of concrete lining in fault-crossing tunnel
Authors: Hu Hui , Lan Youdi , Liu Yun , Qiu Wenge 
Published: January 2024

AbstractUnderstanding the adverse effects of tunnel crossing active faults on tunnel structures is crucial for ensuring their safe operation and construction. This paper presents the results of a series of model tests conducted at a scale of 1:40 using a fault sliding test box. Three sets of fault comparison tests were carried out, namely: (1) the tunnel does not cross the fault, (2) the spring stiffness is reduced, and (3) the model is not reinforced. The objective was to study the failure characteristics of tunnels crossing active faults. The findings reveal that when the hanging wall moves downwards, cracks appear on the surrounding rock surface of the hanging wall, specifically above the tunnel lining crossing the fault. The lining is significantly damaged within the range of − 30–+ 30 cm. All points of axial force exhibit an increasing compression trend. The section of axial force and bending moment near the fault fracture surface is notably larger than that far from the fault fracture surface. The safety factor of the entire structure decreases sharply after dislocation, making the tunnel more susceptible to cracking at various locations such as the vault, arch waist, left and right arch feet, and inverted arch. It has been proven that the shear compression of the fracture surface during fault dislocation is the main cause of longitudinal through cracks in the lining. The use of springs with higher stiffness effectively ensures the reciprocating dislocation of the upper and foot walls, with long duration and large displacement, providing a better simulation of the dislocation of active faults.
Yeast 26S proteasome nuclear import is coupled to nucleus-specific degradation of the karyopherin adaptor protein Sts1
Authors: Breckel Carolyn Allain , Johnson Zane M. , Hickey Christopher M. , Hochstrasser Mark 
Published: January 2024

AbstractIn eukaryotes, the ubiquitin–proteasome system is an essential pathway for protein degradation and cellular homeostasis. 26S proteasomes concentrate in the nucleus of budding yeastSaccharomyces cerevisiaedue to the essential import adaptor protein Sts1 and the karyopherin-α protein Srp1. Here, we show that Sts1 facilitates proteasome nuclear import by recruiting proteasomes to the karyopherin-α/β heterodimer. Following nuclear transport, the karyopherin proteins are likely separated from Sts1 through interaction with RanGTP in the nucleus. RanGTP-induced release of Sts1 from the karyopherin proteins initiates Sts1 proteasomal degradation in vitro. Sts1 undergoes karyopherin-mediated nuclear import in the absence of proteasome interaction, but Sts1 degradation in vivo is only observed when proteasomes successfully localize to the nucleus. Sts1 appears to function as a proteasome import factor during exponential growth only, as it is not found in proteasome storage granules (PSGs) during prolonged glucose starvation, nor does it appear to contribute to the rapid nuclear reimport of proteasomes following glucose refeeding and PSG dissipation. We propose that Sts1 acts as a single-turnover proteasome nuclear import factor by recruiting karyopherins for transport and undergoing subsequent RanGTP-initiated ubiquitin-independent proteasomal degradation in the nucleus.
Nuclear and mitochondrial genetic variants associated with mitochondrial DNA copy number
Authors: Koller Adriana , Filosi Michele , Weissensteiner Hansi , Fazzini Federica , Gorski Mathias , Pattaro Cristian , Schönherr Sebastian , Forer Lukas , Herold Janina M. , Stark Klaus J. , Döttelmayer Patricia , Hicks Andrew A. , Pramstaller Peter P. , Würzner Reinhard , Eckardt Kai-Uwe , Heid Iris M. , Fuchsberger Christian , Lamina Claudia , Kronenberg Florian 
Published: January 2024

AbstractMitochondrial DNA copy number (mtDNA-CN) is a biomarker for mitochondrial dysfunction associated with several diseases. Previous genome-wide association studies (GWAS) have been performed to unravel underlying mechanisms of mtDNA-CN regulation. However, the identified gene regions explain only a small fraction of mtDNA-CN variability. Most of this data has been estimated from microarrays based on various pipelines. In the present study we aimed to (1) identify genetic loci for qPCR-measured mtDNA-CN from three studies (16,130 participants) using GWAS, (2) identify potential systematic differences between our qPCR derived mtDNA-CN measurements compared to the published microarray intensity-based estimates, and (3) disentangle the nuclear from mitochondrial regulation of the mtDNA-CN phenotype. We identified two genome-wide significant autosomal loci associated with qPCR-measured mtDNA-CN: at HBS1L (rs4895440, p = 3.39 × 10–13) and GSDMA (rs56030650, p = 4.85 × 10–08) genes. Moreover, 113/115 of the previously published SNPs identified by microarray-based analyses were significantly equivalent with our findings. In our study, the mitochondrial genome itself contributed only marginally to mtDNA-CN regulation as we only detected a single rare mitochondrial variant associated with mtDNA-CN. Furthermore, we incorporated mitochondrial haplogroups into our analyses to explore their potential impact on mtDNA-CN. However, our findings indicate that they do not exert any significant influence on our results.
Low handgrip strength is associated with worse functional outcomes in long COVID
Authors: do Amaral Camila Miriam Suemi Sato Barros , da Luz Goulart Cássia , da Silva Bernardo Maia , Valente Jefferson , Rezende Anna Gabriela , Fernandes Eduardo , Cubas-Vega Nadia , Borba Mayla Gabriela Silva , Sampaio Vanderson , Monteiro Wuelton , de Melo Gisely Cardoso , Lacerda Marcus , Arêas Guilherme Peixoto Tinoco , Almeida-Val Fernando 
Published: January 2024

AbstractThe diagnosis of long COVID is troublesome, even when functional limitations are present. Dynapenia is the loss of muscle strength and power production that is not caused by neurologic or muscular diseases, being mostly associated with changes in neurologic function and/or the intrinsic force-generating properties of skeletal muscle, which altogether, may partially explain the limitations seen in long COVID. This study aimed to identify the distribution and possible associations of dynapenia with functional assessments in patients with long COVID. A total of 113 patients with COVID-19 were evaluated by functional assessment 120 days post-acute severe disease. Body composition, respiratory muscle strength, spirometry, six-minute walk test (6MWT, meters), and hand-grip strength (HGS, Kilogram-force) were assessed. Dynapenia was defined as HGS < 30 Kgf (men), and < 20 Kgf (women). Twenty-five (22%) participants were dynapenic, presenting lower muscle mass (p < 0.001), worse forced expiratory volume in the first second (FEV1) (p = 0.0001), lower forced vital capacity (p < 0.001), and inspiratory (p = 0.007) and expiratory (p = 0.002) peek pressures, as well as worse 6MWT performance (p < 0.001). Dynapenia, independently of age, was associated with worse FEV1, maximal expiratory pressure (MEP), and 6MWT, (p < 0.001) outcomes. Patients with dynapenia had higher intensive care unit (ICU) admission rates (p = 0.01) and need for invasive mechanical ventilation (p = 0.007) during hospitalization. The HGS is a simple, reliable, and low-cost measurement that can be performed in outpatient clinics in low- and middle-income countries. Thus, HGS may be used as a proxy indicator of functional impairment in this population.
Thinner bats to face hibernation as response to climate warming
Authors: López-Roig Marc , Piera Eduard , Serra-Cobo Jordi 
Published: January 2024

AbstractOne of the principal consequences of climate warming on hibernating mammals could be the loss of optimal conditions for hibernation. Although hibernating mammals, like bats, may be particularly vulnerable to climate warming due to a potential reduction of energy saving during the hibernation, there is a lack of knowledge regarding how they will be affected and how they will respond to this impact. Here, we examine the variation in the body condition of Schreiber’s bent-winged bat (Miniopterus schreibersii) to investigate changes in the optimization energy demand. Using a 20-year dataset (1998–2017), we analyse the temporal trends of body condition in three key stages of the hibernation period: onset and end of hibernation and early activity. Our results indicate that body condition at the onset and end of hibernation have decreased significantly over these 20 years. However, despite this lower body condition, the decrease of mass loss rate in the last decade (although not significant) indicate a greater saving of fat reserves. The significant increase in winter temperatures did not affect body condition or reserve depletion, instead, lower body condition was observed with a higher number of days below 0 °C. Unlike other hibernating bat species, the females had lower fat reserves than males in all three periods considered. This study indicates that hibernation energy requirements could be changing as an adaptation to a warmer climate and that hibernating bats can survive the winter by optimizing their lower accumulation of reserves.
Registered trials on novel therapies for myasthenia gravis: a cross-sectional study on ClinicalTrials.gov
Authors: Li Xingyue , Chen Jinxin , Wang Youtao , Zheng Siwei , Wan Kun , Liu Xiaodong 
Published: January 2024

AbstractNovel biologics in MG therapy research is on the rise. This research aimed to investigate the characteristics of registered trials on novel therapies for myasthenia gravis on ClinicalTrials.gov. This cross-sectional study used a descriptive approach to assess the features of the included trials on ClinicalTrials.gov. We found 62 registered trials from 2007 to 2023 on ClinicalTrials.gov. The results showed a yearly rise in the number of registered trials (r = 0.76, p < 0.001). Following 2017, more industry-sponsored trials were conducted (91.5% [43] vs. 60% [9], p = 0.009), fewer results were released (10.6% [5] vs. 60% [9], p = 0.001), and more trials entered phase 3 (67.4% [31] vs. 20% [2], p = 0.001). The most researched novel medications were neonatal Fc receptor inhibitors (51.2% [21]), complement inhibitors (39.0% [16]), and B cell depletors (14.6% [6]). According to the website’s data, the neonatal Fc receptor inhibitors and complement inhibitors were effective in treating myasthenia gravis patients in three trials (NCT03315130, NCT03669588, and NCT00727194). This study provides valuable insights into the profile of registered trials on novel therapies for myasthenia gravis. More clinical studies are needed in the future to prove the value of its application.
The osteoinductive potential of different root-end filling materials in a rat femur model
Authors: Aksu Seçkin , Delikan Ebru , Küçük Ayşe Özcan , Asoğlu Zehra Demiray , Yılmaz Şakir Necat 
Published: January 2024

AbstractIn pediatric dentistry, the enduring success of root-end filling materials employed for the establishment of apical plugs in immature teeth undergoing endodontic intervention is contingent upon their possessing a robust osteoinductive capacity. Hence, the primary objective of this study was to histologically assess the osteoinductive potential of four distinct dental materials, specifically recommended for retrograde filling applications, utilizing an animal hard tissue model. Within the designed experimental model, two bone defects measuring 2 mm in diameter and 2 mm in depth were created in both femurs of a cohort comprising 21 male Wistar albino rats. The first defect in the right femur was left blank as the control group, and Neo MTA Plus was placed in the second defect. The EndoSequence BCRRM Fast Set Putty was placed in the first of the defects on the left femur, and Endo Repair was placed in the second defect. Subjects were sacrificed after 7, 14, and 28 days of follow-up, and sections were examined to assess the degree of inflammation, connective tissue formation, and new bone formation. The data were statistically evaluated with Kruskal‒Wallis and post hoc Dunn's tests using SPSS 12 software. The bone healing levels of the Neo MTA Plus group were significantly higher than those of the other groups in all periods (p < 0.05). Bone organization in all groups decreased over time, and fibrous tissue was enriched. The results of this study demonstrate that NeoMta Plus has superior osteoinductive properties compared to other materials but that EndoSequence and Endo Repair have the potential to be developed.
Anthropogenic mortality threatens the survival of Canarian houbara bustards
Authors: Alonso Juan C. , Abril-Colón Inmaculada , Ucero Alberto , Palacín Carlos 
Published: January 2024

AbstractAnthropogenic mortality is a major cause of global mortality in terrestrial vertebrates. Quantifying its impact on the dynamics of threatened species is essential to improve their conservation. We investigated cause-specific mortality in Canarian houbara bustards (Chlamydotis undulata fuertaventurae), an endangered subspecies endemic to the Canary Islands. We monitored 51 individuals tagged with solar-powered GSM/GPRS loggers for an average of 3.15 years, and recorded 7 casualties at aerial lines (13.73% of the sample; 5 at power lines, 2 at telephone lines), 1 (1.96%) at a wire fence, 4 road kills (7.84%) and 1 case of predation by cat (1.96%). Cox proportional hazards models showed that anthropogenic and natural annual mortality rates were similar (respectively, 6.20% and 6.36% of the individuals). We estimate that 33–35 houbaras die each year in the Canary Islands due to anthropogenic causes. Population viability models using these data and juvenile productivity values obtained over seven years predicted the extinction of the species in 50 years. Eliminating anthropogenic mortality, the population could be recovered, but would still require management actions to improve habitat quality. Conservation measures to reduce anthropogenic mortality due to power line fatalities, roadkills and predation by cats, as well as to increase productivity, are urgently needed, particularly on Fuerteventura, where houbaras are on the brink of extinction.
Strain tuning MoO3 vibrational and electronic properties
Authors: Puebla Sergio , Li Hao , Çakıroğlu Onur , Sánchez-Viso Estrella , Munuera C. , D’Agosta Roberto , Castellanos-Gomez Andres 
Published: January 2024

AbstractThis work investigates the vibrational and electrical properties of molybdenum trioxide (α-MoO3) upon tensile strain applied along different crystal directions. Using a three-point bending setup in combination with Raman spectroscopy, we report measurements of a blueshift of the Raman modes when uniaxial tensile strain is applied along the a- and c-axis to this material. Furthermore, the electrical measurements reveal an increase in resistance with strain applied along both in-plane directions. The findings from the uniaxial strain and Raman spectroscopy measurements are further confirmed by ab-initio calculations. This study provides valuable insights into the mechanical and vibrational properties of α-MoO3 and its potential use in several applications. This study contributes to the growing body of knowledge on the properties of α-MoO3 and lays the foundation for further exploration of its potential applications. Given MoO3 holding the natural hyperbolic phonon polaritons, attracting significant research interest, this study has the potential to arouse the curiosity of the scientific community.
Antibodies from dengue patients with prior exposure to Japanese encephalitis virus are broadly neutralizing against Zika virus
Authors: Salem Gielenny M. , Galula Jedhan Ucat , Wu Shang-Rung , Liu Jyung-Hurng , Chen Yen-Hsu , Wang Wen-Hung , Wang Sheng-Fan , Song Cheng-Sheng , Chen Fan-Chi , Abarientos Adrian B. , Chen Guan-Wen , Wang Cheng-I , Chao Day-Yu 
Published: January 2024

AbstractExposure to multiple mosquito-borne flaviviruses within a lifetime is not uncommon; however, how sequential exposures to different flaviviruses shape the cross-reactive humoral response against an antigen from a different serocomplex has yet to be explored. Here, we report that dengue-infected individuals initially primed with the Japanese encephalitis virus (JEV) showed broad, highly neutralizing potencies against Zika virus (ZIKV). We also identified a rare class of ZIKV-cross-reactive human monoclonal antibodies with increased somatic hypermutation and broad neutralization against multiple flaviviruses. One huMAb, K8b, binds quaternary epitopes with heavy and light chains separately interacting with overlapping envelope protein dimer units spanning domains I, II, and III through cryo-electron microscopy and structure-based mutagenesis. JEV virus-like particle immunization in mice further confirmed that such cross-reactive antibodies, mainly IgG3 isotype, can be induced and proliferate through heterologous dengue virus (DENV) serotype 2 virus-like particle stimulation. Our findings highlight the role of prior immunity in JEV and DENV in shaping the breadth of humoral response and provide insights for future vaccination strategies in flavivirus-endemic countries.
A marine heatwave drives significant shifts in pelagic microbiology
Authors: Brown Mark V. , Ostrowski Martin , Messer Lauren F. , Bramucci Anna , van de Kamp Jodie , Smith Matthew C. , Bissett Andrew , Seymour Justin , Hobday Alistair J. , Bodrossy Levente 
Published: January 2024

AbstractMarine heatwaves (MHWs) cause disruption to marine ecosystems, deleteriously impacting macroflora and fauna. However, effects on microorganisms are relatively unknown despite ocean temperature being a major determinant of assemblage structure. Using data from thousands of Southern Hemisphere samples, we reveal that during an “unprecedented” 2015/16 Tasman Sea MHW, temperatures approached or surpassed the upper thermal boundary of many endemic taxa. Temperate microbial assemblages underwent a profound transition to niche states aligned with sites over 1000 km equatorward, adapting to higher temperatures and lower nutrient conditions bought on by the MHW. MHW conditions also modulate seasonal patterns of microbial diversity and support novel assemblage compositions. The most significant affects of MHWs on microbial assemblages occurred during warmer months, when temperatures exceeded the upper climatological bounds. Trends in microbial response across several MHWs in different locations suggest these are emergent properties of temperate ocean warming, which may facilitate monitoring, prediction and adaptation efforts.