bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic 3D genome reorganization during senescence: defining cell states through chromatin
Authors: Shaban Haitham A. , Gasser Susan M. 
Published: August 2023

Abstract
Cellular senescence, a cell state characterized by growth arrest and insensitivity to growth stimulatory hormones, is accompanied by a massive change in chromatin organization. Senescence can be induced by a range of physiological signals and pathological stresses and was originally thought to be an irreversible state, implicated in normal development, wound healing, tumor suppression and aging. Recently cellular senescence was shown to be reversible in some cases, with exit being triggered by the modulation of the cell’s transcriptional program by the four Yamanaka factors, the suppression of p53 or H3K9me3, PDK1, and/or depletion of AP-1. Coincident with senescence reversal are changes in chromatin organization, most notably the loss of senescence-associated heterochromatin foci (SAHF) found in oncogene-induced senescence. In addition to fixed-cell imaging, chromatin conformation capture and multi-omics have been used to examine chromatin reorganization at different spatial resolutions during senescence. They identify determinants of SAHF formation and other key features that differentiate distinct types of senescence. Not surprisingly, multiple factors, including the time of induction, the type of stress experienced, and the type of cell involved, influence the global reorganization of chromatin in senescence. Here we discuss how changes in the three-dimensional organization of the genome contribute to the regulation of transcription at different stages of senescence. In particular, the distinct contributions of heterochromatin- and lamina-mediated interactions, changes in gene expression, and other cellular control mechanisms are discussed. We propose that high-resolution temporal and spatial analyses of the chromatin landscape during senescence will identify early markers of the different senescence states to help guide clinical diagnosis.
Neutrophil elastase as a potential biomarker related to the prognosis of gastric cancer and immune cell infiltration in the tumor immune microenvironment
Authors: Jia Wangqiang , Luo Qianwen , Wu Jiang , Shi Yuanchao , Guan Quanlin 
Published: August 2023

AbstractExploring biomarkers interrelated the tumor immune microenvironment (TIME) provides novel ideas for predicting the prognosis of gastric cancer (GC) and developing new treatment strategies. We analyzed the differential gene expression levels between the high and low StromalScore and ImmuneScore groups. Neutrophil elastase (ELANE) was evaluated as a potential biomarker by conducting intersection analysis of the protein–protein interaction network and univariate Cox regression analysis. The expression of ELANE was evaluated by immunohistochemistry. Its prognostic value was evaluated using Kaplan–Meier (K–M) survival curves and multivariate Cox regression analysis and its potential biological molecular mechanism was examined by gene set enrichment analysis (GSEA). We applied the CIBERSORT computing method to analyze the relationship between ELANE and tumor immune-infiltrating cells (TIICs). K–M survival curve showed that higher ELANE expression was closely related to shorter overall survival. The Cox regression analysis indicated that the high expression of ELANE was an independent prognostic risk factor in patients with GC. The GSEA revealed that genes in the ELANE high-expression group were involved in the signaling pathways regulating immune response; genes in the ELANE low-expression group were involved in the signaling pathways that regulate metabolism. ELANE might be participate in the change of TIME from immunodominant to metabolically dominant and its expression was closely related to tumor mutation burden and multiple TIICs. ELANE is a potential biomarker for predicting the GC patients’ survival and prognosis. It influences the tumor immune cell infiltration in the TIME, and affects the TIME to maintain their immune status.
High-resolution mapping and dispersion analyses of volcanic ballistics emitted during the 3rd July 2019 paroxysm at Stromboli
Authors: Bisson M. , Spinetti C. , Gianardi R. , Strehlow K. , De Beni E. , Landi P. 
Published: August 2023

AbstractA detailed mapping of volcanic ballistic projectiles emplaced in a defined area, represents the starting point to derive preparatory data in hazard and risk studies of ballistics phenomena. Considering as case study the 3rd July 2019 paroxysmal eruption occurred at Stromboli volcano, we map and analyse at very high spatial resolution (8 cm) the distribution of the ballistic spatter clasts emplaced on the E flank of the volcano. The resulting map identifies and reproduces as geospatial polygon elements 152,228 spatter clasts with areal dimensions from 0.03 to 4.23 m2. Dispersed on 0.407 km2, the spatters cover an area of 29,000 m2 corresponding to an erupted products volume from 2.3 to 7.0 × 103 m3, calculated here for the first time. Spatial analyses indicate that the area mostly affected by the clasts emplacement is between N67.5 and N135 directions, identifying a preferential deposition between N112.50 and N123.75 directions. The clasts size distribution rapidly decreases with the size increase, highlighting a nearly constant ratio small/large clasts regardless the distance from the vent. Finally, additional investigations reveal that clasts dispersion parameters decrease progressively with the distance from the vent only along one direction (N67.5), highlighting how the morphology influences the deposition and remobilisation of mapped ballistics.
Multi-hazard exposure mapping under climate crisis using random forest algorithm for the Kalimantan Islands, Indonesia
Authors: Heo Sujung , Park Sangjin , Lee Dong Kun 
Published: August 2023

AbstractNumerous natural disasters that threaten people’s lives and property occur in Indonesia. Climate change-induced temperature increases are expected to affect the frequency of natural hazards in the future and pose more risks. This study examines the consequences of droughts and forest fires on the Indonesian island of Kalimantan. We first create maps showing the eleven contributing factors that have the greatest impact on forest fires and droughts related to the climate, topography, anthropogenic, and vegetation. Next, we used RF to create single and multi-risk maps for forest fires and droughts in Kalimantan Island. Finally, using the Coupled Model Intercomparison Project (CMIP6) integrated evaluation model, a future climate scenario was applied to predict multiple risk maps for RCP-SSP2-4.5 and RCP-SSP5-8.5 in 2040–2059 and 2080–2099. The probability of a 22.6% drought and a 21.7% forest fire were anticipated to have an influence on the study’s findings, and 2.6% of the sites looked at were predicted to be affected by both hazards. Both RCP-SSP2-4.5 and RCP-SSP5-8.5 have an increase in these hazards projected for them. Researchers and stakeholders may use these findings to assess risks under various mitigation strategies and estimate the spatial behavior of such forest fire and drought occurrences.
Straintronics in phosphorene via tensile vs shear strains and their combinations for manipulating the band gap
Authors: Solomenko Anastasiia G. , Sahalianov Ihor Y. , Radchenko Taras M. , Tatarenko Valentyn A. 
Published: August 2023

AbstractWe study the effects of the uniaxial tensile strain and shear deformation as well as their combinations on the electronic properties of single-layer black phosphorene. The evolutions of the strain-dependent band gap are obtained using the numerical calculations within the tight-binding (TB) model as well as the first-principles (DFT) simulations and compared with previous findings. The TB-model-based findings show that the band gap of the strain-free phosphorene agrees with the experimental value and linearly depends on both stretching and shearing: increases (decreases) as the stretching increases (decreases), whereas gradually decreases with increasing the shear. A linear dependence is less or more similar as compared to that obtained from the ab initio simulations for shear strain, however disagrees with a non-monotonic behaviour from the DFT-based calculations for tensile strain. Possible reasons for the discrepancy are discussed. In case of a combined deformation, when both strain types (tensile/compression + shear) are loaded simultaneously, their mutual influence extends the realizable band gap range: from zero up to the values respective to the wide-band-gap semiconductors. At a switched-on combined strain, the semiconductor–semimetal phase transition in the phosphorene is reachable at a weaker (strictly non-destructive) strain, which contributes to progress in fundamental and breakthroughs.
Inhibitory effects of Schisandrin C on collagen behavior in pulmonary fibrosis
Authors: Xu Mingchen , Zhao Chenghe , Song Haiming , Wang Chunmei , Li He , Qiu Xudong , Jing He , Zhuang Wenyue 
Published: August 2023

AbstractPulmonary fibrosis (PF) is a serious progressive fibrotic disease that is characterized by excessive accumulation of extracellular matrix (ECM), thus resulting in stiff lung tissues. Lysyl oxidase (LOX) is an enzyme involved in fibrosis by catalyzing collagen cross-linking. Studies found that the ingredients in schisandra ameliorated bleomycin (BLM)-induced PF, but it is unknown whether the anti-PF of schisandra is related to LOX. In this study, we established models of PF including a mouse model stimulated by BLM and a HFL1 cell model induced by transforming growth factor (TGF)-β1 to evaluate the inhibition effects of Schisandrin C (Sch C) on PF. We observed that Sch C treatment decreased pulmonary indexes compared to control group. Treatment of Sch C showed a significant reduction in the accumulation of ECM as evidenced by decreased expressions of α-SMA, FN, MMP2, MMP9, TIMP1 and collagen proteins such as Col 1A1, and Col 3A1. In addition, the expression of LOX in the lung tissue of mice after Sch C treatment was effectively decreased compared with the MOD group. The inhibition effects in vitro were consistent with those in vivo. Mechanistic studies revealed that Sch C significantly inhibited TGF-β1/Smad2/3 and TNF-α/JNK signaling pathways. In conclusion, our data demonstrated that Sch C significantly ameliorated PF in vivo and vitro, which may play an important role by reducing ECM deposition and inhibiting the production of LOX.
Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs
Authors: Sriaporn Chanenath , Campbell Kathleen A , Van Kranendonk Martin J , Handley Kim M 
Published: August 2023

Abstract
Terrestrial hot springs harbor diverse microbial communities whose compositions are shaped by the wide-ranging physico-chemistries of individual springs. The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. We therefore analysed the prevalence and relative abundance of bacteria and archaea in the sediments (n = 76) of hot spring features, in the Taupō Volcanic Zone (New Zealand), spanning large differences in major anion water chemistry, pH (2.0–7.5), and temperature (17.5–92.9 °C). Community composition, based on 16S rRNA amplicon sequence variants (ASVs) was strongly influenced by both temperature and pH. However, certain lineages characterized diverse hot springs. At the domain level, bacteria and archaea shared broadly equivalent community abundances across physico-chemically diverse springs, despite slightly lower bacteria-to-archaea ratios and microbial 16S rRNA gene concentrations at higher temperatures. Communities were almost exclusively dominated by Proteobacteria, Euryarchaeota or Crenarchaeota. Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9–84.2% of samples) and abundant (1.7–12.0% sample relative abundance), and together comprised 44% of overall community abundance. Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. Differences in metabolic gene composition and genome-specific metabolism delineated populations from relatives. Genome coverage calculations showed that populations associated with each lineage were distributed across a physicochemically broad range of hot springs. Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments.
Challenges of decarbonizing global maritime container shipping toward net-zero emissions
Authors: Lu Bo , Ming Xi , Lu Hongman , Chen Deyang , Duan Hongbo 
Published: August 2023

AbstractResponsible for the most significant part of the world’s burning of marine fossil fuels and shipping emissions, global maritime container shipping is under decarbonization pressure. This paper develops an integrated framework of bottom-up emission estimation and upscaling pathway analysis (BEEPA) to measure global maritime container shipping emissions from 2015 to 2020, and project possible pathways toward carbon neutrality by designing typical decarbonization scenarios. The result shows that global total seaborne container emissions fluctuated from 2015 to 2020 with a maximum value of 264 Mt, and the average annual energy consumption is 77.7 Mt (heavy fuel oil-equivalent). Container traffic to/from Asian ports generate the largest volumes of shipping emissions, accounting for about 55% of the global total. Under the most stringent scenario, container shipping emissions peak in 2025 and then quickly decline to 19.6 Mt in 2050, nearing the International Maritime Organization’s goal of reaching net zero emissions by or around 2050. Energy efficiency improvements contribute to emission reduction in the near term, but the trade growth impact still predominates in the shipping emission increase. With the maturity of infrastructural development and technological innovation, the energy transition would be the largest contributor emission reductions over the medium to long term.
Penta-MP5 (M = B, Al, Ga, In) monolayers as high-performance photocatalysts for overall water splitting
Authors: Chen Jiao , Cai Xinyong , Zhang Xiaotao , Wang Hongyan , Ni Yuxiang , Liu Xuefei , Chen Yuanzheng 
Published: August 2023

Phosphorus-rich phosphides penta-MP5 (M = B, Al, Ga, and In) monolayers have excellent electronic, light-harvesting, and transport properties, as well as exhibiting HER and OER activity, making them candidates for water-splitting photocatalysts.
Pyrazole–pyridine–pyrazole (NNN) ruthenium(ii) complex catalyzed acceptorless dehydrogenation of alcohols to aldehydes
Authors: Chen Yinyin , Cui Tianhua , Chen Hua , li Zheng Xue , Fu Haiyan , Li Ruixiang 
Published: August 2023

Complex 1 shows good catalytic activity (up to 99% yield) and excellent selectivity (up to 100%) for the AD of alcohols to aldehydes.
Aetiology of Type 2 diabetes in people with a ‘normal’ body mass index: testing the personal fat threshold hypothesis
Authors: Taylor Roy , Barnes Alison C. , Hollingsworth Kieren G. , Irvine Keaton M. , Solovyova Alexandra S. , Clark Lucy , Kelly Tara , Martin-Ruiz Carmen , Romeres Davide , Koulman Albert , Meek Claire M. , Jenkins Benjamin , Cobelli Claudio , Holman Rury R. 
Published: August 2023

AbstractWeight loss in overweight or obese individuals with Type 2 diabetes (T2D) can normalize hepatic fat metabolism, decrease fatty acid oversupply to β cells and restore normoglycaemia. One in six people has BMI &lt;27 kg/m2 at diagnosis, and their T2D is assumed to have different aetiology. The Personal Fat Threshold hypothesis postulated differing individual thresholds for lipid overspill and adverse effects on β-cell function. To test this hypothesis, people with Type 2 diabetes and body mass index &lt;27kg/m2 (n = 20) underwent repeated 5% weight loss cycles. Metabolic assessments were carried out at stable weight after each cycle and after 12 months. To determine how closely metabolic features returned to normal, 20 matched normoglycemic controls were studied once. Between baseline and 12 months: BMI fell (mean ± SD), 24.8 ± 0.4 to 22.5 ± 0.4 kg/m2 (P&lt;0.0001) (controls: 21.5 ± 0.5); total body fat, 32.1 ± 1.5 to 27.6 ± 1.8% (P&lt;0.0001) (24.6 ± 1.5). Liver fat content and fat export fell to normal as did fasting plasma insulin. Post-meal insulin secretion increased but remained subnormal. Sustained diabetes remission (HbA1c &lt; 48 mmol/mol off all glucose-lowering agents) was achieved by 70% (14/20) by initial weight loss of 6.5 (5.5–10.2)%. Correction of concealed excess intra-hepatic fat reduced hepatic fat export, with recovery of β-cell function, glycaemic improvement in all and return to a non-diabetic metabolic state in the majority of this group with BMI &lt;27 kg/m2 as previously demonstrated for overweight or obese groups. The data confirm the Personal Fat Threshold hypothesis: aetiology of Type 2 diabetes does not depend on BMI. This pathophysiological insight has major implications for management.
The Influence of Shyness on Language Assessment
Authors: Melnick Liesl , Kucker Sarah C. 
Published: August 2023

Purpose:The goal of this study is to examine how shyness affects a child's performance on language assessments that vary in sociability. We hypothesized that accuracy on language tasks would be driven by shyness such that shyer children would perform better on nonsociable tasks compared to sociable tasks.Method:The procedures followed a quasi-experimental design. One hundred twenty-two participants, ages 17–42 months and varying in their temperament, each underwent a series of three language tasks. The order of tasks was randomized, and each task varied in the social interaction required: a looking task, a pointing task, and a production task. Data were collected via Zoom, and parents reported their child's shyness level via the Early Child Behavior Questionnaire.Results:Shyness was compared with participants' accuracy across the three tests while controlling for age and vocabulary percentile. There were significant differences in children's performance across the tasks, with respect to shyness. Shyer children performed worse on the production task compared to less shy children. All children did well on the pointing task regardless of shyness level, but performance was more nuanced on the looking task such that shyer children were at times more accurate but also less likely to respond in general.Conclusions:As shown by these results, shyer and less shy children respond differentially to methods of language assessment that vary in sociability. It is important for clinicians to acknowledge shyness when choosing an appropriate assessment of children's language. Future direction includes assessing performance on standardized assessments.Supplemental Material:https://doi.org/10.23641/asha.23845521
An In Vitro Analysis of a One-Way Arterial Check Valve
Authors: Springer Michael A. , Korth Douglas C. , Guiterrez Pamela J. , Morrow John F. , Stammers Alfred H. 
Published: August 2023

The utilization of a centrifugal pump during extracorporeal circulation may result in retrograde blood flow through the circuit. The non-occlusive characteristics of a centrifugal pump could create a condition where regurgitant flow is possible when the pressure in the cannulated vessel exceeded the pressure in the extracorporeal circuit. The reversal of flow, from patient to pump, could entrain air from multiple points including cannulation sites, suture holes, or open vessels or chambers. The following study was conducted to evaluate the ability of an arterial check valve (ACV) to prevent retrograde flow.
An in vitro circuit was designed to evaluate the flow dynamics of an ACV under a variety of test conditions including the following: flow rates between 0 and 7.5 L/min, and at temperatures of 37°, 25° and 15°C. The design characteristics of the ACV permitted easy priming, aided by gentle turbulence at the junction of the valve attachment to the casing. There was no difference in pressure drop across the ACV at any flow when compared to an identical circuit without the valve. The pressure drop across the ACV never exceeded 5 mmHg, at any temperature, when flow was less than 2 L/min. Retrograde leak volume was determined by creating "back" pressures on the valve, ranging from 25 to 500 mmHg. One ACV malfunctioned at a back pressure of 250 mmHg, and the data for that valve was omitted for comparative purposes. On the remaining valves, leak volume did not exceed 1.2 ml, and was a result of the compliance of the leaflet structures causing a slight volume displacement due to valve motion in a retrograde fashion. The results of this study show that the ACV permitted unimpeded, unidirectional flow at all operating conditions considered clinically relevant, and may be efficacious in alleviating the chance of retrograde circuit flow.
A Perfluorocarbon Emulsion Prime Additive Improves the Electroencephalogram and Cerebral Blood Flow at the Initiation of Cardiopulmonary Bypass
Authors: Vocelka C. , Spiess B. , Soltow L. , Thomas R. , Gohra H. , Akimoto H. , Rothnie C. , Kunzelman K. , Verrier E. , Cochran R.P. 
Published: August 2023

Depression in electroencephalogram (EEG) has been documented clinically and is reproducible in swine at the initiation of cardiopulmonary bypass (CPB) utilizing a crystalloid prime. The physiological cause of this transient alteration in electrical brain activity appears to be associated with the transient drop in arterial pressure. The etiology is unknown but may be attributable to the bolus of the crystalloid prime or micro emboli, either air or fibrin-platelet.
Thirteen swine (17-26 kg) were anesthetized and received 4 mg/kg dexamethasone, and following a tracheotomy were ventilated with halothane in 100% O2. Surgical preparation included: sternotomy and preparation for right atrial- aortic CPB. The CPB circuit consisted of a hollow fiber membrane oxygenator, a hard-shell venous reservoir, a roller pump, and PVC tubing. The circuit was randomly primed with either 1200 ml Plasmalyte-A or 10 ml/kg perfluorocarbon emulsion (PFE) and Plasmalyte-A to total 1200 ml. The animals were monitored continuously for systemic hemodynamics and electrocardiogram, and cerebral monitoring included blood flow and bitemporal EEG. Arterial blood gases were measured and PaCO2 was kept between 30-45 mmHg both before and during CPB. Cerebral blood flow (CBF) was measured pre-CPB and at 10 minutes after initiation of CPB. Bitemporal computerized EEG was analyzed every 60 seconds. Total power of each hemisphere, power in frequency bands, and spectral edge were recorded.
All animals demonstrated a relative decrease in EEG total power at the onset of CPB. Animals that received PFE demonstrated a more stable arterial blood pressure, an increased CBF, and a lesser decrease and an earlier recovery of the EEG power. The differences in hemodynamics and EEG in the PFE prime group may be beneficial in decreasing the neuro-psychological changes associated with CPB and needs further investigation.