bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes
Authors: Kim Mangi , Xi Hong , Park Suhyeon , Yun Yunho , Park Jongsun 
Published: August 2021

AbstractGATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17–20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.
Rapid target validation in a Cas9-inducible hiPSC derived kidney model
Authors: Shamshirgaran Yasaman , Jonebring Anna , Svensson Anna , Leefa Isabelle , Bohlooly-Y Mohammad , Firth Mike , Woollard Kevin J. , Hofherr Alexis , Rogers Ian M. , Hicks Ryan 
Published: August 2021

AbstractRecent advances in induced pluripotent stem cells (iPSCs), genome editing technologies and 3D organoid model systems highlight opportunities to develop new in vitro human disease models to serve drug discovery programs. An ideal disease model would accurately recapitulate the relevant disease phenotype and provide a scalable platform for drug and genetic screening studies. Kidney organoids offer a high cellular complexity that may provide greater insights than conventional single-cell type cell culture models. However, genetic manipulation of the kidney organoids requires prior generation of genetically modified clonal lines, which is a time and labor consuming procedure. Here, we present a methodology for direct differentiation of the CRISPR-targeted cell pools, using a doxycycline-inducible Cas9 expressing hiPSC line for high efficiency editing to eliminate the laborious clonal line generation steps. We demonstrate the versatile use of genetically engineered kidney organoids by targeting the autosomal dominant polycystic kidney disease (ADPKD) genes: PKD1 and PKD2. Direct differentiation of the respective knockout pool populations into kidney organoids resulted in the formation of cyst-like structures in the tubular compartment. Our findings demonstrated that we can achieve > 80% editing efficiency in the iPSC pool population which resulted in a reliable 3D organoid model of ADPKD. The described methodology may provide a platform for rapid target validation in the context of disease modeling.
Perchlorate salts confer psychrophilic characteristics in α-chymotrypsin
Authors: Gault Stewart , Jaworek Michel W. , Winter Roland , Cockell Charles S. 
Published: August 2021

AbstractStudies of salt effects on enzyme activity have typically been conducted at standard temperatures and pressures, thus missing effects which only become apparent under non-standard conditions. Here we show that perchlorate salts, which are found pervasively on Mars, increase the activity of α-chymotrypsin at low temperatures. The low temperature activation is facilitated by a reduced enthalpy of activation owing to the destabilising effects of perchlorate salts. By destabilising α-chymotrypsin, the perchlorate salts also cause an increasingly negative entropy of activation, which drives the reduction of enzyme activity at higher temperatures. We have also shown that α-chymotrypsin activity appears to exhibit an altered pressure response at low temperatures while also maintaining stability at high pressures and sub-zero temperatures. As the effects of perchlorate salts on the thermodynamics of α-chymotrypsin’s activity closely resemble those of psychrophilic adaptations, it suggests that the presence of chaotropic molecules may be beneficial to life operating in low temperature environments.
Long-term outcomes of “open iridectomy” for secondary anterior chamber epithelial iris cysts
Authors: Lan Jie , Liu Ting , Huang Yusen , Pan Xiaojing , Wei Yufen , Xie Pingzhong , Kong Qianqian , Guo Xiang , Xie Lixin 
Published: August 2021

AbstractEpithelial cysts run a high risk of recurrence and conversion to sheet-like ingrowth after surgical intervention. In this retrospective study, we introduced a modified iridectomy for treatment of secondary epithelial iris cysts (EICs) in the anterior chamber. Twenty-nine patients (29 eyes) aged 2–61 years received “open iridectomy” for EICs between April 1995 and July 2019. After viscodissection, most of the cyst wall was cut using a 20-gauge aspiration cutter via a 2.5-mm clear corneal incision. The residue closely adhering to the iris stroma was remained to avoid photophobia and diplopia. At 3 months, best corrected visual acuity was ≥ 20/100 in 55.5% (15/27, except two pediatric patients with poor cooperation) of patients. Among the eight patients suffering partial corneal edema preoperatively, six patients received surgery treatment at 3–6.5 months, and the cornea in the other two patients became transparent after medication. In a mean follow-up of 47.4 months, recurrence occurred in 3 patients at 7, 37, and 118 months, respectively. The percentage of treatment success was 96%, 87%, and 65% at 1, 5, and 10 years, respectively. “Open iridectomy” was effective for EICs, with a minimal invasion, less damage to the corneal endothelium, and a low recurrence rate.
Paleotemperature record of the Middle Devonian Kačák Episode
Authors: Suttner Thomas J. , Kido Erika , Joachimski Michael M. , Vodrážková Stanislava , Pondrelli Monica , Corradini Carlo , Corriga Maria G. , Simonetto Luca , Kubajko Michal 
Published: August 2021

AbstractThe Middle Devonian Epoch, ~ 393–383 million years ago, is known for a peak in diversity and highest latitudinal distribution of coral and stromatoporoid reefs. About 388 million years ago, during the late Eifelian and earliest Givetian, climax conditions were interrupted by the polyphased Kačák Episode, a short-lived period of marine dys-/anoxia associated with climate warming that lasted less than 500 kyr. Reconstruction of the seawater temperature contributes to a better understanding of the climate conditions marine biota were exposed to during the event interval. To date, conodont apatite-based paleotemperatures across the Eifelian–Givetian boundary interval have been published from Belarus, France, Germany and North America (10–36° S paleolatitude). Here we provide new δ18Oapatite data from the Carnic Alps (Austria, Italy) and the Prague Synform (Czech Republic). For better approximation of the paleotemperature record across the Kačák Episode, a latitude-dependent correction for Middle Devonian seawater δ18O is applied. Because δ18Oapatite data from shallow marine sections are influenced by regional salinity variations, calculated mean sea surface temperatures (SST) are restricted to more open marine settings (22–34° S paleolatitude). Water temperatures reach ~ 34 °C in the Prague Synform and ~ 33 °C in the Carnic Alps and suggest that SSTs of the southern hemisphere low latitudes were ~ 6 °C higher than previously assumed for this time interval.
COVID-related psychological distress fully mediates the association from social impact to sleep disturbance among patients with chronic schizophrenia
Authors: Li Dian-Jeng , Chou Li-Shiu , Chou Frank Huang-Chih , Hsu Su-Ting , Hsieh Kuan-Ying , Wu Hui-Ching , Kao Wei-Tsung , Lin Guei-Ging , Chen Wei-Jen , Huang Joh-Jong 
Published: August 2021

AbstractThe aims of the current study were to identify factors associated with sleep disturbance and Coronavirus disease-19 related psychological distress (CPD), and to develop a conceptual model to verify the mediating effect of CPD on the association between social impact and sleep disturbance. This study recruited patients with schizophrenia. Factors associated with the level of sleep disturbance and CPD were identified using univariate linear regression, and further selected into a stepwise multivariate linear regression model. Using structural equation modeling, a mediation model was developed to test the mediating effect of CPD on the association between social impact and sleep disturbance. After estimating with the stepwise and bootstrap regression, higher levels of CPD were associated with higher levels of social anxiety and subjects without a regular diet. Sleep disturbance was associated with a higher level of social anxiety, a history of psychological trauma, chronic disease, and those who did not smoke. The final model confirmed the mediating effects of CPD; whereas, the direct effect from social impact to sleep disturbance did not reach statistical significance. The current study manifests the crucial role of CPD on the association between social impact and sleep disturbance, and timely intervention for CPD is warranted.
Global potential distribution prediction of Xanthium italicum based on Maxent model
Authors: Zhang Yang , Tang Jieshi , Ren Gang , Zhao Kaixin , Wang Xianfang 
Published: August 2021

AbstractAlien invasive plants pose a threat to global biodiversity and the cost of control continues to rise. Early detection and prediction of potential risk areas are essential to minimize ecological and socio-economic costs. In this study, the Maxent model was used to predict current and future climatic conditions to estimate the potential global distribution of the invasive plantXanthium italicum. The model consists of 366 occurrence records (10 repeats, 75% for calibration and 25% for verification) and 10 climate prediction variables. According to the model forecast, the distribution ofX. italicumwas expected to shrink in future climate scenarios with human intervention, which may be mainly caused by the rise in global average annual temperature. The ROC curve showed that the AUC values of the training set and the test set are 0.965 and 0.906, respectively, indicating that the prediction result of this model was excellent. The contribution rates of annual mean temperature, monthly mean diurnal temperature range, standard deviation of temperature seasonal change and annual average precipitation to the geographical distribution ofX. italicumwere 65.3%, 11.2%, 9.0%, and 7.7%, respectively, and the total contribution rate was 93.2%. These four variables are the dominant environmental factors affecting the potential distribution ofX. italicum, and the influence of temperature is greater than that of precipitation. Through our study on the potential distribution prediction ofX. italicumunder the future climatic conditions, it has contribution for all countries to strengthen its monitoring, prevention and control, including early warning.
Impact of land use/land cover changes on water quality and human health in district Peshawar Pakistan
Authors: Ahmad Waqas , Iqbal Javed , Nasir Muhammad Jamal , Ahmad Burhan , Khan Muhammad Tasleem , Khan Shahid Nawaz , Adnan Syed 
Published: August 2021

AbstractThe quality and quantity of groundwater resources are affected by landuse/landcover (LULC) dynamics, particularly the increasing urbanization coupled with high household wastewater discharge and decreasing open lands. This study evaluates temporal changes of groundwater quality for 2012 and 2019, its relation to Landuse/landcover, and its impact on Peshawar's residents (study area), Pakistan. A total of 105 and 112 groundwater samples were collected from tube wells in 2012 and 2019. Samples were then analyzed for seven standard water quality parameters (i.e., pH, electric conductivity (EC), turbidity, chloride, calcium, magnesium, and nitrate). Patient data for waterborne diseases were also collected for the years 2012 and 2019 to relate the impact of groundwater quality on human health. Landsat satellite images were classified for the years 2012 and 2019 to observe landuse/landcover dynamics concerning groundwater quality. Results manifested a decrease in groundwater quality for the year 2019 compared to 2012 and were more highlighted in highly populated areas. The nitrate concentration level was found high in the vicinity of agricultural areas due to the excessive use of nitrogenous fertilizers and pesticides, and thus the methemoglobinemia patients ratio increased by 14% (48–62% for the year 2012 and 2019, respectively). Besides, Urinary Tract Infections, Peptic Ulcer, and Dental Caries diseases increased due to the high calcium and magnesium concentration. The overall results indicate that anthropogenic activities were the main driver of Spatio-temporal variability in groundwater quality of the study area. The study could help district health administration understand groundwater quality trends, make appropriate site-specific policies, and formulate future health regulations.
Circulating syndecan-1 is reduced in pregnancies with poor fetal growth and its secretion regulated by matrix metalloproteinases and the mitochondria
Authors: Garcha Damanpreet , Walker Susan P. , MacDonald Teresa M. , Hyett Jon , Jellins Jessica , Myers Jenny , Illanes Sebastian E. , Nien Jhy K. , Schepeler Manuel , Keenan Emerson , Whigham Carole-Anne , Cannon Ping , Murray Elizabeth , Nguyen Tuong-Vi , Kandel Manju , Masci Joshua , Murphy Ciara , Cruickshank Tess , Pritchard Natasha , Hannan Natalie J. , Brownfoot Fiona , Roddy Mitchell Alexandra , Middleton Anna , Pell Gabrielle , Wong Georgia P. , Tong Stephen , Kaitu’u-Lino Tu’uhevaha J. 
Published: August 2021

AbstractFetal growth restriction is a leading cause of stillbirth that often remains undetected during pregnancy. Identifying novel biomarkers may improve detection of pregnancies at risk. This study aimed to assess syndecan-1 as a biomarker for small for gestational age (SGA) or fetal growth restricted (FGR) pregnancies and determine its molecular regulation. Circulating maternal syndecan-1 was measured in several cohorts; a large prospective cohort collected around 36 weeks’ gestation (n = 1206), a case control study from the Manchester Antenatal Vascular service (285 women sampled at 24–34 weeks’ gestation); two prospective cohorts collected on the day of delivery (36 + 3–41 + 3 weeks’ gestation, n = 562 and n = 405 respectively) and a cohort who delivered for preterm FGR (< 34 weeks). Circulating syndecan-1 was consistently reduced in women destined to deliver growth restricted infants and those delivering for preterm disease. Syndecan-1 secretion was reduced by hypoxia, and its loss impaired proliferation. Matrix metalloproteinases and mitochondrial electron transport chain inhibitors significantly reduced syndecan-1 secretion, an effect that was rescued by coadministration of succinate, a mitochondrial electron transport chain activator. In conclusion, circulating syndecan-1 is reduced among cases of term and preterm growth restriction and has potential for inclusion in multi-marker algorithms to improve detection of poorly grown fetuses.
Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death
Authors: Antiga Laura G. , Sibbens Lode , Abakkouy Yasmina , Decorte Ronny , Van Den Bogaert Wouter , Van de Voorde Wim , Bekaert Bram 
Published: August 2021

AbstractRNA analysis of post-mortem tissues, or thanatotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual. For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death. The results reveal that, after death, two clearly differentiated groups of up- and down-regulated genes can be detected. Pathway analysis suggests active processes that promote cell survival and DNA damage repair, rather than passive degradation, are the source of early post-mortem changes of gene expression in blood. In addition, a generalized linear model with an elastic net restriction predicted post-mortem interval with a root mean square error of 4.75 h. In conclusion, we demonstrate that post-mortem gene expression data can be used as biomarkers to estimate the post-mortem interval though further validation using independent sample sets is required before use in forensic casework.
Indoor and outdoor noise changes due to the COVID-19 lockdown and their effects on individuals’ expectations and preferences
Authors: Caniato Marco , Bettarello Federica , Gasparella Andrea 
Published: August 2021

AbstractThe COVID-19 pandemic significantly modified our urban territories. One of the most strongly affected parameters was outdoor noise, caused by traffic and human activity in general, all of which were forced to stop during the spring of 2020. This caused an indubitable noise reduction both inside and outside the home. This study investigates how people reacted to this new unexpected, unwanted and unpredictable situation. Using field measurements, it was possible to demonstrate how the outdoor sound pressure level clearly decreased. Furthermore, by means of an international survey, it was discovered that people had positive reaction to the lower noise level. This preference was generally not related to home typology or location in the city, but rather to a generalized wish to live in a quieter urban environment.
Urine metabolic phenotyping in children with nocturnal enuresis and comorbid neurobehavioral disorders
Authors: Yu Mei-Ching , Wang Ta-Min , Chiou Yee-Hsuan , Yu Meng-Kung , Lin Chiao-Fan , Chiu Chih-Yung 
Published: August 2021

AbstractNocturnal enuresis (NE) is a common problem among 10% school-aged children. The etiologies underlying childhood NE is complex and not fully understood nowadays. Nevertheless, increasing evidence suggests a potential link between neurobehavioral disorders and enuresis in children. In this study, we aimed to explore novel metabolomic insights into the pathophysiology of NE and also, its association with pediatric psychiatric problems. Urine collected from 41 bedwetting children and 27 healthy control children was analyzed by using 1H-nuclear magnetic resonance spectroscopy from August 2017 to December 2018. At regular follow-up, there were 14 children with refractory NE having a diagnosis of attention deficient hyperactivity disorder (ADHD) or anxiety. Eventually, we identified eight significantly differential urinary metabolites and particularly increased urinary excretion of betaine, creatine and guanidinoacetate linked to glycine, serine and threonine metabolism were associated with a comorbidity of neurobehavioral disorders in refractory bedwetting children. Notably, based on physiological functions of betaine acting as a renal osmolyte and methyl group donor, we speculated its potential role in modulation of renal and/or central circadian clock systems, becoming a useful urinary metabolic marker in diagnosis of treatment-resistant NE in children affected by these two disorders.
Safety and humoral responses to BNT162b2 mRNA vaccination of SARS-CoV-2 previously infected and naive populations
Authors: Efrati Shai , Catalogna Merav , Abu Hamad Ramzia , Hadanny Amir , Bar-Chaim Adina , Benveniste-Levkovitz Patricia , Levtzion-korach Osnat 
Published: August 2021

AbstractSince COVID-19 risk of reinfection is of great concern, the safety and efficacy of the mRNA-based vaccines in previously infected populations should be assessed. We studied 78 individuals previously infected with SARS-CoV-19, who received a single dose of BNT162b2 mRNA COVID-19 vaccine, and 1:2 ratio matched infection-naïve cohort who received two injections. The evaluation procedure included symptom monitoring, and serological tests. Among the post-infected population, the median IgG-S response after the first vaccine dose was 3.35 AU, compared to 2.38 AU after the second vaccine injection in the infection naive group. A strong correlation was demonstrated between IgG-S level before vaccination, and the corresponding responses after a single vaccine dose (r = 0.8, p < 0.001) in the post infected population. Short-term severe symptoms that required medical attention were found in 6.8% among the post-infected individuals, while none were found in the infection naïve population. Our data suggest that a single vaccine dose is sufficient to induce an intense immune response in post-infected population regardless of seropositivity. Although some short-term safety issues were observed compared to the infection naïve population, a single dose regimen can be considered safe in post-infected populations.
Prevalence characteristics of human papillomavirus (HPV) infection among women receiving physical examinations in the Shangcheng District, Hangzhou city, China
Authors: Wang Lu , Yu Chunfeng , Ni Xiaoling , Wang Fang , Wen Caihe , Jin Mei , Chen Juanjuan , Zhang Kunming , Wang Jiahao 
Published: August 2021

AbstractThis paper aimed to investigate the characteristics of female HPV infection in the Shangcheng District, Hangzhou city, China. The retrospective study was designed to analyze the HPV prevalence rate of 22,382 women receiving physical examinations from 2016 to 2020 in the Shangcheng District of Hangzhou city in China. A commercial kit was designed to detect the HPV genotypes. Trends were examined for age-specific groups (≤ 30 years, 31–44 years, 45–54 years, 55–64 years,  ≥ 65 years). A receiver operating characteristic (ROC) analysis was used to assess the correlation of age classification in high risk HPV (HR-HPV) infection. 22.41% (5015/22,382) of samples were HPV positive, 91.28% (4578/5015) of HPV positive women were infected by HR-HPV. The most prevalent HR-HPV genotypes were 16, 52, 18, 58, 56, and 51. The trend of HPV prevalence showed the significant differences in age-specific groups (χ2 = 164.70, P < 0.001). Moreover, the areas under ROC curve (AUC) was 0.712 in 55–64 years group which showed a strong contribution of age classification for HR-HPV infection. This study provided baseline data on the prevalence characteristics of HPV infection and the critical age group of HR-HPV prevalence rate was 55–64 y among the samples receiving physical examinations.