bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel method for single-cell data imputation using subspace regression
Authors: Tran Duc , Tran Bang , Nguyen Hung , Nguyen Tin 
Published: February 2022

AbstractRecent advances in biochemistry and single-cell RNA sequencing (scRNA-seq) have allowed us to monitor the biological systems at the single-cell resolution. However, the low capture of mRNA material within individual cells often leads to inaccurate quantification of genetic material. Consequently, a significant amount of expression values are reported as missing, which are often referred to as dropouts. To overcome this challenge, we develop a novel imputation method, named single-cell Imputation via Subspace Regression (scISR), that can reliably recover the dropout values of scRNA-seq data. The scISR method first uses a hypothesis-testing technique to identify zero-valued entries that are most likely affected by dropout events and then estimates the dropout values using a subspace regression model. Our comprehensive evaluation using 25 publicly available scRNA-seq datasets and various simulation scenarios against five state-of-the-art methods demonstrates that scISR is better than other imputation methods in recovering scRNA-seq expression profiles via imputation. scISR consistently improves the quality of cluster analysis regardless of dropout rates, normalization techniques, and quantification schemes. The source code of scISR can be found on GitHub athttps://github.com/duct317/scISR.
Lower multisensory temporal acuity in individuals with high schizotypal traits: a web-based study
Authors: Marsicano Gianluca , Cerpelloni Filippo , Melcher David , Ronconi Luca 
Published: February 2022

AbstractNatural events are often multisensory, requiring the brain to combine information from the same spatial location and timing, across different senses. The importance of temporal coincidence has led to the introduction of the temporal binding window (TBW) construct, defined as the time range within which multisensory inputs are highly likely to be perceptually bound into a single entity. Anomalies in TBWs have been linked to confused perceptual experiences and inaccurate filtering of sensory inputs coming from different environmental sources. Indeed, larger TBWs have been associated with disorders such as schizophrenia and autism and are also correlated to a higher level of subclinical traits of these conditions in the general population. Here, we tested the feasibility of using a web-based version of a classic audio-visual simultaneity judgment (SJ) task with simple flash-beep stimuli in order to measure multisensory temporal acuity and its relationship with schizotypal traits as measured in the general population. Results show that: (i) the response distribution obtained in the web-based SJ task was strongly similar to those reported by studies carried out in controlled laboratory settings, and (ii) lower multisensory temporal acuity was associated with higher schizotypal traits in the “cognitive-perceptual” domains. Our findings reveal the possibility of adequately using a web-based audio-visual SJ task outside a controlled laboratory setting, available to a more diverse and representative pool of participants. These results provide additional evidence for a close relationship between lower multisensory acuity and the expression of schizotypal traits in the general population.
The impact of COVID-19 stressors on psychological distress and suicidality in a nationwide community survey in Taiwan
Authors: Wu Chia-Yi , Lee Ming-Been , Huong Pham Thi Thu , Chan Chia-Ta , Chen Chun-Yin , Liao Shih-Cheng 
Published: February 2022

AbstractCOVID-19 stressors and psychological stress response are important correlates of suicide risks under the COVID-19 pandemic. This study aimed to investigate the prevalence of COVID-19 stress, its impact on mental health and associated risk factors among the general population during the outbreak of COVID-19 in July 2020 throughout Taiwan. A nationwide population-based survey was conducted using a computer-assisted telephone interview system with a stratified, proportional randomization method for the survey. The questionnaire comprised demographic variables, psychological distress assessed by the five-item Brief Symptom Rating Scale and independent psychosocial variables including COVID-19 stressors, loneliness, suicidality, and health-related self-efficacy. In total, 2094 respondents completed the survey (female 51%). The COVID-19 stress was experienced among 45.4% of the participants, with the most prevalent stressors related to daily life and job/financial concerns. Higher levels of suicidality, loneliness, and a lower level of self-efficacy had significantly higher odds of having COVID-19 stress. The structural equation model revealed that COVID-19 stress was moderately associated with psychological distress and mediated by other psychosocial risk factors. The findings call for more attention on strategies of stress management and mental health promotion for the public to prevent larger scales of psychological consequences in future waves of the COVID-19 pandemic.
Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis)
Authors: Shi Fengyan , Pang Zhijin , Liu Chuanhong , Zhou Li , Tan Chong , Ren Jie , Ye Xueling , Feng Hui , Liu Zhiyong 
Published: February 2022

AbstractAnther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestrisL. ssp.pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA–DEmRNA, 281 DEmiRNA–DElncRNA, and 23 DEmiRNA–DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers ofArabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.
Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1
Authors: Puiggené Òscar , Espinosa María José Cárdenas , Schlosser Dietmar , Thies Stephan , Jehmlich Nico , Kappelmeyer Uwe , Schreiber Stephan , Wibberg Daniel , Kalinowski Joern , Harms Hauke , Heipieper Hermann J. , Eberlein Christian 
Published: February 2022

AbstractThe continuing reports of plastic pollution in various ecosystems highlight the threat posed by the ever-increasing consumption of synthetic polymers. Therefore, Pseudomonas capeferrum TDA1, a strain recently isolated from a plastic dump site, was examined further regarding its ability to degrade polyurethane (PU) compounds. The previously reported degradation pathway for 2,4-toluene diamine, a precursor and degradation intermediate of PU, could be confirmed by RNA-seq in this organism. In addition, different cell fractions of cells grown on a PU oligomer were tested for extracellular hydrolytic activity using a standard assay. Strikingly, purified outer membrane vesicles (OMV) of P. capeferrum TDA1 grown on a PU oligomer showed higher esterase activity than cell pellets. Hydrolases in the OMV fraction possibly involved in extracellular PU degradation were identified by mass spectrometry. On this basis, we propose a model for extracellular degradation of polyester-based PUs by P. capeferrum TDA1 involving the role of OMVs in synthetic polymer degradation.
Crop–livestock integration enhanced soil aggregate-associated carbon and nitrogen, and phospholipid fatty acid
Authors: Bansal Sangeeta , Chakraborty Poulamee , Kumar Sandeep 
Published: February 2022

AbstractIntegrated crop–livestock (ICL) production enhances diversification and provides ecosystem benefits by improving nutrient cycling and energy efficiency, thus, increasing overall farm productivity. However, a detailed study is needed to understand the influence of crop diversification and grazing animals on soil aggregation and associated carbon (C) and nitrogen (N), and microbial properties, especially compared with a grazed native pasture. We investigated the soil aggregate size distribution and associated C and N fractions, glomalin-related soil protein, and soil phospholipid fatty acid (PLFA) to understand the collective influence of livestock grazing of crop residue and cover crops (CC) and compared it with native pasture and non-grazed traditional production systems. The study was conducted in South Dakota at four different locations consisting of three long-term (> 30 years) on-farm sites: 1 (Salem), 2 (Bristol), 3 (Bristol) with three treatments that included ICL (corn,Zea MaysL.-soybean,Glycine maxL.-oats,Avena sativaL.-CC with cattle grazing); natural ecosystem (NE) or native pasture; and control (CNT) (corn–soybean-without grazing or CC). Experimental site 4 (Beresford) with study duration of 3-year consisted of oats, oats with CC, oats with CC + grazing, and grazed pasture mix. Soil samples were collected from 0 to 5 cm depth at all four sites in summer 2019. Data showed that at sites 1 and 2, ICL had significantly (P ≤ 0.5) greater fractionation of 0.053–0.25 mm and > 4 mm aggregates compared with NE and CNT. At site 1, ICL showed significantly higher soil organic carbon (SOC, 36–49%) and higher nitrogen (33–44%) in > 4 mm aggregates than NE and CNT. At site 2, ICL had 32–41% higher SOC than NE and CNT for 0.25–0.5 mm aggregates. At site 1, NE enhanced total phospholipid fatty acid (PLFA), total bacterial biomass, gram (+), gram (−) bacteria than CNT, however, it did not vary significantly than ICL. Grazed pasture mix at site 4 had higher total PLFA (40.81 nmol g−1soil) than the other treatments. The principal components 1 and 2 accounted for 33% and 22% of the variation, respectively, where the majority of the microbial compositions and aggregate-associated C and N were influenced by ICL and NE compared with corn–soybean without grazing or short-term oats/CC/grazing treatments. Integrated crop–livestock system and NE enhanced C and N concentrations in macroaggregates as well as in microaggregates. It is concluded that ICL and NE systems are sustainable prospects in enhancing overall soil health. Integrating crop and livestock improved physicochemical and microbial properties compared to the traditional corn–soybean system.
Characterization of acquired anemia in children by iron metabolism parameters
Authors: Ben-David Yael , Koren Ariel , Colodner Raul , Levin Carina 
Published: February 2022

AbstractInflammatory states are associated with anemia of chronic disease and acute infection. Hepcidin, a regulator of iron metabolism, is involved in iron pathophysiology during inflammation. We investigated biochemical characteristics in children with anemia from different causes. Four patient groups (n = 38; mean age: 12.44 ± 4.35 years) were studied: (1) inflammatory bowel disease (IBD, 10 patients); (2) iron deficiency anemia (IDA, 12); (3) celiac disease (CD, 8); (4) acute infection (AI, 8). Laboratory measurements were evaluated at diagnosis: blood count, serum iron, transferrin, ferritin, vitamin B12, folic acid, CRP, erythropoietin, hepcidin and soluble transferrin receptor (sTfR). IDA patients had the lowest Hgb (6.9 ± 1.7 g/dL), MCV (63.2 ± 7.2 fL), iron (16.8 ± 13.5 µg/dL), ferritin (4.5 ± 4.5 ng/mL) and hepcidin (3.1 ± 0.8 ng/mL) values, and the highest transferrin and sTfR values. AI patients had the highest ferritin (156.2 ± 124.5 ng/mL), CRP (144.6 ± 94 mg/L) and hepcidin (74.67 ± 12.3 ng/ml) values. Overall, hepcidin levels correlated with CRP and with ferritin (r = 0.83 and 0.85, respectively). Elucidating specific etiology-related biochemical profiles in pediatric patients with anemia from different causes using a combination of laboratory biomarkers, including hepcidin, can help physicians treat the anemia.
Non contrast enhanced volumetric histology of blood clots through high resolution propagation-based X-ray microtomography
Authors: Saghamanesh Somayeh , Dumitriu LaGrange Daniela , Reymond Philippe , Wanke Isabel , Lövblad Karl-Olof , Neels Antonia , Zboray Robert 
Published: February 2022

AbstractWe have demonstrated the capability of laboratory propagation-based microtomography (miroCT) in non-destructive 3D virtual histopathology of human blood clots without any contrast agent. The volumetric information are valuable to understand the mechanical properties of clots which are crucial in selecting the most efficient mechanical thrombectomy method for clot extraction. Different clot types retrieved by mechanical thrombectomy from patient victims of acute ischemic stroke were evaluated through propagation-based microCT. The results were correlated with high-resolution scanning electron microscopy (SEM) images, confirming detected cellular and fibrillary structures. Calcifications appeared as glassy opacity areas with relatively intense signal on microCT images, also proved by energy-dispersive spectroscopy and X-ray diffraction. Hyperintense regions on the microCT corresponded to individual or compact aggregates of red blood cells, whereas fibrin dominated volumes appeared at consistently moderate to low normalized microCT values. Red blood cell shapes and sizes are consistent with the SEM observations. Together with other potential parameters, 3D porosity distribution and volume fraction of structures can be easily measured by microCT data. Further development of automated post-processing techniques for X-ray propagation-based micro/nanoCT, also based on machine learning algorithms, can enable high throughput analysis of blood clot composition and their 3D histological features on large sample cohorts.
Longitudinal associations between domains of flourishing
Authors: Chen Ying , Weziak-Bialowolska Dorota , Lee Matthew T. , Bialowolski Piotr , McNeely Eileen , VanderWeele Tyler J. 
Published: February 2022

AbstractThe longitudinal interrelationships between domains of human well-being or flourishing remain understudied empirically. While different aspects of flourishing may be sought as their own end, it is also the case that well-being in one domain may influence well-being in other domains. Using longitudinal data form a sample of employees from a large national employer in the United States (N = 1209, mean age = 43.52 years, age range 20–74 years), this study examined the temporal associations between various domains of flourishing, based on a 40-item index that assessed six domains of flourishing. These domains include emotional health, physical health, meaning and purpose, character strengths, social connectedness, and financial security. A set of linear regression models were used to regress subsequent composite flourishing on flourishing domain-specific scores at baseline. The results indicated that all domains were each independently associated with greater composite flourishing subsequently. The strongest and most robust links were observed for meaning and purpose (β = 0.19, 95% confidence interval [CI] 0.13, 0.25), social connectedness (β = 0.17, 95% CI 0.12, 0.22), and financial security (β = 0.32, 95% CI 0.28, 0.37). Further analyses that regressed subsequent composite flourishing on individual item indicators at baseline suggested that, out of all 40 items, one item under the character domain “I always act to promote good in all circumstances, even in difficult and challenging situations” and one item in the physical health domain (“Based on my past health, I expect to be healthy long into the future”) had the most robust association with subsequent composite flourishing. Implications of these results for understanding the constituents of a flourishing life and for refinement of the flourishing assessments are discussed.
Blood pressure and mortality after percutaneous coronary intervention: a population-based cohort study
Authors: Lee Chung-woo , Lee Joo Kyung , Choi Yeon Joo , Kim Hyunjin , Han Kyungdo , Jung Jin-hyung , Kim Do Hoon , Park Joo-Hyun 
Published: February 2022

AbstractRevascularization procedures, including percutaneous coronary intervention (PCI), for coronary artery disease (CAD) are increasingly performed in Korea. However, studies on blood pressure control targets in these patients remain insufficient. To assess the relationship between baseline blood pressure and all-cause mortality in CAD patients who underwent PCI. A population-based retrospective cohort study based on the national claims database of the Korean National Health Insurance System, which represents the entire Korean population. A total 38,330 patients with a history of PCI for CAD between 2005 and 2008 were recruited and followed up for all-cause mortality until December 31, 2017. Baseline systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured, and they were classified into eight SBP and DBP groups each. The hazard ratios (HRs) for all-cause mortality were measured for each group. The pattern of SBP and DBP in this population followed a J-curve relationship for all-cause mortality, with the nadir point at 119 and 74 mmHg, respectively. In subjects aged > 60 years, high SBP (≥ 160 mmHg) and high DBP (≥ 90 mmHg) were significantly related to death. Moreover, in subjects aged > 60 years, low DBP (< 70 mmHg) was significantly related to mortality. There is a J-curve relationship between baseline blood pressure and all-cause mortality in patients who underwent PCI, and intensive lowering of blood pressure may be beneficial for these patients. However, the elderly population needs more attention as excessive BP lowering, particularly DBP, could instead increase the risk of death.
Effects of long-term Tai-Chi Chuan practice on whole-body balance control during obstacle-crossing in the elderly
Authors: Kuo Chien-Chung , Chen Sheng-Chang , Chen Tsan-Yang , Ho Tsung-Jung , Lin Jaung-Geng , Lu Tung-Wu 
Published: February 2022

AbstractOlder people are subject to an increased risk of falling compared to the young, especially during obstacle negotiation. This study aimed to quantify the effects of long-term Tai-Chi Chuan (TCC) practice on the balance control during obstacle-crossing in older people in terms of the inclination angles (IA) of the body’s centre of mass (COM) relative to the centre of pressure (COP), and the rate of change of IA (RCIA). Fifteen healthy older adults who had practised TCC for at least 13 years and 15 healthy controls without any experience in TCC performed obstacle-crossing in a gait laboratory. The TCC group showed significantly greater leading and trailing toe-obstacle clearances but smaller trailing stride lengths when compared to controls. In the sagittal plane, the TCC group showed significantly smaller average anterior IA when the COM was anterior to the COP but greater average posterior IA when the COM was posterior to the COP, with significantly smaller average and peak RCIA over the crossing cycle. Long-term TCC practitioners showed an obstacle-crossing technique for less risk of tripping and better balance control, as indicated respectively by significantly increased toe-obstacle clearances and more posterior COM position relative to the COP with smaller anterior IA and RCIA during leading crossing and greater posterior IA and frontal RCIA at trailing-toe crossing. These benefits appeared to be related to the main features of TCC movements that emphasized maintaining balance during single-leg support and keeping the body weight on the trailing limb during the slow weight-shifting of double-limb support.
Microstructural changes of white matter fiber tracts induced by insular glioma revealed by tract-based spatial statistics and automatic fiber quantification
Authors: Wang Xiangdong , Zhou Chunyao , Wang Yinyan , Wang Lei 
Published: February 2022

AbstractGliomas typically grow along white matter fiber tracts, yet their invasion patterns remain unclear. This study assessed the effect of insular glioma on large white matter fiber tracts and the microstructural subcortical changes associated with clinical outcomes in patients with insular glioma. Twenty-five patients with insular glioma were enrolled and divided into left and right groups according to tumor lateralization. The control group comprised 14 healthy volunteers. Subjects in both the glioma and control groups underwent diffusion tensor magnetic resonance imaging at 3.0 T. The characteristics of white matter fiber bundles were analyzed using tract-based spatial statistics and automatic fiber quantification. Both Automatic Fiber Quantification and Tract-Based Spatial Statistics revealed that patients with insular glioma had significantly lower fractional anisotropy (FA) values in the inferior frontal-occipital fasciculus and uncinate fasciculus ipsilateral to the tumor, than the controls. Fractional anisotropy associated with mean diffusivity values several large fiber tracts showed potential on tumor-grade distinguishing. Diffusion metrics can sensitively detect microstructural changes in tumor progression. Insular glioma significantly affects the microstructure of white matter fibers proximal to the tumor. The range of white matter fiber bundles affected differs according to the grade of the glioma. These changes are mainly associated with early-stage tumor invasion.
Amyloid-β42 stimulated hippocampal lactate release is coupled to glutamate uptake
Authors: Hascup Erin R. , Sime Lindsey N. , Peck Mackenzie R. , Hascup Kevin N. 
Published: February 2022

AbstractSince brain glucose hypometabolism is a feature of Alzheimer’s disease (AD) progression, lactate utilization as an energy source may become critical to maintaining central bioenergetics. We have previously shown that soluble amyloid-β (Aβ)42 stimulates glutamate release through the α7 nicotinic acetylcholine receptor (α7nAChR) and hippocampal glutamate levels are elevated in the APP/PS1 mouse model of AD. Accordingly, we hypothesized that increased glutamate clearance contributes to elevated extracellular lactate levels through activation of the astrocyte neuron lactate shuttle (ANLS). We utilized an enzyme-based microelectrode array (MEA) selective for measuring basal and phasic extracellular hippocampal lactate in male and female C57BL/6J mice. Although basal lactate was similar, transient lactate release varied across hippocampal subregions with the CA1 > CA3 > dentate for both sexes. Local application of Aβ42 stimulated lactate release throughout the hippocampus of male mice, but was localized to the CA1 of female mice. Coapplication with a nonselective glutamate or lactate transport inhibitor blocked these responses. Expression levels of SLC16A1, lactate dehydrogenase (LDH) A, and B were elevated in female mice which may indicate compensatory mechanisms to upregulate lactate production, transport, and utilization. Enhancement of the ANLS by Aβ42-stimulated glutamate release during AD progression may contribute to bioenergetic dysfunction in AD.