bluuebunny/crossref_metadata_2025_split huggingface dataset:
The allometry of cellular DNA and ribosomal gene content among microbes and its use for the assessment of microbiome community structure
Authors: de Salceda Luis Gonzalez , Garcia-Pichel Ferran 
Published: February 2021

Abstract
BackgroundThe determination of taxon-specific composition of microbiomes by combining high-throughput sequencing of ribosomal genes with phyloinformatic analyses has become routine in microbiology and allied sciences. Systematic biases to this approach based on the demonstrable variability of ribosomal operon copy number per genome were recognized early. The more recent realization that polyploidy is probably the norm, rather than the exception, among microbes from all domains of life, points to an even larger source bias.ResultsWe found that the number of 16S or 18S RNA genes per cell, a combined result of the number of RNA gene loci per genome and ploidy level, follows an allometric power law of cell volume with an exponent of 2/3 across 6 orders of magnitude in small subunit copy number per cell and 9 orders of magnitude in cell size. This stands in contrast to cell DNA content, which follows a power law with an exponent of ¾.ConclusionIn practical terms, that relationship allows for a single, simple correction for variations in both copy number per genome and ploidy level in ribosomal gene analyses of taxa-specific abundance. In biological terms, it points to the uniqueness of ribosomal gene content among microbial properties that scale with size.
The potential genes mediate the pathogenicity of allogeneic CD4+T cell in aGVHD mouse model
Authors: Yu Zheng-Yu , Qin Chen-Chen , Cao Min , He Xiao-Ya , Ren Han-Yun , Liu Hui-Hui 
Published: February 2021

Abstract
Acute graft-versus-host disease (aGVHD) remains a significant and severe complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT). Due to the occurrence of aGVHD, allo-HSCT significantly increases the mortality rate compared with autologous hematopoietic stem cell transplantation (auto-HSCT). As a transcriptome sequencing technique, ribonucleic acid sequencing (RNA-Seq) is used to study alternative splicing and other forms of alternative isoform expression. Major histocompatibility complex (MHC)-matched and MHC-mismatched mouse bone marrow transplant (BMT) models were built to detect the difference of CD4+ lymphocyte in different tissues based on RNA-seq analysis. Four critical pathways were identified by enrichment analysis, including a lymphoid and a non-lymphoid cell, chemokine receptor binding chemokine, cytokine and cytokine receptor interaction pathway. At the same time, 11 novel hub genes that are most likely to participate in immunoregulatory and enriched pathways were identified, which were further validated by qRT-PCR. Besides, Cxcl7 was verified at the protein level. In summary, we revealed that DEGs and pathways related to immunoregulation played a vital role in the onset of aGVHD. These findings may provide some new clues for probing the pathogenesis and treatment of aGVHD.
Dynamics of a Discrete-time Pioneer–climax Model
Authors: Gilbertson Nora , Kot Mark 
Published: February 2021

Abstract
We present a simple mathematical model for the dynamics of a successional pioneer–climax system using difference equations. Each population is subject to inter- and intraspecific competition; population density growth is dependent on the combined densities of both species. Nine different geometric cases, corresponding to different orientations of the zero-growth isoclines, are possible for this system. We fully characterize the long-term dynamics of the model for each of the nine cases, uncovering diverse sets of potential behaviors. Competitive exclusion of the pioneer species and exclusion of the climax species are both possible depending on the relative strength of competition. Stable coexistence of both species may also occur; in two cases, a coexistence state is destabilized through a Neimark–Sacker bifurcation and an attracting invariant circle is born. The invariant circle eventually disappears into thin air in a heteroclinic or homoclinic bifurcation, leading to the sudden transition of the system to an exclusion state. Neither global bifurcation has been observed in a discrete-time pioneer–climax model before. The homoclinic bifurcation is novel to all pioneer–climax models. We conclude by discussing the ecological implications of our results.
Three saprobic Dothideomycetes from the aerial parts of mangrove trees with polyphenism in Striatiguttula
Authors: Kumar Vinit , Thambugala Kasun M , Sarma V Venkatesh , Cheewangkoon R , Wen Ting Chi 
Published: February 2021

Abstract
Fungi inhabiting the aerial parts of two mangrove trees, Nypa fruticans, and Rhizophora apiculata, were studied from the central region of Thailand, utilizing morpho-molecular characteristics. Three different fungal taxa were isolated including Rhytidhysteron kirshnacephalus sp. nov., Lasiodiplodia citricola and Striatiguttula phoenicis. Sexual morphs are reported for these three taxa and the asexual morph of Striatiguttula phoenicis is identified based on molecular data. This is the first asexual morph report for the genus Striatiguttula as well as the family Striatiguttulaceae. The new isolate of Striatiguttula phoenicis differs slightly from other extant species in the genus in terms of measurements of ascomata, asci, ascospores, and thickness of peridium. Also, a pigmented hamathecium was observed in this species. The morphological results are congruent to the phylogenetic results of previous studies and support Striatiguttula phoenicis as a new host record from Nypa fruticans. Rhytidhysteron kirshnacephalus was collected from dead twigs of a standing Rhizophora apiculata in Cha-am and it has significant morphological and molecular differences to support its establishment as a novel taxon. Phylogenetically, Rhytidhysteron kirshnacephalus forms a sister clade to Rh. magnoliae, but has different ascomatal characters, including, smooth margins without striations and black pruina. Lasiodiplodia citricola is another species from Cha-am and a new record from Thai mangroves. Detailed descriptions of the isolates, along with their potential ecological roles, are provided. We have also provided the occurrence of fungi from the aerial parts of mangrove trees worldwide.
Spatial-temporal Assessment of historical and projected drought events over Isiolo County, Kenya using Self Calibrating Palmer Drought Severity Index
Authors: Ochieng phillip , Nyandega Isaiah , Wambua Boniface 
Published: February 2021

Abstract
This study was to determine the spatiotemporal characteristics of historical and projected drought events throughout Isiolo County, Kenya, through using self-calibrating Palmer drought severity index (scPDSI). The scPDSI is a complex and robust drought index that applies the water balance model by incorporating the role played by evapotranspiration and soil properties on drought analysis therefore making it appropriate to identify the linkages between meteorological, agricultural and hydrological droughts. The historical scPDSI was computed at a monthly timescale using a 39-year long monthly mean precipitation data from Climate Hazard Group Infrared Precipitation with Station (CHIRPS) and monthly average temperature data from the Climate Research Unit (CRU). The climatological (1950-1996) available water holding capacity (AWHC) of the soil was obtained from Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biochemical dynamics at a spatial resolution of 1o x 1o. The projected scPDSI under Representative Concentration Pathways (RCPs) was computed using bias corrected monthly temperature and precipitation model output data from Coordinated Regional Climate Downscaling Experiment (CORDEX). The datasets were extracted for ten grid points in the County. The scPDSI was used to assess the historical and projected duration, severity, and intensity of droughts. The major significant historical and projected drought events and their characteristics were clearly identified using the run theory. ScPDSI runs have shown that more severe drought events dominated the period between 1980 and 2000. ScPDSI had the longest dry event duration of 61 months and a severity of 126.412 with adverse effects on the eastern locations. The projected drought events identified Mar 2046 –Mar 2048 under RCP4.5 to be the most severe drought lasting for 25 months with severity of 59.292 while under RCP8.5 run Nov 2042 – Nov 2046 is identified as the most severe, 114.362 with the duration of water stress anticipated to last for 49 months. To examine the spatial variability of the drought events in the County, the Empirical Orthogonal Analysis (EOF) was applied to the historical and projected scPDSI time series. The EOF results indicated that the two leading eigen vectors accounted for over 85% of the spatial variability for both historical and projected droughts under the RCPs. Subsequently, the Mann-Kendall (MK) test was applied to the projected scPDSI, temperature and precipitation timeseries in order to determine the local expected drought trends. The MK test of the identified significant increase in trend for temperatures under RCP8.5 and precipitation under RCP4.5 towards the end of the last decade under the study period considered. Both scenarios showed a decline in trends of drought events in Isiolo County from 2020-2050.
Effects of management of infection source of echinococcosis in Linzhi, Tibet autonomous region of China
Authors: Wang Ying , Ma Bing-Cheng , Wang Liying , Quzhen Gongsang , Pang Hua-Sheng 
Published: February 2021

Abstract
Background Echinococcosis is highly endemic in western and northern China, Tibet Autonomous Region (TAR) is the most serious prevalent area. Linzhi is located in southeastern part of TAR. Dogs are the primary infection source for the transmission of echinococcosis to humans. A control and prevention campaign based on dog management has been implemented in the past three years. This study aims to evaluate the effects of dog management on the infection rate of dogs.Methods Data of dog population, registration and de-worming of seven counties/district in Linzhi between 2017 and 2019 were obtained from the annual prevention and control report. Domestic dog fecal samples were collected from each endemic town of seven counties/district in Linzhi in 2019 to determine the infection of domestic dogs using coproantigen ELISA. Data analysis was processed using SPSS statistics to compare dog infection rate between 2016 and 2019 by chi-square test, and maps were mapped using ArcGIS.Results In Linzhi, domestic dog population has decreased from 17407 in 2017 to 12663 in 2019, whilethe registration rate has increased from 75.9% in 2017 to 98.6% in 2019. Similarly, stray dog populationhas decreased from 14336 in 2017 to 11837 in 2019, while sheltered ratehas increased from 84.6% in 2017 to 96.6% in 2019.Dog de-worming frequency has increased from four times per annum in 2017 to 12 times in 2019, indicating that approximately every dog was dewormed monthly. A total number of 2715 dog fecal samples were collected for coproantigen ELISA assay. The dog infection rate was 2.8% (77/2715) in 2019, which was significantly lower than7.3% (45/618) in 2016 (P<0.05).Conclusions Increased dog registration, decreased dog population, and increased dog de-worming frequency contributed to significantly decreased the dog infection rate in Linzhi, TAR. Control and prevention campaign based on dog management could significantly decrease dog infection with Echinococcus spp. in echinococcosis endemic areas.
The Use of Virtual Reality to Reduce Stress among Night-Shift Anesthesiologists: Study Protocol for a Cross-Over Trial
Authors: Chen Chaojin , Chen Liubing , Shen Ning , Luo Chenfang , Wang Ren , Fang Hongyi , Zhang Qi , Hei Ziqing 
Published: February 2021

Abstract
Background: Because of the lack of anesthesia workforce, anesthesiologists are forced to work overtime and more night shifts; this can disturb their biological rhythm and cause severe stress and depression, potentially leading to negative and even devastating outcomes for both themselves and patients. Virtual reality (VR), which is a new method to reduce stress and pain for patients, has been widely used in biomedical fields. The purpose of this study is to evaluate the potential effectiveness of VR technology in reducing stress among night-shift anesthesiologists.Methods: In this randomized controlled, crossover, single-center clinical trial, a total of 30 anesthesiologists will be enrolled and randomized in a 1:1 allocation to either the VR immersion group (intervention group) or the routine night-shift group (control group) with a washout of 1 week. Anesthesiologists in the intervention group will undergo VR immersion twice, while anesthesiologists in the control group will not watch VR videos during the night shift. The primary outcome will be the difference in the NASA Task Load Index (NASA-TLX) score between the two groups. Secondary outcomes will include the Chinese Perceived Stress Scale (CPSS), perceived stress scores (Visual Analogue Scale (VAS)) and Multidimensional Fatigue Inventory (MFI-20) scores; levels of satisfaction among the participants; incidence of arrhythmia; and incidence of chest tightness, headache, and palpitations.Discussion: It is unknown whether the use of VR technology during the night shift can reduce stress among anesthesiologists. With the widespread use of VR technology, a positive result in this trial could spur hospitals to apply VR technology to reduce stress among night-shift doctors in every department and provide a relatively relaxed working environment.Trial registration: ChiCTR2000031025
Different effects of monophasic pulses and biphasic pulses applied by a bipolar stimulation electrode in the rat hippocampal CA1 region
Authors: Yuan Yue , Zheng Lvpiao , Feng Zhouyan , Yang Gangsheng 
Published: February 2021

Abstract
Background: Electrical pulse stimulations have been applied in brain for treating certain diseases such as movement disorders. High-frequency stimulations (HFS) of biphasic pulses have been used in clinic stimulations, such as deep brain stimulation (DBS), to minimize the risk of tissue damages caused by the electrical stimulations. However, HFS sequences of monophasic pulses have often been used in animal experiments for studying neuronal responses to the stimulations. It is not clear yet what the differences of the neuronal responses to the HFS of monophasic pulses from the HFS of biphasic pulses are. Methods: To investigate the neuronal responses to the two types of pulses, orthodromic-HFS (O-HFS) and antidromic-HFS (A-HFS) of biphasic and monophasic pulses (1-min) were delivered by bipolar electrodes respectively to the Schaffer collaterals (i.e., afferent fibers) and the alveus fibers (i.e., efferent fibers) of the rat hippocampal CA1 region in-vivo. Evoked population spikes of CA1 pyramidal neurons to the HFSs were recorded in the CA1 region. In addition, single pulses of antidromic- and orthodromic-test stimuli were applied before and after HFSs to evaluate the baseline and the recovery of neuronal activity, respectively. Results: Spreading depression (SD) appeared during sequences of 200 Hz monophasic O-HFS with a high incidence (4/5), but did not appear during corresponding 200 Hz biphasic O-HFS (0/6). A preceding burst of population spikes appeared before the SD waveforms. Then, the SD propagated slowly, silenced neuronal firing temporarily and resulted in partial recovery of orthodromically-evoked population spikes (OPS) after the end of O-HFS. No SD events appeared during the O-HFS with a lower frequency of 100 Hz of monophasic or biphasic pulses (0/5 and 0/6, respectively), neither during the A-HFS of 200 Hz pulses (0/9). The antidromically-evoked population spikes (APS) after 200 Hz biphasic A-HFS recovered to baseline level within ~2 min. However, the APS only recovered partially after the 200 Hz A-HFS of monophasic pulses.Conclusions: The O-HFS with a higher frequency of monophasic pulses can induce the abnormal neuron activity of SD and the A-HFS of monophasic pulses can cause a persisting attenuation of neuronal excitability, indicating neuronal damages caused by monophasic stimulations in brain tissues. The results provide guidance for proper stimulation protocols in clinic and animal experiments.
Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa
Authors: Gwarinda Hazel B. , Tessema Sofonias K. , Raman Jaishree , Greenhouse Bryan , Birkholtz Lyn-Marie 
Published: February 2021

Abstract
Background South Africa aims to eliminate malaria transmission by 2023. However, despite sustained vector control efforts and case management interventions, the Vhembe District remains a malaria transmission hotspot. To better understand Plasmodium falciparum transmission dynamics in the area, this study characterized the genetic diversity of parasites circulating within the Vhembe District.Methods A total of 1153 falciparum-positive rapid diagnostic tests (RDTs) were randomly collected from seven clinics within the district, over three consecutive years (2016, 2017 and 2018) during the wet and dry malaria transmission seasons. Using 26 neutral microsatellite markers, differences in genetic diversity were described using a multiparameter scale of multiplicity of infection (MOI), inbreeding metric (Fws), number of unique alleles (A), expected heterozygosity (He), multilocus linkage disequilibrium (LD) and genetic differentiation, and were associated with temporal and geospatial variances. Results A total of 747 (65%) samples were successfully genotyped. Moderate to high genetic diversity (mean He = 0.74 ± 0.03) was observed in the parasite population. This was ascribed to high allelic richness (mean A = 12.2 ± 1.2). The majority of samples (99%) had unique multi-locus genotypes, indicating high genetic diversity in the sample set. Complex infections were observed in 66% of samples (mean MOI = 2.13 ± 0.04), with 33% of infections showing high within-host diversity as described by the Fws metric. Low, but significant LD (standardised index of association, ISA = 0.08, P < 0.001) was observed that indicates recombination of distinct clones. Limited impact of temporal (FST range -0.00005 to 0.0003) and spatial (FST = –0.028 to 0.023) variation on genetic diversity existed during the sampling timeframe and study sites respectively. Conclusion Consistent with the Vhembe District’s classification as a 'high' transmission setting within South Africa, P. falciparum diversity in the area was moderate to high and complex. This study showed that genetic diversity within the parasite population reflects the continued residual transmission observed in the Vhembe District. This data can be used as a reference point for the assessment of the effectiveness of on-going interventions over time, the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance.
RDmap: A Map for Exploring Rare Diseases
Authors: Yang Jian , Dong Cong , Duan Huilong , Shu Qiang , Li Haomin 
Published: February 2021

Abstract
Background: The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians. A map for visualizing, locating and navigating rare diseases based on similarity will help clinicians and researchers understand and easily explore these diseases. Methods: A distance matrix of rare diseases included in Orphanet was measured by calculating the quantitative distance among phenotypes and pathogenic genes based on Human Phenotype Ontology (HPO) and Gene Ontology (GO), and each disease was mapped into Euclidean space. A rare disease map, enhanced by clustering classes and disease information, was developed based on ECharts. Results: A rare disease map called RDmap was published at http://rdmap.nbscn.org. Total 3,287 rare diseases are included in the phenotype-based map, and 3,789 rare genetic diseases are included in the gene-based map; 1,718 overlapping diseases are connected between two maps. RDmap works similarly to the widely used Google Map service and supports zooming and panning. The phenotype similarity base disease location function performed better than traditional keyword searches in an in silico evaluation, and 20 published cases of rare diseases also demonstrated that RDmap can assist clinicians in seeking the rare disease diagnosis. Conclusion: RDmap is the first user-interactive map-style rare disease knowledgebase. It will help clinicians and researchers explore the increasingly complicated realm of rare genetic diseases.
Preparation of a hybrids APT@MIL by one-step solvent-thermal method for effectively degrading organics
Authors: Zhang Yaping , Gao Di , He Yufeng , Li Bozhen , Song Pengfei , Wang Rongmin 
Published: February 2021

Abstract
The attapulgite (APT), a typical nano-rod structured clay was introduced to MIL-101(Fe), a typical eco-friendly iron-based Metal-Organic Framework material (MOF), during the preparation by a one-step solvothermal method, which afforded a novel APT and MOF hybrid (APT@MIL). Based on the characterization of SEM, FT-IR and XRD, it was found that the rod-like crystals of APT determined the size of MIL-101(Fe) while maintaining its regular octahedral crystal form, and the crystal size of MIL-101(Fe) in APT@MIL enlarged 4 times. It was also discovered that the rod-like APT were evenly distributed in MIL-101(Fe) crystals. Using APT@MIL as the photocatalyst, some organic dyes were photodegraded in simulated sunlight. The analysis indicated that APT@MIL has high adsorption and photodegradation activity, the removal rate of methylene blue was up to 99.5%. Finally, the photocatalytic activity of APT@MIL was verified by UV-Vis DRS, photoluminescence spectra. The thermodynamic adsorption, kinetic characteristics adsorption, and removal mechanism of APT@MIL are also discussed. In summary, a novel hybrid material APT@MIL was successfully prepared with good adsorption and photocatalytic performance. It is expected to be used in photocatalytic degradation of dye wastewater.