bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity
Authors: Islam M. Rafiul , Hoque M. Nazmul , Rahman M. Shaminur , Alam A. S. M. Rubayet Ul , Akther Masuda , Puspo J. Akter , Akter Salma , Sultana Munawar , Crandall Keith A. , Hossain M. Anwar 
Published: August 2020

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.
Maternal stress or sleep during pregnancy are not reflected on telomere length of newborns
Authors: Ämmälä Antti-Jussi , Vitikainen Emma I. K. , Hovatta Iiris , Paavonen Juulia , Saarenpää-Heikkilä Outi , Kylliäinen Anneli , Pölkki Pirjo , Porkka-Heiskanen Tarja , Paunio Tiina 
Published: August 2020

AbstractTelomeres play an important role in maintaining chromosomal integrity. With each cell division, telomeres are shortened and leukocyte telomere length (LTL) has therefore been considered a marker for biological age. LTL is associated with various lifetime stressors and health-related outcomes. Transgenerational effects have been implicated in newborns, with maternal stress, depression, and anxiety predicting shorter telomere length at birth, possibly reflecting the intrauterine growth environment. Previous studies, with relatively small sample sizes, have reported an effect of maternal stress, BMI, and depression during pregnancy on the LTL of newborns. Here, we attempted to replicate previous findings on prenatal stress and newborn LTL in a sample of 1405 infants using a qPCR-based method. In addition, previous research has been expanded by studying the relationship between maternal sleep quality and LTL. Maternal prenatal stress, anxiety, depression, BMI, and self-reported sleep quality were evaluated with self-reported questionnaires. Despite sufficient power to detect similar or even considerably smaller effects than those previously reported in the literature, we were unable to replicate the previous correlation between maternal stress, anxiety, depression, or sleep with LTL. We discuss several possible reasons for the discrepancies between our findings and those previously described.
Mechanisms protect airborne green microalgae during long distance dispersal
Authors: Chiu Chia-Sheng , Chiu Pai-Ho , Yong Tze Ching , Tsai Hsin-Pei , Soong Keryea , Huang Hsiang-En , Chen Ching-Nen Nathan 
Published: August 2020

AbstractViable microalgae occur in the air. Whether they can survive the stresses such as UV, desiccation and freezing temperatures at high altitudes during long distance dispersal is rarely studied. If yes, what mechanisms confer the tolerance? Four freshwater airborne green microalgae were isolated from Dongsha Atoll in the South China Sea, classified as Scenedesmus sp. DSA1, Coelastrella sp. DSA2, Coelastrella sp. DSA3 and Desmodesmus sp. DSA6 based on their morphologies and ITS sequences. Their survival rates under UV stress were tightly correlated with their cell wall thickness. All the four airborne green microalgae survived the air-dry stress on benchtop followed by − 20 °C freeze–desiccation stress for 4 weeks, but not the two waterborne green microalgae Desmodesmus sp. F5 and Neodesmus sp. UTEX 2219-4 used as controls. Three of the four airborne microalgae survived the lyophilization treatment, excluding Desmodesmus sp. DSA6 and the two waterborne microalgae. The four airborne microalgae produced carotenoids under prolonged stress conditions, which might help detoxify the reactive oxygen species generated under environmental stresses and shield from the high-light stress in the air. Characterization of these airborne microalgae may help answer how the descendants of green algae survived on the land about 450 MYA.
Metabolomics approach revealed robust changes in amino acid and biogenic amine signatures in patients with schizophrenia in the early course of the disease
Authors: Parksepp Madis , Leppik Liisa , Koch Kadri , Uppin Kärt , Kangro Raul , Haring Liina , Vasar Eero , Zilmer Mihkel 
Published: August 2020

AbstractThe primary objective of this study was to evaluate how schizophrenia (SCH) spectrum disorders and applied antipsychotic (AP) treatment affect serum level of amino acids (AAs) and biogenic amines (BAs) in the early course of the disorder. We measured 21 different AAs and 10 BAs in a sample of antipsychotic (AP)-naïve first-episode psychosis (FEP) patients (n = 52) at baseline, after 0.6-year as well as after 5.1-year treatment compared to control subjects (CSs, n = 37). Serum levels of metabolites were determined with AbsoluteIDQ p180 kit using flow injection analysis tandem mass spectrometry and liquid chromatography technique. Elevated level of taurine and reduced level of proline and alpha-aminoadipic acid (alpha-AAA) were established as metabolites with significant change in AP-naïve FEP patients compared to CSs. The following 0.6-year treatment restored these alterations. However, further continuous 5.1-year AP treatment changed the metabolic profile substantially. Significantly elevated levels of asparagine, glutamine, methionine, ornithine and taurine, alongside with decreased levels of aspartate, glutamate and alpha-AAA were observed in the patient group compared to CSs. These biomolecule profile alterations provide further insights into the pathophysiology of SCH spectrum disorders and broaden our understanding of the impact of AP treatment in the early stages of the disease.
A retrospective analysis of the dynamic transmission routes of the COVID-19 in mainland China
Authors: Jiang Xiandeng , Chang Le , Shi Yanlin 
Published: August 2020

AbstractThe fourth outbreak of the Coronaviruses, known as the COVID-19, has occurred in Wuhan city of Hubei province in China in December 2019. We propose a time-varying sparse vector autoregressive (VAR) model to retrospectively analyze and visualize the dynamic transmission routes of this outbreak in mainland China over January 31–February 19, 2020. Our results demonstrate that the influential inter-location routes from Hubei have become unidentifiable since February 4, 2020, whereas the self-transmission in each provincial-level administrative region (location, hereafter) was accelerating over February 4–15, 2020. From February 16, 2020, all routes became less detectable, and no influential transmissions could be identified on February 18 and 19, 2020. Such evidence supports the effectiveness of government interventions, including the travel restrictions in Hubei. Implications of our results suggest that in addition to the origin of the outbreak, virus preventions are of crucial importance in locations with the largest migrant workers percentages (e.g., Jiangxi, Henan and Anhui) to controlling the spread of COVID-19.
WGCNA reveals key gene modules regulated by the combined treatment of colon cancer with PHY906 and CPT11
Authors: Xing Shuqin , Wang Yafei , Hu Kaiwen , Wang Fen , Sun Tao , Li Quanwang 
Published: August 2020

Abstract
Irinotecan (CPT11) is one of the most effective drugs for treating colon cancer, but its severe side effects limit its application. Recently, a traditional Chinese herbal preparation, named PHY906, has been proved to be effective for improving therapeutic effect and reducing side effects of CPT11. The aim of the present study was to provide novel insight to understand the molecular mechanism underlying PHY906-CPT11 intervention of colon cancer. Based on the GSE25192 dataset, for different three treatments (PHY906, CPT11, and PHY906-CPT11), we screened out differentially expressed genes (DEGs) and constructed a co-expression network by weighted gene co-expression network analysis (WGCNA) to identify hub genes. The key genes of the three treatments were obtained by merging the DEGs and hub genes. For the PHY906-CPT11 treatment, a total of 18 key genes including Eif4e, Prr15, Anxa2, Ddx5, Tardbp, Skint5, Prss12 and Hnrnpa3, were identified. The results of functional enrichment analysis indicated that the key genes associated with PHY906-CPT11 treatment were mainly enriched in ‘superoxide anion generation’ and ‘complement and coagulation cascades’. Finally, we validated the key genes by Gene Expression Profiling Interactive Analysis (GEPIA) and RT-PCR analysis, the results indicated that EIF4E, PRR15, ANXA2, HNRNPA3, NCF1, C3AR1, PFDN2, RGS10, GNG11, and TMSB4X might play an important role in the treatment of colon cancer with PHY906-CPT11. In conclusion, a total of 18 key genes were identified in the present study. These genes showed strong correlation with PHY906-CPT11 treatment in colon cancer, which may help elucidate the underlying molecular mechanism of PHY906-CPT11 treatment in colon cancer.
Long noncoding RNA Hotair facilitates retinal endothelial cell dysfunction in diabetic retinopathy
Authors: Zhao Di , Zhao Yanyan , Wang Jiao , Wu Lina , Liu Yanling , Zhao Shuiying , Guo Feng , Ma Xiaojun , Zhang Haohao , Li Zhizhen , Meng Dongdong , Xu Lijun , Zhang Lixia , Liu Junqi , Qin Guijun 
Published: August 2020

Abstract
Background: Retinal endothelial cell (REC) dysfunction induced by diabetes mellitus (DM) is an important pathological step of diabetic retinopathy (DR). Long noncoding RNAs (lncRNAs) have emerged as novel modulators in DR. The present study aimed to investigate the role and mechanism of lncRNA Hotair in regulating DM-induced REC dysfunction.
Methods: The retinal vascular preparations and immunohistochemical staining assays were conducted to assess the role of Hotair in retinal vessel impairment in vivo. The EdU, transwell, cell permeability, CHIP, luciferase activity, RIP, RNA pull-down, and Co-IP assays were employed to investigate the underlying mechanism of Hotair-mediated REC dysfunction in vitro.
Results: Hotair expression was significantly increased in diabetic retinas and high glucose (HG)-stimulated REC. Hotair knockdown inhibited the proliferation, invasion, migration, and permeability of HG-stimulated REC in vitro and reduced the retinal acellular capillaries and vascular leakage in vivo. Mechanistically, Hotair bound to LSD1 to inhibit VE-cadherin transcription by reducing the H3K4me3 level on its promoter and to facilitate transcription factor HIF1α-mediated transcriptional activation of VEGFA. Furthermore, LSD1 mediated the effects of Hotair on REC function under HG condition.
Conclusion: The Hotair exerts its role in DR by binding to LSD1, decreasing VE-cadherin transcription, and increasing VEGFA transcription, leading to REC dysfunction. These findings revealed that Hotair is a potential therapeutic target of DR.
An Evaluation of an Integrated Stuttering and Parent-Administered Self-Regulation Program for Early Developmental Stuttering Disorders
Authors: Druker Kerianne , Mazzucchelli Trevor , Hennessey Neville , Beilby Janet 
Published: August 2020

Purpose
This study reports findings from a clinical trial that implemented an early stuttering treatment program integrated with evidence-based parenting support (EBPS) to children who stutter (CWS) with concomitant self-regulation challenges manifested in elevated attention-deficit/hyperactivity disorder (eADHD) symptoms and compared those outcomes to CWS receiving stuttering treatment without EBPS.

Method

Participants were 76 preschool CWS and their parent(s). Thirty-six of these children presented with eADHD and were quasirandomized into two groups: stuttering treatment only (eADHD
standard
) or stuttering treatment integrated with EBPS (eADHD
integrated
). The remaining children did not meet criteria for eADHD symptoms and received stuttering treatment only (No-eADHD
standard
). Pre, post, and 3-month follow-up measures of stuttering treatment outcomes as well as treatment effects on measures of child behavior difficulties and parenting practices were examined.

Results

Significant reduction in stuttering was found for all groups. However, the eADHD
integrated
group showed a greater reduction in stuttering frequency than the eADHD
standard
group, and at follow-up, stuttering frequencies in the eADHD
integrated
group matched those of children in the No-eADHD
standard
group, while stuttering in the eADHD
standard
group remained significantly higher. Children with eADHD symptoms who received the integrated program also required significantly less stuttering intervention time than those children with eADHD symptoms who received stuttering treatment only. Families in the eADHD
integrated
group reported large and significant improvements in child behavior and parenting practices.

Conclusion
This study provides support for an early treatment program for CWS. The integrated stuttering and self-regulation management program for CWS with eADHD symptoms proved successful for fluency and behavioral improvements, which were sustained at follow-up.
Phosphorylated CtIP bridges DNA to promote annealing of broken ends
Authors: Öz Robin , Howard Sean M. , Sharma Rajhans , Törnkvist Hanna , Ceppi Ilaria , KK Sriram , Kristiansson Erik , Cejka Petr , Westerlund Fredrik 
Published: August 2020

Significance
The DNA of our cells is constantly exposed to various types of damaging agents. One of the most critical types of damage is when both strands of the DNA break, and thus such breaks need to be efficiently repaired. It is known that CtIP promotes nucleases in DNA break repair. Here we show that CtIP can also hold the two DNA strands together in solution when DNA is free to move, using novel methodology that allows the monitoring of thousands of single DNA molecules in nanofabricated devices. DNA bridging likely facilitates the enzymatic repair steps and identifies novel CtIP functions that are crucial for repairing broken DNA.
Make us difficult
Authors: Mehl Seth 
Published: August 2020

AbstractThis paper introduces a previously undiscussed English construction, termed themake us difficultconstruction. Examples of the construction are presented, from theInternational Corpus of Englishand theCorpus of Global Web-Based English, and a quantitative analysis is conducted of the construction’s text frequency and variant rates. Quantitative data on specific usage patterns is employed to inform an analysis of the construction and its productivity, and recommendations are made for future research.
Effects of land-use and climate change on sediment and nutrient retention in Guizhou, China
Authors: Han Huiqing , Yang Jianqiang , Ma Geng , Liu Yue , Zhang Linan , Chen Siying , Ma Shuliang 
Published: August 2020

ABSTRACT

Introduction
Sediment and nutrient retention have significant impacts on agricultural productivity and water quality. Obvious changes of climate and land-use have deeply affected freshwater ecosystem services in the last several decades. Nevertheless, it is unclear what the differences are in the impact of climate and land-use changes on freshwater ecosystem services.

Outcomes
The impacts of climate and land-use change on sediment and nutrient retention (two essential freshwater ecosystem services) were evaluated with the help of the Integrated Valuation of Environmental Services and Tradeoffs (InVEST) model. The results from the study area suggest a decreasing trend in sediment and nutrient retention from 1995 to 2015 when climate and land-use were changed simultaneously. A decreasing trend in sediment retention and an increasing trend in nutrient retention were presented under scenario A (climate change from 1995 to 2015 with land-use unchanged), while the sediment exported and nutrient retention exhibited a decreasing trend except sediment retained under scenario B (land-use change from 1995 to 2015 with unchanged climate). Rainfall erosivity and soil erodibility were more sensitive to the output of sediment retention, while retention efficiency produced more of an effect on nutrient retention.

Discussion and Conclusion
Climate change played a dominant role in the change in sediment retention, while land-use change had a more significant effect on nutrient retention change than climate change. The results of this study provide explicitinformation for land-use managers to reduce the negative effects associated with sediment and nutrient retention.
Compact coplanar waveguide fed wideband directional antenna for medical diagnosis
Authors: Rokunuzzaman Md , Ahmed Asif , Baum Thomas , Rowe Wayne S T 
Published: August 2020

Abstract
This paper presents a compact coplanar waveguide fed antenna for medical diagnosis of the human head. Early diagnosis of the sophisticated organs inside the human body is possible through microwave medical imaging, which has recently achieved its popularity due to its numerous advantages. The crucial functional element for microwave medical imaging is the antenna. The antenna presented in this paper is conceived and evaluated in contact with an inhomogeneous human head tissue medium, increasing the signal penetration by removing the antenna–air–tissue transition loss. A combination of a meandered line and circular slot are utilized to achieve wideband performance at a subwavelength size. A rectangular cavity is introduced at the back of the antenna to attain directional radiation towards the inhomogeneous human head phantom. The antenna achieves increased bandwidth covering the lower microwave frequency region for medical diagnosis of a human head while minimizing ill-directed radiated fields which interfere with imaging computations. The salient characteristics of compact size, high near-field directionality, lower microwave operating frequency range and low impact on the skin surface make the proposed antenna a suitable candidate for microwave imaging of the human head.
Formation and stability of conformal spirals in confined 2D crystals
Authors: Silva Fillipe C O , Menezes Raí M , Cabral Leonardo R E , de Souza Silva Clécio C 
Published: August 2020

Abstract
We investigate the ground-state and dynamical properties of nonuniform two-dimensional (2D) clusters of long-range interacting particles. We demonstrate that, when the confining external potential is designed to produce an approximate 1/r
2 density profile, the particles crystallize into highly ordered structures featuring spiral crystalline lines. Despite the strong inhomogeneity of the observed configurations, most of them are characterized by small density of topological defects, typical of conformal crystals, and the net topological charge induced by the simply-connected geometry of the system is concentrated near the cluster center. These crystals are shown to be robust with respect to thermal fluctuations up to a certain threshold temperature, above which the net charge is progressively redistributed from the center to the rest of the system and the topological order is lost. The crystals are also resilient to the shear stress produced by a small nonuniform azimuthal force field, rotating as a rigid body (RB). For larger forces, topological defects proliferate and the RB rotation gives place to plastic flow.
A friction-coupled measurement model of a 3D scanning probe with unequal stiffness
Authors: Zheng Weikang , Liu Zhigang , Guo Junkang 
Published: August 2020

Abstract
The friction force during the scanning of a three-dimensional (3D) probe inevitably leads to undesired tangential displacement, the processing of which is challenging, especially for probes with unequal stiffness. In this paper, a new friction-coupled measurement model of the probe is deduced based on the principle of mechanics so as to realize the positioning and tracking of any friction force between the stylus ball and the sample surface. Considering the two features of the time-varying normal displacement in the scanning and the 3D unequal stiffness of the probe, this paper reveals the nonlinear bidirectional conversion between the 3D resultant force and the resultant displacement at the measuring end. The measurement deviations and the geometric relationship among the frictional force, equivalent force, normal contact force and friction-coupled force are theoretically analyzed. In addition, the finite element analysis (FEA) and calibration experiment analyze the force characteristics and sensitivity of the probe, and obtain the friction-coupled measurement model for actual measurement. The designed measurement experiment on the scanning trajectory compares the calculation difference of the displacement and azimuth angles with and without friction, and obtains a conclusion consistent with the theory and simulation.
Sparse feature extraction based on periodical convolutional sparse representation for fault detection of rotating machinery
Authors: Ding Chuancang , Zhao Ming , Lin Jing 
Published: August 2020

Abstract
Sparse fault transient extraction is the primary step in rotating machine fault detection. In the present paper, periodical convolutional sparse representation (PCSR) is proposed for reliable separation of fault transients imbedded in raw vibration signals. Specifically, a sparse optimization problem of PCSR is constructed, in which periodical fault transients and harmonic components are sparsely represented by a learned dictionary and Fourier dictionary, and the periodicity and group sparsity of sparse coefficients related to sparse fault transients are also incorporated. Meanwhile, to further promote the sparsity of the sparse coefficients, a non-convex function is also introduced into the optimization problem. In addition, an iterative algorithm is developed to resolve the constructed sparse optimization problem, and the parameter selection method is also investigated to ensure the fault transient extraction ability of PCSR. The performance of the proposed PCSR is assessed via a synthetic and actual vibration signal. The results illustrate that the proposed PCSR has an excellent ability in fault transient extraction and machine fault detection.