bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lower extremity joint-level responses to pelvis perturbation during human walking
Authors: Vlutters Mark , van Asseldonk Edwin H. F. , van der Kooij Herman 
Published: September 2018

AbstractThe human leg joints play a major role in balance control during walking. They facilitate leg swing, and modulate the ground (re)action forces to prevent a fall. The aim of this study is to provide and explore data on perturbed human walking to gain a better understanding of balance recovery during walking through joint-level control. Healthy walking subjects randomly received anteroposterior and mediolateral pelvis perturbations at the instance of toe-off. The open-source modeling tool OpenSim was used to perform inverse kinematics and inverse dynamics analysis. We found hip joint involvement in accelerating and then halting leg swing, suggesting active preparation for foot placement. Additionally, responses in the stance leg’s ankle and hip joints contribute to balance recovery by decreasing the body’s velocity in the perturbation direction. Modulation also occurs in the plane perpendicular to the perturbation direction, to safeguard balance in both planes. Finally, the recorded muscle activity suggests both spinal and supra-spinal mediated contributions to balance recovery, scaling with perturbation magnitude and direction. The presented data provide a unique and multi-joint insight in the complexity of both frontal and sagittal plane balance control during human walking in terms of joint angles, moments, and power, as well as muscle EMG responses.
The terpenes of leaves, pollen, and nectar of thyme (Thymus vulgaris) inhibit growth of bee disease-associated microbes
Authors: Wiese Natalie , Fischer Juliane , Heidler Jenifer , Lewkowski Oleg , Degenhardt Jörg , Erler Silvio 
Published: September 2018

AbstractHoney bees are highly prone to infectious diseases, causing colony losses in the worst case. However, they combat diseases through a combination of their innate immune system and social defence behaviours like foraging for health-enhancing plant products (e.g. nectar, pollen and resin). Plant secondary metabolites are not only highly active against bacteria and fungi, they might even enhance selective foraging and feeding decisions in the colony. Here, we tested six major plant terpenes and their corresponding acetates, characterizing six natural Thymus vulgaris chemotypes, for their antimicrobial activity on bacteria associated with European foulbrood. Comparison of the inhibitory activity revealed the highest activity for carvacrol and thymol whereas the acetates mostly did not inhibit bacterial growth. All terpenes and acetates are present in the nectar and pollen of thyme, with pollen containing concentrations higher by several orders of magnitude. The physiological response was tested on forager and freshly emerged bees by means of antennal electroantennography. Both responded much stronger to geraniol and trans-sabinene hydrate compared to carvacrol and thymol. In conclusion, bee-forageable thyme product terpenes (mainly from pollen) yield effective antibiotic activity by reducing the growth of bee disease-associated bacteria and can be detected with different response levels by the honey bees’ antennae. This is a further step forward in understanding the complex pathogen-pollinator-plant network.
OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
Authors: Boudellioua Imane , Kulmanov Maxat , Schofield Paul N. , Gkoutos Georgios V. , Hoehndorf Robert 
Published: September 2018

AbstractAn increasing number of disorders have been identified for which two or more distinct alleles in two or more genes are required to either cause the disease or to significantly modify its onset, severity or phenotype. It is difficult to discover such interactions using existing approaches. The purpose of our work is to develop and evaluate a system that can identify combinations of alleles underlying digenic and oligogenic diseases in individual whole exome or whole genome sequences. Information that links patient phenotypes to databases of gene–phenotype associations observed in clinical or non-human model organism research can provide useful information and improve variant prioritization for genetic diseases. Additional background knowledge about interactions between genes can be utilized to identify sets of variants in different genes in the same individual which may then contribute to the overall disease phenotype. We have developed OligoPVP, an algorithm that can be used to prioritize causative combinations of variants in digenic and oligogenic diseases, using whole exome or whole genome sequences together with patient phenotypes as input. We demonstrate that OligoPVP has significantly improved performance when compared to state of the art pathogenicity detection methods in the case of digenic diseases. Our results show that OligoPVP can efficiently prioritize sets of variants in digenic diseases using a phenotype-driven approach and identify etiologically important variants in whole genomes. OligoPVP naturally extends to oligogenic disease involving interactions between variants in two or more genes. It can be applied to the identification of multiple interacting candidate variants contributing to phenotype, where the action of modifier genes is suspected from pedigree analysis or failure of traditional causative variant identification.
Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity
Authors: Callejas-Hernández Francisco , Rastrojo Alberto , Poveda Cristina , Gironès Núria , Fresno Manuel 
Published: September 2018

AbstractChagas disease is a complex illness caused by the protozoan Trypanosoma cruzi displaying highly diverse clinical outcomes. In this sense, the genome sequence elucidation and comparison between strains may lead to disease understanding. Here, two new T. cruzi strains, have been sequenced, Y using Illumina and Bug2148 using PacBio, assembled, analyzed and compared with the T. cruzi annotated genomes available to date. The assembly stats from the new sequences show effective improvement of T. cruzi genome over the actual ones. Such as, the largest contig assembled (1.3 Mb in Bug2148) in de novo attempts and the highest mean assembly coverage (71X for Y). Our analysis reveals a new genomic expansion and greater complexity for those multi-copy gene families related to infection process and disease development, such as Trans-sialidases, Mucins and Mucin Associated Surface Proteins, among others. On one side, we demonstrate that multi-copy gene families are located near telomeric regions of the “chromosome-like” 1.3 Mb contig assembled of Bug2148, where they likely suffer high evolutive pressure. On the other hand, we identified several strain-specific single copy genes that might help to understand the differences in infectivity and physiology among strains. In summary, our results indicate that T. cruzi has a complex genomic architecture that may have promoted its evolution.
Multivariate analysis of short time series in terms of ensembles of correlation matrices
Authors: Vyas Manan , Guhr T. , Seligman T. H. 
Published: September 2018

AbstractWhen dealing with non-stationary systems, for which many time series are available, it is common to divide time in epochs, i.e. smaller time intervals and deal with short time series in the hope to have some form of approximate stationarity on that time scale. We can then study time evolution by looking at properties as a function of the epochs. This leads to singular correlation matrices and thus poor statistics. In the present paper, we propose an ensemble technique to deal with a large set of short time series without any consideration of non-stationarity. Given a singular data matrix, we randomly select subsets of time series and thus create an ensemble of non-singular correlation matrices. As the selection possibilities are binomially large, we will obtain good statistics for eigenvalues of correlation matrices, which are typically not independent. Once we defined the ensemble, we analyze its behavior for constant and block-diagonal correlations and compare numerics with analytic results for the corresponding correlated Wishart ensembles. We discuss differences resulting from spurious correlations due to repetitive use of time-series. The usefulness of this technique should extend beyond the stationary case if, on the time scale of the epochs, we have quasi-stationarity at least for most epochs.
Urinary Exosomal and cell-free DNA Detects Somatic Mutation and Copy Number Alteration in Urothelial Carcinoma of Bladder
Authors: Lee Dong Hyeon , Yoon Hana , Park Sanghui , Kim Jeong Seon , Ahn Young-Ho , Kwon Kihwan , Lee Donghwan , Kim Kwang Hyun 
Published: September 2018

AbstractUrothelial bladder carcinoma (UBC) is characterized by a large number of genetic alterations. DNA from urine is a promising source for liquid biopsy in urological malignancies. We aimed to assess the availability of cell-free DNA (cfDNA) and exosomal DNA (exoDNA) in urine as a source for liquid biopsy in UBC. We included 9 patients who underwent surgery for UBC and performed genomic profiling of tumor samples and matched urinary cfDNA and exoDNA. For mutation analysis, deep sequencing was performed for 9 gene targets and shallow whole genome sequencing (sWGS) was used for the detection of copy number variation (CNV). We analyzed whether genetic alteration in tumor samples was reflected in urinary cfDNA or exoDNA. To measure the similarity between copy number profiles of tumor tissue and urinary DNA, the Pearson’s correlation coefficient was calculated. We found 17 somatic mutations in 6 patients. Of the 17 somatic mutations, 14 and 12 were identified by analysis of cfDNA and exoDNA with AFs of 56.2% and 65.6%, respectively. In CNV analysis using sWGS, although the mean depth was 0.6X, we found amplification of MDM2, ERBB2, CCND1 and CCNE1, and deletion of CDKN2A, PTEN and RB1, all known to be frequently altered in UBC. CNV plots of cfDNA and exoDNA showed a similar pattern with those from the tumor samples. Pearson’s correlation coefficients of tumor vs. cfDNA (0.481) and tumor vs. exoDNA (0.412) were higher than that of tumor vs. normal (0.086). We successfully identified somatic mutations and CNV in UBC using urinary cfDNA and exoDNA. Urinary exoDNA could be another source for liquid biopsy. Also, CNV analysis using sWGS is an alternative strategy for liquid biopsy, providing data from the whole genome at a low cost.
A magnetically recyclable photocatalyst with commendable dye degradation activity at ambient conditions
Authors: Pant Abhilasha , Tanwar Ruchika , Kaur Bikramjit , Mandal Uttam Kumar 
Published: September 2018

AbstractAn efficient, economical, environment-friendly and easy separable catalyst to treat environmental contaminants is an enduring attention in recent years due to their great potential for environmental protection and remediation. Here we have reported the excellent performance of polyaniline activated heterojunctured Ni0.5Zn0.5Fe2O4 catalyst to degrade azo dye in an aqueous solution at ambient condition. The catalyst was prepared via a simple facile polymerization procedure. The physicochemical properties and structure of the synthesized catalyst was confirmed by TGA, PXRD, FTIR, SEM, HRTEM, XPS, EDX, and DRS techniques. The developed catalyst has shown an accelerated degradation ability of an organic pollutant Orange ll Sodium salt azo dye about 100% for the dye concentration of 50 ppm within five minutes at ambient conditions with 1 g/l loading of catalyst. Simple facile synthesis, easy separation by an external magnet, good reusability and high degradation capability of the catalyst may promote the practical applications of the heterostructured catalyst at ambient condition for water remediation. The present study also explored possible credible charge transfer directions and mechanism of photocatalysis supported by trapping experiments and electrochemical impedance spectroscopy (EIS) measurement for the effective improvement of photocatalytic activity and enhancement of the visible light adsorption.
Comparative study of substrate free and amniotic membrane scaffolds for cultivation of limbal epithelial sheet
Authors: Lee Hyun Jung , Nam Sang Min , Choi Sae Kyung , Seo Kyoung Yul , Kim Hyun Ok , Chung So-Hyang 
Published: September 2018

AbstractTransplantation of cultivated limbal epithelial transplantation has been proven to restore the corneal surface in limbal stem cell deficiency (LSCD). Here we comparatively investigated the optimized conditions and the efficiency of limbal epithelial sheet growth in three media conditions as well as with substrate free (transwell), human amniotic membrane (HAM) sutured onto transwell inserts (HAMTW), and HAM slide scaffold (HAMS). Outcomes evaluated were outgrowth sheet size from limbal explants, expression of stem/progenitor cell markers p63α, ABCG2 and CK15, and colony formation efficiency (CFE). Additionally, limbal epithelial sheets on HAMS were transplanted into corneas of LSCD rabbit models. Limbal epithelial sheets with 5% human AB serum showed the greatest increase in ABCG2 efflux activity (JC1low), p63α expression, and CFE compared in both conditions without HAM and with HAM, respectively. The outgrowth sheet size, cell yield, and Ki67 expression were increased in limbal epithelial sheets on HAMS compared to transwell and HAMTW. ABCG2 efflux activity, p63α and CK15 expressions, and CFE were also increased in limbal epithelial sheets on HAMS as well. In corneas of transplanted rabbit LSCD models, p63α expressions were noted in the basal layers and CK12 expressions were observed in superficial layers. Cultivation of limbal epithelial sheet on HAMS with xeno-free medium enhances the growth and stemness of limbal epithelial sheets.
Heterogeneity of a landscape influences size of home range in a North American cervid
Authors: Walter W. David , Evans Tyler S. , Stainbrook David , Wallingford Bret D. , Rosenberry Christopher S. , Diefenbach Duane R. 
Published: September 2018

AbstractIn the northeastern United States, chronic wasting disease has recently been detected in white-tailed deer (Odocoileus virginianus) populations, and understanding the relationship between landscape configuration and home range may improve disease surveillance and containment efforts. The objectives of our study were to compare size of home range for deer occupying a continuum of forested landscapes and to investigate relationships between size of home range and measures of landscape configuration. We used a movement-based kernel density estimator to estimate home range at five spatial scales among deer across study areas. We developed 7 linear regression models that used measures of the configuration of the forested landscape to explain size of home range. We observed differences in size of home range between sexes among areas that differed based on landscape configuration. We documented size of home range changed with various metrics that identifying connectivity of forested patches. Generally, size of home range increased with an increasing proportion of homogenous forest. Our results suggest that deer in our region occupy a landscape at hierarchically-nested scales that is controlled by the connectivity of the forested landscape across local or broad geographical regions.
Arrowtail RNA for Ligand Display on Ginger Exosome-like Nanovesicles to Systemic Deliver siRNA for Cancer Suppression
Authors: Li Zhefeng , Wang Hongzhi , Yin Hongran , Bennett Chad , Zhang Huang-ge , Guo Peixuan 
Published: September 2018

AbstractExosomes have shown increasing potential as delivery vesicles for therapy, but challenges like cost/yield, drug payload, and targeting specificity still exist. Plant derived exosome-like nanoparticles have been reported as a promising substitution and exhibit biocompatibility through oral, intranasal administration; however, systemic delivery of siRNA by exosome-like nanoparticles directly isolated from plants has not been reported. Recently, we reported the control of RNA orientation to decorate human derived exosome with cell targeting ligands for specific delivery of siRNA to tumors. Here, we expand to the application of arrowtail RNA nanoparticles for displaying ligands on ginger derived exosome-like nanovesicles (GDENs) for siRNA delivery and tumor inhibition through IV administration. Cushion ultracentrifugation coupled with equilibrium density gradient ultracentrifugation were used for purifying GDENs that displayed size, density, and morphology similar to human derived exosomes. Folic acid (FA), as a ligand, was displayed on the surface of GDENs for targeted delivery of survivin siRNA to KB cancer models. In vitro gene knockdown efficacy by FA-3WJ/GDENs/siRNA complex was comparable to transfection. We observed inhibition of tumor growth on a xenograft model by intravenous administration, which reveals the potential of GDENs as an economic delivery system for siRNA.
Diagnostic value of plasma tryptophan and symmetric dimethylarginine levels for acute kidney injury among tacrolimus-treated kidney transplant patients by targeted metabolomics analysis
Authors: Zhang Feng , Wang Qinghua , Xia Tianyi , Fu Shangxi , Tao Xia , Wen Yan , Chan Shen’an , Gao Shouhong , Xiong Xiaojuan , Chen Wansheng 
Published: September 2018

AbstractFew literatures have evaluated the exact role of metabolomics in the identification process of potential biomarkers for acute kidney injury among the patients receiving renal transplantation. On top of this, the success of metabolomics in biomarker translation seems to lie in the robust quantitative method. As such, a single-center retrospective observational study was conducted enrolling 42 patients underwent renal transplantation with/without acute kidney injury, as well as 24 healthy volunteers, in Shanghai Changzheng Hospital. Plasma amino acid metabolic patterns for the participants were investigated by targeted UHPLC-MS/MS metabolic profiling. The most significant changes of the explored metabolites were related to the disturbance of tryptophan metabolism and arginine metabolism. Abnormal circulating tryptophan and symmetric dimethylarginine were identified to be potential biomarkers of acute kidney injury, combination of which showed a higher area under receiver-operator curve value (AUC = 0.901), improved sensitivity (0.889) and specificity (0.831) compared with creatinine only. Overall, these results revealed that targeted metabolomics analysis would be a potent and promising strategy for identification and pre-validation of biomarkers of acute kidney injury in renal transplantation patients.
A novel antimicrobial peptide acting via formyl peptide receptor 2 shows therapeutic effects against rheumatoid arthritis
Authors: Park Yoo Jung , Park Byunghyun , Lee Mingyu , Jeong Yu Sun , Lee Ha Young , Sohn Dong Hyun , Song Jason Jungsik , Lee Joon Ha , Hwang Jae Sam , Bae Yoe-Sik 
Published: September 2018

AbstractIn oriental medicine, centipede Scolopendra subspinipes mutilans has long been used as a remedy for rheumatoid arthritis (RA), a well-known chronic autoimmune disorder. However, the molecular identities of its bioactive components have not yet been extensively investigated. We sought to identify bioactive molecules that control RA with a centipede. A novel antimicrobial peptide (AMP) (scolopendrasin IX) was identified from Scolopendra subspinipes mutilans. Scolopendrasin IX markedly activated mouse neutrophils, by enhancing cytosolic calcium increase, chemotactic cellular migration, and generation of superoxide anion in neutrophils. As a target receptor for scolopendrasin IX, formyl peptide receptor (FPR)2 mediates neutrophil activation induced by the AMP. Furthermore, scolopendrasin IX administration strongly blocked the clinical phenotype of RA in an autoantibody-injected model. Mechanistically, the novel AMP inhibited inflammatory cytokine synthesis from the joints and neutrophil recruitment into the joint area. Collectively, we suggest that scolopendrasin IX is a novel potential therapeutic agent for the control of RA via FPR2.
In Utero Heat Stress Alters the Offspring Epigenome
Authors: Skibiel A. L. , Peñagaricano F. , Amorín R. , Ahmed B. M. , Dahl G. E. , Laporta J. 
Published: September 2018

AbstractExposure to intrauterine heat stress during late gestation affects offspring performance into adulthood. However, underlying mechanistic links between thermal insult in fetal life and postnatal outcomes are not completely understood. We examined morphology, DNA methylation, and gene expression of liver and mammary gland for bull calves and heifers that were gestated under maternal conditions of heat stress or cooling (i.e. in utero heat stressedvs. in utero cooled calves). Mammary tissue was harvested from dairy heifers during their first lactation and liver from bull calves at birth. The liver of in utero heat stressed bull calves contained more cells and the mammary glands of in utero heat stressed heifers were comprised of smaller alveoli. We identified more than 1,500 CpG sites differently methylated between maternal treatment groups. These CpGs were associated with approximately 400 genes, which play a role in processes, such asdevelopment,innate immune defense, cell signaling, andtranscription and translation. We also identified over 100 differentially expressed genes in the mammary gland with similar functions. Interestingly, fifty differentially methylated genes were shared by both bull calf liver and heifer mammary gland. Intrauterine heat stress alters the methylation profile of liver and mammary DNA and programs their morphology in postnatal life, which may contribute to the poorer performance of in utero heat stressed calves.
Mutations at the hydrophobic core affect Hal3 trimer stability, reducing its Ppz1 inhibitory capacity but not its PPCDC moonlighting function
Authors: Santolaria Carlos , Velázquez Diego , Strauss Erick , Ariño Joaquín 
Published: September 2018

AbstractS.cerevisiaeHal3 (ScHal3) is a moonlighting protein that, is in its monomeric state, regulates the Ser/Thr protein phosphatase Ppz1, but also joins ScCab3 (and in some instances the Hal3 paralog Vhs3) to form an unusual heterotrimeric phosphopantothenoylcysteine decarboxylase (PPCDC) enzyme. PPCDC is required for CoA biosynthesis and in most eukaryotes is a homotrimeric complex with three identical catalytic sites at the trimer interfaces. However, inS.cerevisiaethe heterotrimeric arrangement results in a single functional catalytic center. Importantly, the specific structural determinants that direct Hal3’s oligomeric state and those required for Ppz1 inhibition remain largely unknown. We mutagenized residues in the predicted hydrophobic core of ScHal3 (L403–L405) and the plantArabidopsis thalianaHal3 (AtHal3, G115–L117) oligomers and characterized their properties as PPCDC components and, for ScHal3, also as Ppz1 inhibitor. We found that in AtHal3 these changes do not affect trimerization or PPCDC function. Similarly, mutation of ScHal3 L403 has no effect. In contrast, ScHal3 L405E fails to form homotrimers, but retains the capacity to bind Cab3—explaining its ability to rescue ahal3 vhs3synthetically lethal mutation. Remarkably, the L405E mutation decreases Hal3’s ability to interact with and to inhibit Ppz1, confirming the importance of the oligomer/monomer equilibrium in Hal3’s Ppz1 regulating function.