bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histones from Avian Erythrocytes Exhibit Antibiofilm activity against methicillin-sensitive and methicillin-resistant Staphylococcus aureus
Authors: Rose-Martel Megan , Kulshreshtha Garima , Ahferom Berhane Nahom , Jodoin Joelle , Hincke Maxwell T. 
Published: April 2017

AbstractStaphylococcus aureus, a human pathogen associated with many illnesses and post-surgical infections, can resist treatment due to the emergence of antibiotic-resistant strains and through biofilm formation. The current treatments for chronic biofilm infections are antibiotics and/or surgical removal of the contaminated medical device. Due to higher morbidity and mortality rates associated with overuse/misuse of antibiotics, alternate treatments are essential. This study reports the antibiofilm activity of avian erythrocyte histones against methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). Fluorescence and scanning electron microscopy revealed membrane damage to bacteria in histone-treated biofilms. Histones and indolicidin (positive control) increased the expression of apsS and apsR, which are associated with the Antimicrobial Peptide (AMP) sensor/regulator system in S. aureus. The expression of dltB, and vraF, associated with AMP resistance mechanisms, were under histone inducible control in the biofilm-embedded bacterial cells. The time kill kinetics for histones against S. aureus revealed a rapid biocidal activity (<5 min). Purified erythrocyte-specific histone H5 possessed 3–4 fold enhanced antimicrobial activity against planktonic cells compared to the histone mixture (H1, H2A, H2B, H3, H4, H5). These results demonstrate the promise of histones and histone-like derivatives as novel antibiotics against pathogens in their planktonic and biofilm forms.
FKBP65-dependent peptidyl-prolyl isomerase activity potentiates the lysyl hydroxylase 2-driven collagen cross-link switch
Authors: Chen Yulong , Terajima Masahiko , Banerjee Priyam , Guo Houfu , Liu Xin , Yu Jiang , Yamauchi Mitsuo , Kurie Jonathan M. 
Published: April 2017

AbstractBruck Syndrome is a connective tissue disease associated with inactivating mutations in lysyl hydroxylase 2 (LH2/PLOD2) or FK506 binding protein 65 (FKBP65/FKBP10). However, the functional relationship between LH2 and FKBP65 remains unclear. Here, we postulated that peptidyl prolyl isomerase (PPIase) activity of FKBP65 positively modulates LH2 enzymatic activity and is critical for the formation of hydroxylysine-aldehyde derived intermolecular collagen cross-links (HLCCs). To test this hypothesis, we analyzed collagen cross-links in Fkbp10-null and –wild-type murine embryonic fibroblasts. Although LH2 protein levels did not change, FKBP65 deficiency significantly diminished HLCCs and increased the non-hydroxylated lysine-aldehyde–derived collagen cross-links (LCCs), a pattern consistent with loss of LH2 enzymatic activity. The HLCC-to-LCC ratio was rescued in FKBP65-deficient murine embryonic fibroblasts by reconstitution with wild-type but not mutant FKBP65 that lacks intact PPIase domains. Findings from co-immunoprecipitation, protein-fragment complementation, and co-immunofluorescence assays showed that LH2 and FKBP65 are part of a common protein complex. We conclude that FKBP65 regulates LH2-mediated collagen cross-linking. Because LH2 promotes fibrosis and cancer metastasis, our findings suggest that pharmacologic strategies to target FKBP65 and LH2 may have complementary therapeutic activities.
Mediation of transitional B cell maturation in the absence of functional Bruton’s tyrosine kinase
Authors: Tanwar Shalini , Dhar Atika , Varanasi Vineeth , Mukherjee Tapas , Boppana Ramanamurthy , Basak Soumen , Bal Vineeta , George Anna , Rath Satyajit 
Published: April 2017

AbstractX-linked immune-deficient (Xid) mice, carrying a mutation in Bruton’s tyrosine kinase (Btk), have multiple B cell lineage differentiation defects. We now show that, while Xid mice showed only mild reduction in the frequency of the late transitional (T2) stage of peripheral B cells, the defect became severe when the Xid genotype was combined with either a CD40-null, a TCRbeta-null or an MHC class II (MHCII)-null genotype. Purified Xid T1 and T2 B cells survived poorlyin vitrocompared to wild-type (WT) cells. BAFF rescued WT but not Xid T1 and T2 B cells from death in culture, while CD40 ligation equivalently rescued both. Xid transitional B cellsex vivoshowed low levels of the p100 protein substrate for non-canonical NF-kappaB signalling.In vitro, CD40 ligation induced equivalent activation of the canonical but not of the non-canonical NF-kappaB pathway in Xid and WT T1 and T2 B cells. CD40 ligation efficiently rescued p100-null T1 B cells from neglect-induced deathin vitro. These data indicate that CD40-mediated signals, likely from CD4 T cells, can mediate peripheral transitional B cell maturation independent of Btk and the non-canonical NF-kappaB pathway, and thus contribute to the understanding of the complexities of peripheral B cell maturation.
Alpha-lipoic acid ameliorates the epithelial mesenchymal transition induced by unilateral ureteral obstruction in mice
Authors: Cho Hyun Seop , Kim Jin Hyun , Jang Ha Nee , Lee Tae Won , Jung Myeong Hee , Kim Tae Ho , Chang Se-Ho , Park Dong Jun 
Published: April 2017

AbstractThe epithelial-to-mesenchymal transition (EMT) is one of mechanisms that induce renal interstitial fibrosis. Understanding EMT in renal fibrosis has important therapeutic implications for patients with kidney disease. Alpha-lipoic acid (ALA) is a natural compound with antioxidant properties. Studies for ALA are performed in acute kidney injury with renal tubular apoptosis, renal inflammation, and oxidative stress. We investigated the effects of ALA on EMT-mediated renal interstitial fibrosis in mice with unilateral ureteral obstruction (UUO). UUO mice developed severe tubular atrophy and tubulointerstitial fibrosis, with a robust EMT response and ECM deposition after 7 postoperative days. In contrast, ALA-treated UUO mice showed only moderate injury and minimal fibrosis and also larger reductions in the expression of ECM proteins, inflammatory factors, and EMT markers. ALA was shown to be involved in the suppression of infiltrating macrophages associated with EMT and the progression of interstitial fibrosis. It also lessened the destruction of the tubular basement membrane, by reducing the expression of matrix metalloproteinases. This is the first study to show that ALA modulates EMT in a UUO mouse model. Our results suggest that ALA merits further exploration as a therapeutic agent in the prevention and treatment of chronic kidney disease.
Human health alters the sustainability of fishing practices in East Africa
Authors: Fiorella Kathryn J. , Milner Erin M. , Salmen Charles R. , Hickey Matthew D. , Omollo Dan O. , Odhiambo Abdi , Mattah Brian , Bukusi Elizabeth A. , Fernald Lia C. H. , Brashares Justin S. 
Published: April 2017

Significance
We accept that the environment influences human health, but we know little about how human health affects the environment. However, millions of people around the world rely on natural resources for food and livelihoods and confront a high burden of illness. Experience of illness may change people’s physical capacities, outlook, and planning horizons and shape how they engage with the environment. We analyze these impacts in fishing communities of Lake Victoria, Kenya. Although illness may cause the sickest individuals not to fish, many fishers continue fishing but shift their methods. When sick, fishers use methods that are less physically demanding but illegal and environmentally destructive. Our findings suggest that environmental sustainability may be integrally shaped by the health of resource users.
Anomalous Anderson localization behaviors in disordered pseudospin systems
Authors: Fang A. , Zhang Z. Q. , Louie Steven G. , Chan C. T. 
Published: April 2017

Significance
Wave propagation through a 1D disordered potential is always confined spatially due to the constructive interference in the backward direction. This “Anderson localization” behavior applies to all previously known 1D disordered systems in nature. Here, we show that wave propagating in 2D pseudospin-1 systems with 1D disorder has unique localization behaviors. In all conventional materials, stronger disorder always induces stronger localization. However, the localization in pseudospin-1 systems actually becomes weaker after the randomness increases beyond a critical value and a sharp transition separates the localization behavior into two regimes with different localization characteristics. Pseudospin-1 systems have been achieved in artificial crystals such as metamaterials and ultracold atom systems, which would be interesting platforms to observe the anomalous localization behaviors.
SMARCE1 is required for the invasive progression of in situ cancers
Authors: Sokol Ethan S. , Feng Yu-Xiong , Jin Dexter X. , Tizabi Minu D. , Miller Daniel H. , Cohen Malkiel A. , Sanduja Sandhya , Reinhardt Ferenc , Pandey Jai , Superville Daphne A. , Jaenisch Rudolf , Gupta Piyush B. 
Published: April 2017

Significance
More than half of ductal carcinoma in situ (DCIS) lesions will never progress to invasive breast cancers. However, the factors that drive invasion are not well understood. Our findings establish SMARCE1 as a clinically relevant factor that promotes the invasive progression of early-stage breast cancers. SMARCE1 drives invasion by serving as a master regulator of genes encoding proinvasive ECM and proteases required to degrade basement membrane. In functional studies in 3D cultures and animal models, SMARCE1 is dispensable for tumor growth but is required for the invasive and metastatic progression of cancers. In patients, SMARCE1 expression specifically identifies early-stage breast, lung, and ovarian cancers that are likely to eventually progress and metastasize.
Optimization of a Plaque Neutralization Test (PNT) to Identify the Exposure History of Pacific Herring to Viral Hemorrhagic Septicemia Virus (VHSV)
Authors: Hart Lucas M. , MacKenzie Ashley , Purcell Maureen K. , Powers Rachel L. , Hershberger Paul K. 
Published: April 2017

Abstract
Methods for a plaque neutralization test (PNT) were optimized for the detection and quantification of viral hemorrhagic septicemia virus (VHSV) neutralizing activity in the plasma of Pacific Herring Clupea pallasii. The PNT was complement dependent, as neutralizing activity was attenuated by heat inactivation; further, neutralizing activity was mostly restored by the addition of exogenous complement from specific-pathogen-free Pacific Herring. Optimal methods included the overnight incubation of VHSV aliquots in serial dilutions (starting at 1:16) of whole test plasma containing endogenous complement. The resulting viral titers were then enumerated using a viral plaque assay in 96-well microplates. Serum neutralizing activity was virus-specific as plasma from viral hemorrhagic septicemia (VHS) survivors demonstrated only negligible reactivity to infectious hematopoietic necrosis virus, a closely related rhabdovirus. Among Pacific Herring that survived VHSV exposure, neutralizing activity was detected in the plasma as early as 37 d postexposure and peaked at approximately 64 d postexposure. The onset of neutralizing activity was slightly delayed in fish reared at 7.4°C relative to those in warmer temperatures (9.9°C and 13.1°C); however, neutralizing activity persisted for at least 345 d postexposure in all temperature treatments. It is anticipated that this novel ability to assess VHSV neutralizing activity in Pacific Herring will enable retrospective comparisons between prior VHS infections and year-class recruitment failures. Additionally, the optimized PNT could be employed as a forecasting tool capable of identifying the potential for future VHS epizootics in wild Pacific Herring populations.
Received November 7, 2016; accepted January 14, 2017 Published online April 4, 2017
Inhibition of Grass Carp Reovirus Infection by DNA Aptamers against S10 Protein
Authors: Liang Hongru , Fu Xiaozhe , Liu Lihui , Lin Qiang , Guo Huizhi , Li Yonggang , Liu JiaXu , Huang Zhibin , Li Ningqiu 
Published: April 2017

Abstract
Grass Carp reovirus (GCRV) is one of the most pathogenic agents among aquareovirus isolates and has the ability to cause a severe epidemic outbreak of hemorrhagic disease, thus resulting in both a high mortality rate during the culture of Grass Carp Ctenopharyngodon idella and an enormous economic loss. Aptamers have been demonstrated to have strong promising applications in antiviral drug development. In the present study, a complementary DNA fragment encoding the S10 gene of GCRV was cloned. The S10 protein was expressed and purified. Aptamers for S10 protein were selected by the method of selective evolution of ligands by exponential enrichment (SELEX), and their characteristics and antiviral actions were examined. All targeting-selected aptamers formed a similar structure, forming a 5–7 base loop at the terminus. The results show that the aptamers could inhibit the GCRV infection. The most significant inhibitory effect was obsereved when the aptamers were added to the cell culture for 1 h before the cells were infected by GCRV. Our data showed that these novel molecular agents could be considered suitable candidates for anti-GCRV therapy.
Received August 23, 2016; accepted February 5, 2017Published online April 5, 2017
Sex, Obesity, and Blood Pressure Among African American Adolescents: The Jackson Heart KIDS Pilot Study
Authors: Bruce Marino A , Beech Bettina M , Norris Keith C , Griffith Derek M , Sims Mario , Thorpe Roland J 
Published: April 2017

Abstract

BACKGROUND
This study examined the degree to which sex, weight status, and the presence of hypertension and obesity in parents/grandparents were associated with systolic (SBP) and diastolic (DBP) blood pressure (BP) among African American youth in a pilot offspring study examining obesity-related cardiovascular disease (CVD) risks among adolescents.

METHODS
Data for this study were drawn from 212 adolescents (mean age 15.2 ± 2.2 years, 50.5% female) participating in the Jackson Heart Kids Pilot Study – an offspring cohort study examining cardiovascular disease risks among descendants of Jackson Heart Study participants. SBP (mean 114.4 ± 11.8 mm Hg) and DBP (mean 66.8 ± 9.0 mm Hg) were the primary outcomes. Weight status (46.1% normal weight, 30.1% overweight, 23.6% obese) was the key independent variable. Other covariates were attempts to lose weight, fruit and vegetable consumption, physical activity, and spirituality.

RESULTS
Fully adjusted linear regression models of the total sample produced results indicating that obesity was associated with BP (SBP: β = 7.08, P &lt; 0.01; DBP: β = 8.14, P &lt; 0.001). Sex-stratified analyses indicated that overweight and obesity were associated with SBP (overweight: β = 6.77, P &lt; 0.01; obese: β = 11.65, P &lt; 0.001) and obesity was correlated with DBP (β = 9.86, P &lt; 0.001) among males. For females, overweight was correlated with SBP (β = 4.11, P &lt; 0.05) while obesity was associated with DBP (β = 6.98, P &lt; 0.01). Attempting to lose weight was inversely related to SBP (β = −4.01, P &lt; 0.05) in the full sample and among males (β = −11.94, P &lt; 0.001). Familial presence of hypertension and/or obesity was significantly associated with SBP among adolescent females but not males.

CONCLUSIONS
The relationship between weight status, familial hypertension and obesity status, and BP among adolescents vary by sex. This study underscores the need for additional research investigating the relationship between individual sex, weight status, BP and familial BP, and obesity status on risk among African American adolescents.
StrandScript: evaluation of Illumina genotyping array design and strand correction
Authors: Wang Jing , Samuels David C , Shyr Yu , Guo Yan 
Published: April 2017

Abstract

Summary
After the introduction of high-throughput sequencing, genotyping arrays continue to be a viable source for conducting large-scale genetic studies. Currently, Illumina is one of the largest genotyping array manufacturers. One technical issue that has always plagued the post-processing of Illumina genotyping array data is the strand definition. Against convention, Illumina uses their own definition of strand, which is inconsistent with the standard reference forward and reverse definition. This issue has been a major obstacle in the consistency of reporting, meta-analysis and correct interpretation of phenotype association results. To date, the strand issue has not been adequately addressed, prompting us to develop StrandScript, a tool that can convert all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer Illumina array designs. Furthermore, StrandScript can examine an Illumina genotyping array manifest file and can detect all problematic SNPs, including SNPs with wrong RS ID and SNPs with mismatched probe sequences. Here, we introduce StrandScript’s design and development, and demonstrate its effectiveness using real genotyping data.

Availability and Implementation
https://github.com/seasky002002/Strandscript

Supplementary information
Supplementary data are available at Bioinformatics online.
Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data
Authors: Alzahrani Majed , Kuwahara Hiroyuki , Wang Wei , Gao Xin 
Published: April 2017

Abstract

Motivation
Growth phenotype profiling of genome-wide gene-deletion strains over stress conditions can offer a clear picture that the essentiality of genes depends on environmental conditions. Systematically identifying groups of genes from such high-throughput data that share similar patterns of conditional essentiality and dispensability under various environmental conditions can elucidate how genetic interactions of the growth phenotype are regulated in response to the environment.

Results
We first demonstrate that detecting such ‘co-fit’ gene groups can be cast as a less well-studied problem in biclustering, i.e. constant-column biclustering. Despite significant advances in biclustering techniques, very few were designed for mining in growth phenotype data. Here, we propose Gracob, a novel, efficient graph-based method that casts and solves the constant-column biclustering problem as a maximal clique finding problem in a multipartite graph. We compared Gracob with a large collection of widely used biclustering methods that cover different types of algorithms designed to detect different types of biclusters. Gracob showed superior performance on finding co-fit genes over all the existing methods on both a variety of synthetic data sets with a wide range of settings, and three real growth phenotype datasets for E. coli, proteobacteria and yeast.

Availability and Implementation
Our program is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Supplementary information
Supplementary data are available at Bioinformatics online.
EzMap: a simple pipeline for reproducible analysis of the human virome
Authors: Czeczko Patrick , Greenway Steven C , de Koning A P Jason 
Published: April 2017

Abstract

Summary
In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract WGS reads by mapping to a reference human assembly. The relative abundance of each virus present is estimated using a maximum likelihood approach that accounts for genome size, and results are presented with interactive visualizations and taxonomy-based summaries that enable rapid insights. The pipeline is automated to run on both workstations and computing clusters for all steps. EzMap automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA.

Availability and Implementation
EzMap is freely available at https://github.com/dekoning-lab/ezmap.

Supplementary information
Supplementary data are available at Bioinformatics online.
ploidyNGS: visually exploring ploidy with Next Generation Sequencing data
Authors: Augusto Corrêa dos Santos Renato , Goldman Gustavo Henrique , Riaño-Pachón Diego Mauricio 
Published: April 2017

Abstract

Summary
ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way.

Availability and Implementation
ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R.
Machine learning in computational biology to accelerate high-throughput protein expression
Authors: Sastry Anand , Monk Jonathan , Tegel Hanna , Uhlen Mathias , Palsson Bernhard O , Rockberg Johan , Brunk Elizabeth 
Published: April 2017

Abstract

Motivation
The Human Protein Atlas (HPA) enables the simultaneous characterization of thousands of proteins across various tissues to pinpoint their spatial location in the human body. This has been achieved through transcriptomics and high-throughput immunohistochemistry-based approaches, where over 40 000 unique human protein fragments have been expressed in E. coli. These datasets enable quantitative tracking of entire cellular proteomes and present new avenues for understanding molecular-level properties influencing expression and solubility.

Results
Combining computational biology and machine learning identifies protein properties that hinder the HPA high-throughput antibody production pipeline. We predict protein expression and solubility with accuracies of 70% and 80%, respectively, based on a subset of key properties (aromaticity, hydropathy and isoelectric point). We guide the selection of protein fragments based on these characteristics to optimize high-throughput experimentation.

Availability and implementation
We present the machine learning workflow as a series of IPython notebooks hosted on GitHub (https://github.com/SBRG/Protein_ML). The workflow can be used as a template for analysis of further expression and solubility datasets.

Supplementary information
Supplementary data are available at Bioinformatics online.