bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baicalin from Scutellaria baicalensis blocks respiratory syncytial virus (RSV) infection and reduces inflammatory cell infiltration and lung injury in mice
Authors: Shi Hengfei , Ren Ke , Lv Baojie , Zhang Wei , Zhao Ying , Tan Ren Xiang , Li Erguang 
Published: October 2016

AbstractThe roots of Scutellaria baicalensis has been used as a remedy for inflammatory and infective diseases for thousands of years. We evaluated the antiviral activity against respiratory syncytial virus (RSV) infection, the leading cause of childhood infection and hospitalization. By fractionation and chromatographic analysis, we determined that baicalin was responsible for the antiviral activity of S. baicalensis against RSV infection. The concentration for 50% inhibition (IC50) of RSV infection was determined at 19.9 ± 1.8 μM, while the 50% cytotoxic concentration (CC50) was measured at 370 ± 10 μM. We then used a mouse model of RSV infection to further demonstrate baicalin antiviral effect. RSV infection caused significant lung injury and proinflammatory response, including CD4 and CD8 T lymphocyte infiltration. Baicalin treatment resulted in reduction of T lymphocyte infiltration and gene expression of proinflammatory factors, while the treatment moderately reduced RSV titers recovered from the lung tissues. T lymphocyte infiltration and cytotoxic T lymphocyte modulated tissue damage has been identified critical factors of RSV disease. The study therefore demonstrates that baicalin subjugates RSV disease through antiviral and anti-inflammatory effect.
Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment
Authors: Weber Christian , Koutero Mikael , Dillies Marie-Agnes , Varet Hugo , Lopez-Camarillo Cesar , Coppée Jean Yves , Hon Chung-Chau , Guillén Nancy 
Published: October 2016

AbstractAmoebiasis is a human infectious disease due to the amoeba parasiteEntamoeba histolytica. The disease appears in only 20% of the infections. Diversity in phenotypes may occur within the same infectious strain in the gut; for instance, parasites can be commensal (in the intestinal lumen) or pathogenic (inside the tissue). The degree of pathogenesis of clinical isolates varies greatly. These findings raise the hypothesis that genetic derivation may account for amoebic diverse phenotypes. The main goal of this study was to analyse gene expression changes of a single virulent amoebic strain in different environmental contexts where it exhibit different degrees of virulence, namely isolated from humans and maintained through animal liver passages, in contact with the human colon and short or prolongedin vitroculture. The study reveals major transcriptome changes in virulent parasites upon contact with human colon explants, including genes related to sugar metabolism, cytoskeleton rearrangement, stress responses and DNA repair. Furthermore, in long-term cultured parasites, drastic changes in gene expression for proteins with functions for proteasome and tRNA activities were found. Globally we conclude that rapid changes in gene expression rather than genetic derivation can sustain the invasive phenotype of a single virulent isolate ofE. histolytica.
Multilayer Dye Aggregation at Dye/TiO2 Interface via π…π Stacking and Hydrogen Bond and Its Impact on Solar Cell Performance: A DFT Analysis
Authors: Zhang Lei , Liu Xiaogang , Rao Weifeng , Li Jingfa 
Published: October 2016

AbstractMultilayer dye aggregation at the dye/TiO2 interface of dye-sensitized solar cells is probed via first principles calculations, using p-methyl red azo dye as an example. Our calculations suggest that the multilayer dye aggregates at the TiO2 surface can be stabilized by π…π stacking and hydrogen bond interactions. Compared with previous two-dimensional monolayer dye/TiO2 model, the multilayer dye aggregation model proposed in this study constructs a three-dimensional multilayer dye/TiO2 interfacial structure, and provides a better agreement between experimental and computational results in dye coverage and dye adsorption energy. In particular, a dimer forms by π…π stacking interactions between two neighboring azo molecules, while one of them chemisorbs on the TiO2 surface; a trimer may form by introducing one additional azo molecule on the dimer through a hydrogen bond between two carboxylic acid groups. Different forms of multilayer dye aggregates, either stabilized by π…π stacking or hydrogen bond, exhibit varied optical absorption spectra and electronic properties. Such variations could have a critical impact on the performance of dye sensitized solar cells.
Biofluid metabotyping of occupationally exposed subjects to air pollution demonstrates high oxidative stress and deregulated amino acid metabolism
Authors: Pradhan Surya Narayan , Das Aleena , Meena Ramovatar , Nanda Ranjan Kumar , Rajamani Paulraj 
Published: October 2016

AbstractOccupational exposure to air pollution induces oxidative stress and prolonged exposure increases susceptibility to cardiovascular and respiratory diseases in several working groups. Biofluid of these subjects may reflect perturbed metabolic phenotypes. In this study we carried out a comparative molecular profiling study using parallel biofluids collected from subjects (n = 85) belonging to auto rickshaw drivers (ARD), traffic cops (TC) and office workers (OW). Higher levels of oxidative stress and inflammation markers in serum of ARD subjects were observed as compared to OW and TC. Uni and multivariate analyses of metabolites identified in urine by 1H NMR revealed 11 deregulated molecules in ARD subjects and involved in phenylalanine, histidine, arginine and proline metabolism. Despite contribution of confounding factors like exposure period, dietary factors including smoking and alcohol status, our results demonstrate existence of exposure specific metabotypes in biofluids of ARD, OW and TC groups. Monitoring serum oxidative stress and inflammation markers and urine metabolites by NMR may be useful to characterize perturbed metabolic phenotypes in populations exposed to urban traffic air pollution.
An investigation on the aqueous-phase hydrodeoxygenation of various methoxy-substituted lignin monomers on Pd/C and HZSM-5 catalysts
Authors: Zhang Cong , Qi Jingbo , Xing Jing , Tang Si-Fu , Song Liang , Sun Yuanyuan , Zhang Chuanhui , Xin Hongchuan , Li Xuebing 
Published: October 2016

Aqueous phase catalytic upgrading of lignin monomers to hydrocarbons via hydrodeoxygenation (HDO) has been explored using a combination of Pd/C and HZSM-5 catalysts under 2 MPa of H2 (ambient temperature).
Subjective Reports of Trouble Tolerating Sound in Daily Life versus Loudness Discomfort Levels
Authors: Zaugg Tara L. , Thielman Emily J. , Griest Susan , Henry James A. 
Published: October 2016

Purpose
A retrospective analysis of tonal and speech loudness discomfort levels (LDLs) relative to a subjective report of sound tolerance (SRST) was performed to explore the relation between the 2 commonly used clinical measures.

Method
Tonal LDLs and SRST were measured for 139 U.S. military veterans who were recruited into a study providing intervention for tinnitus. Spearman's rank correlation coefficients were computed to assess the relation between the tonal and speech LDLs and the SRST.

Results
Only weak correlations were found between tonal LDLs and SRST and between speech LDLs and SRST.

Conclusion
If LDLs ratings of SRST measured the same phenomenon, the measures would be strongly negatively correlated. The weak correlations found between the measures suggest that LDLs do not accurately represent a patient's ability to tolerate sound in daily life.
One‐pot synthesis of flake Cu1.81S/C composite for high‐performance supercapactiors electrodes
Authors: Hu Haihua , Sui Yanwei , Zhou Yaoyao , Qi Jiqiu , Wei Fuxiang , He Yezeng , Meng Qingkun , Sun Zhi , Zhao Yulong 
Published: October 2016

One‐pot fabrication of flake Cu1.81S/C composite with size of 300 nm was successfully demonstrated in this work. As the supercapacitor electrode material, the obtained Cu1.81S/C composite sample displayed good cycling stability of 83.6% capacitance retention after 1000 cycles and high specific capacitance of 617 F g−1 at current density of 0.5 A g−1. The excellent electrochemical performance is mainly attributed to flake nanostructure, which provides large electrode‐electrolyte contact area and facilitates an easy access of electrolyte ions to the electrode surface. This result provides a new pathway for the fabrication of high‐performance electrode material for supercapacitors.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery
Authors: Zhang Jin , Mardis Elaine R , Maher Christopher A 
Published: October 2016

Abstract

Motivation
While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens.

Results
We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens.

Availability and Implementation
INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo.

Supplementary information
Supplementary data are available at Bioinformatics online.
Discovery of a 0.42-s pulsar in the ultraluminous X-ray source NGC 7793 P13
Authors: Israel G. L. , Papitto A. , Esposito P. , Stella L. , Zampieri L. , Belfiore A. , Rodríguez Castillo G. A. , De Luca A. , Tiengo A. , Haberl F. , Greiner J. , Salvaterra R. , Sandrelli S. , Lisini G. 
Published: October 2016

Abstract
NGC 7793 P13 is a variable (luminosity range ∼100) ultraluminous X-ray source proposed to host a stellar-mass black hole of less than 15 M⊙ in a binary system with orbital period of 64 d and a 18–23 M⊙ B9Ia companion. Within the EXTraS (Exploring the X-ray Transient and variable Sky) project, we discovered pulsations at a period of ∼0.42 s in two XMM–Newton observations of NGC 7793 P13, during which the source was detected at LX ∼ 2.1 × 1039 and 5 × 1039 erg s−1 (0.3–10 keV band). These findings unambiguously demonstrate that the compact object in NGC 7793 P13 is a neutron star accreting at super-Eddington rates. While standard accretion models face difficulties accounting for the pulsar X-ray luminosity, the presence of a multipolar magnetic field with B ∼ few × 1013 G close to the base of the accretion column appears to be in agreement with the properties of the system.
A Revised Host Galaxy Association for GRB 020819B: A High-Redshift Dusty Starburst, Not a Low-Redshift Gas-Poor Spiral
Authors: Perley Daniel A. , Krühler Thomas , Schady Patricia , Michałowski Michał J. , Thöne Christina C. , Petry Dirk , Graham John F. , Greiner Jochen , Klose Sylvio , Schulze Steve , Kim Sam 
Published: October 2016

Abstract
The purported spiral host galaxy of GRB 020819B at z = 0.41 has been seminal in establishing our view of the diversity of long-duration gamma-ray burst environments: optical spectroscopy of this host provided evidence that GRBs can form even at high metallicities, while millimetric observations suggested that GRBs may preferentially form in regions with minimal molecular gas. We report new observations from VLT (MUSE and X-shooter) which demonstrate that the purported host is an unrelated foreground galaxy. The probable radio afterglow is coincident with a compact, highly star-forming, dusty galaxy at z = 1.9621. The revised redshift naturally explains the apparent nondetection of CO(3-2) line emission at the afterglow site from ALMA. There is no evidence that molecular gas properties in GRB host galaxies are unusual, and limited evidence that GRBs can form readily at super-Solar metallicity.
Testing the Interpersonal Theory of Suicide in Chronic Pain
Authors: Wilson Keith G. , Heenan Adam , Kowal John , Henderson Peter R. , McWilliams Lachlan A. , Castillo Dyana 
Published: October 2016

Objective:
The interpersonal theory of suicide offers a conceptual framework for understanding suicidal ideation (SI) that may be applicable to individuals with chronic pain. The theory emphasizes the importance of 2 interpersonal constructs as precursors to SI: perceived burdensomeness (the belief that one has become a burden to others) and thwarted belongingness (a lack of social integration or connection). Our objective was to test the interpersonal theory of suicide in people with chronic pain.

Methods:
Hierarchical regression analysis was used in a cross-sectional study of 282 patients of an interdisciplinary pain clinic. The Beck Scale for Suicide Ideation was the criterion measure of SI, and independent variables included both general and pain-specific predictors.

Results:
After adjusting for other known or putative risk factors related to pain and mental health, perceived burdensomeness significantly predicted SI, whereas thwarted belongingness did not. As expected according to theory, the interaction between perceived burdensomeness and thwarted belongingness was also significant; perceived burdensomeness was a strong predictor of SI at high levels of thwarted belongingness, but only marginally at low levels. Other independent predictors were male sex, number of prior suicide attempts, and hopelessness.

Discussion:
These findings are in line with some, but not all, of the major predictions of the interpersonal theory of suicide. In general, however, they support the relevance of the theory for individuals with chronic pain.
A Randomized Trial of Palliative Care Discussions Linked to an Automated Early Warning System Alert
Authors: Picker David , Dans Maria , Heard Kevin , Bailey Thomas , Chen Yixin , Lu Chenyang , Kollef Marin H. 
Published: October 2016

Objective:
To determine whether an Early Warning System could identify patients wishing to focus on palliative care measures.

Design:
Prospective, randomized, pilot study.

Setting:
Barnes-Jewish Hospital, Saint Louis, MO (January 15, 2015, to December 12, 2015).

Patients:
A total of 206 patients; 89 intervention (43.2%) and 117 controls (56.8%).

Interventions:
Palliative care in high-risk patients targeted by an Early Warning System.

Measurements and Main Results:
Advanced directive documentation was significantly greater prior to discharge in the intervention group (37.1% vs 15.4%; p < 0.001) as were first-time requests for advanced directive documentation (14.6% vs 0.0%; p < 0.001). Documentation of resuscitation status was also greater prior to discharge in the intervention group (36.0% vs 23.1%; p = 0.043). There was no difference in the number of patients requesting a change in resuscitation status between groups (11.2% vs 9.4%; p = 0.666). However, changes in resuscitation status occurred earlier and on the general medicine units for the intervention group compared to the control group. The number of patients transferred to an ICU was significantly lower for intervention patients (12.4% vs 27.4%; p = 0.009). The median (interquartile range) ICU length of stay was significantly less for the intervention group (0 [0–0] vs 0 [0–1] d; p = 0.014). Hospital mortality was similar (12.4% vs 10.3%; p = 0.635).

Conclusions:
This study suggests that automated Early Warning System alerts can identify patients potentially benefitting from directed palliative care discussions and reduce the number of ICU transfers.
Transcanalicular Laser-Assisted Dacryocystorhinostomy With Endonasal Augmentation in Primary Nasolacrimal Duct Obstruction: Our Experience
Authors: Goel Ruchi , Nagpal Smriti , Kumar Sushil , Meher Ravi , Kamal Saurabh , Garg Sonam 
Published: October 2016

Purpose:
To evaluate and compare the success rate of transcanalicular laser-assisted dacryocystorhinostomy with endonasal augmentation, with and without intubation, in patients suffering from primary acquired nasolacrimal duct obstruction, at 1 year of follow up.

Methods:
A prospective, randomized interventional pilot study was conducted at a tertiary care center, in accordance with the guidelines of Declaration of Helsinki. Sixty eyes of 60 adult patients with primary acquired nasolacrimal duct obstruction were included. The participants were divided randomly into 2 equal groups (A and B-without and with bicanalicular intubation, respectively). An osteotomy was first created using 980 nm diode laser (set at 8W continuous mode) transcanalicularly and then enlarged intranasally using Blakesley’s nasal forceps, followed by bicanalicular silicon intubation in group B patients. The tubes were removed at the end of 8 weeks. The ostium size was assessed endoscopically at 8 weeks and again at the end of follow up, at 1 year. A successful outcome was defined in terms of ostium patency at the end of 1 year. The results were analyzed at the end of a follow up of 1 year, using various statistical tests (p < 0.05).

Results:
The mean age of the patients was 35.3 ± 15.89 years, with 23 male and 37 female patients, the 2 groups having a similar male:female ratio. An overall success rate of 90% was achieved at the end of 1 year with no statistically significant difference between the groups. Postoperative complications like tube displacement and punctal, canalicular injury were more in the intubated group. The average osteotomy size was 8.06 ± 5.4 mm2 at the end of 1 year.

Conclusions:
Transcanalicular laser-assisted dacryocysto rhinostomy, with endonasal augmentation, is a scarless, effective, daycare procedure, for treatment of primary acquired nasolacrimal duct obstruction with no additional advantage offered by silicone intubation.
Non-Exenteration Management of Sino-Orbital Fungal Disease
Authors: Athavale Dnyaneshwar D. , Jones Robin , O’Donnell Brett A. , Forer Martin , Biggs Nigel 
Published: October 2016

Purpose:
To describe the non-exenteration management of sino-orbital fungal infection, a life-threatening condition for which orbital exenteration is generally considered a first-line treatment.

Methods:
A retrospective case series is presented of 7 orbits in 6 consecutive patients admitted and treated at 2 major metropolitan tertiary teaching hospitals in Sydney, New South Wales, Australia.

Results:
Seven orbits in 6 consecutive patients with sino-orbital fungal infection were treated conservatively with surgical debridement and intravenous antifungal agents. Four patients were immunosuppressed and the other 2 patients were otherwise healthy. All presented with pain, proptosis, or loss of vision. Causative organisms found were Mucormycoses, Aspergillus, and Scedosporium prolificans. Exenteration was avoided in all patients as part of their planned management and 5 patients, including 1 with bilateral disease, survived their disease without exenteration. Medical treatment included intravenous liposomal amphotericin B or voriconazole. A single immunosuppressed patient deteriorated and as a last resort, exenteration was performed, but this made no difference to his clinical course and in retrospect could have been avoided as he died of multiple cerebral metastases diagnosed shortly after his deterioration.

Conclusion:
The authors recommend that patients with sino-orbital fungal disease preferably be treated conservatively, without orbital exenteration.
Epigenetic Mediators Between Childhood Socioeconomic Disadvantage and Mid-Life Body Mass Index: The New England Family Study
Authors: Loucks Eric B. , Huang Yen-Tsung , Agha Golareh , Chu Su , Eaton Charles B. , Gilman Stephen E. , Buka Stephen L. , Kelsey Karl T. 
Published: October 2016

ABSTRACTObjectiveChildhood socioeconomic disadvantage is associated with adulthood obesity risk; however, epigenetic mechanisms are poorly understood. This work's objective was to evaluate whether associations of childhood socioeconomic disadvantage with adulthood body mass index (BMI) are mediated by DNA methylation.MethodsParticipants were 141 men and women from the New England Family Study, prospectively followed prenatally through a mean age of 47 years. Epigenomewide DNA methylation was evaluated in peripheral blood and adipose tissue obtained at adulthood, using the Infinium HumanMethylation450K BeadChip. Childhood socioeconomic status (SES) at age 7 years was assessed directly from parents' reports. Offspring adiposity was directly assessed using BMI at a mean age of 47 years. Associations of SES, DNA methylation, and BMI were estimated using least square estimators. Statistical mediation analyses were performed using joint significance test and bootstrapping.ResultsOf CpG sites significant at the 25% false discovery rate level in epigenomewide methylation BMI analyses, 91 sites in men and 71 sites in women were additionally significant for SES-methylation associations (p< .001) in adipose tissue. Many involved genes biologically relevant for development of obesity, including fatty acid synthase, transmembrane protein 88, signal transducer and activator of transcription 3, and neuritin 1. There was no evidence of epigenetic mediation in peripheral blood leukocytes.ConclusionsDNA methylation at specific genes may be mediators of associations between childhood socioeconomic disadvantage and mid-life BMI in adipose tissue. Findings motivate continued efforts to study if and how childhood socioeconomic disadvantage is biologically embedded at the level of the epigenome in regions etiologically relevant for adiposity.
TheE. colimolecular phenotype under different growth conditions
Authors: Caglar Mehmet U. , Houser John R. , Barnhart Craig S. , Boutz Daniel R. , Carroll Sean M. , Dasgupta Aurko , Lenoir Walter F. , Smith Bartram L. , Sridhara Viswanadham , Sydykova Dariya K. , Wood Drew Vander , Marx Christopher J. , Marcotte Edward M. , Barrick Jeffrey E. , Wilke Claus O. 
Published: October 2016

AbstractModern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset ofE. coligrown under 34 different conditions. Additionally, we provide measurements of doubling times andin-vivometabolic fluxes through the central carbon metabolism. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling ofE. coligene regulation, transcription, and translation.