bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrophoresis assisted time-of-flow mass spectrometry using hollow nanomechanical resonators
Authors: Chaudhari Swathi , Chaudhari Kamalesh , Kim Seokbeom , Khan Faheem , Lee Jungchul , Thundat Thomas 
Published: June 2017

AbstractThis report discusses the first demonstration of electrophoresis assisted time-of-flow mass spectrometry using ‘U’ shaped hollow nanomechanical resonators (HNR). Capillary electrophoresis was coupled with the HNR based mass detection to overcome low ionic conductivity of channels embedded in the HNR preventing direct in-situ electrophoretic separation. The flow of analytes through the HNR was achieved by balancing the hydrodynamic pressure to override the electromotive force and inhibit the motion of analytes towards the anode for capillary electrophoresis. The resonance frequency shifts of the HNR vibrating around 1.5 MHz were correlated with the time of the passage of the protein bands to construct the mass spectrum. The proposed concept was demonstrated by constructing a mass spectrum of egg white proteins in the molecular weight range of 14–250 kDa. When compared to regular polyacrylamide gel electrophoresis, our method not only provides a precise and fast readout but also avoids the use of chemical staining. This study paves a new route for low-cost and on-chip mass spectrometers with ultra-miniaturized dimensions.
Brain-derived neurotrophic factor is regulated via MyD88/NF-κB signaling in experimental Streptococcus pneumoniae meningitis
Authors: Xu Danfeng , Lian Di , Zhang Zhijie , Liu Ying , Sun Jiaming , Li Ling 
Published: June 2017

AbstractStreptococcus pneumoniae meningitis is an intractable disease of the central nervous system (CNS). Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophic family and found to participate in the immune inflammatory response. In this study, we investigated if activation of the classical inflammatory signaling pathway, myeloid differentiation factor 88 (MyD88)/nuclear factor-kappa B (NF-κB), regulates BDNF expression in experimental S. pneumoniae meningitis. MyD88 knockout (myd88−/−) mice and wild-type littermates were infected intracisternally with S. pneumoniae suspension. Twenty-four hours after inoculation, histopathology of brains was evaluated. Cytokine and chemokine in brains and spleens was analyzed using ELISA. NF-κB activation was evaluated using EMSA. Cortical and hippocampal BDNF was assessed using RT-PCR and ELISA, respectively. BDNF promoter activity was evaluated using ChIP-PCR. myd88−/− mice showed an obviously weakened inflammatory host response. This diminished inflammation was consistent with worse clinical parameters, neuron injury, and apoptosis. Deficiency in MyD88 was associated with decreased BDNF expression. Furthermore, we identified a valid κB-binding site in the BDNF promoter, consistent with activation of NF-κB induced by inflammation. To sum up, MyD88/NF-κB signaling has a crucial role in up-regulating BDNF, which might provide potential therapeutic targets for S. pneumoniae meningitis.
Economic development, flow of funds, and the equilibrium interaction of financial frictions
Authors: Moll Benjamin , Townsend Robert M. , Zhorin Victor 
Published: June 2017

Significance
Variation in the type of financial frictions faced by households and firms is an overlooked dimension of regional heterogeneity that has the potential to explain cross-regional factor flows and differences in concentration of economic activity. Our research combines a theoretical model with a complexity and variety of data from Thailand. The theoretical model features variation in financial regimes, moral hazard, and limited commitment, inferred from the data. In a counterfactual experiment we explore the effects of protecting wages in urban areas from incoming migrants and protecting rural areas from capital outflow. Economic life in cities would suffer enormously, as would rural and national productivity, with an increase in overall inequality.
Grain boundary precipitation in Inconel 718 and ATI 718Plus
Authors: Hassan Bilal , Corney Jonathan 
Published: June 2017

Grain boundary precipitates in Inconel 718 and ATI 718Plus are important to control during hot working processes, since they can control the grain size. Precipitating excessive or insufficient amounts can be detrimental to the final component. Therefore, it is important for manufacturers to understand the formation and kinetics of grain boundary precipitation and the effect this has on mechanical properties. This review considers the background of grain boundary precipitation, including the effect of the thermal stability of γ′ and γ″ phases. In addition, the effect of stress on the grain boundary phases and their precipitation kinetics in different conditions are also included. Also, the impact of grain boundary precipitation on the mechanical properties is explored. This review was submitted as part of the 2017 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged
Nitrate analogs as attractants for soybean cyst nematode
Authors: Hosoi Akito , Katsuyama Tsutomu , Sasaki Yasuyuki , Kondo Tatsuhiko , Yajima Shunsuke , Ito Shinsaku 
Published: June 2017

Abstract
Soybean cyst nematode (SCN) Heterodera glycines Ichinohe, a plant parasite, is one of the most serious pests of soybean. In this paper, we report that SCN is attracted to nitrate and its analogs. We performed attraction assays to screen for novel attractants for SCN and found that nitrates were attractants for SCN and SCN recognized nitrate gradients. However, attraction of SCN to nitrates was not observed on agar containing nitrate. To further elucidate the attraction mechanism in SCN, we performed attraction assays using nitrate analogs (, , ). SCN was attracted to all nitrate analogs; however, attraction of SCN to nitrate analogs was not observed on agar containing nitrate. In contrast, SCN was attracted to azuki root, irrespective of presence or absence of nitrate in agar media. Our results suggest that the attraction mechanisms differ between plant-derived attractant and nitrate.
Investigation of radon level in air and tap water of workplaces at Thailand Institute of Nuclear Technology, Thailand
Authors: Sola P , Youngchuay U , Kongsri S , Kongtana A 
Published: June 2017

Abstract
Thailand Institute of Nuclear Technology (TINT) has continuously monitored radiation exposure and radionuclide in workplaces specifically radon gas to estimate effective dose for workers. Radon exposure is the second leading cause of lung cancer in the world. In this study, radon in air and tap water at building no. 3, 7, 8, 9 and 18 on Ongkharak site of TINT have been measured for 5 years from 2012 to 2016. Radon level in air and tap water were investigated on 83 stations (workplaces) and 54 samples, respectively. Radon concentrations in air and tap water were measured by using the pulsed ionization chamber (ATMOS 12 DPX). Indoor radon concentrations in air were in the range of 12-138 Bq.m-3 with an average value of 30.13±17.05 Bq.m-3. Radon concentrations in tap water were in the range of 0.10 to 2.89 Bq.l-1 with an average value of 0.51±0.55 Bq.l-1. The results of radon concentrations at TINT were below the US Environmental Protection Agency (US EPA) safety limit of 148 Bq.m-3 and 150 Bq.l-1, for, air and tap water, respectively. The average effective dose for TINT’s workers due to indoor radon exposure was approximately 0.20±0.11 mSv.y-1. The value is 100 times less than the annual dose limit for limit occupational radiation worker defined by the International Commission on Radiological Protection (ICRP). As a result, the TINT’s workplaces are radiologically safe from radon content in air and tap water.
Group galaxy number density profiles far out: Is the ‘one-halo’ term NFW out to &gt;10 virial radii?
Authors: Trevisan M. , Mamon G. A. , Stalder D. H. 
Published: June 2017

Abstract
While the density profiles (DPs) of Lambda cold dark matter haloes obey the Navarro, Frenk & White (NFW) law out to roughly one virial radius, rvir, the structure of their outer parts is still poorly understood, because the one-halo term describing the halo itself is dominated by the two-halo term representing the other haloes picked up. Using a semi-analytical model, we measure the real-space one-halo number DP of groups out to 20rvir by assigning each galaxy to its nearest group above mass Ma, in units of the group rvir. If Ma is small (large), the outer DP of groups falls rapidly (slowly). We find that there is an optimal Ma for which the stacked DP resembles the NFW model to 0.1 dex accuracy out to 13 virial radii. We find similar long-range NFW surface DPs (out to 10rvir) in the Sloan Digital Sky Survey observations using a galaxy assignment scheme that combines the non-linear virialized regions of groups with their linear outer parts. The optimal Ma scales as the minimum mass of the groups that are stacked to a power 0.25–0.3. The NFW model thus does not solely originate from violent relaxation. Moreover, populating haloes with galaxies using halo occupation distribution models must proceed out to much larger radii than usually done.
Progestogens for Maintenance Tocolysis in Women With a Short Cervix
Authors: Facchinetti Fabio , Vergani Patrizia , Di Tommaso Mariarosaria , Marozio Luca , Acaia Barbara , Vicini Roberto , Pignatti Lucrezia , Locatelli Anna , Spitaleri Marina , Benedetto Chiara , Zaina Barbara , D'Amico Roberto ,   on behalf of the PROTECT Collaborative Group
Published: June 2017

OBJECTIVE:
To assess the efficacy of progestogens for maintenance tocolysis in women undelivered after their first preterm labor episode.

METHODS:
Women with singleton pregnancies between 22 0/7 and 31 6/7 weeks of gestation with arrested preterm labor and a cervical length 25 mm or less at hospital discharge were eligible. Patients with a previous preterm birth were excluded. In a randomized controlled trial conducted in five university hospitals, women were randomized to receive vaginal progesterone (200 mg per day) or intramuscular 17α-hydroxyprogesterone caproate (341 mg per week) or to an observation groups (control group). The primary outcome was the proportion of women with preterm birth at less than 37 weeks of gestation. A sample size of 160 per group (n=480) was planned to compare vaginal progesterone and 17α-hydroxyprogesterone caproate groups with those in the control group. The sample size estimation was based on the hypothesis that the risk of experiencing preterm birth in the control group would be 30% and that 17α-hydroxyprogesterone caproate or progesterone would decrease this risk to 15%. A P value of <.025 was defined as statistically significant. At planned interim analysis (n=254), the trial was stopped for futility.

RESULTS:
Between July 2010 and June 2015, 257 women were eligible and 254 were subsequently randomly assigned to vaginal progesterone (n=86), 17α-hydroxyprogesterone caproate (n=87), or observation (n=81). Nineteen (8%) were excluded from the analysis because they either dropped out or information was missing, leaving 235 women available for analysis. Demographic characteristics were similar across groups. The preterm birth rate did not differ significantly between groups: 23% in the 17α-hydroxyprogesterone caproate group, 39% in the vaginal progesterone group, and 22% in the women in the control group (P=.949 for 17α-hydroxyprogesterone caproate compared with the women in the control group and P=.027 for vaginal progesterone compared with women in the control group).

CONCLUSION:
The use of progestogens for maintenance tocolysis in women with a short cervix did not reduce the rate of preterm birth.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT01178788.
POSTERIOR VITRECTORHEXIS: A SURGICAL MODIFICATION FOR INTRAOCULAR FOREIGN BODY REMOVAL THROUGH LIMBAL ROUTE
Authors: Baskaran Prabu , Bhandari Sahil , Govindarajan Madanagopalan V. 
Published: June 2017

Purpose:
To describe a modified surgical technique of creating a posterior capsule opening for removal of retained intraocular foreign body, what we call as retroillumination-assisted posterior vitrectorhexis.

Methods:
Vitrectomy probe through pars plana route is used to create a well-controlled circular posterior vitrectorhexis.

Results:
A uniformly circular posterior capsule opening is created after standard pars plana vitrectomy for the removal of foreign body.

Conclusion:
Posterior vitrectorhexis is a well-controlled technique in the setting of a penetrating injury that can facilitate safe removal of different sizes of intraocular foreign body simultaneously preserving capsular support.
Relationship Between Serum Glucose Levels and Intraocular Pressure, a Population-based Cross-sectional Study
Authors: Cohen Eytan , Kramer Michal , Shochat Tzippy , Goldberg Elad , Krause Ilan 
Published: June 2017

Purpose:
The purpose of this study is to assess the relationship between serum glucose levels and intraocular pressure (IOP) both in subjects with impaired fasting glucose (IFG) as well as in subjects with diabetes mellitus (DM).

Materials and Methods:
Data of a cross-sectional sample of 18,406 subjects who underwent routine annual screening at a tertiary medical center in 2000 to 2013 were analyzed.

Results:
Mean (SD) age of the subjects was 46 (10) years; 68% were male. Mean (95% confidence interval) IOP measured 13.1 (13.0-13.1) mm Hg in subjects with normal glucose levels, 13.7 (13.6-13.8) mm Hg in subjects with IFG, and 14.3 (14.1-14.4) mm Hg in subjects with diabetes. The difference in IOP between subjects with normal and abnormal (DM or IFG) serum glucose levels were significant, even after adjusting for age, body mass index, and hypertension (P<0.0001). There was a positive linear correlation between serum glucose levels and IOP in both men (r=0.12; P<0.0001) and women (r=0.17; P<0.0001). For every 10 mg/dL increase in fasting serum glucose, IOP increased by 0.09 mm Hg in men and by 0.11 mm Hg in women.

Conclusions:
This study demonstrated that similar to subjects with DM, subjects with IFG also have IOP levels that are higher than those with normal serum glucose. Moreover, there is a direct correlation between fasting serum glucose levels and changes in IOP. These findings highlight another end-organ effect of uncontrolled glucose levels.
Advances in vascular thiol isomerase function
Authors: Flaumenhaft Robert 
Published: June 2017

Purpose of reviewThe present review will provide an overview of several recent advances in the field of vascular thiol isomerase function.Recent findingsThe initial observation that protein disulfide isomerase (PDI) functions in thrombus formation occurred approximately a decade ago. At the time, there was little understanding regarding how PDI or other vascular thiol isomerases contribute to thrombosis. Although this problem is far from solved, the past few years have seen substantial progress in several areas that will be reviewed in this article. The relationship between PDI structure and its function has been investigated and applied to identify domains of PDI that are critical for thrombus formation. The mechanisms that direct thiol isomerase storage and release from platelets and endothelium have been studied. New techniques including kinetic-based trapping have identified substrates that vascular thiol isomerases modify during thrombus formation. Novel inhibitors of thiol isomerases have been developed that are useful both as tools to interrogate PDI function and as potential therapeutics. Human studies have been conducted to measure circulating PDI in disease states and evaluate the effect of oral administration of a PDI inhibitor on ex-vivo thrombin generation.SummaryCurrent findings indicate that thiol isomerase-mediated disulfide bond modification in receptors and plasma proteins is an important layer of control of thrombosis and vascular function more generally.
Retrospective Analysis of Catheter-Acquired Urinary Tract Infection
Authors: Retelski Julia , Richardson Tammy , Mahabaleshwarkar Rohan , Gohs Frank X. , Spencer Melanie D. 
Published: June 2017

Aims:
The objective of this study was to determine if a diagnosis of stroke was associated with a higher incidence of catheter-associated urinary tract infections (CAUTIs). Secondary aims included examining the effect of healthcare-related variables including antibiotic and steroid use, length of stay before catheter insertion, and duration of catheter use on the incidence of CAUTI in stroke patients.

Design:
This was a retrospective chart review analysis set in a large teaching hospital in the Southeastern United States.

Methods:
A total of 300 patients with indwelling urinary catheter use who also had a stroke diagnosis were randomly selected and matched (on age, gender, race, and admission date) to 300 randomly selected patients with indwelling urinary catheter use and without stroke. Bivariate statistical tests included Wilcoxon signed-rank test and McNemar’s test, whereas the multivariate test consisted of generalized estimating equations.

Results:
The incidence of CAUTIs in stroke patients was significantly higher than that in nonstroke patients (6.0% vs 1.7%, P = .005). In the multivariable generalized estimating equations analysis, stroke patients were found to be approximately 3.5 times more likely to experience CAUTI compared with nonstroke patients (odds ratio = 3.53; 95% confidence interval, 1.24–10.03; P = .018). The proportion of patients who used steroids was greater among stroke patients who experienced CAUTI compared with those who did not experience CAUTI (55.6% vs 24.5%, P = .004).

Conclusion:
Stroke patients were more likely to develop CAUTI compared with nonstroke patients. These patients should be considered as key targets when implementing interventions aimed at reducing CAUTIs. Use of steroids may be associated with a higher likelihood of CAUTI in stroke patients.

Implications:
Clinical nurse specialists are directly influential in preventing CAUTIs. This study provides evidence regarding the association between stroke and CAUTI to clinical nurse specialists to help them plan CAUTI prevention initiatives.
FUSTr: a tool to find gene Families Under Selection in Transcriptomes
Authors: Cole T. Jeffrey , Brewer Michael S. 
Published: June 2017

AbstractFUSTr is a tool for finding genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. When applied to previously studied spider toxin families as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection. FUSTr provides a tool capable of utilizing multi-processor high-performance computational facilities and is scalable for large transcriptomic biodiversity datasets.AvailabilityFUSTr is freely available under a GNU license and can be downloaded athttps://github.com/tijeco/FUSTr.Contactcoleti16@students.ecu.edu
A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferation
Authors: Reeves Daniel B. , Duke Elizabeth R. , Wagner Thor A. , Palmer Sarah E. , Spivak Adam M. , Schiffer Joshua T. 
Published: June 2017

AbstractAntiretroviral therapy (ART) suppresses viral replication in people living with HIV. Yet, infected cells persist for decades on ART and viremia returns if ART is stopped. Persistence has been attributed to viral replication in an ART sanctuary and long-lived and1or proliferating latently infected cells. Using ecological methods and existing data, we infer that >99% of infected cells are members of clonal populations after one year of ART. We reconcile our results with observations from the first months of ART, demonstrating mathematically how a “fossil record” of historic HIV replication permits observed viral evolution even while most new infected cells arise from proliferation. Together, our results imply cellular proliferation generates a majority of infected cells during ART. Therefore, reducing proliferation could decrease the size of the HIV reservoir and help achieve a functional cure.
COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome
Authors: Rodrigues Richard R. , Rodgers Nyle C. , Wu Xiaowei , Williams Mark A. 
Published: June 2017

AbstractMicrobial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val < 0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.
Homology-based hydrogen bond information improves crystallographic structures in the PDB
Authors: Beusekom Bart van , Touw Wouter G. , Tatineni Mahidhar , Somani Sandeep , Rajagopal Gunaretnam , Luo Jinquan , Gilliland Gary L. , Perrakis Anastassis , Joosten Robbie P. 
Published: June 2017

AbstractCrystallographic structure models in the Protein Data Bank (PDB) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures, especially at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. Using approximately 60 years of CPU-time in massively parallel computing, we constructed a new instance of the PDB-REDO databank, a novel resource to help biologists gain insight on protein families or on specific structures, as we demonstrate with examples.