bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acid-sensing ion channels are expressed in the ventrolateral medulla and contribute to central chemoreception
Authors: Song Nana , Guan Ruijuan , Jiang Qian , Hassanzadeh Comron J. , Chu Yuyang , Zhao Xiaomei , Wang Xia , Yang Dawei , Du Qijun , Chu Xiang-Ping , Shen Linlin 
Published: December 2016

AbstractThe role of acid-sensing ion channels (ASICs) in the ventrolateral medulla (VLM) remains uncertain. Here, we found that ASIC1a and ASIC2 are widely expressed in rat medulla, and the expression level is higher at neonatal stage as compared to adult stage. The two ASIC subunits co-localized in medualla neurons. Furthermore, pH reduction triggered typical ASIC-type currents in the medulla, including the VLM. These currents showed a pH50 value of 6.6 and were blocked by amiloride. Based on their sensitivity to psalmotoxin 1 (PcTx1) and zinc, homomeric ASIC1a and heteromeric ASIC1a/2 channels were likely responsible for acid-mediated currents in the mouse medulla. ASIC currents triggered by pH 5 disappeared in the VLM neurons from ASIC1−/−, but not ASIC2−/− mice. Activation of ASICs in the medulla also triggered neuronal excitation. Moreover, microinjection of artificial cerebrospinal fluid at a pH of 6.5 into the VLM increased integrated phrenic nerve discharge, inspiratory time and respiratory drive in rats. Both amiloride and PcTx1 inhibited the acid-induced stimulating effect on respiration. Collectively, our data suggest that ASICs are highly expressed in the medulla including the VLM, and activation of ASICs in the VLM contributes to central chemoreception.
Comparison of non-Gaussian and Gaussian diffusion models of diffusion weighted imaging of rectal cancer at 3.0 T MRI
Authors: Zhang Guangwen , Wang Shuangshuang , Wen Didi , Zhang Jing , Wei Xiaocheng , Ma Wanling , Zhao Weiwei , Wang Mian , Wu Guosheng , Zhang Jinsong 
Published: December 2016

AbstractWater molecular diffusion in vivo tissue is much more complicated. We aimed to compare non-Gaussian diffusion models of diffusion-weighted imaging (DWI) including intra-voxel incoherent motion (IVIM), stretched-exponential model (SEM) and Gaussian diffusion model at 3.0 T MRI in patients with rectal cancer, and to determine the optimal model for investigating the water diffusion properties and characterization of rectal carcinoma. Fifty-nine consecutive patients with pathologically confirmed rectal adenocarcinoma underwent DWI with 16 b-values at a 3.0 T MRI system. DWI signals were fitted to the mono-exponential and non-Gaussian diffusion models (IVIM-mono, IVIM-bi and SEM) on primary tumor and adjacent normal rectal tissue. Parameters of standard apparent diffusion coefficient (ADC), slow- and fast-ADC, fraction of fast ADC (f), α value and distributed diffusion coefficient (DDC) were generated and compared between the tumor and normal tissues. The SEM exhibited the best fitting results of actual DWI signal in rectal cancer and the normal rectal wall (R2 = 0.998, 0.999 respectively). The DDC achieved relatively high area under the curve (AUC = 0.980) in differentiating tumor from normal rectal wall. Non-Gaussian diffusion models could assess tissue properties more accurately than the ADC derived Gaussian diffusion model. SEM may be used as a potential optimal model for characterization of rectal cancer.
Placental antibody transfer efficiency and maternal levels: specific for measles, coxsackievirus A16, enterovirus 71, poliomyelitis I-III and HIV-1 antibodies
Authors: Fu Chuanxi , Lu Long , Wu Hao , Shaman Jeffrey , Cao Yimin , Fang Fang , Yang Qiongying , He Qing , Yang Zhicong , Wang Ming 
Published: December 2016

AbstractMaternal antibodies transported across the placenta can provide vital immunity against infectious pathogens for infants. We here examine maternal antibody (MA) levels and their association with neonatal antibody levels. Pregnant women of gestational age ≥35 weeks were enrolled at a Guangzhou China hospital and mother-infant paired sera were collected. Measles IgG antibody was detected using ELISA assay, neutralizing antibodies titers against coxsackievirus A16 (CA16), enterovirus 71 (EV71), PV I-III and HIV-1 were performed. 711 mother-infant pairs were enrolled and positive relationships for paired serums were found (r: 0.683–0.918). 81.6%, 87.0%, and 82.3% of mothers, and 87.3%, 72.7%, and 72.2% of newborns were positive for measles, CA16 and EV71 antibodies respectively. The highest Neonatal: maternal ratio (NMR) was found in measles (1.042) and the ratios for the other pathogens ranged from 0.84 to 1.00. Linear regressions showed that log(NMR) decreased by a factor of 0.04–15.43 as log(MA) levels increased. A second analysis restricted to maternal positive measles sera revealed that MA measles of was still inversely associated with NMR. Low NMR was found in high MA HIV + serums among 22 paired sera. MA levels appear to play a role determining transplacental antibody transfer; further study is needed to reveal the mechanism.
InGaAs metamorphic laser (1064 nm) power converters with over 40% efficiency
Authors: Kalyuzhnyy N.A. , Mintairov S.A. , Nadtochiy A.M. , Nevedomskiy V.N. , Rybalchenko D.V. , Shvarts M.Z. 
Published: December 2016

Grown by metalorganic vapour phase epitaxy (MOVPE) InxGa1−xAs metamorphic laser power converters have been considered. Metamorphic buffer designs with high quality top layers have been developed. Photovoltaic converters with In0.24Ga0.76As photoactive area and optimised buffer have demonstrated efficiency 41.4% for 1064 nm monochromatic radiation conversion and ∼40% for laser power conversion.
Robust DoA estimation in case of multipath environment for a sense and avoid airborne radar
Authors: Bonacci David , Vincent François , Gigleux Benjamin 
Published: December 2016

This study deals with the sense and avoid problem for an helicopter. The objective of such a system is to early detect collision targets (typically high‐voltage wires). The direction of arrival (DoA) of the target is then a crucial information. In severe multipath environments (flight over a river, for instance), classical DoA estimation schemes dramatically degrade. The authors make use of a method based on the maximum likelihood (ML) principle that can resolve two highly correlated and close targets. The major drawback of ML algorithms, namely the computational burden, is removed using an approximation for closely space targets. The contribution of this study is twofold. The authors first extend the approximated ML DoA estimation to the case of non‐uniform linear antennas and complete the procedure by a detection scheme. Second, they attest the validity of this new processing on real radar data. Hence, they show that the proposed procedure is able to detect a high‐voltage wire, over a river, at ranges up to 1 km, where a capon beamformer cannot.
Optical and antibacterial properties of synthesised silver nanoparticles
Authors: Acharya Debashish , Mohanta Bidhan , Pandey Piyush , Singha Malabika , Nasiri Farnaj 
Published: December 2016

In the present study, tri‐sodium citrate has been used as both the reducing agent and stabiliser for the synthesis of silver nanoparticles (AgNPs). Sodium borohydride (NaBH4) was used in various concentrations. The absorbance of AgNP solution was measured after the addition of NaBH4. The samples were characterised by ultraviolet‐visible spectroscopy after 5, 10, 15, 25, 60 and 120 min of synthesis to investigate the stability of AgNPs for different concentrations of NaBH4. Transmission electron microscopy revealed the nanostructure of the prepared samples with average sizes as 18, 20 and 29 nm. Photoluminescence spectra of these AgNPs showed maximum emission at wavelengths 473, 470 and 469 nm, respectively, when excited at 350 nm. Further, Disk diffusion test showed that all the prepared samples are good candidates for antibacterial activity while AgNPs of average size 18 nm were found most effective against the tested Gram‐positive and Gram‐negative bacteria.
Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium
Authors: Biase Fernando H. , Rabel Chanaka , Guillomot Michel , Hue Isabelle , Andropolis Kalista , Olmstead Colleen A. , Oliveira Rosane , Wallace Richard , Le Bourhis Daniel , Richard Christophe , Campion Evelyne , Chaulot-Talmon Aurélie , Giraud-Delville Corinne , Taghouti Géraldine , Jammes Hélène , Renard Jean-Paul , Sandra Olivier , Lewin Harris A. 
Published: December 2016

SignificanceCloning cattle by somatic cell nuclear transfer (SCNT) is an agriculturally important technology and is also used as a model system for the study of mammalian development. The SCNT process is inefficient, typically yielding fewer than 10% live offspring. The majority of losses are the result of embryonic death, failure of the implantation process, and development of a defective placenta. A critical period is the implantation window, when survival of the conceptus depends on factors including genetics, epigenetics, and the communication between conceptus and the endometrium. Our study of gene expression in cloned conceptuses and endometrial tissues during the periimplantation period enhances understanding of the mechanisms that lead to pregnancy failure in SCNT cloning. The results have wide implications for cloning of other mammals.
Computational design of a homotrimeric metalloprotein with a trisbipyridyl core
Authors: Mills Jeremy H. , Sheffler William , Ener Maraia E. , Almhjell Patrick J. , Oberdorfer Gustav , Pereira José Henrique , Parmeggiani Fabio , Sankaran Banumathi , Zwart Peter H. , Baker David 
Published: December 2016

Significance
This article reports the computational design of a threefold symmetric, self-assembling protein homotrimer containing a highly stable noncanonical amino acid-mediated metal complex within the protein interface. To achieve this result, recently developed protein–protein interface design methods were extended to include a metal-chelating noncanonical amino acid containing a bipyridine functional group in the design process. Bipyridine metal complexes can give rise to photochemical properties that would be impossible to achieve with naturally occurring amino acids alone, suggesting that the methods reported here could be used to generate novel photoactive proteins.
Evolution of a mass spectrometry-grade protease with PTM-directed specificity
Authors: Tran Duc T. , Cavett Valerie J. , Dang Vuong Q. , Torres Héctor L. , Paegel Brian M. 
Published: December 2016

Significance
Protein posttranslational modifications (PTMs) regulate virtually every aspect of cellular function. Mapping PTMs is a key application of protein mass spectrometry (MS), which analyzes thousands of peptides generated in enzymatic protein digests. There are currently only about seven naturally occurring proteases for generating these digests, and with the exception of trypsin, most are poor or promiscuous enzymes that are not ideal for MS. This protease “toolbox” has remained essentially unchanged for decades. In this study, the directed evolution of trypsin’s proteolytic specificity resulted in the discovery of a mutant protease that efficiently cleaves at citrullinated arginines, affording a powerful PTM site identification tool and promising a Darwinian wellspring of new, custom proteases.
Hierarchical CRMP2 posttranslational modifications control NaV1.7 function
Authors: Dustrude Erik T. , Moutal Aubin , Yang Xiaofang , Wang Yuying , Khanna May , Khanna Rajesh 
Published: December 2016

SignificanceThe voltage-gated sodium channel NaV1.7 is important for electrogenesis in sensory neurons. Insertion within the membrane is required for function of NaV1.7. However, the mechanisms determining how NaV1.7 is trafficked to neuronal cell membranes are poorly understood. Here, we elucidate a signaling program involving a complex and intriguing posttranslational modification regime of collapsin response mediator protein 2 (CRMP2), an NaV1.7-binding protein. NaV1.7 surface localization and currents are controlled by CRMP2 modifications. Activity of NaV1.7 is thought to modulate neuronal excitability that codes for several sensory modalities, including chronic pain, as inferred from human pain disorders caused by mutations in NaV1.7 channels. Understanding the role of cross-talk between CRMP2 modifications in modulation of NaV1.7 activity opens routes to exploit this system for pain.
CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing
Authors: Piao Yongjun , Lee Seong Keon , Lee Eun-Joon , Robertson Keith D , Shi Huidong , Ryu Keun Ho , Choi Jeong-Hyeon 
Published: December 2016

Abstract

Motivation
Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin accessibility from MAPit-BGS and NOMe-seq.

Results
In this article, we present CAME (Chromatin Accessibility and Methylation), a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods.

Availability and Implementation
CAME is implemented in java and the program is freely available online at http://sourceforge.net/projects/came/

Supplementary information
Supplementary data are available at Bioinformatics online.
PhosD: inferring kinase–substrate interactions based on protein domains
Authors: Qin Gui-Min , Li Rui-Yi , Zhao Xing-Ming 
Published: December 2016

AbstractMotivationIdentifying the kinase–substrate relationships is vital to understanding the phosphorylation events and various biological processes, especially signal transductions. Although large amount of phosphorylation sites have been detected, unfortunately, it is rarely known which kinases activate those sites. Despite distinct computational approaches have been proposed to predict the kinase–substrate interactions, the prediction accuracy still needs to be improved.ResultsIn this paper, we propose a novel probabilistic model named as PhosD to predict kinase–substrate relationships based on protein domains with the assumption that kinase–substrate interactions are accomplished with kinase–domain interactions. By further taking into account protein–protein interactions, our PhosD outperforms other popular approaches on several benchmark datasets with higher precision. In addition, some of our predicted kinase–substrate relationships are validated by signaling pathways, indicating the predictive power of our approach. Furthermore, we notice that given a kinase, the more substrates are known for the kinase the more accurate its predicted substrates will be, and the domains involved in kinase–substrate interactions are found to be more conserved across proteins phosphorylated by multiple kinases. These findings can help develop more efficient computational approaches in the future.Availability and ImplementationThe data and results are available at http://comp-sysbio.org/phosdSupplementary informationSupplementary data are available at Bioinformatics online.
Gag-Specific CD8 T-Cell Proliferation Is Associated With Higher Peripheral Blood Levels of Transforming Growth Factor-β and Gut-Homing T Cells in Youths Perinatally Infected With Human Immunodeficiency Virus-1: The ANRS-EP38-IMMIP Study
Authors: Warszawski Josiane , Avettand-Fenoel Véronique , Rouzioux Christine , Scott-Algara Daniel , Montange Thomas , Didier Céline , Le Chenadec Jérôme , Viard Jean-Paul , Dollfus Catherine , Blanche Stéphane , Buseyne Florence 
Published: December 2016

AbstractBackgroundGag-specific T lymphocytes play a key role in the control of human immunodeficiency virus (HIV) replication. Their restoration will be important for future reservoir targeting strategies. In this study, we aimed to identify immune correlates of Gag-specific CD8 T-cell proliferation in youths with perinatally acquired HIV-1 infection.MethodsThe ANRS-EP38-IMMIP study included youths of 15 to 24 years of age. Fifty-three were taking combination anti-retroviral therapy and aviremic at the time of the study and had undergone valid 5-6-carboxyfluorescein diacetate succimidyl ester-based flow cytometry T-cell proliferation assays. Plasma analytes were quantified by enzyme-linked immunosorbent assay or multiplex assays. Peripheral blood cells were phenotyped by flow cytometry. Logistic regression was used to study the association between Gag-specific T-cell proliferation and immune markers.ResultsPatients with Gag-specific CD8 T-cell proliferation had higher levels of plasma transforming growth factor (TGF)-β1, a lower proportion of naive cells among regulatory T cells (Tregs), and higher percentages of CD4 and CD8 T cells expressing the α4β7 integrin or CD161 molecule than those without a Gag-specific response. These associations were significant based on analyses including potential confounders.ConclusionsPreserved Gag-specific CD8 T-cell proliferation was associated with higher TGF-β1 levels and increased percentages of T cells with a gut-homing phenotype at least 15 years after HIV infection during the perinatal period.
Properdin Levels in Individuals with Chemotherapy-Induced Neutropenia
Authors: Tsyrkunou Artsiom , Agarwal Sarika , Koirala Bibek , Finberg Robert W. , Nath Rajneesh , Barton Bruce , Levitz Stuart M. , Wang Jennifer P. , Ram Sanjay 
Published: December 2016

AbstractBackgroundNeutrophils produce and carry key components of the alternative pathway (AP) of complement, including properdin (P). The effect of chemotherapy-induced absolute neutropenia on circulating P levels and AP function has not been previously established.MethodsWe prospectively measured free P levels in serum from 27 individuals expected to develop neutropenia after administration of chemotherapy for hematological malignancies in preparation for hematopoietic stem cell transplantation and here describe the relationship between serum P levels and the neutrophil count over time.ResultsWhen the absolute neutrophil count (ANC) was &gt;500 cells/mm3 pre-chemotherapy, P levels were significantly higher than P levels associated with an ANC ≤500 cells/mm3 (median values 8392 ng/mL and 6355 ng/mL, respectively; P = .001). Pairwise comparison between pre-chemotherapy P levels and P levels at initial or last documented neutropenia before recovery showed a significant decline (P &lt; .0001). No correlation was observed between P levels during neutropenia and after recovery of neutropenia in 20 subjects for which postneutropenia samples were obtained. A small but significant (P = .02) decrease in AP hemolytic activity was noted between baseline (preneutropenia) and samples obtained at the onset of neutropenia, but only with low (6.25%) and not higher (12.5 or 25%) serum concentrations.ConclusionsA decline in P levels and AP activity could contribute to the increased risk of infection in neutropenic patients and warrants further study.
Hepatitis B Virus Incidence and Risk Factors Among Human Immunodeficiency Virus-1 Negative Men Who Have Sex With Men in Kenya
Authors: Wahome Elizabeth , Ngetsa Caroline , Mwambi John , Gelderblom Huub C. , Manyonyi Gloria Omosa , Micheni Murugi , Hassan Amin , Price Matt A. , Graham Susan M. , Sanders Eduard J. 
Published: December 2016

Abstract
No data exist on hepatitis B virus (HBV) incidence among African men who have sex with men (MSM). We tested plasma samples archived between 2005 and 2014 for HBV core antibody or surface antigen seroconversion in a cohort of 312 initially human immunodeficiency virus (HIV)-1-negative MSM with no evidence of prior HBV infection. Hepatitis B virus incidence was 6.0/100 person-years (95% confidence interval [CI], 3.9–9.1). Hepatitis B virus acquisition was associated with being uncircumcised (adjusted incidence rate ratio [aIRR], 5.0; 95% CI, 1.5–16.8), recent HIV-1 acquisition (aIRR, 2.9; 95% CI, 1.1–7.7), rape (aIRR, 5.0; 95% CI, 1.2–20.4), and any tertiary education (aIRR, 3.2; 95% CI, 1.1–9.7). African MSM have a substantial risk of HBV acquisition and require vaccination urgently.
Oseltamivir Use Among Children and Adults Hospitalized With Community-Acquired Pneumonia
Authors: Oboho Ikwo K. , Bramley Anna , Finelli Lyn , Fry Alicia , Ampofo Krow , Arnold Sandra R. , Self Wesley H. , Williams Derek J. , Courtney D. Mark , Zhu Yuwei , Anderson Evan J. , Grijalva Carlos G. , McCullers Jonathan A. , Wunderink Richard G. , Pavia Andrew T. , Edwards Kathryn M. , Jain Seema 
Published: December 2016

Abstract

Background
Data on oseltamivir treatment among hospitalized community-acquired pneumonia (CAP) patients are limited.

Methods
Patients hospitalized with CAP at 6 hospitals during the 2010−2012 influenza seasons were included. We assessed factors associated with oseltamivir treatment using logistic regression.

Results
Oseltamivir treatment was provided to 89 of 1627 (5%) children (&lt;18 years) and 143 of 1051 (14%) adults. Among those with positive clinician-ordered influenza tests, 39 of 61 (64%) children and 37 of 48 (77%) adults received oseltamivir. Among children, oseltamivir treatment was associated with hospital A (adjusted odds ratio [aOR], 2.76; 95% confidence interval [CI], 1.36−4.88), clinician-ordered testing performed (aOR, 2.44; 95% CI, 1.47−5.19), intensive care unit (ICU) admission (aOR, 2.09; 95% CI, 1.27−3.45), and age ≥2 years (aOR, 1.43; 95% CI, 1.16−1.76). Among adults, oseltamivir treatment was associated with clinician-ordered testing performed (aOR, 8.38; 95% CI, 4.64−15.12), hospitals D and E (aOR, 3.46−5.11; 95% CI, 1.75−11.01), Hispanic ethnicity (aOR, 2.06; 95% CI, 1.18−3.59), and ICU admission (aOR, 2.05; 95% CI, 1.34−3.13).

Conclusions
Among patients hospitalized with CAP during influenza season, oseltamivir treatment was moderate overall and associated with clinician-ordered testing, severe illness, and specific hospitals. Increased clinician education is needed to include influenza in the differential diagnosis for hospitalized CAP patients and to test and treat patients empirically if influenza is suspected.
An Uncommon Site of Streptococcus pneumoniae Colonization Leading to Recurrent Pneumococcal Disease
Authors: Sendi Parham , Moser Schaub Eva Maria , Nirgianakis Konstantinos , Hathaway Lucy J. , Bittel Pascal , Goldblatt David , Streit Sven 
Published: December 2016

Abstract
This report describes a case of relapsing pneumococcal peritonitis. The postulated source of infection was vaginal colonization and secondary adherence of pneumococci to an intrauterine contraceptive device. After immunization with a conjugate pneumococcal vaccine, her antibody levels were observed. She remained infection free at the 2-year follow-up investigation.