bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of hydrogen-rich water on depressive-like behavior in mice
Authors: Zhang Yi , Su Wen-Jun , Chen Ying , Wu Teng-Yun , Gong Hong , Shen Xiao-Liang , Wang Yun-Xia , Sun Xue-Jun , Jiang Chun-Lei 
Published: March 2016

AbstractEmerging evidence suggests that neuroinflammation and oxidative stress may be major contributors to major depressive disorder (MDD). Patients or animal models of depression show significant increase of proinflammatory cytokine interleukin-1β (IL-1β) and oxidative stress biomarkers in the periphery or central nervous system (CNS). Recent studies show that hydrogen selectively reduces cytotoxic oxygen radicals and hydrogen-rich saline potentially suppresses the production of several proinflammatory mediators. Since current depression medications are accompanied by a wide spectrum of side effects, novel preventative or therapeutic measures with fewer side effects might have a promising future. We investigated the effects of drinking hydrogen-rich water on the depressive-like behavior in mice and its underlying mechanisms. Our study show that hydrogen-rich water treatment prevents chronic unpredictable mild stress (CUMS) induced depressive-like behavior. CUMS induced elevation in IL-1β protein levels in the hippocampus and the cortex was significantly attenuated after 4 weeks of feeding the mice hydrogen-rich water. Over-expression of caspase-1 (the IL-1β converting enzyme) and excessive reactive oxygen species (ROS) production in the hippocampus and prefrontal cortex (PFC) was successfully suppressed by hydrogen-rich water treatment. Our data suggest that the beneficial effects of hydrogen-rich water on depressive-like behavior may be mediated by suppression of the inflammasome activation resulting in attenuated protein IL-1β and ROS production.
Visualizing spatial distribution of alectinib in murine brain using quantitative mass spectrometry imaging
Authors: Aikawa Hiroaki , Hayashi Mitsuhiro , Ryu Shoraku , Yamashita Makiko , Ohtsuka Naoto , Nishidate Masanobu , Fujiwara Yasuhiro , Hamada Akinobu 
Published: March 2016

AbstractIn the development of anticancer drugs, drug concentration measurements in the target tissue have been thought to be crucial for predicting drug efficacy and safety. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is commonly used for determination of average drug concentrations; however, complete loss of spatial information in the target tissue occurs. Mass spectrometry imaging (MSI) has been recently applied as an innovative tool for detection of molecular distribution of pharmacological agents in heterogeneous targets. This study examined the intra-brain transitivity of alectinib, a novel anaplastic lymphoma kinase inhibitor, using a combination of matrix-assisted laser desorption ionization–MSI and LC-MS/MS techniques. We first analyzed the pharmacokinetic profiles in FVB mice and then examined the effect of the multidrug resistance protein-1 (MDR1) using Mdr1a/b knockout mice including quantitative distribution of alectinib in the brain. While no differences were observed between the mice for the plasma alectinib concentrations, diffuse alectinib distributions were found in the brain of the Mdr1a/b knockout versus FVB mice. These results indicate the potential for using quantitative MSI for clarifying drug distribution in the brain on a microscopic level, in addition to suggesting a possible use in designing studies for anticancer drug development and translational research.
Ovarian cancer treatment with a tumor-targeting and gene expression-controllable lipoplex
Authors: He Zhi-Yao , Deng Feng , Wei Xia-Wei , Ma Cui-Cui , Luo Min , Zhang Ping , Sang Ya-Xiong , Liang Xiao , Liu Li , Qin Han-Xiao , Shen Ya-Li , Liu Ting , Liu Yan-Tong , Wang Wei , Wen Yan-Jun , Zhao Xia , Zhang Xiao-Ning , Qian Zhi-Yong , Wei Yu-Quan 
Published: March 2016

AbstractOverexpression of folate receptor alpha (FRα) and high telomerase activity are considered to be the characteristics of ovarian cancers. In this study, we developed FRα-targeted lipoplexes loaded with an hTERT promoter-regulated plasmid that encodes a matrix protein (MP) of the vesicular stomatitis virus, F-LP/pMP(2.5), for application in ovarian cancer treatment. We first characterized the pharmaceutical properties of F-LP/pMP(2.5). The efficient expression of the MP-driven hTERT promoter in SKOV-3 cells was determined after an in-vitro transfection assay, which was significantly increased compared with a non-modified LP/pMP(2.5) group. F-LP/pMP(2.5) treatment significantly inhibited the growth of tumors and extended the survival of mice in a SKOV-3 tumor model compared with other groups. Such an anti-tumor effect was due to the increased expression of MP in tumor tissue, which led to the induction of tumor cell apoptosis, inhibition of tumor cell proliferation and suppression of tumor angiogenesis. Furthermore, a preliminary safety evaluation demonstrated a good safety profile of F-LP/pMP(2.5) as a gene therapy agent. Therefore, FRα-targeted lipoplexes with therapeutic gene expression regulated by an hTERT promoter might be a promising gene therapy agent and a potential translational candidate for the clinical treatment of ovarian cancer.
Variable climatic conditions dominate recent phytoplankton dynamics in Chesapeake Bay
Authors: Harding, Lawrence W. , Mallonee Michael E. , Perry Elgin S. , Miller W. David , Adolf Jason E. , Gallegos Charles L. , Paerl Hans W. 
Published: March 2016

AbstractVariable climatic conditions strongly influence phytoplankton dynamics in estuaries globally. Our study area is Chesapeake Bay, a highly productive ecosystem providing natural resources, transportation, and recreation for nearly 16 million people inhabiting a 165,000-km2 watershed. Since World War II, nutrient over-enrichment has led to multiple ecosystem impairments caused by increased phytoplankton biomass as chlorophyll-a (chl-a). Doubled nitrogen (N) loadings from 1945–1980 led to increased chl-a, reduced water clarity, and low dissolved oxygen (DO), while decreased N loadings from 1981–2012 suggest modest improvement. The recent 30+ years are characterized by high inter-annual variability of chl-a, coinciding with irregular dry and wet periods, complicating the detection of long-term trends. Here, we synthesize time-series data for historical and recent N loadings (TN, NO2 + NO3), chl-a, floral composition, and net primary productivity (NPP) to distinguish secular changes caused by nutrient over-enrichment from spatio-temporal variability imposed by climatic conditions. Wet years showed higher chl-a, higher diatom abundance, and increased NPP, while dry years showed lower chl-a, lower diatom abundance, and decreased NPP. Our findings support a conceptual model wherein variable climatic conditions dominate recent phytoplankton dynamics against a backdrop of nutrient over-enrichment, emphasizing the need to separate these effects to gauge progress toward improving water quality in estuaries.
VIP: an integrated pipeline for metagenomics of virus identification and discovery
Authors: Li Yang , Wang Hao , Nie Kai , Zhang Chen , Zhang Yi , Wang Ji , Niu Peihua , Ma Xuejun 
Published: March 2016

AbstractIdentification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP (“Virus Identification Pipeline”), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP.
Sub-10 nm feature chromium photomasks for contact lithography patterning of square metal ring arrays
Authors: Park Woongkyu , Rhie Jiyeah , Kim Na Yeon , Hong Seunghun , Kim Dai-Sik 
Published: March 2016

AbstractAdvances in photolithographic processes have allowed semiconductor industries to manufacture smaller and denser chips. As the feature size of integrated circuits becomes smaller, there has been a growing need for a photomask embedded with ever narrower patterns. However, it is challenging for electron beam lithography to obtain <10 nm linewidths with wafer scale uniformity and a necessary speed. Here, we introduce a photolithography-based, cost-effective mask fabrication method based on atomic layer deposition and overhang structures for sacrificial layers. Using this method, we obtained sub-10 nm square ring arrays of side length 50 μm, and periodicity 100 μm on chromium film, on 1 cm by 1 cm quartz substrate. These patterns were then used as a contact-lithography photomask using 365 nm I-line, to generate metal ring arrays on silicon substrate.
Prognostic value of platelet to lymphocyte ratio in non-small cell lung cancer: evidence from 3,430 patients
Authors: Gu Xiaobin , Sun Shaoqian , Gao Xian-Shu , Xiong Wei , Qin Shangbin , Qi Xin , Ma Mingwei , Li Xiaoying , Zhou Dong , Wang Wen , Yu Hao 
Published: March 2016

AbstractThis study was designed to explore the association between elevated platelet to lymphocyte ratio (PLR) and prognosis of patients with non-small cell lung cancer (NSCLC) by meta-analysis. A total of 11 studies with 3,430 subjects were included and the combined hazard ratio (HR) and 95% confidence intervals (95% CI) were calculated. The data showed that elevated PLR predicted poor overall survival (OS) (HR = 1.42; 95% CI: 1.25–1.61, p < 0.001; I2 = 63.6, Ph = 0.002) and poor disease-free survival (DFS)/progression-free survival (PFS) (HR = 1.19; 95% CI: 1.02–1.4, p = 0.027; I2 = 46.8, Ph = 0.111). Subgroup analysis showed elevated PLR did not predict poor OS in patients included in large sample studies (HR = 1.44; 95% CI: 0.94–2.21, p = 0.098) whereas petients with Caucasian ethnicity (HR = 1.59; 95% CI: 1.27–1.98, p < 0.001) and PLR cut-off value >180 (HR = 1.61; 95% CI: 1.3–1.99, p < 0.001) had enhanced prognostic efficiency for OS. Subgroup analysis also demonstrated that high PLR did not predict poor DFS/PFS in Asian patients. In conclusion, our meta-analysis suggested that elevated PLR was associated with poor OS and DFS/PFS in NSCLC. In addition, high PLR especially predicted poor OS in Caucasians but had no association with poor DFS/PFS in Asians.
Extension and denature temperature of dsDNA molecules at various magnetic forces by using magnetic tweezers
Authors: Chung Yung‐Chiang , Tsai Cheng‐Wei , Lin Shih‐Hao 
Published: March 2016

Stretching experiments on lambda‐deoxyribonucleic acid (DNA) were carried out in microfluidic channel using a microscope, micro‐flow pump, and electromagnet. The micro‐flow channel was fabricated by using micro electromechanical technology, and the electromagnet was analyzed by software to simulate the magnetic field distribution. The magnetic field was 248.6 gauss at a current of 0.5 A, and the system could exert 20.4 pN of force on a magnetic bead with diameter of 2.8 μm. When the buffer temperature was 25 °C, the average length of lambda‐DNA molecules was 1.9 μm without magnetic field. In a magnetic field of 248.6 gauss, the extension was 7.2 μm, the total length was 9.1 μm, and the coefficient of elasticity was 2.83 × 10−6N/m. When the buffer temperature was 45 °C, the average length was 4.6 μm without magnetic field. At 45 °C in a magnetic field of 248.6 gauss, the extension was 11.9 μm, the total length was 16.5 μm, and the coefficient of elasticity was 1.71 × 10−6N/m. Besides, the denature temperature of dsDNA decreases with increasing magnetic force, and the temperature difference can be higher than 7 °C. This system can be used to measure the related properties of macromolecules.
Multibit ferroelectric field-effect transistor with epitaxial-like Pb(Zr,Ti)O3
Authors: Park Jae Hyo , Kim Hyung Yoon , Seok Ki Hwan , Kiaee Zohreh , Lee Sol Kyu , Joo Seung Ki 
Published: March 2016

Being able to control grain boundaries during the phase transformation when processing a ferroelectric thin-film is crucial for the successful development of practical multibit ferroelectric memory. A novel development of ferroelectric thin-film crystallization processing for realizing epitaxial-like single crystals via artificial nucleation by Pt-seeding is reported here. Dividing the nucleation and growth mechanism by Pt-seeding, it is possible to obtain large and uniform rectangular-shaped ferroelectric grains, large enough to fabricate a field-effect transistor (FET) in the inside of the crystal grain. The fabricated ferroelectric FET, Pt/Pb(Zr,Ti)O3/ZrTiO4/Si, showed a large memory window (∼2.2 V), a low operation voltage (∼6 V), and an ultra-fast program/erase speed (∼10−6 s). Moreover, there was no degradation after 1015 cycles of bipolar fatigue testing and the sample even showed a long retention time after 1 yr. All of these characteristics correspond to the best performance among all types of ferroelectric field-effect transistors reported thus far.
At the request of the Editor-in-Chief and AIP Publishing this article is being retracted. The Journal of Applied Physics retracts the referenced article due to the duplication of figures and significant overlap with other publications by the authors, and because of concerns about the accuracy of the description of the devices and materials from which the reported results were obtained. The article is retracted from the scientific record effective 6 November 2017.
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Authors: Hall Andrew Brantley , Papathanos Philippos-Aris , Sharma Atashi , Cheng Changde , Akbari Omar S. , Assour Lauren , Bergman Nicholas H. , Cagnetti Alessia , Crisanti Andrea , Dottorini Tania , Fiorentini Elisa , Galizi Roberto , Hnath Jonathan , Jiang Xiaofang , Koren Sergey , Nolan Tony , Radune Diane , Sharakhova Maria V. , Steele Aaron , Timoshevskiy Vladimir A. , Windbichler Nikolai , Zhang Simo , Hahn Matthew W. , Phillippy Adam M. , Emrich Scott J. , Sharakhov Igor V. , Tu Zhijian Jake , Besansky Nora J. 
Published: March 2016

SignificanceInterest in male mosquitoes has been motivated by the potential to develop novel vector control strategies, exploiting the fact that males do not feed on blood or transmit diseases, such as malaria. However, genetic studies of maleAnophelesmosquitoes have been impeded by the lack of molecular characterization of the Y chromosome. Here we show that theAnopheles gambiaeY chromosome contains a very small repertoire of genes, with massively amplified tandem arrays of a small number of satellites and transposable elements constituting the vast majority of the sequence. These genes and repeats evolve rapidly, bringing about remodeling of the Y, even among closely related species. Our study provides a long-awaited foundation for studying mosquito Y chromosome biology and evolution.
Comparison of density determination of liquid samples by density meters
Authors: Buchner C , Wolf H , Vámossy C , Lorefice S , Lenard E , Spohr I , Mares G , Perkin M , Parlic-Risovic T , Grue L -L , Tammik K , Andel I van , Zelenka Z 
Published: March 2016

Hydrostatic density determinations of liquids as reference material are mainly performed by National Metrology Institutes to provide means for calibrating or checking liquid density measuring instruments such as oscillation-type density meters. These density meters are used by most of the metrology institutes for their calibration and scientific work.
The aim of this project was to compare the results of the liquid density determination by oscillating density meters of the participating laboratories. The results were linked to CCM.D.K-2 partly via Project EURAMET.M.D.K-2 (1019) "Comparison of liquid density standards" by hydrostatic weighing piloted by BEV in 2008.
In this comparison pentadecane, water and of oil with a high viscosity were measured at atmospheric pressure using oscillation type density meter. The temperature range was from 15 °C to 40 °C.
The measurement results were in some cases discrepant. Further studies, comparisons are essential to explore the capability and uncertainty of the density meters

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Holomorphic isometries of the complex unit ball into irreducible bounded symmetric domains
Authors: Mok Ngaiming 
Published: March 2016

LetΩ⊂S\Omega \subset Sbe an irreducible bounded symmetric domain of rank≥2\ge 2embedded as an open subset in its dual Hermitian symmetric manifoldSSof the compact type. Writec1(S)=(p+2)δc_1(S) = (p+2)\delta,δ∈H2(S,Z)≅Z\delta \in H^2(S,\mathbb {Z}) \cong \mathbb {Z}being the positive generator. We prove that there exists a nonstandard holomorphic embedding of the(p+1)(p+1)-dimensional complex unit ballBp+1B^{p+1}intoΩ\Omegawhich is isometric with respect to canonical Kähler-Einstein metricsggresp. hhnormalized so that minimal disks are of constant Gaussian curvature−2-2. We construct such holomorphic isometries using varieties of minimal rational tangents (VMRTs). We also prove thatn≤p+1n \le p+1for any holomorphic isometryf:(Bn,g)→(Ω,h)f: (B^n,g) \to (\Omega ,h). Our proofs rely on an extension theorem for holomorphic isometries of Mok (2012), the asymptotic behavior due to Klembeck (1978) of standard complete Kähler metrics on strictly pseudoconvex domains, and the fine structure of boundaries of bounded symmetric domains in their Harish-Chandra realizations due to Wolf (1972).
pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data
Authors: Vanderkam Dan , Aksoy B. Arman , Hodes Isaac , Perrone Jaclyn , Hammerbacher Jeff 
Published: March 2016

Abstract
pileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library.
Availability and implementation: The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license.
Contact: correspondence@hammerlab.org
Analysis of clinical decision support system malfunctions: a case series and survey
Authors: Wright Adam , Hickman Thu-Trang T , McEvoy Dustin , Aaron Skye , Ai Angela , Andersen Jan Marie , Hussain Salman , Ramoni Rachel , Fiskio Julie , Sittig Dean F , Bates David W 
Published: March 2016

AbstractObjective To illustrate ways in which clinical decision support systems (CDSSs) malfunction and identify patterns of such malfunctions.Materials and Methods We identified and investigated several CDSS malfunctions at Brigham and Women’s Hospital and present them as a case series. We also conducted a preliminary survey of Chief Medical Information Officers to assess the frequency of such malfunctions.Results We identified four CDSS malfunctions at Brigham and Women’s Hospital: (1) an alert for monitoring thyroid function in patients receiving amiodarone stopped working when an internal identifier for amiodarone was changed in another system; (2) an alert for lead screening for children stopped working when the rule was inadvertently edited; (3) a software upgrade of the electronic health record software caused numerous spurious alerts to fire; and (4) a malfunction in an external drug classification system caused an alert to inappropriately suggest antiplatelet drugs, such as aspirin, for patients already taking one. We found that 93% of the Chief Medical Information Officers who responded to our survey had experienced at least one CDSS malfunction, and two-thirds experienced malfunctions at least annually.Discussion CDSS malfunctions are widespread and often persist for long periods. The failure of alerts to fire is particularly difficult to detect. A range of causes, including changes in codes and fields, software upgrades, inadvertent disabling or editing of rules, and malfunctions of external systems commonly contribute to CDSS malfunctions, and current approaches for preventing and detecting such malfunctions are inadequate.Conclusion CDSS malfunctions occur commonly and often go undetected. Better methods are needed to prevent and detect these malfunctions.
IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples
Authors: Hintzsche Jennifer , Kim Jihye , Yadav Vinod , Amato Carol , Robinson Steven E , Seelenfreund Eric , Shellman Yiqun , Wisell Joshua , Applegate Allison , McCarter Martin , Box Neil , Tentler John , De Subhajyoti , Robinson William A , Tan Aik Choon 
Published: March 2016

AbstractObjective Currently, there is a disconnect between finding a patient’s relevant molecular profile and predicting actionable therapeutics. Here we develop and implement the Integrating Molecular Profiles with Actionable Therapeutics (IMPACT) analysis pipeline, linking variants detected from whole-exome sequencing (WES) to actionable therapeutics.Methods and materials The IMPACT pipeline contains 4 analytical modules: detecting somatic variants, calling copy number alterations, predicting drugs against deleterious variants, and analyzing tumor heterogeneity. We tested the IMPACT pipeline on whole-exome sequencing data in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples with known EGFR mutations. We also used IMPACT to analyze melanoma patient tumor samples before treatment, after BRAF-inhibitor treatment, and after BRAF- and MEK-inhibitor treatment.Results IMPACT Food and Drug Administration (FDA) correctly identified known EGFR mutations in the TCGA lung adenocarcinoma samples. IMPACT linked these EGFR mutations to the appropriate FDA-approved EGFR inhibitors. For the melanoma patient samples, we identified NRAS p.Q61K as an acquired resistance mutation to BRAF-inhibitor treatment. We also identified CDKN2A deletion as a novel acquired resistance mutation to BRAFi/MEKi inhibition. The IMPACT analysis pipeline predicts these somatic variants to actionable therapeutics. We observed the clonal dynamic in the tumor samples after various treatments. We showed that IMPACT not only helped in successful prioritization of clinically relevant variants but also linked these variations to possible targeted therapies.Conclusion IMPACT provides a new bioinformatics strategy to delineate candidate somatic variants and actionable therapies. This approach can be applied to other patient tumor samples to discover effective drug targets for personalized medicine.IMPACT is publicly available at http://tanlab.ucdenver.edu/IMPACT.