bluuebunny/crossref_metadata_2025_split huggingface dataset:
Will hypolimnetic waters become anoxic in all deep tropical lakes?
Authors: Fukushima Takehiko , Matsushita Bunkei , Subehi Luki , Setiawan Fajar , Wibowo Hendro 
Published: March 2017

AbstractTo elucidate trends of hypolimnetic oxygen concentrations, vertical distributions of dissolved oxygen were measured in eight deep tropical bodies of water (one natural lake with two basins, five natural lakes, and one reservoir) in Indonesia. A comparison of those concentrations with previously reported data revealed that shoaling of hypolimnetic oxygen-deficient (around a few decimeters to a few meter per year) water had occurred in all of the lakes. Calculated areal hypolimnetic oxygen depletion rates were 0.046–5.9 g m−2 y−1. The oligomictic or meromictic characteristics of the bodies of water suppressed circulation and mixing in the hypolimnions and thus resulted in continuous shoaling of the uppermost oxygen-deficient layers. In some lakes, millions of fish sometimes died suddenly, probably owing to upward movement of oxygen-deficient water to near the surface during periods of strong winds. In the future, the rate of shoaling will be accelerated by human impacts in the basins and by climate warming, the influence of which has already been manifested by rising water temperatures in these lakes. Appropriate monitoring and discussions of future restoration challenges are urgently needed to prevent the hypolimnions of the lakes from becoming completely anoxic.
Activation of ERK1/2 Causes Pazopanib Resistance via Downregulation of DUSP6 in Synovial Sarcoma Cells
Authors: Yokoyama Nobuhiko , Matsunobu Tomoya , Matsumoto Yoshihiro , Fukushi Jun-ichi , Endo Makoto , Hatano Mihoko , Nabeshima Akira , Fukushima Suguru , Okada Seiji , Iwamoto Yukihide 
Published: March 2017

AbstractSynovial sarcoma (SS) is a rare high-grade malignant mesenchymal tumour with a relatively poor prognosis despite intensive multimodal therapy. Although pazopanib, a multi-kinase inhibitor, is often used for advanced SS, most cases eventually become resistant to pazopanib. In the present study, we investigated the mechanisms of acquired pazopanib resistance in SS. To examine acquired pazopanib resistance, two SS cell lines, SYO-1 and HS-SY-II, were isolated after multiple selection steps with increasing concentrations of pazopanib. SYO-1 was also used in vivo. Then, pazopanib-resistant clones were investigated to assess potential mechanisms of acquired pazopanib resistance. Stable pazopanib-resistant clones were established and exhibited enhanced cell cycle progression, cell growth with increased ERK1/2 phosphorylation, and higher sensitivity than parental cells to a MEK-inhibitor, trametinib, both in vitro and in vivo. Furthermore, addition of low-dose trametinib partially reversed the pazopanib resistance. In the pazopanib-resistant clones, dual specificity phosphatase 6 (DUSP6) was downregulated. Inhibition of DUSP6 expression in parental HS-SY-II cells partially recapitulated acquired pazopanib resistance. Acquired pazopanib resistance in SS was associated with activation of ERK1/2 through downregulation of DUSP6 expression. Simultaneous treatment with pazopanib and a MEK inhibitor could be a promising strategy to overcome pazopanib resistance in SS.
Nine phenylethanoid glycosides from Magnolia officinalis var. biloba fruits and their protective effects against free radical-induced oxidative damage
Authors: Ge Lanlan , Zhang Wenhui , Zhou Gao , Ma Bingxin , Mo Qigui , Chen Yuxin , Wang Youwei 
Published: March 2017

AbstractTo systematically study the chemical constituents in Magnolia officinalis var. biloba fruits, nine phenylethanoid glycosides were isolated by solvent extraction, silica gel, and preparative high-performance liquid chromatography (HPLC). Their structures were elucidated by 1D and 2D NMR analyses, including COSY, HMQC and HMBC correlations, and HPLC analysis of sugar residue. Nine phenylethanoid glycosides, namely, magnoloside Ia (1), magnoloside Ic (2), crassifolioside (3), magnoloside Ib (4), magnoloside IIIa (5), magnoloside IVa (6), magnoloside IIa (7), magnoloside IIb (8) and magnoloside Va (9), were first isolated from the n-butanol fraction of Magnolia officinalis var. biloba fruits alcohol extract. Free radical scavenging activities of the nine phenylethanoid glycosides were assessed using the DPPH, ABTS, and superoxide anion radical scavenging assays. Simultaneously, protective effects of all compounds against free radical-induced oxidative damage were evaluated by two different kinds of mitochondrial damage model. The protective effects were assessed by mitochondrial swelling, the formations of malondialdehyde (MDA) and lipid hydroperoxide (LOOH), the activities of catalase (CAT), glutathione reductase (GR) and superoxide dismutase (SOD). All phenylethanoid glycosides showed significant protective effects.
A canine model of tracheal stenosis induced by cuffed endotracheal intubation
Authors: Su Zhuquan , Li Shiyue , Zhou Ziqing , Chen Xiaobo , Gu Yingying , Chen Yu , Zhong Changhao , Zhong Minglu , Zhong Nanshan 
Published: March 2017

AbstractPostintubation tracheal stenosis is a complication of endotracheal intubation. The pathological mechanism and risk factors for endotracheal intubation-induced tracheal stenosis remain not fully understood. We aimed to establish an animal model and to investigate risk factors for postintubation tracheal stenosis. Beagles were intubated with 4 sized tubes (internal diameter 6.5 to 8.0 mm) and cuff pressures of 100 to 200 mmHg for 24 hr. The status of tracheal wall was evaluated by bronchoscopic and histological examinations. The model was successfully established by cuffed endotracheal intubation using an 8.0 mm tube and an intra-cuff pressure of 200 mmHg for 24 hr. When the intra-cuff pressures were kept constant, a larger sized tube would induce a larger tracheal wall pressure and more severe injury to the tracheal wall. The degree of tracheal stenosis ranged from 78% to 91% at 2 weeks postextubation. Histological examination demonstrated submucosal infiltration of inflammatory cells, hyperplasia of granulation tissue and collapse of tracheal cartilage. In summary, a novel animal model of tracheal stenosis was established by cuffed endotracheal intubation, whose histopathological feathers are similar to those of clinical cases of postintubation tracheal stenosis. Excessive cuff pressure and over-sized tube are the risk factors for postintubation tracheal stenosis.
Origin of high oxygen reduction reaction activity of Pt12 and strategy to obtain better catalyst using sub-nanosized Pt-alloy clusters
Authors: Miyazaki Kasumi , Mori Hirotoshi 
Published: March 2017

AbstractIn the present study, methods to enhance the oxygen reduction reaction (ORR) activity of sub-nanosized Pt clusters were investigated in a theoretical manner. Using ab initio molecular dynamics and Monte Carlo simulations based on density functional theory, we have succeeded in determining the origin of the superior ORR activity of Pt12 compared to that of Pt13. That is, it was clarified that the electronic structure of Pt12 fluctuates to a greater extent compared to that of Pt13, which leads to stronger resistance against catalyst poisoning by O/OH. Based on this conclusion, a set of sub-nanosized Pt-alloy clusters was also explored to find catalysts with better ORR activities and lower financial costs. It was suggested that Ga4Pt8, Ge4Pt8, and Sn4Pt8 would be good candidates for ORR catalysts.
Investigation on the plasmon Talbot effect of finite-sized periodic arrays of metallic nanoapertures
Authors: Li Wenli , Li Haoyong , Gao Bo , Yu Yiting 
Published: March 2017

AbstractWe present an in-depth and systematical investigation on the plasmon Talbot effect of finite-sized two-dimensional (2D) periodic metallic nanoaperture arrays. The nanoaperture shapes, fill factor, lattice distribution, array size, film thickness, material property and polarization state of the incident light are considered, and the inherent influencing rules are summarized via the three-dimensional (3D) finite-difference time-domain (FDTD) numerical simulations. The nanoaperture shapes, fill factor or array size seems to express a tiny influence on Talbot effect, which shows a good agreement with our previously reported experimental results. Besides, square lattice brings out a much more uniform Talbot pattern than the triangular distribution, and the smaller array period should be taken to estimate the Talbot distance when it comes to a rectangular distribution. Furthermore, the thickness of Au film is suggested to within the range of 50~100 nm, which gives a broadest Talbot contour. It is also found out that the elliptical shape of hotspots is closely related to the linearly polarization state of the light source, showing an asymmetric electromagnetic field. The research contributes to a better understanding of the optical transmission features through periodic metallic nanoaperture arrays, which provides opportunities for the potential applications such as nanofabrication, optoelectronics, and imaging.
Integration of solar photovoltaic with battery to single‐phase grid
Authors: Saxena Nupur , Singh Bhim , Vyas Anoop Lal 
Published: March 2017

This work deals with the control of a solar photovoltaic array and a battery storage integrated into a grid. It has versatile control strategy as it provides with maximum power point tracking, battery charging/discharging and a grid current at unity power factor. This configuration along with its control helps in feeding a constant power to the grid and maintains the controlled power dynamics in the system. The control performs a voltage control of the boost converter, current control of grid and DC‐link voltage control along with current control of the battery and adapts itself according to the environmental conditions such as no/low solar insolation and absence of battery storage. The proposed system is designed for a maximum power of 5 kW and simulated in MATLAB‐based environment. Test results on a prototype developed in the laboratory verify the simulated results. Under steady‐state condition, the total harmonic distortions of grid voltage and current are within the range of an IEEE 519 standard. Simulations and experimental results of the proposed system are demonstrated for various dynamic changes.
Digital impedance pilot relaying scheme for STATCOM compensated TL for fault phase classification with fault location
Authors: Singh Arvind R. , Patne Nita R. , Kale Vijay S. , Khadke Piyush 
Published: March 2017

This study presents calculation of fundamental frequency‐based per phase digital impedance pilot relaying (DIPR) scheme for static synchronous compensator (STATCOM) compensated transmission line (TL) using two end synchronised measurement. DIPR involves computation of absolute value of ratio of estimated phasor sum of voltages to the phasor sum of currents of both ends. DIPR inherently differentiate between internal and external faults on the line. For all internal faults, computed value of DIPR ratio is equivalent to system and TL impedance value whereas for external faults, it is equal to line capacitance impedance value. This novel pilot relaying scheme is easy to set once the system parameters are estimated and has the ability to detect all types of faults and correctly classify faulty phase with mid‐point connected STATCOM on TL. This scheme is immune to effect of STATCOM compensation mode, level of injection and its dynamic response. Also it is not affected by line charging capacitive current and fault transient resistance. The fault distance is estimated using the STATCOM current injection information for various types of fault with high accuracy, considering maximum fault resistance of 20 Ω. Accuracy and effectiveness of this scheme is evaluated in EMTDC/PSCAD simulation for 230 kV, 300 km, mid‐point STATCOM compensated TL and in hardware setup with mid‐point STATCOM on 100 V supply voltage having 200 km TL in offline mode. Results bring out the robustness, reliability and superiority of proposed novel pilot relaying scheme with fault location algorithm.
A Comparison of Size Structure, Age, and Growth of Red Snapper from Artificial and Natural Habitats in the Western Gulf of Mexico
Authors: Streich Matthew K. , Ajemian Matthew J. , Wetz Jennifer J. , Williams Jason A. , Shipley J. Brooke , Stunz Gregory W. 
Published: March 2017

AbstractRed SnapperLutjanus campechanussupport economically important fisheries in the Gulf of Mexico (GOM) and have been classified as overfished since the first stock assessment was conducted in 1988. Although the stock is now showing signs of recovery, management could benefit from a better understanding of regional or even habitat‐level differences in stock demographics, as these dynamics ultimately determine overall stock productivity. From 2012 to 2014, we used a fishery‐independent vertical line survey to assess Red Snapper relative abundance, size and age structure, and growth parameters at standing oil and gas platforms, decommissioned platform artificial reefs, and natural banks in the western GOM. We captured 1,170 Red Snapper ranging from 275 to 855 mm TL. Vertical line CPUE data showed no differences among the three habitat types. Ages determined for 1,143 individuals ranged from 2 to 30 years; however, most (90%) were younger than age 8. Size and age frequencies revealed that natural banks supported a greater proportion of large and relatively old fish compared to standing platforms or artificial reefs, although this difference was heavily influenced by a single bank that had significantly larger and older Red Snapper than other sites. Mean age was not significantly different among habitat types. Among a suite of growth models fitted to size‐at‐age data, the logistic model provided the best fit and suggested that fish from artificial reefs reached larger sizes at age than fish from either standing platforms or natural banks. Our study provides the first estimates of habitat‐specific growth parameters for Red Snapper in the western GOM, and this information can benefit future stock assessments. This study also highlights the potential benefits of artificial reefs to Red Snapper and indicates that all habitats could contribute similarly to stock productivity on a per‐unit‐area basis.Received December 21, 2016; accepted March 14, 2017 Published online May 26, 2017
Invited Commentary: A Landmark Study Launched in a Public Health
Maelstrom
Authors: Engels Eric A. , Rabkin Charles S. , Goedert James J. 
Published: March 2017

Abstract
The acquired immune deficiency syndrome (AIDS) epidemic was first recognized in 1981, and it quickly became a public health emergency. In a 1987 paper in the American Journal of Epidemiology (Am J Epidemiol. 1987;126(2): 310–318), Richard Kaslow et al. described the launch of the Multicenter AIDS Cohort Study (MACS), a cohort study of homosexual men in 4 US cities, the purpose of which was to better understand the natural history of AIDS and its determinants. The MACS enrolled participants through a range of community contacts. These efforts facilitated rapid recruitment, but given the targeted approaches, participants tended to comprise high-risk social networks. At baseline, 4%–26% of participants at the 4 sites reported having a sexual partner who had developed AIDS. Kaslow et al. also described baseline testing for the causative agent of AIDS, the human immunodeficiency virus (HIV). HIV seroprevalence was remarkably high, ranging from 11%–26% across age groups in Pittsburgh to 38%–53% in Los Angeles. The major turning point in the epidemic occurred in 1995–1996 when combination antiretroviral therapy was introduced, effectively blocking HIV replication and markedly reducing AIDS morbidity and mortality. The MACS cohort continues to be followed actively 3 decades after its launch and has proven to be an important resource for information on HIV infection and AIDS.
EUPAN enables pan-genome studies of a large number of eukaryotic genomes
Authors: Hu Zhiqiang , Sun Chen , Lu Kuang-chen , Chu Xixia , Zhao Yue , Lu Jinyuan , Shi Jianxin , Wei Chaochun 
Published: March 2017

Abstract

Summary
Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms.

Availability and Implementation
EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
annotatr: genomic regions in context
Authors: Cavalcante Raymond G , Sartor Maureen A 
Published: March 2017

Abstract

Motivation
Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof.

Results
We developed the annotatr Bioconductor package to flexibly and quickly summarize and plot annotations of genomic regions. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of graphics functions are implemented to easily plot numerical or categorical data associated with the regions across the annotations, and across annotation intersections, providing insight into how characteristics of the regions differ across the annotations. We demonstrate that annotatr is up to 27× faster than comparable R packages. Overall, annotatr enables a richer biological interpretation of experiments.

Availability and Implementation
http://bioconductor.org/packages/annotatr/ and https://github.com/rcavalcante/annotatr

Supplementary information
Supplementary data are available at Bioinformatics online.
The obesity paradox, extreme obesity, and long-term outcomes in older adults
with ST-segment elevation myocardial infarction: results from the NCDR
Authors: Neeland Ian J. , Das Sandeep R. , Simon DaJuanicia N. , Diercks Deborah B. , Alexander Karen P. , Wang Tracy Y. , de Lemos James A. 
Published: March 2017

Abstract

Aims
To investigate the obesity paradox and association of extreme obesity with long-term outcomes among older ST-segment elevation myocardial infarction (STEMI) patients.

Methods and results
Nineteen thousand four hundred and ninety-nine patients ≥65 years with STEMI surviving to hospital discharge in NCDR ACTION Registry-GWTG linked to Centers for Medicare and Medicaid Services outcomes between 2007 and 2012 were stratified by body mass index (BMI) (kg/m2) into normal weight (18.5–24.9), overweight (25–29.9), class I (30–34.9), class II (35–39.9), and class III/extreme obese (≥40) categories. Multivariable-adjusted associations were evaluated between BMI categories and mortality by Cox proportional hazards models, and days alive and out of hospital (DAOH) by generalized estimating equations, within 3 years after discharge. Seventy percent of patients were overweight/obese and 3% extremely obese. Normal weight patients were older and more likely to smoke; while extremely obese patients were younger and more likely to be female and black, with lower socioeconomic status and more comorbidity (P ≤ 0.001). A U-shaped association was observed between BMI categories and mortality: patients with class I obesity were at lowest risk, while normal weight [hazard ratio (HR) 1.30, 95% confidence interval (CI) 1.15–1.47] and extremely obese patients (HR 1.33, 95% CI 1.02–1.74) had higher mortality. Normal weight [odds ratio (OR) 0.79, 95% CI 0.68–0.90] and extremely obese (OR 0.73, 95% CI 0.54–0.99) individuals also had lower odds of DAOH.

Conclusion
Mild obesity is associated with lower long-term risk in older STEMI patients, while normal weight and extreme obesity are associated with worse outcomes. These findings highlight hazards faced by an increasing number of older individuals with normal weight or extreme obesity and cardiovascular disease.
HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters
Authors: Brenner Bluma G. , Ibanescu Ruxandra-Ilinca , Oliveira Maureen , Roger Michel , Hardy Isabelle , Routy Jean-Pierre , Kyeyune Fred , Quiñones-Mateu Miguel E. , Wainberg Mark A. ,   on behalf of the Montreal PHI Cohort Study Group
Published: March 2017

AbstractObjectives: Viral phylogenetics revealed two patterns of HIV-1 spread among MSM in Quebec. While most HIV-1 strains (n = 2011) were associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and 2015. Herein, tissue culture selections ascertained if large cluster lineages possessed higher replicative fitness than singleton/small cluster isolates, allowing for viral escape from integrase inhibitors.Methods: Primary HIV-1 isolates from large 20+ cluster (n = 11) or singleton/small cluster (n = 6) networks were passagedin vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective drug pressure.Results: Large cluster HIV-1 isolates selected for resistance to dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K (n = 7), S153Y (n = 1) or H51Y (n = 1) mutations as the dominant quasi-species within 8–12 weeks as compared with small cluster lineages where R263K (n = 1/6), S153Y (1/6) or WT species (4/6) were observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G, N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations leading to viral escape (&gt;10 μM) by week 24.Conclusions: Further studies are needed to understand virological features of large cluster viruses that may favour their transmissibility, replicative competence and potential to escape selective antiretroviral drug pressure.