bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dating the period when intensive anthropogenic activity began to influence the Sanjiang Plain, Northeast China
Authors: Cong Jinxin , Gao Chuanyu , Zhang Yan , Zhang Shaoqing , He Jiabao , Wang Guoping 
Published: February 2016

AbstractDating the start of intensive anthropogenic influence on ecosystems is important for identifying the conditions necessary for ecosystem recovery. However, few studies have focused on determining when anthropogenic influences on wetland began through sedimentary archives. To fill this critical gap in our knowledge, combustion sources and emission intensities, reconstructed via black carbon (BC) and polycyclic aromatic hydrocarbons (PAHs) were analyzed in two wetlands in the Sanjiang Plain in Northeast China. 14C provided age control for the sedimentary records. By combining previous sedimentary and archaeological studies, we attempt to date the beginning of intensive anthropogenic influences on the Sanjiang Plain. Our results showed that BC deposition fluxes increased from 0.02 to 0.7 g C/m2.yr during the last 10,000 years. An upward trend was apparent during the last 500 years. Before 1200 cal yr BP, human activities were minor, such that the wetland ecosystem in the Sanjiang Plain before this period may represent the reference conditions that for the recovery of these wetlands. As the human population increased after 1200 cal yr BP, combustion sources changed and residential areas became a major source of BC and PAHs. In this way, the wetland ecosystem gradually became more heavily influenced by human activities.
A Label-Free Electrochemical Impedance Cytosensor Based on Specific Peptide-Fused Phage Selected from Landscape Phage Library
Authors: Han Lei , Liu Pei , Petrenko Valery A. , Liu Aihua 
Published: February 2016

AbstractOne of the major challenges in the design of biosensors for cancer diagnosis is to introduce a low-cost and selective probe that can recognize cancer cells. In this paper, we combined the phage display technology and electrochemical impedance spectroscopy (EIS) to develop a label-free cytosensor for the detection of cancer cells, without complicated purification of recognition elements. Fabrication steps of the cytosensing interface were monitored by EIS. Due to the high specificity of the displayed octapeptides and avidity effect of their multicopy display on the phage scaffold, good biocompatibility of recombinant phage, the fibrous nanostructure of phage and the inherent merits of EIS technology, the proposed cytosensor demonstrated a wide linear range (2.0 × 102 − 2.0 × 108 cells mL−1), a low limit of detection (79 cells mL−1, S/N = 3), high specificity, good inter-and intra-assay reproducibility and satisfactory storage stability. This novel cytosensor designing strategy will open a new prospect for rapid and label-free electrochemical platform for tumor diagnosis.
Angiotensin II centrally induces frequent detrusor contractility of the bladder by acting on brain angiotensin II type 1 receptors in rats
Authors: Kawamoto Bunya , Shimizu Shogo , Shimizu Takahiro , Higashi Youichirou , Honda Masashi , Sejima Takehiro , Saito Motoaki , Takenaka Atsushi 
Published: February 2016

AbstractAngiotensin (Ang) II plays an important role in the brain as a neurotransmitter and is involved in psychological stress reactions, for example through activation of the sympatho-adrenomedullary system. We investigated the effects of centrally administered Ang II on the micturition reflex, which is potentially affected by the sympatho-adrenomedullary system and brain Ang II receptors in urethane-anesthetized (1.0 g/kg, intraperitoneally) male rats. Central administration of Ang II (0.01, 0.02 and 0.07 nmol per rat, intracerebroventricularly, icv) but not vehicle rapidly and dose-dependently decreased the urinary bladder intercontraction interval, without altering the bladder detrusor pressure. Central administration of antagonists of Ang II type 1 but not type 2 receptors inhibited the Ang II-induced shortening of intercontraction intervals. Administration of the highest dose of Ang II (0.07 nmol per rat, icv) but not lower doses (0.01 and 0.02 nmol per rat, icv) elevated the plasma concentration of adrenaline. Bilateral adrenalectomy reduced Ang II-induced elevation in adrenaline, but had no effect on the Ang II-induced shortening of the intercontraction interval. These data suggest that central administration of Ang II increases urinary frequency by acting on brain Ang II type 1 receptors, independent of activation of the sympatho-adrenomedullary system.
One-step catalytic asymmetric synthesis of all-
syn
deoxypropionate motif from propylene: Total synthesis of (2
R
,4
R
,6
R
,8
R
)-2,4,6,8-tetramethyldecanoic acid
Authors: Ota Yusuke , Murayama Toshiki , Nozaki Kyoko 
Published: February 2016

Significance
Synthetic strategies for deoxypropionate motif reported to date mainly use iterative elongations, thus requiring many reaction steps to obtain the desired natural product. Additionally, such methods also require the preparation of complex building blocks. Here, we have developed a one-step construction of deoxypropionate motif by stereo-controlled propylene oligomerization. Our method using propylene as a very simple building block provides the shortest, three-step access to a natural product whose preparation conventionally required at least 10 steps. Furthermore, multiple oligomers with different number of deoxypropionate units can be isolated from the same oligomerization product, enabling the construction of library. Because deoxypropionate motif is found in a variety of biologically active compounds, our method would impact the field of synthetic organic chemistry.
Site-directed spectroscopy of cardiac myosin-binding protein C reveals effects of phosphorylation on protein structural dynamics
Authors: Colson Brett A. , Thompson Andrew R. , Espinoza-Fonseca L. Michel , Thomas David D. 
Published: February 2016

Significance
Contractility in cardiac muscle is finely tuned in response to changing circulatory demands, and phosphorylation of cardiac myosin-binding protein C (cMyBP-C) plays an important role in this regulation of function. The molecular mechanism of this regulation is not well understood because the N-terminal region [domains C0–C2 (C0C2)] containing the phosphorylatable region of cMyBP-C is highly dynamic and disordered, thus inaccessible to standard structural techniques. Therefore, we used site-directed spectroscopic probes (fluorescence and magnetic resonance) and computational simulations that are optimized for analyzing dynamic disorder. We found that phosphorylation makes C0C2 more compact and less disordered in the linker region and phosphorylation motif, and a new binding site simultaneously emerges. Our results provide insight into muscle contraction with implications for heart failure.
Reaction Decoder Tool (RDT): extracting features from chemical reactions
Authors: Rahman Syed Asad , Torrance Gilliean , Baldacci Lorenzo , Martínez Cuesta Sergio , Fenninger Franz , Gopal Nimish , Choudhary Saket , May John W. , Holliday Gemma L. , Steinbeck Christoph , Thornton Janet M. 
Published: February 2016

Abstract
Summary: Extracting chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features.
Availability and implementation: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder
Contact: asad@ebi.ac.uk or s9asad@gmail.com
Offshore Medical Schools Are Buying Clinical Clerkships in U.S. Hospitals: The Problem and Potential Solutions
Authors: Halperin Edward C. , Goldberg Robert B. 
Published: February 2016

U.S. medical education faces a threat from for-profit Caribbean medical schools which purchase clinical rotation slots for their students at U.S. hospitals. These offshore schools are monetizing a system that was previously characterized as a duty—the duty of the current generation of physicians to educate their successors. Offshore schools purchase clinical rotation slots using funds largely derived from federally subsidized student loans. This leads to pressure on U.S. schools to pay for clinical clerkships and is forcing some of them to find new clinical training sites.
For-profit Caribbean schools largely escape the type of scrutiny that U.S. schools face from U.S. national accreditation organizations. They also enroll large classes of students with lower undergraduate GPAs and Medical College Admission Test scores than those of students at U.S. medical schools; their students take and pass Step 1 of the United States Medical Licensing Examination at a substantially lower rate than that of U.S. medical students; and their students match for residencies at a fraction of the rate of U.S. medical school graduates.
Among the potential solutions proposed by the authors are passing laws to hold for-profit Caribbean schools to standards for board passage rates, placing restrictions on federal student loans, monitoring attrition rates, and denying offshore schools access to U.S. clinical training sites unless they meet accreditation standards equivalent to those of U.S. medical schools.
The Impact of Robotic versus Conventional Coronary Artery Bypass Grafting on In-Hospital Narcotic Use: A Propensity-Matched Analysis
Authors: Raad Wissam N. , Forest Stephen , Follis Marco , Friedmann Patricia , DeRose Joseph J. 
Published: February 2016

Objective The aim of this study was to compare narcotic use in the perioperative hospital stay as a measure of pain in patients undergoing robotic versus conventional coronary artery bypass grafting (CABG). Methods Propensity score matching of patients undergoing robotically assisted CABG and conventional CABG over a period of 5 years was performed. A retrospective chart review was performed to identify the total amount of narcotics used by both groups calculated as morphine equivalent dosing (MED). Results From 2007 to 2012, 154 patients underwent robotic CABG, and 1660 underwent conventional CABG. Propensity matching resulted in 142 patients in each group. Patients undergoing robotic CABG received less blood transfusion, were more frequently extubated in the operating room, and had a shorter length of stay. The robotic group had a lower MED than the conventional group as defined by the primary end point[181 (11) vs 251 (8)]. If intraoperative narcotic use was eliminated, there was no difference in MED from postoperative days 0 to 3. Conclusions Patients undergoing robotic CABG use fewer narcotics over the first three hospital days than patients undergoing conventional CABG. The surrogate of narcotics use for postoperative pain shows that the minithoracotomy of robotic CABG may result in either less or equivalent pain than the sternotomy of conventional CABG.
Brief Report: HIV Infection Is Associated With Worse Bone Material Properties, Independently of Bone Mineral Density
Authors: Güerri-Fernández Robert , Molina Daniel , Villar-García Judit , Prieto-Alhambra Daniel , Mellibovsky Leonardo , Nogués Xavier , González-Mena Alicia , Guelar Ana , Trenchs-Rodríguez Marta , Herrera-Fernández Sabina , Horcajada Juan Pablo , Díez-Pérez Adolfo , Knobel Hernando 
Published: February 2016

Abstract:
Low bone mineral density (BMD) in HIV-infected individuals has been documented in an increasing number of studies. However, it is not clear whether it is the infection itself or the treatment that causes bone impairment. Microindentation measures bone material strength (Bone Material Strength index) directly. We recruited 85 patients, 50 infected with HIV and 35 controls. Median Bone Material Strength index was 84.5 (interquartile range 83–87) in HIV-infected patients and 90 (88.5–93) in controls (P < 0.001). No significant differences in BMD between cases and controls at any of the sites examined (total hip, femoral neck, and lumbar spine). HIV infection is associated with bone damage, independently of BMD.
Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon-capture
Authors: Teasdale Luisa C. , Köehler Frank , Murray Kevin D. , O’Hara Tim , Moussalli Adnan 
Published: February 2016

ABSTRACTThe qualification of orthology is a significant challenge when developing large, multiloci phylogenetic datasets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts, and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete gene data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon-capture targeting 490 of the 500 genes (those with at least one exon > 120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2,825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and Agalma-equivalent dataset (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a broad range of evolutionary depths, and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.
“Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly”
Authors: Grime John M. A. , Dama James F. , Ganser-Pornillos Barbie K. , Woodward Cora L. , Jensen Grant J. , Yeager Mark J. , Voth Gregory A. 
Published: February 2016

Abstract:The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.
Characterization and Transposon Mutagenesis of the Maize (Zea mays)Pho1Gene Family - Submission to PLOS Journals
Authors: Salazar-Vidal M. Nancy , Acosta-Segovia Edith , Sanchez-Leon Nidia , Ahern Kevin R. , Brutnell Thomas P. , Sawers Ruairidh J. H. 
Published: February 2016

AbstractPhosphorus is an essential nutrient for all plants, but also one of the least mobile, and consequently least available, in the soil. Plants have evolved a series of molecular, metabolic and developmental adaptations to increase the acquisition of phosphorus and to maximize the efficiency of use within the plant. In Arabidopsis (Arabidopsis thaliana), the AtPHO1 protein regulates and facilitates the distribution of phosphorus within the plant. To investigate the role of PHO1 in maize (Zea mays), the B73 reference genome was searched for homologous sequences and four genes identified that were designatedZmPho1;1, ZmPho1;2a, ZmPho1;2bandZmPho1;3. ZmPho1;2aandZmPho1;2bare the most similar to AtPho1, and represent candidate co-orthologs that we hypothesize to have been retained following whole genome duplication. Tissue-and phosphate-specific differences in the accumulation ofZmPho1;2aandZmPho1;2btranscripts were observed, indicating regulatory divergence. Furthermore, evidence was obtained for the phosphate-regulated production of anti-sense transcripts associated with bothZmPho1;2aandZmPho1;2b, suggesting the possibility of regulatory crosstalk between paralogs. To characterize functional divergence betweenZmPho1;2aandZmPho1;2b, a program of transposon mutagenesis was initiated using the Ac/Ds system, and, here, we report the generation of novel alleles ofZmPho1;2aandZmPho1;2b.
A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification
Authors: Fulop Daniel , Ranjan Aashish , Ofner Itai , Covington Michael F. , Chitwood Daniel H. , West Donelly , Ichihashi Yasunori , Headland Lauren , Zamir Daniel , Maloof Julin N. , Sinha Neelima R. 
Published: February 2016

ABSTRACTQuantitative Trait Locus (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as theSolanum pennelliiIntrogression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar andS. pennelli. This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix ofBC2andBC3lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existingS. pennelliiIL population, with which it shares parents. Using the BILs we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous Hidden Markov Model for genotyping the lines, and by using state of the art sparse regression techniques for QTL mapping.
Transcriptional pulsing of a nucleolar transgene
Authors: Vaňková Hausnerová Viola , Křížek Pavel , Hagen Guy M. , Lanctôt Christian 
Published: February 2016

AbstractThe pulsatile nature of transcription has recently emerged as an important property of gene expression. Here we report on the characterization of a RNA polymerase II transgene that is transcribed in the nucleolus. Using the MS2-GFP reporter system and live cell imaging, we found that the synthesis of a MS2-tagged transcript in the nucleolus was discontinuous in all of the cells that were observed, with periods of activity lasting from 15 minutes to 21 hours. The frequency of pulse lengths could be fitted with an exponential function, from which we determined that transcription occurs on average for periods of 20 minutes. These ON periods alternate with periods of inactivity which last on average 29 minutes. The post-mitotic reactivation of transcription was found to be asynchronous in daughter cell pairs. Our observation of discontinuous transcriptional activity in the nucleolus may reflect cycling in the assembly and disassembly of active chromatin structure in and/or around the rDNA genes.
A curvature correction turbulent model for computations of cloud cavitating flows
Authors: Zhao Yu , Wang Guoyu , Huang Biao 
Published: February 2016

Purpose– The purpose of this paper is to assess the predictive capability of the streamline curvature correction model (CCM) and investigate the unsteady vortex behavior of the cloud cavitating flows around a hydrofoil.Design/methodology/approach– The design of the paper is based on introducing the curvature correction method to the originalk-εmodel. Calculations of unsteady cloud cavitating flows around a Clark-Y hydrofoil are performed using both the CCM and the baseline model.Findings– Compared with the baseline model, better agreements are observed between the predictions of the CCM model and experimental data, especially the cavity shedding process. Based on the computations, it is demonstrated that streamline curvature correction of the CCM model can effectively decrease predicted turbulence kinetic energy and eddy viscosity in cavity shedding region. This leads to the better prediction for the recirculation zone located downstream of the attached cavity, and dynamics of this recirculation zone contribute to the formation and development of the re-entrant jet.Originality/value– The authors apply streamline curvature correction to the calculations of unsteady cloud cavitating flows and discuss the interactions between the cavitation unsteadiness and vortex structures to get an insight of the correction mechanics.
Co-seismic and post-seismic behavior of an existed shallow foundation and super structure system on a natural sand/silt layered ground
Authors: Bao Xiaohua , Ye Guanlin , Ye Bin , Fu Yanbin , Su Dong 
Published: February 2016

Purpose
– The purpose of this paper is to evaluate the co-seismic and post-seismic behaviors of an existed soil-foundation system in an actual alternately layered sand/silt ground including pore water pressure, acceleration response, and displacement et al. during and after earthquake.

Design/methodology/approach
– The evaluation is performed by finite element method and the simulation is performed using an effective stress-based 2D/3D soil-water coupling program DBLEAVES. The calculation is carried out through static-dynamic-static three steps. The soil behavior is described by a new rotational kinematic hardening elasto-plastic cyclic mobility constitutive model, while the footing and foundation are modeled as elastic rigid elements.

Findings
– The shallow (short-pile type) foundation has a better capacity of resisting ground liquefaction but large differential settlement occurred. Moreover, most part of the differential settlement occurred during earthquake motion. Attention should be paid not only to the liquefaction behavior of the ground during the earthquake motion, but also the long-term settlement after earthquake should be given serious consideration.

Originality/value
– The co-seismic and post-seismic behavior of a complex ground which contains sand and silt layers, especially long-term settlement over a period of several weeks or even years after the earthquake, has been clarified sufficiently. In some critical condition, even if the seismic resistance is satisfied with the design code for building, detailed calculation may reveal the risk of under estimation of differential settlement that may give rise to serious problems.