bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification, Characterization and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas
Authors: Unno Hideaki , Matsuyama Kazuki , Tsuji Yoshiteru , Goda Shuichiro , Hiemori Keiko , Tateno Hiroaki , Hirabayashi Jun , Hatakeyama Tomomitsu 
Published: July 2016

AbstractA novel mannose-specific lectin, named CGL1 (15.5 kDa), was isolated from the oyster Crassostrea gigas. Characterization of CGL1 involved isothermal titration calorimetry (ITC), glycoconjugate microarray and frontal affinity chromatography (FAC). This analysis revealed that CGL1 has strict specificity for the mannose monomer and for high mannose-type N-glycans (HMTGs). Primary structure of CGL1 did not show any homology with known lectins but did show homology with proteins of the natterin family. Crystal structure of the CGL1 revealed a unique homodimer in which each protomer was composed of 2 domains related by a pseudo two-fold axis. Complex structures of CGL1 with mannose molecules showed that residues have 8 hydrogen bond interactions with O1, O2, O3, O4 and O5 hydroxyl groups of mannose. The complex interactions that are not observed with other mannose-binding lectins revealed the structural basis for the strict specificity for mannose. These characteristics of CGL1 may be helpful as a research tool and for clinical applications.
Transient Grating Spectroscopy in Magnetic Thin Films: Simultaneous Detection of Elastic and Magnetic Dynamics
Authors: Janušonis J. , Jansma T. , Chang C. L. , Liu Q. , Gatilova A. , Lomonosov A. M. , Shalagatskyi V. , Pezeril T. , Temnov V. V. , Tobey R. I. 
Published: July 2016

AbstractSurface magnetoelastic waves are coupled elastic and magnetic excitations that propagate along the surface of a magnetic material. Ultrafast optical techniques allow for a non-contact excitation and detection scheme while providing the ability to measure both elastic and magnetic components individually. Here we describe a simple setup suitable for excitation and time resolved measurements of high frequency magnetoelastic waves, which is based on the transient grating technique. The elastic dynamics are measured by diffracting a probe laser pulse from the long-wavelength spatially periodic structural deformation. Simultaneously, a magnetooptical measurement, either Faraday or Kerr effect, is sensitive to the out-of-plane magnetization component. The correspondence in the response of the two channels probes the resonant interaction between the two degrees of freedom and reveals their intimate coupling. Unraveling the observed dynamics requires a detailed understanding of the spatio-temporal evolution of temperature, magnetization and thermo-elastic strain in the ferromagnet. Numerical solution of thermal diffusion in two dimensions provides the basis on which to understand the sensitivity in the magnetooptic detection.
The reemergence of long-term potentiation in aged Alzheimer’s disease mouse model
Authors: Huh Seonghoo , Baek Soo-Ji , Lee Kyung-Hwa , Whitcomb Daniel J. , Jo Jihoon , Choi Seong-Min , Kim Dong Hyun , Park Man-Seok , Lee Kun Ho , Kim Byeong C. 
Published: July 2016

AbstractMouse models of Alzheimer’s disease (AD) have been developed to study the pathophysiology of amyloid β protein (Aβ) toxicity, which is thought to cause severe clinical symptoms such as memory impairment in AD patients. However, inconsistencies exist between studies using these animal models, specifically in terms of the effects on synaptic plasticity, a major cellular model of learning and memory. Whereas some studies find impairments in plasticity in these models, others do not. We show that long-term potentiation (LTP), in the CA1 region of hippocampal slices from this mouse, is impared at Tg2576 adult 6–7 months old. However, LTP is inducible again in slices taken from Tg2576 aged 14–19 months old. In the aged Tg2576, we found that the percentage of parvalbumin (PV)-expressing interneurons in hippocampal CA1-3 region is significantly decreased, and LTP inhibition or reversal mediated by NRG1/ErbB signaling, which requires ErbB4 receptors in PV interneurons, is impaired. Inhibition of ErbB receptor kinase in adult Tg2576 restores LTP but impairs depotentiation as shown in aged Tg2576. Our study suggests that hippocampal LTP reemerges in aged Tg2576. However, this reemerged LTP is an insuppressible form due to impaired NRG1/ErbB signaling, possibly through the loss of PV interneurons.
Arbitrarily tunable orbital angular momentum of photons
Authors: Pan Yue , Gao Xu-Zhen , Ren Zhi-Cheng , Wang Xi-Lin , Tu Chenghou , Li Yongnan , Wang Hui-Tian 
Published: July 2016

AbstractOrbital angular momentum (OAM) of photons, as a new fundamental degree of freedom, has excited a great diversity of interest, because of a variety of emerging applications. Arbitrarily tunable OAM has gained much attention, but its creation remains still a tremendous challenge. We demonstrate the realization of well-controlled arbitrarily tunable OAM in both theory and experiment. We present the concept of general OAM, which extends the OAM carried by the scalar vortex field to the OAM carried by the azimuthally varying polarized vector field. The arbitrarily tunable OAM we presented has the same characteristics as the well-defined integer OAM: intrinsic OAM, uniform local OAM and intensity ring and propagation stability. The arbitrarily tunable OAM has unique natures: it is allowed to be flexibly tailored and the radius of the focusing ring can have various choices for a desired OAM, which are of great significance to the benefit of surprising applications of the arbitrary OAM.
Network Analysis Implicates Alpha-Synuclein (Snca) in the Regulation of Ovariectomy-Induced Bone Loss
Authors: Calabrese Gina , Mesner Larry D. , Foley Patricia L. , Rosen Clifford J. , Farber Charles R. 
Published: July 2016

AbstractThe postmenopausal period in women is associated with decreased circulating estrogen levels, which accelerate bone loss and increase the risk of fracture. Here, we gained novel insight into the molecular mechanisms mediating bone loss in ovariectomized (OVX) mice, a model of human menopause, using co-expression network analysis. Specifically, we generated a co-expression network consisting of 53 gene modules using expression profiles from intact and OVX mice from a panel of inbred strains. The expression of four modules was altered by OVX, including module 23 whose expression was decreased by OVX across all strains. Module 23 was enriched for genes involved in the response to oxidative stress, a process known to be involved in OVX-induced bone loss. Additionally, module 23 homologs were co-expressed in human bone marrow. Alpha synuclein (Snca) was one of the most highly connected “hub” genes in module 23. We characterized mice deficient in Snca and observed a 40% reduction in OVX-induced bone loss. Furthermore, protection was associated with the altered expression of specific network modules, including module 23. In summary, the results of this study suggest that Snca regulates bone network homeostasis and ovariectomy-induced bone loss.
Over Ten Years of Experience with a Modified Right Atrial Anastomosis in Orthotopic Heart Transplantation: Follow-up and Comparison with the Biatrial and Bicaval Technique
Authors: Panholzer Bernd , Fritzsche Katharina , Broch Ole , Renner Jochen , Friedrich Christine , Rahimi-Barfeh Azizolah , Reinecke Alexander , Cremer Jochen , Haneya Assad , Huenges Katharina 
Published: July 2016

Background In 1997, a modified right atrial anastomosis (cavoatrial technique) for orthotopic heart transplantation (oHTx) was first developed in our institution. The purpose of this study is to report our long-term experience with this technique compared with biatrial and bicaval technique.
Methods Retrospectively, 202 consecutive oHTx between 1997 and 2013 were analyzed. The applied transplantation techniques were biatrial (n = 108), bicaval (n = 22), and cavoatrial (n = 72).
Results Demographic data were similar in all groups. The cardiopulmonary bypass and cross-clamp time were significantly shorter in the biatrial group. Follow-up echocardiographic examination showed excellent results in all groups with no relevant differences. After 1 year, occurrence of severe tricuspid regurgitation (biatrial 1.9% vs bicaval 0.0% vs cavoatrial 1.4%) was low in all groups. Rate of permanent pacemaker implantations was also low (12.0% vs 5.0% vs 11.1%). There were no significant differences in survival between the groups.
Conclusion The cavoatrial technique can be a safe and simple alternative for heart transplantation. Easy handling and similar reduced postoperative complications encourage the use of this technique.
Trends and Factors Influencing the Length, Compensatory Growth, and Size-Selective Mortality of Juvenile Bristol Bay, Alaska, Sockeye Salmon at Sea
Authors: Yasumiishi Ellen M. , Farley Ed V. , Ruggerone Gregory T. , Agler Beverly A. , Wilson Lorna I. 
Published: July 2016

Abstract
The productivity of Bristol Bay, Alaska, Sockeye Salmon Oncorhynchus nerka increased during the mid-1970s. This increase is believed to be partially due to an increase in early marine growth associated with the 1976–1977 cool-to-warm shift in summer sea surface temperature (SST). The body size of juvenile salmon during their first year at sea is believed to regulate their ability to survive over winter. The back-calculated smolt length, first-year ocean growth, and total juvenile length of Sockeye Salmon from five Bristol Bay river systems (Egegik, Kvichak, Naknek, Ugashik, and Wood) and two smolt ages were used to examine trends and factors influencing total juvenile length, compensatory growth, and size-selective mortality in the first year in the ocean from 1962 to 2007. Juvenile length increased in relation to summer sea temperature, the 1977–2001 and 2002–2007 warm temperature regimes, smolt length, and compensatory growth. Compensatory growth—an inverse relationship between first-year ocean growth and smolt size—increased over time as well as after the 1976–1977 climate regime shift, was more common in age-1.0 fish than in age-2.0 juveniles, and was important in determining the length of juvenile Sockeye Salmon from the Wood River (the shorter fish among rivers and smolt ages). The coefficient of variation in length did not change with SST, suggesting that size-selective mortality occurred prior to the end of the first year at sea for all 10 fish groups. The predictor variables that were significant in the models varied among river systems and smolt ages. This study demonstrated that the frequency of compensatory growth and the total lengths of juvenile Sockeye Salmon during their first year at sea increased with summer SST (range, 7.5–10.5°C) in the eastern Bering Sea, a possible mechanism for the increased productivity of Bristol Bay Sockeye Salmon associated with warmer sea temperatures.
Received June 2, 2015; accepted February 23, 2016
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
Authors: Krupa Paweł , Mozolewska Magdalena A. , Wiśniewska Marta , Yin Yanping , He Yi , Sieradzan Adam K. , Ganzynkowicz Robert , Lipska Agnieszka G. , Karczyńska Agnieszka , Ślusarz Magdalena , Ślusarz Rafał , Giełdoń Artur , Czaplewski Cezary , Jagieła Dawid , Zaborowski Bartłomiej , Scheraga Harold A. , Liwo Adam 
Published: July 2016

Abstract
Summary: Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six single-domain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CαRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes.
Availability and Implementation: Freely available on the web at http://www.unres.pl/ .
Contact: has5@cornell.edu
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
Authors: Devailly Guillaume , Mantsoki Anna , Joshi Anagha 
Published: July 2016

Abstract
Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments chromatin immuno-precipitation followed by sequencing, RNA-sequencing and Cap Analysis of Gene Expression) provided by a user, to the data in the public domain. Heat*seq currently contains over 12 000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualize user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.
Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/ . Source code: https://github.com/gdevailly .
Contact: Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
w4CSeq: software and web application to analyze 4C-seq data
Authors: Cai Mingyang , Gao Fan , Lu Wange , Wang Kai 
Published: July 2016

Abstract
Summary: Circularized Chromosome Conformation Capture followed by deep sequencing (4C-Seq) is a powerful technique to identify genome-wide partners interacting with a pre-specified genomic locus. Here, we present a computational and statistical approach to analyze 4C-Seq data generated from both enzyme digestion and sonication fragmentation-based methods. We implemented a command line software tool and a web interface called w4CSeq, which takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis and presents results in a user-friendly manner. Besides providing users with the list of candidate interacting sites/regions, w4CSeq generates figures showing genome-wide distribution of interacting regions, and sketches the enrichment of key features such as TSSs, TTSs, CpG sites and DNA replication timing around 4C sites.
Availability and Implementation: Users can establish their own web server by downloading source codes at https://github.com/WGLab/w4CSeq . Additionally, a demo web server is available at http://w4cseq.wglab.org .
Contact: kaiwang@usc.edu or wangelu@usc.edu
Supplementary information : Supplementary data are available at Bioinformatics online.
Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees
Authors: Yamada Kazunori D. , Tomii Kentaro , Katoh Kazutaka 
Published: July 2016

Abstract
Motivation: Large multiple sequence alignments (MSAs), consisting of thousands of sequences, are becoming more and more common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking of large MSAs has been difficult. Recently, such assessments have been made possible through the HomFam and ContTest benchmark protein datasets. Along with the development of these datasets, an interesting theory was proposed: chained guide trees increase the accuracy of MSAs of structurally conserved regions. This theory challenges the basis of progressive alignment methods and needs to be examined by being compared with other known methods including computationally intensive ones.
Results: We used HomFam, ContTest and OXFam (an extended version of OXBench) to evaluate several methods enabled in MAFFT: (1) a progressive method with approximate guide trees, (2) a progressive method with chained guide trees, (3) a combination of an iterative refinement method and a progressive method and (4) a less approximate progressive method that uses a rigorous guide tree and consistency score. Other programs, Clustal Omega and UPP, available for large MSAs, were also included into the comparison. The effect of method 2 (chained guide trees) was positive in ContTest but negative in HomFam and OXFam. Methods 3 and 4 increased the benchmark scores more consistently than method 2 for the three datasets, suggesting that they are safer to use.
Availability and Implementation: http://mafft.cbrc.jp/alignment/software/
Contact: katoh@ifrec.osaka-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
A calibration method for realistic neutron dosimetry in radiobiological experiments assisted by MCNP simulation
Authors: Shahmohammadi Beni Mehrdad , Krstic Dragana , Nikezic Dragoslav , Yu Kwan Ngok 
Published: July 2016

Abstract
Many studies on biological effects of neutrons involve dose responses of neutrons, which rely on accurately determined absorbed doses in the irradiated cells or living organisms. Absorbed doses are difficult to measure, and are commonly surrogated with doses measured using separate detectors. The present work describes the determination of doses absorbed in the cell layer underneath a medium column ( DA ) and the doses absorbed in an ionization chamber ( DE ) from neutrons through computer simulations using the MCNP-5 code, and the subsequent determination of the conversion coefficients R (= DA / DE ). It was found that R in general decreased with increase in the medium thickness, which was due to elastic and inelastic scattering. For 2-MeV neutrons, conspicuous bulges in R values were observed at medium thicknesses of about 500, 1500, 2500 and 4000 μm, and these were attributed to carbon, oxygen and nitrogen nuclei, and were reflections of spikes in neutron interaction cross sections with these nuclei. For 0.1-MeV neutrons, no conspicuous bulges in R were observed (except one at ~2000 μm that was due to photon interactions), which was explained by the absence of prominent spikes in the interaction cross-sections with these nuclei for neutron energies &lt;0.1 MeV. The ratio R could be increased by ~50% for small medium thickness if the incident neutron energy was reduced from 2 MeV to 0.1 MeV. As such, the absorbed doses in cells ( DA ) would vary with the incident neutron energies, even when the absorbed doses shown on the detector were the same.
The Niche for Escherichia coli Sequence Type 131 Among Veterans: Urinary Tract Abnormalities and Long-Term Care Facilities
Authors: Drekonja Dimitri M. , Kuskowski Michael A. , Anway Ruth , Johnston Brian D. , Johnson James R. 
Published: July 2016

Abstract
Background.  Antimicrobial resistance among Escherichia coli is increasing, driven largely by the global emergence of sequence type 131 (ST131). However, the clinical significance of ST131 status is unknown. Among veterans, we assessed whether ST131 causes more severe, persistent, or recurrence-prone infections than non-ST131 E. coli.
Methods.  Isolates were assessed by polymerase chain reaction for membership in ST131 and relevant subclones thereof (H30R and H30Rx) and by broth microdilution for susceptibility to 11 antibiotics. Clinical and epidemiological data were systematically abstracted from the medical record. Between-group comparisons were made using t tests and Fisher's exact test.
Results.  Of the 311 unique E. coli isolates, 61 (19.6%) represented ST131. Of these, most (51 of 61, 83.6%) represented the H30R subclone; only 5 of 51 (9.8%) represented H30Rx. Relative to non-ST131 and non-H30R isolates, neither ST131 nor H30R were associated with more severe disease, worse clinical outcomes, or more robust hosts. Instead, both were more likely to be isolated from patients without manifestations of infection (for ST131, 36.1% vs 21.2% [P = .02]; for H30R, 39% vs 21% [P = .008]) and who had prior healthcare contact or long-term care facility (LTCF) exposure (for ST131, 33% vs 14% [P = .002]; for H30R, 37% vs 14% [P &lt; .001]). Despite a greater likelihood of discordant initial therapy, outcomes did not differ between ST131 and H30R isolates vs other E. coli isolates.
Conclusions.  Among veterans, ST131 and its H30R subclone were associated with LTCF-exposed hosts but not with worse outcomes.
Linkage to Care, Early Infant Diagnosis, and Perinatal Transmission Among Infants Born to HIV-Infected Nigerian Mothers: Evidence From the Healthy Beginning Initiative
Authors: Pharr Jennifer R. , Obiefune Michael C. , Ezeanolue Chinenye O. , Osuji Alice , Ogidi Amaka G. , Gbadamosi Semiu , Patel Dina , Iwelunmor Juliet , Yang Wei , Ogedegbe Gbenga , Ehiri John E. , Sam-Agudu Nadia A. , Ezeanolue Echezona E. 
Published: July 2016

Background:
In 2014, Nigeria accounted for 33% of all new childhood HIV infections that occurred among the 22 Global Plan priority countries where 80% of HIV-infected women reside. Even with a vertical HIV transmission rate of 27%, only 6% of infants born to HIV-infected women in Nigeria receive early infant diagnosis (EID). This article reports rates of antiretroviral prophylaxis, EID, and mother-to-child transmission in a congregation-based Healthy Beginning Initiative (HBI) designed to increase HIV testing among pregnant women in southeast Nigeria.

Methods:
This is a nested cohort study of HIV-exposed infants (HEI) within the HBI trial originally designed as a 2-arm cluster randomized trial. HIV-infected mothers and infants were followed between January 2013 and August 2014.

Results:
Across both arms of the study, 72 HIV-infected women delivered 69 live infants (1 set of twins) and 4 had miscarriages. Of the 69 live-born HEI, HIV status was known for 71% (49/69), 16% (11/69) died before sample collection, and 13% (9/69) were lost to follow-up. Complete information was available for 84% of HEI (58/69), of which 64% (37/58) received antiretroviral prophylaxis. Among the 49 infants tested for HIV, 88% (43/49) received EID within 2 months and 12% (6/49) received antibody testing after 18 months. The mother-to-child transmission rate was 8.2% (4/49).

Conclusions:
EID was higher and HIV transmission rate was lower among the HBI participants compared to reported rates in 2014. However, further progress is needed to achieve goals of elimination of infant HIV infection.