bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning identifies SNPs predictive of advanced coronary artery calcium in ClinSeq® and Framingham Heart Study cohorts
Authors: Oguz Cihan , Sen Shurjo K , Davis Adam R , Fu Yi-Ping , O’Donnell Christopher J , Gibbons Gary H 
Published: January 2017

ABSTRACTOne goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits and requires systems level approaches. To this end, we employed random forests (RF) and neural networks (NN) for predictive modeling of coronary artery calcification (CAC), which is an intermediate end-phenotype of coronary artery disease (CAD). Model inputs were derived from advanced cases in the ClinSeq®discovery cohort (n=16) and the FHS replication cohort (n=36) from 89th−99thCAC score percentile range, and age-matching controls (ClinSeq® n=16, FHS n=36) with no detectable CAC (all subjects were Caucasian males). These inputs included clinical variables (CLIN), genotypes of 57 SNPs associated with CAC in past GWAS (SNP Set-1), and an alternative set of 56 SNPs (SNP Set-2) ranked highest in terms of their nominal correlation with advanced CAC state in the discovery cohort. Predictive performance was assessed by computing the areas under receiver operating characteristics curves (AUC). Within the discovery cohort, RF models generated AUC values of 0.69 with CLIN, 0.72 with SNP Set-1, and 0.77 with their combination. In the replication cohort, SNP Set-1 was again more predictive (AUC=0.78) than CLIN (AUC=0.61), but also more predictive than the combination (AUC=0.75). In contrast, in both cohorts, SNP Set-2 generated enhanced predictive performance with or without CLIN (AUC> 0.8). Using the 21 SNPs of SNP Set-2 that produced optimal predictive performance in both cohorts, we developed NN models trained with ClinSeq® data and tested with FHS data and replicated the high predictive accuracy (AUC>0.8) with several topologies, thereby identifying several potential susceptibility loci for advanced CAD. Several CAD-related biological processes were found to be enriched in the network of genes constructed from these loci. In both cohorts, SNP Set-1 derived from past CAC GWAS yielded lower performance than SNP Set-2 derived from “extreme” CAC cases within the discovery cohort. Machine learning tools hold promise for surpassing the capacity of conventional GWAS-based approaches for creating predictive models utilizing the complex interactions between disease predictors intrinsic to the pathogenesis of polygenic disorders.
Staphylococcus aureusBiofilm Removal by Targeting Biofilm-Associated Extracellular Proteins
Authors: Shukla Sudhir K. , Rao T. Subba 
Published: January 2017

AbstractAimAmong cell surface proteins, biofilm-associated protein promotes biofilm development inStaphylococcus aureusstrains. Aim of this study was to investigate proteinase-mediated biofilm dispersion in different isolates ofS. aureus.Methods and ResultsMicrotitre plate based biofilm assay showed that 2 μg/mL proteinase K significantly inhibited biofilm development inbap-positiveS. aureusV329 as well as otherS. aureusstrains, i.e. SA7, SA10, SA33, SA352 and but not inbap-mutant M556 and SA392 (a weak biofilm producing strain). However, proteinase K treatment onS. aureusplanktonic cells showed that there was no inhibition of planktonic growth at any concentration of proteinase K when tested up to 32 μg/mL. This observation ruled out the possibility ofS. aureusbiofilm inhibition by altering the cell viability. Proteinase K treatment upon 24 h old preformed biofilms showed an enhanced dispersion ofbap-positive V329 and SA7, SA10, SA33 and SA352 biofilms, however, proteinase K did not affect thebap-mutantS. aureusM556 and SA392 biofilms. Biofilm compositions study before and after proteinase K treatment indicated that Bap might also be involved in eDNA retention in the biofilm matrix that aid in biofilm stability. When proteinase K was used in combination with antibiotics, a synergistic effect in antibiotic efficacy was observed against all biofilm formingS. aureusstrains.ConclusionProteinase K inhibited biofilms growth inS. aureusbovine mastitis isolates but did not affect their planktonic growth. An enhanced dispersion of preformedS. aureusbiofilms was observed upon proteinase K treatment. Proteinase K treatment with antibiotics showed a synergistic effect againstS. aureusbiofilms.Significance of the studyThe study suggests that dispersingS. aureusby protease can be of use while devising strategies againstS. aureusbiofilms. Proteinase K treatment has a wider scope for control ofS. aureusbiofilms.
Production of Multilayer Cell Mass from Olfactory Stem Cell and Its Utilization Potential in Nervous Tissue Regeneration
Authors: Oztel Olga N. , Allahverdiyev Adil , Karaaltin Aysegul Batioglu , Bağırova Melahat , Ovali Ercument 
Published: January 2017

AbstractBackgroundExperimental studies performed with human olfactory nerve stem cells haveshown that these cells can ameliorate nerve cell regeneration. Developing a method of repairing nerve damage solely using stem cells without the need of any supporting material is important.MethodsA multilayer cell mass was obtained from olfactory tissue-derived mesenchymal stem cells with high viability and proliferation capability using a protocol devoid of scaffolds or any other artificial supporting material. First, human olfactory tissue-derived mesenchymal stem cells were isolated, cultured, and characterized. Next, consecutive passages were conducted to obtain multilayer cell growth. The resulting cell mass could be suitable for tissue engineering models as well as nerve cell or tissue regeneration studies in the future.ResultsViability and adhesive properties of the resulting cell mass were examined and found to be suitable for use in nerve tissue regeneration.ConclusionIt is suggested that anin vitro-produced olfactory stem cell mass can be applied to a very small damaged region and could have a high potential for microenvironment formation.
Prolonged exposure does not increase soil microbial community response to warming along geothermal gradients
Authors: Radujković Dajana , Verbruggen Erik , Sigurdsson Bjarni D. , Leblans Niki I. W. , Vicca Sara , Weedon James T. 
Published: January 2017

ABSTRACTPredicting effects of climate change on ecosystem functioning requires knowledge of soil microbial community responses to warming. We used natural geothermal gradients (from +1°C to +19°C above ambient) in two subarctic grasslands to test the hypothesis that long-term exposure (>50 years) intensifies microbial community responses to warming compared to short-term exposure (5-7 years). Community profiles from amplicon sequencing of bacterial and fungal rRNA genes did not support this hypothesis: significant changes relative to ambient were observed from +9°C and upwards in the long-term and from 7°C to 11°C / +3°C to +5°C and upwards in the short-term, for bacteria and fungi, respectively. Our results suggest that bacterial communities in high-latitude grasslands will not undergo lasting shifts in community composition under the warming predicted for the coming 100 years. Fungal communities do appear to be temperature sensitive to the warming within this range, but only for short-term exposures.
Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission
Authors: Mullon Charles , Lehmann Laurent 
Published: January 2017

AbstractHuman evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to off-spring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the “learning-reproduction trade-off”) significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is more efficient than between unrelated individuals.
A Molecular Signature for Anastasis, Recovery from the Brink of Apoptotic Cell Death
Authors: Sun Gongping , Guzman Elmer , Zhou Hongjun Robin , Kosik Kenneth S. , Montell Denise J. 
Published: January 2017

AbstractDuring apoptosis, executioner caspase activity has been considered a point of no return. However, recent studies show that cells can survive caspase activation following transient apoptotic stimuli, a process named anastasis. To identify a molecular signature, we performed whole transcriptome RNA sequencing of untreated, apoptotic, and recovering HeLa cells. We found that anastasis is an active, two-stage program. During the early stage, cells transition from growth-arrested to growing. In the late stage, cells change from proliferating to migratory. Strikingly, some early recovery mRNAs were elevated first during apoptosis, implying that dying cells poise to recover, even while still under apoptotic stress. Furthermore, TGFβ-induced Snail expression is required for anastasis, and recovering cells exhibit prolonged elevation of pro-angiogenic factors. This study demonstrates similarities in the anastasis genes, pathways, and cell behaviors to those activated in wound healing. This study identifies a repertoire of potential targets for therapeutic manipulation of this process.
Family history and APOE4 risk for Alzheimer’s Disease impact the neural correlates of episodic memory by early midlife
Authors: Rajah M. N. , Wallace L. M. K. , Ankudowich E. , Yu E. H. , Swierkot A. , Patel R. , Chakravarty M. M. , Naumova D. , Pruessner J. , Joober R. , Gauthier S. , Pasvanis S. 
Published: January 2017

AbstractEpisodic memory impairment is a consistent, pronounced deficit in pre-clinical stages of late-onset Alzheimer’s disease (AD). Individuals with risk factors for AD exhibit altered brain function several decades prior to the onset of AD-related symptoms. In the current event-related fMRI study of spatial context memory we tested the hypothesis that middle-aged adults (MA; 40-58yrs) with a family history of late onset AD (MA+FH), or a combined +FH and apolipoprotein E ε4 allele risk factors for AD (MA+FH+APOE4), will exhibit differences in encoding and retrieval-related brain activity, compared to – FH –APOE4 MA controls. We also hypothesized that the two at-risk MA groups will exhibit distinct patterns of correlation between brain activity and memory performance, compared to controls. To test these hypotheses we conducted multivariate task, and behavior, partial least squares analysis of fMRI data obtained during successful context encoding and retrieval. Our results indicate that even though there were no significant group differences in context memory performance, there were significant differences in brain activity and brain-behavior correlations involving hippocampus, inferior parietal cortex, cingulate, and precuneus in MA with AD risk factors, compared to controls. In addition, we observed that brain activity and brain-behavior correlations in anterior-medial PFC and in ventral visual cortex differentiated the two MA risk groups from each other, and from MAcontrols. Our results indicate that functional differences in episodic memory-related regions are present by early midlife in adults with +FH and +APOE-4 risk factors for late onset AD, compared to middle-aged controls.
The complex origins of strigolactone signalling in land plants
Authors: Bythell-Douglas Rohan , Rothfels Carl J. , Stevenson Dennis W.D. , Graham Sean W. , Wong Gane Ka-Shu , Nelson David C. , Bennett Tom 
Published: January 2017

ABSTRACTStrigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an α/β hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor, and likely recognizes an uncharacterized, endogenous signal. Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. Here, we have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analyzed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We identify characteristic structural features of D14 and KAI2 proteins, and use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2, and not D14 proteins. Furthermore, we show that probable SL receptors in non-seed plants do not have D14-like structure. Our results suggest that SL perception has relatively relaxed structural requirements, and that the evolution from KAI2-like to D14-like protein structure in the DDK lineage may have been driven by interactions with protein partners, rather than being required for SL perception itself.
Do journal data sharing mandates work? Life sciences evidence from Dryad
Authors: Thelwall Mike , Kousha Kayvan 
Published: January 2017

Purpose
Data sharing is widely thought to help research quality and efficiency. Data sharing mandates are increasingly being adopted by journals and the purpose of this paper is to assess whether they work.

Design/methodology/approach
This study examines two evolutionary biology journals, Evolution and Heredity, that have data sharing mandates and make extensive use of Dryad. It uses a quantitative analysis of presence in Dryad, downloads and citations.

Findings
Within both journals, data sharing seems to be complete, showing that the mandates work on a technical level. Low correlations (0.15-0.18) between data downloads and article citation counts for articles published in 2012 within these journals indicate a weak relationship between data sharing and research impact. An average of 40-55 data downloads per article after a few years suggests that some use is found for shared life sciences data.

Research limitations/implications
The value of shared data uses is unclear.

Practical implications
Data sharing mandates should be encouraged as an effective strategy.

Originality/value
This is the first analysis of the effectiveness of data sharing mandates.
Numerical analysis of skewed squirrel-cage induction motor taking into account interbar current using 3-D finite element method
Authors: Kawase Yoshihiro , Yamaguchi Tadashi , Iwai Yoshiki , Akiyama Koki , Toida Naotaka , Furukawa Tomoyasu , Kawano Hiroshi 
Published: January 2017

Purpose
The interbar current of a squirrel-cage induction motor (IM) flows in the steel sheets when the secondary conductor is not insulated from the laminated steel sheets. It was reported that the interbar current loss was increased when skewing the rotor core. This paper aims to analyze a skewed IM using the three-dimensional (3D) finite element method. The effects of rotor skew on the interbar current are clarified.

Design/methodology/approach
In this paper, a skewed squirrel-cage IM is analyzed in three patterns of skewed angle. The calculated results were compared with each other. If all laminated steel sheets are divided by the mesh with actual thickness, the huge calculation time is required. In the method applied in the study, several steel sheets are divided by the mesh with the actual thickness and some steel sheets are assumed to be the steel lump between them to shorten the calculation time.

Findings
The paper describes that the distribution of interbar current loss when rotor is skewed is different from that when rotor is not skewed. In addition, the paper suggests that the larger the skew angle becomes, the larger the interbar current loss becomes.

Originality/value
In this paper, a skewed IM with the consideration of the interbar current in the laminated steel sheets was analyzed using the 3D finite element method. The influences of the rotor skew on the interbar current are clarified.
Mathematical modeling and harmonic analysis of SISFCL
Authors: Sarkar Debraj , Roy Debabrata , Choudhury Amalendu Bikash , Yamada Sotoshi 
Published: January 2017

Purpose
A saturated iron core superconducting fault current limiter (SISFCL) has an important role to play in the present-day power system, providing effective protection against electrical faults and thus ensuring an uninterrupted supply of electricity to the consumers. Previous mathematical models developed to describe the SISFCL use a simple flux density-magnetic field intensity curve representing the ferromagnetic core. As the magnetic state of the core affects the efficient working of the device, this paper aims to present a novel approach in the mathematical modeling of the device with the inclusion of hysteresis.

Design/methodology/approach
The Jiles–Atherton’s hysteresis model is utilized to develop the mathematical model of the limiter. The model is numerically solved using MATLAB. To support the validity of model, finite element model (FEM) with similar specifications was simulated.

Findings
Response of the limiter based on the developed mathematical model is in close agreement with the FEM simulations. To illustrate the effect of the hysteresis, the responses are compared by using three different hysteresis characteristics. Harmonic analysis is performed and comparison is carried out utilizing fast Fourier transform and continuous wavelet transform. It is observed that the core with narrower hysteresis characteristic not only produces a better current suppression but also creates a higher voltage drop across the DC source. It also injects more harmonics in the system under fault condition.

Originality/value
Inclusion of hysteresis in the mathematical model presents a more realistic approach in the transient analysis of the device. The paper provides an essential insight into the effect of the core hysteresis characteristic on the device performance.
Small-signal discrete-time modeling of digitally controlled three-phase PWM boost rectifier under balanced voltage
Authors: Zeng Zhiyong , Jin Xiaoliang , Zhao Rongxiang 
Published: January 2017

Purpose
The model for digitally controlled three-phase pulse width modulation (PWM) boost rectifiers is a sampled data model, which is different from the continuous time domain models presented in previous studies. The controller, which is tuned according to the model in continuous time domain and discretized by approximation methods, may exhibit some unpredictable performances and even result in unstable systems under some extreme situations. Consequently, a small-signal discrete-time model of digitally controlled three-phase PWM boost rectifier is required. The purpose of this paper is to provide a simple but accurate small-signal discrete-time model of digital controlled three-phase PWM boost rectifier, which explains the effect of the sampling period, modulator and time delays on system dynamic and improves the control performance.

Design/methodology/approach
Based on the Laplace domain analysis and the waveforms of up-down-count modulator, the small signal model of digital pulse width modulation (DPWM) in the Laplace domain is presented. With a combination of state-space average and a discrete-time modeling technique, a simplified large signal discrete time model is developed. With rotation transformation and feed-forward decoupling, the large-signal model is decoupled into a single input single output system with rotation transformation. Then, an integrated small signal model in the Laplace domain is constructed that included the time delay and modulation effect. Implementing the modified z-transform, a small-signal discrete-time model is derived from the integrated small signal model.

Findings
In a digital control system, besides the circuit parameters, the location of pole of open-loop transfer function is also related to system sampling time, affecting the system stability, and the time delay determines the location of the zero of open-loop transfer function, affecting the system dynamic. In addition to the circuit parameters discussed in previous literature, the right half plane (RHP) zero is also determined by the sampling period and the time delay. Furthermore, the corner frequency of the RHP zero is mainly determined by the sampling period.

Originality/value
The model developed in this paper, accounting for the effect of the sampling period, modulator and time delays on the system dynamic, give a sufficient insight into the behavior of the digitally controlled three-phase PWM rectifier. It can also explain the effect of sampling period and control delay time on system dynamic, accurately predict the system stability boundary and determine the oscillation frequency of the current loop in critical stable. The experimental results verify that the model is a simple and accurate control-oriented small-signal discrete-time model for the digitally controlled three-phase PWM boost rectifier.