bluuebunny/crossref_metadata_2025_split huggingface dataset:
Categorizing biological information based on function–morphology for bioinspired conceptual design
Authors: Lee Sooyeon , McAdams Daniel A. , Morris Elissa 
Published: December 2016

AbstractA function-based keyword search is a concept generation methodology studied in the bioinspired design area that conveys textual biological inspiration for engineering design. Current keyword search methods are inefficient primarily due to the knowledge gap between engineering and biology domains. To improve current keyword search methods, we propose an algorithm that extracts and organizes morphology-based solutions from biological text. WordNet is utilized to discover morphological solutions in biological text. The novel algorithm also adapts latent semantic analysis and the expectation–maximization algorithm to categorize morphological solutions and group biological text. We introduce a novel penalty function that reflects the distance between functions (problems) and morphologies (solutions). The penalty function allows the algorithm to extract morphological solutions directly related to a design problem. We compare the output of the algorithm to manually extracted solutions for validation. A case study is included to exemplify the utility of the developed algorithm. Upon implementation of the algorithm, engineering designers can discover innovative solutions in biological text in a straightforward, efficient manner.
Incidence and factors associated with emergency department visits for recurrent skin and soft tissue infections in patients in California, 2005–2011
Authors: MAY L. , KLEIN E. Y. , MARTINEZ E. M. , MOJICA N. , MILLER L. G. 
Published: December 2016

SUMMARYMore than 2 million visits for skin and soft tissue infections (SSTIs) are seen in US emergency departments (EDs) yearly. Up to 50% of patients with SSTIs, suffer from recurrences, but associated factors remain poorly understood. We performed a retrospective study of patients with primary diagnosis of SSTI between 2005 and 2011 using California ED discharge data from the State Emergency Department Databases and State Inpatient Databases. Using a multivariable logistic regression, we examined factors associated with a repeat SSTI ED visits up to 6 months after the initial SSTI. Among 197 371 SSTIs, 16·3% were associated with a recurrent ED visit. We found no trend in recurrent visits over time (χ2 trend = 0·68, P = 0·4). Race/ethnicity, age, geographical location, household income, and comorbidities were all associated with recurrent visits. Recurrent ED visits were associated with drug/alcohol abuse or liver disease [odds ratio (OR) 1·4, 95% confidence interval (CI) 1·3–1·4], obesity (OR 1·3, 95% CI 1·2–1·4), and in infections that were drained (OR 1·1, 95% CI 1·1–1·1) and inversely associated with hospitalization after initial ED visit (OR 0·4, 95% CI 0·3–0·4). In conclusion, we found several patient-level factors associated with recurrent ED visits. Identification of these high-risk groups is critical for future ED-based interventions.
The longevity of desorbing and adsorbing rice seeds
Authors: Hay Fiona R. , Timple Stephen 
Published: December 2016

AbstractIn each of two experiments, freshly harvested seeds of two cultivars of rice were dried and then rehydrated to different moisture levels. In experiment 1, seed equilibrium relative humidity (eRH) and moisture content (MC) were determined at each moisture level so that moisture desorption and adsorption isotherms could be constructed. Seed storage experiments were also carried out for seeds equilibrated at each moisture level, in sealed aluminium foil packets at 45°C. In experiment 2, storage experiments at 45°C were carried out on seeds dried to 12% MC and seeds dried to lower moisture levels and then rehydrated to 12% MC.The moisture adsorption isotherm was shifted to lower MC at a given eRH compared with the desorption isotherm. This hysteresis effect was seen both when seeds were dried to <6% MC and then allowed to adsorb moisture to different levels, and when seeds were dried to different levels (10, 8, 6 or 4% MC) and then allowed to adsorb moisture up to 12% MC. The log-log relationship between seed longevity, σ [the standard deviation of the normal distribution of seed deaths over time, as defined in the Ellis and Roberts (1980) seed viability equations] and seed storage MC did not vary depending on whether the seeds were desorbing or adsorbing moisture. The relationship between σ and eRH was better described by a log-log model than a log-linear model and did vary depending on whether seeds were desorbing or adsorbing moisture: at a given eRH, the longevity of adsorbing seeds was greater than that of desorbing seeds. The implications for seed storage are discussed.
Do Cognitive and Physical Functions Age in Concert from Age 70 to 76? Evidence from the Lothian Birth Cohort 1936
Authors: Ritchie Stuart J. , Tucker-Drob Elliot M. , Starr John M. , Deary Ian J. 
Published: December 2016

AbstractThe present study concerns the relation of mental and bodily characteristics to one another during ageing. The ‘common cause’ theory of ageing proposes that declines are shared across multiple, seemingly-disparate functions, including both physical and intellectual abilities. The concept of ‘reserve’ suggests that healthier cognitive (and perhaps bodily) functions from early in life are protective against the effects of senescence across multiple domains. In three waves of physical and cognitive testing data from the longitudinal Lothian Birth Cohort 1936 (n = 1,091 at age 70 years; n = 866 at 73; n = 697 at 76), we used multivariate growth curve modeling to test the ‘common cause’ and ‘reserve’ hypotheses. Support for both concepts was mixed: although levels of physical functions and cognitive functions were correlated with one another, physical functions did not decline together, and there was little evidence for shared declines in physical and mental functions. Early-life intelligence, a potential marker of system integrity, made a significant prediction of the levels, but not the slopes, of later life physical functions. These data suggest that common causes, which are likely present within cognitive functions, are not as far-reaching beyond the cognitive arena as has previously been suggested. They also imply that bodily reserve may be similar to cognitive reserve in that it affects the level, but not the slope, of ageing-related declines.
Critical exponents and scaling invariance in the absence of a critical point
Authors: Saratz N. , Zanin D. A. , Ramsperger U. , Cannas S. A. , Pescia D. , Vindigni A. 
Published: December 2016

AbstractThe paramagnetic-to-ferromagnetic phase transition is classified as a critical phenomenon due to the power-law behaviour shown by thermodynamic observables when the Curie point is approached. Here we report the observation of such a behaviour over extraordinarily many decades of suitable scaling variables in ultrathin Fe films, for certain ranges of temperature T and applied field B. This despite the fact that the underlying critical point is practically unreachable because protected by a phase with a modulated domain structure, induced by the dipole–dipole interaction. The modulated structure has a well-defined spatial period and is realized in a portion of the (T, B) plane that extends above the putative critical temperature, where thermodynamic quantities do not display any singularity. Our results imply that scaling behaviour of macroscopic observables is compatible with an avoided critical point.
Efficiency limits for photoelectrochemical water-splitting
Authors: Fountaine Katherine T. , Lewerenz Hans Joachim , Atwater Harry A. 
Published: December 2016

AbstractTheoretical limiting efficiencies have a critical role in determining technological viability and expectations for device prototypes, as evidenced by the photovoltaics community’s focus on detailed balance. However, due to their multicomponent nature, photoelectrochemical devices do not have an equivalent analogue to detailed balance, and reported theoretical efficiency limits vary depending on the assumptions made. Here we introduce a unified framework for photoelectrochemical device performance through which all previous limiting efficiencies can be understood and contextualized. Ideal and experimentally realistic limiting efficiencies are presented, and then generalized using five representative parameters—semiconductor absorption fraction, external radiative efficiency, series resistance, shunt resistance and catalytic exchange current density—to account for imperfect light absorption, charge transport and catalysis. Finally, we discuss the origin of deviations between the limits discussed herein and reported water-splitting efficiencies. This analysis provides insight into the primary factors that determine device performance and a powerful handle to improve device efficiency.
A chromosome-level genome assembly of the Asian arowana, Scleropages formosus
Authors: Li Jia , Bian Chao , Hu Yinchang , Mu Xidong , Shen Xueyan , Ravi Vydianathan , Kuznetsova Inna S. , Sun Ying , You Xinxin , Qiu Ying , Zhang Xinhui , Yu Hui , Huang Yu , Xu Pao , Gu Ruobo , Xu Junmin , Orbán László , Venkatesh Byrappa , Shi Qiong 
Published: December 2016

AbstractAsian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq). In addition, we obtained draft genome assemblies of the red and green varieties. Finally, we annotated 22,016, 21,256 and 21,524 protein-coding genes in the genome assemblies of golden, red and green varieties respectively. Our data were deposited in publicly accessible repositories to promote biological research and molecular breeding of Asian arowana.
Biogenic synthesis of Zinc oxide nanostructures from Nigella sativa seed: Prospective role as food packaging material inhibiting broad-spectrum quorum sensing and biofilm
Authors: Al-Shabib Nasser A. , Husain Fohad Mabood , Ahmed Faheem , Khan Rais Ahmad , Ahmad Iqbal , Alsharaeh Edreese , Khan Mohd Shahnawaz , Hussain Afzal , Rehman Md Tabish , Yusuf Mohammad , Hassan Iftekhar , Khan Javed Masood , Ashraf Ghulam Md , Alsalme Ali , Al-Ajmi Mohamed F. , Tarasov Vadim V. , Aliev Gjumrakch 
Published: December 2016

AbstractBacterial spoilage of food products is regulated by density dependent communication system called quorum sensing (QS). QS control biofilm formation in numerous food pathogens and Biofilms formed on food surfaces act as carriers of bacterial contamination leading to spoilage of food and health hazards. Agents inhibiting or interfering with bacterial QS and biofilm are gaining importance as a novel class of next-generation food preservatives/packaging material. In the present study, Zinc nanostructures were synthesised using Nigella sativa seed extract (NS-ZnNPs). Synthesized nanostructures were characterized hexagonal wurtzite structure of size ~24 nm by UV-visible, XRD, FTIR and TEM. NS-ZnNPs demonstrated broad-spectrum QS inhibition in C. violaceum and P. aeruginosa biosensor strains. Synthesized nanostructures inhibited QS regulated functions of C. violaceum CVO26 (violacein) and elastase, protease, pyocyanin and alginate production in PAO1 significantly. NS-ZnNPs at sub-inhibitory concentrations inhibited the biofilm formation of four-food pathogens viz. C. violaceum 12472, PAO1, L. monocytogenes, E. coli. Moreover, NS-ZnNPs was found effective in inhibiting pre-formed mature biofilms of the four pathogens. Therefore, the broad-spectrum inhibition of QS and biofilm by biogenic Zinc oxide nanoparticles and it is envisaged that these nontoxic bioactive nanostructures can be used as food packaging material and/or as food preservative.
Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs
Authors: Tomov Martin L. , Olmsted Zachary T. , Dogan Haluk , Gongorurler Eda , Tsompana Maria , Otu Hasan H. , Buck Michael , Chang Eun-Ah , Cibelli Jose , Paluh Janet L. 
Published: December 2016

AbstractThe realization of personalized medicine through human induced pluripotent stem cell (iPSC) technology can be advanced by transcriptomics, epigenomics, and bioinformatics that inform on genetic pathways directing tissue development and function. When possible, population diversity should be included in new studies as resources become available. Previously we derived replicate iPSC lines of African American, Hispanic-Latino and Asian self-designated ethnically diverse (ED) origins with normal karyotype, verified teratoma formation, pluripotency biomarkers, and tri-lineage in vitro commitment. Here we perform bioinformatics of RNA-Seq and ChIP-seq pluripotency data sets for two replicate Asian and Hispanic-Latino ED-iPSC lines that reveal differences in generation of contractile cardiomyocytes but similar and robust differentiation to multiple neural, pancreatic, and smooth muscle cell types. We identify shared and distinct genes and contributing pathways in the replicate ED-iPSC lines to enhance our ability to understand how reprogramming to iPSC impacts genes and pathways contributing to cardiomyocyte contractility potential.
Examining the Validity of the Phonon Gas Model in Amorphous Materials
Authors: Lv Wei , Henry Asegun 
Published: December 2016

AbstractThe idea of treating phonon transport as equivalent to transport through a gas of particles is termed the phonon gas model (PGM), and it has been used almost ubiquitously to try and understand heat conduction in all solids. However, most of the modes in disordered materials do not propagate and thus may contribute to heat conduction in a fundamentally different way than is described by the PGM. From a practical perspective, the problem with trying to apply the PGM to amorphous materials is the fact that one cannot rigorously define the phonon velocities for non-propagating modes, since there is no periodicity. Here, we tested the validity of the PGM for amorphous materials by assuming the PGM is applicable, and then, using a combination of lattice dynamics, molecular dynamics (MD) and experimental thermal conductivity data, we back-calculated the phonon velocities for the vibrational modes. The results of this approach show that if the PGM was valid, a large number of the mid and high frequency modes would have to have either imaginary or extremely high velocities to reproduce the experimental thermal conductivity data. Furthermore, the results of MD based relaxation time calculations suggest that in amorphous materials there is little, if any, connection between relaxation times and thermal conductivity. This then strongly suggests that the PGM is inapplicable to amorphous solids.
Comprehensive evaluation of molecular enhancers of the isothermal exponential amplification reaction
Authors: Mok Ellie , Wee Eugene , Wang Yuling , Trau Matt 
Published: December 2016

AbstractThe exponential amplification reaction (EXPAR) is an emerging isothermal nucleic acid amplification method with high potential for molecular diagnostics due to its isothermal nature and high amplification efficiency. However, the use of EXPAR is limited by the high levels of non-specific amplification. Hence, methods that can improve the specificity of EXPAR are desired to facilitate its widespread adoption in practice. Herein, we proposed a strategy to improve EXPAR performance by using molecular enhancers. Eight small molecules were investigated, including ethylene glycol, propylene glycol, betaine, dimethyl sulfoxide (DMSO), trehalose, tetramethylammonium chloride (TMAC), bovine serum albumin (BSA) and single-stranded binding (SSB) proteins. A combination of kinetic and end-point analysis was adopted to investigate how these molecules affected EXPAR performance. Trehalose, TMAC, BSA and SSB proteins were found to have positive effects on EXPAR with trehalose being able to increase the efficiency of EXPAR. In contrast, TMAC, BSA and SSB proteins were shown to increase the specificity of EXPAR. We applied our findings to demonstrate the combination of trehalose and TMAC could simultaneously improve both the efficiency and specificity of an EXPAR-based miRNA detection method. The information provided in this study may serve as a reference to benefit the wider isothermal amplification community.
Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis
Authors: Gutiérrez-Fernández Javier , Saleh Malek , Alcorlo Martín , Gómez-Mejía Alejandro , Pantoja-Uceda David , Treviño Miguel A. , Voß Franziska , Abdullah Mohammed R. , Galán-Bartual Sergio , Seinen Jolien , Sánchez-Murcia Pedro A. , Gago Federico , Bruix Marta , Hammerschmidt Sven , Hermoso Juan A. 
Published: December 2016

AbstractThe human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca2+-binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp_Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.
Ascl3 transcription factor marks a distinct progenitor lineage for non-neuronal support cells in the olfactory epithelium
Authors: Weng Pei-Lun , Vinjamuri Mridula , Ovitt Catherine E. 
Published: December 2016

AbstractThe olfactory epithelium (OE) is composed of olfactory sensory neurons (OSNs), sustentacular supporting cells, and several types of non-neuronal cells. Stem and progenitor cells are located basally, and are the source of all cell types needed to maintain OE homeostasis. Here, we report that Ascl3, a basic helix-loop-helix transcription factor, is expressed in the developing OE. Lineage tracing experiments demonstrate that the non-neuronal microvillar cells and Bowman’s glands are exclusively derived from Ascl3+ progenitor cells in the OE during development. Following chemically-induced injury, Ascl3 expression is activated in a subset of horizontal basal cells (HBCs), which repopulate all microvillar cells and Bowman’s glands during OE regeneration. After ablation of Ascl3-expressing cells, the OE can regenerate, but lacks the non-neuronal microvillar and Bowman’s gland support cells. These results demonstrate that Ascl3 marks progenitors that are lineage-committed strictly to microvillar cells and Bowman’s glands, and highlight the requirement for these cell types to support OE homeostasis.
Sequential information in a great ape utterance
Authors: Fedurek Pawel , Zuberbühler Klaus , Dahl Christoph D. 
Published: December 2016

AbstractBirdsong is a prime example of acoustically sophisticated vocal behaviour, but its complexity has evolved mainly through sexual selection to attract mates and repel sexual rivals. In contrast, non-human primate calls often mediate complex social interactions, but are generally regarded as acoustically simple. Here, we examine arguably the most complex call in great ape vocal communication, the chimpanzee (Pan troglodytes schweinfurthii) ‘pant hoot’. This signal consists of four acoustically distinct phases: introduction, build-up, climax and let-down. We applied state-of-the-art Support Vector Machines (SVM) methodology to pant hoots produced by wild male chimpanzees of Budongo Forest, Uganda. We found that caller identity was apparent in all four phases, but most strongly in the low-amplitude introduction and high-amplitude climax phases. Age was mainly correlated with the low-amplitude introduction and build-up phases, dominance rank (i.e. social status) with the high-amplitude climax phase, and context (reflecting activity of the caller) with the low-amplitude let-down phase. We conclude that the complex acoustic structure of chimpanzee pant hoots is linked to a range of socially relevant information in the different phases of the call, reflecting the complex nature of chimpanzee social lives.
Exploring the Relationship Between Eye Movements and Electrocardiogram Interpretation Accuracy
Authors: Davies Alan , Brown Gavin , Vigo Markel , Harper Simon , Horseman Laura , Splendiani Bruno , Hill Elspeth , Jay Caroline 
Published: December 2016

AbstractInterpretation of electrocardiograms (ECGs) is a complex task involving visual inspection. This paper aims to improve understanding of how practitioners perceive ECGs, and determine whether visual behaviour can indicate differences in interpretation accuracy. A group of healthcare practitioners (n = 31) who interpret ECGs as part of their clinical role were shown 11 commonly encountered ECGs on a computer screen. The participants’ eye movement data were recorded as they viewed the ECGs and attempted interpretation. The Jensen-Shannon distance was computed for the distance between two Markov chains, constructed from the transition matrices (visual shifts from and to ECG leads) of the correct and incorrect interpretation groups for each ECG. A permutation test was then used to compare this distance against 10,000 randomly shuffled groups made up of the same participants. The results demonstrated a statistically significant (α  0.05) result in 5 of the 11 stimuli demonstrating that the gaze shift between the ECG leads is different between the groups making correct and incorrect interpretations and therefore a factor in interpretation accuracy. The results shed further light on the relationship between visual behaviour and ECG interpretation accuracy, providing information that can be used to improve both human and automated interpretation approaches.