bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Left–Right Asymmetries on Voice Quality in Simulated Paramedian Vocal Fold Paralysis
Authors: Samlan Robin A. , Story Brad H. 
Published: February 2017

Purpose
The purpose of this study was to determine the vocal fold structural and vibratory symmetries that are important to vocal function and voice quality in a simulated paramedian vocal fold paralysis.

Method
A computational kinematic speech production model was used to simulate an exemplar “voice” on the basis of asymmetric settings of parameters controlling glottal configuration. These parameters were then altered individually to determine their effect on maximum flow declination rate, spectral slope, cepstral peak prominence, harmonics-to-noise ratio, and perceived voice quality.

Results
Asymmetry of each of the 5 vocal fold parameters influenced vocal function and voice quality; measured change was greatest for adduction and bulging. Increasing the symmetry of all parameters improved voice, and the best voice occurred with overcorrection of adduction, followed by bulging, nodal point ratio, starting phase, and amplitude of vibration.

Conclusions
Although vocal process adduction and edge bulging asymmetries are most influential in voice quality for simulated vocal fold motion impairment, amplitude of vibration and starting phase asymmetries are also perceptually important. These findings are consistent with the current surgical approach to vocal fold motion impairment, where goals include medializing the vocal process and straightening concave edges. The results also explain many of the residual postoperative voice limitations.
Quantum interpolation for high-resolution sensing
Authors: Ajoy Ashok , Liu Yi-Xiang , Saha Kasturi , Marseglia Luca , Jaskula Jean-Christophe , Bissbort Ulf , Cappellaro Paola 
Published: February 2017

Significance
Nanoscale magnetic resonance imaging enabled by quantum sensors is a promising path toward the outstanding goal of determining the structure of single biomolecules at room temperature. We develop a technique, which we name “quantum interpolation,” to improve the frequency resolution of these quantum sensors far beyond limitations set by the experimental controlling apparatus. The method relies on quantum interference to achieve high-fidelity interpolation of the quantum dynamics between hardware-allowed time samplings, thus allowing high-resolution sensing. We demonstrate over two orders of magnitude resolution gains, and discuss applications of our work to high-resolution nanoscale magnetic resonance imaging.
Intrinsically disordered proteins drive enamel formation via an evolutionarily conserved self-assembly motif
Authors: Wald Tomas , Spoutil Frantisek , Osickova Adriana , Prochazkova Michaela , Benada Oldrich , Kasparek Petr , Bumba Ladislav , Klein Ophir D. , Sedlacek Radislav , Sebo Peter , Prochazka Jan , Osicka Radim 
Published: February 2017

SignificanceFormation of the hardest mineralized tissue in vertebrates, tooth enamel, relies on a unique set of enamel matrix proteins (EMPs). These EMPs assemble into a 3D extracellular organic matrix that directs the deposition of calcium and phosphate ions into hydroxyapatite crystallites. However, the molecular basis of EMP assembly into the organic matrix remains poorly understood. This study shows that self-assembly of the key EMPs, ameloblastin and amelogenin, involves a short linear amino acid motif that is evolutionarily conserved from the first tetrapods to man. Functionality of this motif in ameloblastin is shown to be essential for organization of the enamel organic matrix and for proper organization of hydroxyapatite crystallites into the compact bundles that determine the structure and mechanical resistance of enamel.
Insights into immune system development and function from mouse T-cell repertoires
Authors: Sethna Zachary , Elhanati Yuval , Dudgeon Crissy R. , Callan Curtis G. , Levine Arnold J. , Mora Thierry , Walczak Aleksandra M. 
Published: February 2017

SignificanceThe immune system defends against pathogens in part via a diverse population of T cells that display different surface receptor proteins [T-cell receptors (TCRs)] designed to recognize MHC-presented foreign peptides. Receptor diversity is produced by an initial random gene recombination process, followed by selection for proteins that fold correctly and bind weakly to self-peptides. Using data from mice of different ages, from embryo to young adult, we quantify the changes with time in the way receptors are generated and selected for function. We find a strong increase in repertoire diversity, occurring shortly after birth, due to a sharp increase in the number of random nucleotide insertions in the primitive TCR gene recombination process. Differences between thymic and blood TCR sequence distributions allow us to infer subtle details of this “turning on” of the mouse immune system.
Red Snapper Distribution on Natural Habitats and Artificial Structures in the Northern Gulf of Mexico
Authors: Karnauskas Mandy , Walter John F. , Campbell Matthew D. , Pollack Adam G. , Drymon J. Marcus , Powers Sean 
Published: February 2017

Abstract
In 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, patchy “hot spots” at a variety of depths along the Alabama coast and the west Florida shelf. Red Snapper biomass and fecundity estimates were higher for the northwestern GOM than for the northeastern GOM, as the latter area contained mostly smaller, younger individuals. The existence of similar surveys on petroleum platforms and artificial reefs also enabled us to calculate their relative contribution to Red Snapper distribution compared with that of natural habitats. We estimated that for the youngest age-classes, catch rates were approximately 20 times higher on artificial structures than on natural reefs. Despite the high catch rates observed on artificial structures, they represent only a small fraction of the total area in the northern GOM; thus, we estimated that they held less than 14% of Red Snapper abundance. Because artificial structures—particularly petroleum platforms—attract mostly the youngest individuals, their contribution was even lower in terms of total population biomass (7.8%) or spawning potential (6.4%). Our estimates of Red Snapper relative abundance, biomass, and spawning potential can be used to design spatial management strategies or as inputs to spatial modeling techniques.
Realisms and Indexicalities of Photographic Propositions
Authors: Ball Christopher 
Published: February 2017

AbstractIn the eras of both film-based and digital photography, and to differing degrees and with differing consequences in documentary and art photography, the role of indexicality in establishing the veracity of the image has been paramount in photo theory. There is a need, however, for expanding the ways we think about indexicality in photography. In addition to the familiar concepts of the trace, citation, reference, social diacritics, interactional cues, and artists’ intentions, the indexicality of photography may be better understood through appeal to less direct, or more densely mediated, modalities of indexicality. These include qualia (hypostatically abstracted -nesses), dicentization (the upshifting of icons into indexes of contiguity), and propositionality (the assertion of messages subject to truth claims).
The Open Throat: Deceptive Sounds, Facts of Firstness, and the Interactional Emergence of Voice
Authors: Harkness Nicholas 
Published: February 2017

AbstractThis article develops a Peircean conceptualization of qualia as “facts of firstness” by examining the pedagogical pragmatics of a voice lesson in which an intersubjective orientation to vocal sound via listening becomes a subjective orientation to voice production via bodily feeling. I focus specifically on various attempts by a teacher and a student collaboratively to repair and cultivate the student’s voice by generating and isolating qualia across proprioceptive and introspective dimensions. By tracing the sensuous semiotic modes through which qualia become crucial pragmatic signals in the process of “opening” the student’s throat, I demonstrate how these facts of firstness function as cultural emergents that are produced by and accessible through communicative, interactional, intersubjective conduct.
Signatura rerum: Semiotics of the Subnuclear
Authors: Roy Arpita 
Published: February 2017

AbstractOn July 4, 2012, experimental physicists on the Large Hadron Collider near Geneva, in Switzerland, announced the historic discovery of the Higgs boson. After analyzing trillions of proton-to-proton collisions, two teams of physicists concluded that signatures of diphotons in the final state were evidence of the long-sought-after Higgs particle. The answerability of a particle search to polysemic signals raises a deeply provocative question: In what ways does a sign facilitate the discovery of a thing? Drawing on fieldwork at the Large Hadron Collider complex, this article attempts to probe the semiosis of signatures as a palimpsest of inherent possibilities spanning the width of the universe, which is neither a contingent ordering of the Saussurean kind nor a brick-by-brick Peircean construct. What it eloquently foregrounds is the capacity of a class of signs to reflect the presence of objects, even those that are materially nonexistent, which resolves many a metaphysical perplexity involving language, thought, and reality. In the process, this article makes a case for the role of meaningful, qualitative evaluations, which lie at the root of experimental searches, and explains how these qualitative evaluations are a more trustworthy source of discoveries in particle physics than metrics or magnitudes.
Qualia as Value and Knowledge: Histories of European Porcelain
Authors: Gal Susan 
Published: February 2017

AbstractPorcelain is, today, a familiar material of dishes, figurines, vases, and tiles. As commodities, they are enregistered social indexicals, so that the aphorism fits: you are what you drink, eat, or in this case eat on—or know how to admire as collector or connoisseur. This does not yet tell us, however, what qualities are picked out as shared by object and user, on what axis of social distinction. I argue that this everyday material, exactly because of the varied qualities it has been presumed to embody, has been swept up in changing regimes of knowledge, in economic strategies, and in making political and ethical discourses persuasive. In European history over the last few centuries, it has been embedded in diverse axes of differentiation, enlisted and changed not only as sign but also as material in strikingly different ontological projects.
Qualia and Ontology: Language, Semiotics, and Materiality; an Introduction
Authors: Chumley Lily 
Published: February 2017

AbstractQualia—sensory experiences of abstract qualities such as heat, texture, color, sound, stink, hardness, and so on—focus attention on prototypically “material” entities. But how is the ontological category of materiality constituted by conventional qualities, or qualisigns? For instance, how does the sound made by knuckles knocking on a table come to be an exemplary experience of, and a conventional sign for, “materiality”? What ontologies might undermine the seeming naturalness of this category, and to what effect? This issue contributes to the growing literature on semiotic approaches to materiality by arguing that attention to qualia, as sensorial and somatic experiences mediated by cultural qualisigns of value (Munn 1986), offers a useful analytic approach to the dialectics of matter (substrate, affordance) and nonmatter (idea, concept, category). The articles in this issue describe how modes of being and becoming are represented in and organized by discourses on qualia and demonstrate the crucial role of qualia and qualisigns in “ontological politics” (Mol 1999).
Supplementary comparison EURAMET.L-S23 (#1269) high precision roundness measurement by error separation techniques
Authors: Prieto Emilio , Muñoz Rafael , Arce Aelio A , Bergmans Rob , Kotte Gerard , Holmberg Maria , Svendsmark Maria , Toftegaard Jens Bo , Astrua Milena , Pisani Marco , Saraiva Fernanda , Eusebio Liliana , Nouira Hichem , Salgado José 
Published: February 2017

At its meeting in October 2012, the EURAMET Technical Committee for Length, EURAMET TC-L, decided that a key comparison on high precision roundness measurement by multi-step method shall be carried out with CEM acting as the pilot laboratory. The roundness standards to be calibrated were chosen to be a glass hemisphere with a diameter of about 50 mm and a sphere with a diameter of about 30 mm.
A goal of the key comparisons for topics in dimensional metrology is to demonstrate the equivalence of routine calibration services offered by NMIs to clients, as listed in appendix C of the Mutual Recognition Agreement (MRA). To this end, participants in this comparison agreed to use the same apparatus and methods as routinely applied to client artefacts. The comparison was registered in March 2013 as Project EURAMET 1269 and at KCDB as supplementary comparison EURAMET.L-S23.2013.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Renal Sympathetic Denervation: A Viable Option for Treating Resistant Hypertension
Authors: Schlaich Markus P 
Published: February 2017

Abstract
Accumulating evidence from mainly uncontrolled clinical studies with various types of ablation catheters have shown that renal denervation (RDN) can be applied safely and is effective in lowering blood pressure (BP) in patients with treatment-resistant hypertension. Sustained BP lowering has been documented up to 3 years. Furthermore, RDN has been associated with regression of target organ damage, such as left ventricular hypertrophy, arterial stiffness, and others. Several studies indicate potential benefit in other common clinical conditions associated with increased sympathetic tone including chronic kidney disease and heart failure. However, the recently published Symplicity HTN-3 study, the largest and most rigorously designed sham-controlled clinical trial, while confirming the safety of the procedure, failed to demonstrate a BP lowering effect beyond that of a sham procedure in patients with resistant hypertension. Efforts to unravel the reasons for the discrepant results from Symplicity HTN-3 have focused on a range of potential confounders including anatomical and procedural aspects. Indeed, data from post-hoc analyses indicate that sufficient RDN may not have been achieved in the majority of patients in Symplicity HTN-3. Furthermore, recent evidence from human postmortem and functional animal studies revealed new insights into the anatomical distribution of renal nerves and their accessibility by intravascular approaches. Initial results from recent clinical trials integrating these important findings indeed seem to confirm that RDN remains a viable option for the treatment of hypertension. Thorough further investigations will be key to determine the true potential of RDN in clinical conditions characterized by increased sympathetic drive.
Healthy Lifestyle and Blood Pressure Variability in Young Adults
Authors: Maseli Anna , Aeschbacher Stefanie , Schoen Tobias , Fischer Andreas , Jung Manuel , Risch Martin , Risch Lorenz , Conen David 
Published: February 2017

Abstract

BACKGROUND
The aim of this study was to assess the relationships between healthy lifestyle metrics and blood pressure variability (BPV) in young and healthy adults.

METHODS
A population-based sample of 1,999 individuals aged 25–41 years was investigated. A lifestyle-score from 0 (most unhealthy) to 7 (most healthy) was calculated by giving one point for each of the following components: never smoking cigarettes, adhering to a healthy diet, performing moderate or intense physical activity, having a body mass index &lt;25 kg/m2, a total cholesterol &lt;200 mg/dl, a glycated hemoglobin &lt;5.7%, or a conventional BP &lt;120/80 mm Hg. Standardized ambulatory 24-hour BP measurements were obtained in all individuals. BPV was defined as the SD of all individual ambulatory BP recordings. We constructed multivariable linear regression models to assess the relationships between the lifestyle-score and BPV. None of the results were adjusted for multiple testing.

RESULTS
Median age was 37 years and 46.8% were men. With increasing lifestyle-score, systolic and diastolic BPV is decreasing linearly (P for trend &lt;0.0001), even after multivariable adjustment. Per 1-point increase in lifestyle-score, the β-coefficient (95% confidence interval) for systolic and diastolic 24-hour BPV was −0.03 (−0.03; −0.02) and −0.04 (−0.05; −0.03), respectively, both P for trend &lt;0.0001. These relationships were attenuated but remained statistically significant after additional adjustment for mean individual BP.

CONCLUSION
In this study of young and healthy adults, adopting a healthy lifestyle was associated with a lower BPV. These associations were independent of mean BP levels.
AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs
Authors: Jiang Biaobin , Kloster Kyle , Gleich David F , Gribskov Michael 
Published: February 2017

Abstract
Motivation: Diffusion-based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood-based and module-based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function–function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two-layer network model.
Results: We first construct a Bi-relational graph (Birg) model comprised of both protein–protein association and function–function hierarchical networks. We then propose two diffusion-based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two-layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training.
Availability and Implementation: The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank.
Supplementary information: Supplementary data are available at Bioinformatics online.
Succinct colored de Bruijn graphs
Authors: Muggli Martin D , Bowe Alexander , Noyes Noelle R , Morley Paul S , Belk Keith E , Raymond Robert , Gagie Travis , Puglisi Simon J , Boucher Christina 
Published: February 2017

Abstract

Motivation
In 2012, Iqbal et al. introduced the colored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at ‘detecting and genotyping simple and complex genetic variants in an individual or population’. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which requires additional information to be succinctly encoded as well as support for non-standard traversal operations.

Results
Our data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible.

Availability and Implementation
https://github.com/cosmo-team/cosmo/tree/VARI

Supplementary information
Supplementary data are available at Bioinformatics online.
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection
Authors: Moal Iain H , Barradas-Bautista Didier , Jiménez-García Brian , Torchala Mieczyslaw , van der Velde Arjan , Vreven Thom , Weng Zhiping , Bates Paul A , Fernández-Recio Juan 
Published: February 2017

Abstract

Motivation
In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction.

Results
Atomic modeling of protein–protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100.

Availability and Implementation
IRaPPA has been implemented in the SwarmDock server (http://bmm.crick.ac.uk/∼SwarmDock/), pyDock server (http://life.bsc.es/pid/pydockrescoring/) and ZDOCK server (http://zdock.umassmed.edu/), with code available on request.

Supplementary information
Supplementary data are available at Bioinformatics online.