bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
Authors: Stat Michael , Huggett Megan J. , Bernasconi Rachele , DiBattista Joseph D. , Berry Tina E. , Newman Stephen J. , Harvey Euan S. , Bunce Michael 
Published: September 2017

AbstractEffective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using ‘tree of life’ (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing ‘universal’ PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.
Observation of enhanced superconductivity in the vicinity of Ar-induced nano-cavities in Pb(111)
Authors: Song Sang Yong , Seo Jungpil 
Published: September 2017

AbstractLocal variations of superconductivity have been studied using scanning tunneling microscopy around nano-cavities formed by Ar ions embedded in Pb(111). Various factors including the density of states at Fermi energy, electron–phonon couplings, and quantum well states, which are known to affect superconductivity, have been examined. We show that the superconductivity is enhanced near the nano-cavities and propose that quantum effects such as quantum confinement, proximity effect and multi-gap effect are possibly involved in determining the superconducting gap of this system. These results have important implications for the characterization and understanding of superconductivity at a nanometer scale.
Morphologically normalized left ventricular motion indicators from MRI feature tracking characterize myocardial infarction
Authors: Piras Paolo , Teresi Luciano , Puddu Paolo Emilio , Torromeo Concetta , Young Alistair A. , Suinesiaputra Avan , Medrano-Gracia Pau 
Published: September 2017

AbstractWe characterized motion attributes arising from LV spatio-temporal analysis of motion distributions in myocardial infarction. Time-varying 3D finite element shape models were obtained in 300 Controls and 300 patients with myocardial infarction. Inter-individual left ventricular shape differences were eliminated using parallel transport to the grand mean of all cases. The first three principal component (PC) scores were used to characterize trajectory attributes. Scores were tested with ANOVA/MANOVA using patient disease status (Infarcts vs. Controls) as a factor. Infarcted patients had significantly different magnitude, orientation and shape of left ventricular trajectories in comparison to Controls. Significant differences were found for the angle between PC scores 1 and 2 in the endocardium, and PC scores 1 and 3 in the epicardium. The largest differences were found in the magnitude of endocardial motion. Endocardial PC scores in shape space showed the highest classification power using support vector machine, with higher total accuracy in comparison to previous methods. Shape space performed better than size-and-shape space for both epicardial and endocardial features. In conclusion, LV spatio-temporal motion attributes accurately characterize the presence of infarction. This approach is easily generalizable to different pathologies, enabling more precise study of the pathophysiological consequences of a wide spectrum of cardiac diseases.
Characterization of the antifungal functions of a WGA-Fc (IgG2a) fusion protein binding to cell wall chitin oligomers
Authors: Liedke Susie Coutinho , Miranda Daniel Zamith , Gomes Kamilla Xavier , Gonçalves Jorge Luis S. , Frases Susana , Nosanchuk Joshua D. , Rodrigues Marcio L. , Nimrichter Leonardo , Peralta José Mauro , Guimarães Allan J. 
Published: September 2017

AbstractThe majority of therapeutic strategies for mycosis require the protracted administration of antifungals, which can result in significant toxicities and have unacceptable failure rates. Hence, there is an urgent need for the development of improved therapeutic approaches, and monoclonal antibody-based drugs are potentially a powerful alternative to standard antifungals. To develop a broad antibody-like reagent against mycosis, wheat germ agglutinin (WGA) was linked to the effector Fc region of murine IgG2a. The resultant WGA-Fc displayed high affinity to purified chitin and bound efficiently to fungal cell walls, co-localizing with chitin, in patterns ranging from circular (Histoplasma capsulatum) to punctate (Cryptococcus neoformans) to labeling at the bud sites (Candida albicans and Saccharomyces cerevisiae). WGA-Fc directly inhibited fungal growth in standard cultures. WGA-Fc opsonization increased fungal phagocytosis, as well augmented the antifungal functions by macrophages. Prophylactic administration of WGA-Fc fully protected mice against H. capsulatum, correlating with a reduction in lung, spleen and liver fungal burdens. Administration of WGA-Fc also dramatically diminished pulmonary inflammation. Hence, the opsonic activity of WGA-Fc effectively modulates fungal cell recognition and promotes the elimination of fungal pathogens. Therefore, we propose WGA-Fc as a potential “pan-fungal” therapeutic that should be further developed for use against invasive mycoses.
Cortical afferents onto the nucleus Reticularis thalami promote plasticity of low-threshold excitability through GluN2C-NMDARs
Authors: Fernandez Laura M. J. , Pellegrini Chiara , Vantomme Gil , Béard Elidie , Lüthi Anita , Astori Simone 
Published: September 2017

AbstractThalamus and cortex represent a highly integrated processing unit that elaborates sensory representations. Interposed between cortex and thalamus, the nucleus Reticularis thalami (nRt) receives strong cortical glutamatergic input and mediates top-down inhibitory feedback to thalamus. Despite growing appreciation that the nRt is integral for thalamocortical functions from sleep to attentional wakefulness, we still face considerable gaps in the synaptic bases for cortico-nRt communication and plastic regulation. Here, we examined modulation of nRt excitability by cortical synaptic drive in Ntsr1-Cre x ChR2tg/+ mice expressing Channelrhodopsin2 in layer 6 corticothalamic cells. We found that cortico-nRt synapses express a major portion of NMDA receptors containing the GluN2C subunit (GluN2C-NMDARs). Upon repetitive photoactivation (10 Hz trains), GluN2C-NMDARs induced a long-term increase in nRt excitability involving a potentiated recruitment of T-type Ca2+ channels. In anaesthetized mice, analogous stimulation of cortical afferents onto nRt produced long-lasting changes in cortical local field potentials (LFPs), with delta oscillations being augmented at the expense of slow oscillations. This shift in LFP spectral composition was sensitive to NMDAR blockade in the nRt. Our data reveal a novel mechanism involving plastic modification of synaptically recruited T-type Ca2+ channels and nRt bursting and indicate a critical role for GluN2C-NMDARs in thalamocortical rhythmogenesis.
Aligned hierarchical Ag/ZnO nano-heterostructure arrays via electrohydrodynamic nanowire template for enhanced gas-sensing properties
Authors: Yin Zhouping , Wang Xiaomei , Sun Fazhe , Tong Xiaohu , Zhu Chen , Lv Qiying , Ye Dong , Wang Shuai , Luo Wei , Huang YongAn 
Published: September 2017

AbstractGas sensing performance can be improved significantly by the increase in both the effective gas exposure area and the surface reactivitiy of ZnO nanorods. Here, we propose aligned hierarchical Ag/ZnO nano-heterostructure arrays (h-Ag/ZnO-NAs) via electrohydrodynamic nanowire template, together with a subsequent hydrothermal synthesis and photoreduction reaction. The h-Ag/ZnO-NAs scatter at top for higher specific surface areas with the air, simultaneously contact at root for the electrical conduction. Besides, the ZnO nanorods are uniformly coated with dispersed Ag nanoparticles, resulting in a tremendous enhancement of the surface reactivity. Compared with pure ZnO, such h-Ag/ZnO-NAs exhibit lower electrical resistance and faster responses. Moreover, they demonstrate enhanced NO2 gas sensing properties. Self-assembly via electrohydrodynamic nanowire template paves a new way for the preparation of high performance gas sensors.
Neurons and a sensory organ in the pedipalps of male spiders reveal that it is not a numb structure
Authors: Sentenská Lenka , Müller Carsten H.G. , Pekár Stano , Uhl Gabriele 
Published: September 2017

AbstractThe primary function of male copulatory organs is depositing spermatozoa directly into the female reproductive tract. Typical male copulatory organs are sensorily active. This is in contrast to the copulatory organs of male spiders (i.e. palpal bulbi), which have been assumed to lack nerves and muscles until recently. Neurons have been found within the bulbus of the spider Hickmania troglodytes, a taxon basal to all Neocribellata. We provide the first evidence for neurons and an internalized multi-sensillar sensory organ in the bulbus of an entelegyne spider (Philodromus cespitum). The sensory organ likely provides mechanical or chemical feedback from the intromitting structure, the embolus. We found further neurons associated with two glands within the bulbus, one of which is likely responsible for sperm extrusion during mating. These findings provide a new framework for studies on reproductive behaviour and sexual selection in spiders.
Predictors of Surgical Outcome in Isolated Tricuspid Valve Endocarditis: Single Center Experience of 60 Patients
Authors: Singer Mahmoud , Mohsen Tarek , Roushdy Amr , Akl Alsayed , Mashaal Marwa , Alkady Hesham 
Published: September 2017

Background Tricuspid valve (TV) endocarditis may be associated with serious complications, and 25% of patients require surgical intervention. However, indications and outcomes of surgery are not clearly identified. In this study, 60 patients are retrospectively reviewed to determine preoperative predictors of surgical outcome.
Patients and Methods Sixty patients with isolated TV endocarditis who underwent surgery in the period between January 2012 and December 2016 are reviewed retrospectively from the medical records of Cairo University Hospitals. Forty-two (70%) patients were males, and 18 (30%) were females with a mean age of 29.3 ± 10.6 years. Eleven patients had an underlying cardiac lesion, and 27 patients were intravenous (IV)-drug addicts.
Results TV repair could be done in nine (15%) patients, and the rest received TV replacement with biological valves. Twenty-four (40%) patients experienced postoperative complications. On multivariate analysis, a vegetation size >2.2 cm was a significant preoperative predictor for embolic complications and prolonged ventilation. In-hospital mortality occurred in 10 (16.67%) patients. Significant preoperative predictors of mortality were pulmonary embolization, congestive heart failure (HF), and the presence of pericardial effusion. During a mean follow-up period of 25 ± 12.6 months with echocardiography, two (4%) IV drug user patients developed recurrence of infection and needed reoperation.
Conclusion Surgery for tricuspid valve endocarditis (TVE) can be performed with good early and mid-term results. A large size of vegetations >2.2 cm is a significant risk factor for embolic complications. Preoperative predictors of in-hospital mortality according to our study are pulmonary embolization, congestive heart failure, and pericardial effusion.
Transfusionstrigger in der orthopädischen Endoprothetik
Authors: Holten Dirk , Zaar Peter , Kessler Stefan 
Published: September 2017

Zusammenfassung
Studienziel Die Etablierung einer Transfusionstriggercheckliste ist eine kostengünstige und einfach zu implementierende fremdblutsparende Maßnahme aus dem Patient-Blood-Management. Ziel dieser Studie war es, den Effekt dieser Einzelmaßnahme auf die Transfusionsraten und die klinischen Verläufe in der orthopädischen Endoprothetik zu untersuchen.
Methode 893 Patienten zur elektiven Hüft- oder Knie-TEP-Implantation wurden in 2 6-Monats-Zeiträumen untersucht: 481 Patienten vor und 412 Patienten nach Implementierung der Transfusionstriggercheckliste. Zusätzlich zu demografischen Daten wurden Hämoglobinkonzentrationen präoperativ, am 5. postoperativen Tag und vor jeder Transfusion erhoben, um den perioperativen Blutverlust und die Transfusionsschwelle (Hämoglobinkonzentration vor Transfusion) in beiden Gruppen zu errechnen und miteinander zu vergleichen. Die Transfusionsraten und die Krankenhausverweildauer wurden ausgewertet.
Ergebnisse Die Transfusionsraten sanken von 12,3% (HTEP) und 12,3% (KTEP) auf 4,7% (HTEP) und 3,2% (KTEP) nach Implementierung der Transfusionstriggercheckliste. Die durchschnittliche hämoglobinbasierte Transfusionsschwelle sank von 8,17 auf 7,13 g/dl. Die Krankenhausverweildauer sank von 10,20 (HTEP) und 10,59 (KTEP) Tagen auf 9,48 (HTEP) und 9,81 (KTEP) Tage.
Schlussfolgerung Wir haben in dieser Untersuchung gezeigt, dass die Transfusionstriggerkontrolle – in unserem Fall in Form einer Checkliste – zu den effektivsten fremdblutsparenden Maßnahmen im Patient-Blood-Management zählt. Im Bereich der orthopädischen Endoprothetik unserer Einrichtung ließen sich hierdurch die Transfusionsrate und der Transfusionsindex um über 65% senken. Die Krankenhausverweildauer als Marker eines komplizierten Verlaufs und als betriebswirtschaftlich relevante Größe verlängerte sich durch den Verzicht auf einen Großteil der Transfusionen nicht.
What happens to the basic level in language?
Authors: Győri Gábor 
Published: September 2017

AbstractIt is a common assumption that basic level categories are cognitive units that share perceptual and linguistic characteristics at the same time. They are taken to be perceptual and functional gestalts designated by words that have a special status with regard to lexical development in children and frequency of occurrence and usefulness in everyday communication. Despite this connectedness of the two aspects of the basic level they do not go hand in hand. The perceptual side of basic level categorization is primary to language and exists independently of it. Basic level categories emerge naturally in the human perceptual-cognitive system as a result of our biological make-up in order to facilitate a proper functioning and orientation in our environment. The linguistic side relies on perception but is at the same time determined by several other factors. Basic level designations do not directly represent perceptual information because they contain additional conceptual knowledge reflecting cultural conceptualizations. This dissociation between the two sides can be seen on the one hand in the inconsistencies between perceptual qualities of entities and the way in which these entities are grouped together in linguistic basic level categories. On the other hand it is revealed through crosslinguistic discrepancies in category boundaries as delineated by words that are considered basic level terms and seemingly correspond in their semantics. An explanation of these phenomena requires that we do not handle the basic level as one phenomenon in which the perceptual and linguistic aspects merge but keep the two sides of the basic level apart while paying attention to their specific connections and influences on each other.
A crosslinguistic study into culturally motivated resemblances and variations in transferred epithet metaphors in Chinese and English
Authors: Sun Yi , Yang Yishu , Kirner-Ludwig Monika 
Published: September 2017

Abstract
It has been postulated that a cognitive approach may lend itself well to the study of transferred epithets, as this traditional rhetoric device possesses all the essences of metaphor from the perspective of Cognitive Linguistics. Transferred epithet metaphors are gradually cognitively cultivated upon human beings’ repetitive and recursive experiences of the real world and it has been well established that they cannot be separated from culture’s limitations or reformulation. The coupling between experientialism and culture in transferred epithet metaphors necessitates the establishment of a double paradigm to comprehensively and profoundly delve into the twofold restraints.
Judgments under emotioncy’s influence
Authors: Pishghadam Reza , Abbasnejad Hannaneh 
Published: September 2017

Abstract
Following a number of studies on discovering the controlling dormant forces in linguistic biases, this study attempts to introduce the concept of emotioncy as a driving force in explicating the causes of prejudice manifested through biases in speech. To this end, two scales for measuring individuals’ bias and their emotioncy levels were devised and validated through Rasch measurement. A total number of 341 participants were asked to take the scales. Afterward, structural equation modeling (SEM) was employed to investigate the probable relationships between sub-constructs of the scales. The results indicated that as individuals’ emotioncy level increases, the bias level decreases. In other words, involvement slides people toward being less judgmental and thus less biased in language, while exvolvement leads people toward using more abstract words, and therefore more biased language. In the end, implications of the findings were discussed in the realm of judgment and decision making.
Sipros Ensemble improves database searching and filtering for complex metaproteomics
Authors: Guo Xuan , Li Zhou , Yao Qiuming , Mueller Ryan S , Eng Jimmy K , Tabb David L , Hervey William Judson , Pan Chongle 
Published: September 2017

Abstract

Motivation
Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics.

Results
Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers.

Availability and implementation
Freely available under the GNU GPL license at http://sipros.omicsbio.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bending the laws of optics with metamaterials: an interview with John Pendry
Authors: Ball Philip 
Published: September 2017

Abstract
Metamaterials show us that nature's laws might not always be as fixed as they seem to be. One of the laws of optics, for example, states that a light ray passing from one transparent medium to another—air to water or glass, say—is bent at the interface by an amount that depends on the so-called refractive indices of the two media. And all transparent materials have a refractive index greater than that of a vacuum (or, roughly speaking, of air), which is set equal to 1. Or do they? In the 1960s, the Russian physicist Victor Veselago explained what would be needed, in theory, for a material to have a refractive index that is not only less than 1 but in fact negative, so that it bends light the ‘wrong way’.
Veselago's idea was all but forgotten until it was unearthed in the late 1990s by electrical engineer David Smith. He was wondering if it might be possible to make a ‘scaled-up’ version of such a material, built from ‘artificial atoms’ and later called a metamaterial, which could show this effect at longer wavelengths than those of light, in the microwave part of the spectrum. By happy coincidence, physicist Sir John Pendry of Imperial College London, UK, had already come up with a prescription for making a similar structure from loops of wire. Smith and his colleagues created a negative-refractive-index metamaterial in 1999—and it was only in the course of publishing this work that they rediscovered Veselago's prescient paper from 1967. Smith later moved to Duke University in North Carolina and teamed up with Pendry to develop a general theory—transformation optics—that described how such substances can manipulate the paths of light in new and unexpected ways. In 2006 they designed and built a metamaterial device with a far more remarkable property: it could bend light (rather, microwave) rays around an object to render it invisible.
With that dramatic innovation, the field of metamaterials was well and truly launched. NSR spoke with John Pendry about the history and prospects of this intersection of physics, materials science and engineering.
Disparities in Health Care Utilization of Adults With Traumatic Brain Injuries Are Related to Insurance, Race, and Ethnicity: A Systematic Review
Authors: Gao Shiyao , Kumar Raj G. , Wisniewski Stephen R. , Fabio Anthony 
Published: September 2017

Objective:
To characterize racial/ethnic and insurance disparities in the utilization of healthcare services among US adults with traumatic brain injury (TBI).

Methods:
The PubMed database was used to search for articles that directly examined the association between race/ethnicity and insurance disparities and healthcare utilization among patients with TBI. Eleven articles that met the criteria and were published between June 2011 and June 2016 were finally included in the review.

Results:
Lack of insurance was significantly associated with decreased use of inhospital and posthospital healthcare services among patients with TBI. However, mixed results were reported for the associations between insurance types and healthcare utilization. The majority of studies reported that racial/ethnic minorities were less likely to use inhospital and posthospital healthcare services, while some studies did not indicate any significant relation between race/ethnicity and healthcare utilization among patients with TBI.

Conclusions:
This review provides evidence of a relation between insurance status and healthcare utilization among US adults with TBI. Insurance status may also account for some portion of the relation between race/ethnicity and healthcare utilization.
Testicular Torsion Pain Honeymoons
Authors: Mellick Larry Bruce , Sinex James 
Published: September 2017

Abstract
A subset of testicular torsion patients report resolution of their initial severe pain that is followed by variable periods of hours to days of reduced or absent pain. Other patients report only mild pain that is described as gradual in onset. Because of delayed initial presentations or less than timely returns for secondary evaluation, these pain honeymoons may be partially responsible for poor clinical outcomes of the torsed spermatic cords and ischemic testicles.