bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nicolaus Clenardus’Institutiones grammaticae Latinae(1538)
Authors: Swiggers Pierre 
Published: May 2018

SummaryIn 1538 the Flemish humanist language scholar Nicolaus Clenardus (1493–1542) published a grammar of Latin in Braga (Portugal), theInstitutiones grammaticae Latinae. The grammar, the fruit of his public teaching in Braga, was the third in a series of grammars written by Clenardus: while active in Louvain (until 1531) he had published grammars of Hebrew (1529) and of Greek (1530). Clenardus’ Latin grammar is basically a didactic grammar, closely linked to his teaching in Portugal, for which he introduced an innovative methodology. It essentially consists of a morphological and syntactic part, followed by a series of mostly syntactic remarks and by a survey of principles of prosody and versification. Clenardus’ exposition is marked by a strong focus on formal markings (lists of nominal and verbal endings), and by the extensive integration of lexical information into the grammatical frame. Clenardus generally refrains from giving definitions of terms and concepts, and theoretical explanations are eschewed in favour of empirical exemplification. TheInstitutiones grammaticae Latinaeprovides its users with a large amount of examples, the majority of which stem from colloquial humanist Latin usage, but there are also various examples taken from classical Latin authors.
“Our Chief Political Editor reads between the lines of the Chancellor’s Budget speech”
Authors: Fetzer Anita 
Published: May 2018

Abstract
This paper examines the multilayeredness of computer-mediated political discourse, focussing on the interdependencies between the contextual constraints and requirements of the medium on the one hand, and contextualisation, indexicality of communicative action and conversational implicature on the other. Particular attention is given to implicit and entextualised references to differences between what is said and what is meant in the communicative act of follow-up, to the importation of context and provision of background information, to their function with respect to the interactional organisation of (non)credibility and argumentative (non)coherence, and to the co-construction of discourse common ground. Within the context of computer-mediated political discourse, these references are used strategically to accommodate the contextual constraints and requirements of a multilayered reception format and their multilayered felicity conditions, and to support speaker-intended interpretation of multilayered discourse on the production side.
Commenting on in-memoriam columns
Authors: Weizman Elda 
Published: May 2018

Abstract
The discussion in this paper proposes to shed light on a hitherto under-researched area: commenting on in-memoriam columns. Borrowing the basic notions of deliberative and epidictic genres from classical rhetoric and accommodating them to a pragmatic study of online interaction between commenters and columnists, readers’ comments are conceived as follow-ups, which necessarily re-contextualize the initiating column. The mixed character of the initiating columns, which combine deliberative and epidictic features, encourages the commenters to choose between different readings of the columns in context, and exercise their discursive power in re-contextualizing the commenting/column interaction. The analysis suggests that in the data discussed here, commenters manifest clear preference for the epidictic. By so doing, they depart from norms of deliberation manifest in habitual political commenting. On a more general level, the analysis supports the initial claim, namely that by choosing between different readings of the initiating columns and following-up on them, commenters have the discursive power to shape and re-shape the interaction through preferred commenting strategies.
A chimeric mutant analysis in yeast cells suggests BiP independent regulation of the mammalian endoplasmic reticulum-stress sensor IRE1α
Authors: Mai Thanh Chi , Munakata Takeo , Tran Duc Minh , Takagi Hiroshi , Kimata Yukio 
Published: May 2018

ABSTRACT
An endoplasmic reticulum (ER)-located transmembrane protein, Ire1, triggers cytoprotective events upon ER stress. Chimeric yeast Ire1 carrying the luminal domain of the mammalian major Ire1 paralogue IRE1α is upregulated in ER-stressed yeast cells, but is poorly associated with the ER-located chaperone BiP even under non-stressed conditions. This observation contradicts the theory that BiP is the master regulator of IRE1α.
Body mass changes during training in elite rugby union: Is a single test of hydration indices reliable?
Authors: Black Katherine Elizabeth , Black Alistair David , Baker Dane , Fairbairn Kirsty 
Published: May 2018

AbstractThere is limited research studying fluid and electrolyte balance in rugby union players, and a paucity of information regarding the test–retest reliability. This study describes the fluid balance of elite rugby union players across multiple squads and the reliability of fluid balance measures between two equivalent training sessions. Sixty‐one elite rugby players completed a single fluid balance testing session during a game simulation training session. A subsample of 21 players completed a second fluid balance testing session during an equivalent training session. Players were weighed in minimal clothing before and after each training session. Each player was provided with their own drinks which were weighed before and after each training session. More players gained body weight (9 (14.8%)) during training than lost greater than 2% of their initial body mass (1 (1.6%)). Pre‐training body mass and rate of fluid loss were significantly associated (r = 0.318, p = .013). There was a significant correlation between rate of fluid loss in sessions 1 (1.74 ± 0.32 L h−1) and 2 (1.10 ± 0.31 L. h−1), (r = 0.470, p = .032). This could be useful for nutritionists working with rugby squads to identify players with high sweat losses.
Endothelial Differentiated Adipose-Derived Stem Cells Improvement of Survival and Neovascularization in Fat Transplantation
Authors: Harris William M , Plastini Michael , Kappy Nikolas , Ortiz Telisha , Chang Shaohua , Brown Spencer , Carpenter Jeffrey P , Zhang Ping 
Published: May 2018

Abstract

Background
Adipose-derived stem cells (ASCs) assisted lipotransfer have been considered to facilitate the survival of fat grafts. However, emerging evidence of insufficient vascularization is another obstacle for fat graft survival in cell-assisted lipotransfer.

Objectives
This study evaluated if endothelial phenotype ASCs with fat lipoaspirate improves survival and neovascularization in fat transplantation

Methods
ASCs were isolated from human periumbilical fat tissue and cultured in endothelial growth medium for 2 weeks. Fat lipoaspirate was mixed with fresh adipose stroma vascular fraction (SVF), endothelial differentiated ASCs (EC/ASCs), and fat lipoaspirate alone. Three fat mixtures were subcutaneously injected into the adult male Sprague–Dawley rat’s dorsum at 3 locations. At 8 weeks after transplantation, the grafted fat lipoaspirates were harvested, and the extracted fat was evaluated using photographic, survival weights measurements and histological examination. Neo-vascularization was quantified by immunofluorescence and real-time RT-PCR.

Results
Grafts from the EC/ASC assisted group had a higher survival rate, morphologic integrity, and most uniform lipid droplets. They also revealed less inflammation and fibrosis with increased number of vessels by histological and immunofluorescence analysis. Quantitative RT-PCR analysis indicated that the expression levels of EC-specific markers of CD31 and vWF were higher in the EC/ASC group compared with in the control and fat with SVF transplants.

Conclusions
These results indicated that co-implantation of fat lipoaspirate with ASCs differentiated toward an endothelial phenotype improves both survival and neovascularization of the transplanted fat lipoaspirate, which might provide benefits and represents a promising strategy for clinical application in autologous fat transplantation.
Enhancing Facelift With Simultaneous Submalar Implant Augmentation
Authors: Delaney Sean , Kridel Russell W H 
Published: May 2018

AbstractBackgroundThe midface is particularly prone to the senescent changes of soft tissue ptosis and volume loss, which in individuals with aging or low adiposity can manifest as submalar hollowing. Facelift alone in those with submalar hollowing inadequately addresses the volume loss and may result in a gaunt appearance postoperatively. Submalar implant augmentation is a powerful tool for permanent midface volume restoration for a more youthful and natural contour, as opposed to soft tissue fillers that diminish over time. When performed together, submalar augmentation and facelift synergistically enhance facial rejuvenation results.ObjectivesDetermine the long-term safety and efficacy of submalar implant augmentation as an adjunct to facelift.MethodsRetrospective review evaluating results and complications in all consecutive patients who had submalar implant augmentation with SMAS-plication facelift in a single surgeon private practice setting from January 1, 1991, to December 31, 2017.ResultsForty-eight patients underwent submalar augmentation with simultaneous facelift with an overall satisfaction rate of 95.7%. Complications included 2.1%transient infraorbital hypoesthesia, 1.1% prolonged swelling, and 1.1% capsular contraction that required a minor adjustment under local anesthesia. No infection, implant migration, or extrusion or facial nerve injury occurred.ConclusionsSubmalar implant augmentation is a safe and effective means of enhancing facelift results through midface volume restoration, subperiosteal release, and improved soft tissue suspension in a more favorable vector. Submalar implant augmentation performed simultaneously with facelift may be an attractive alternative to repeated soft tissue filler or fat injections for patients with submalar hollowing who are interested in facial rejuvenation surgery.
DeepMirTar: a deep-learning approach for predicting human miRNA targets
Authors: Wen Ming , Cong Peisheng , Zhang Zhimin , Lu Hongmei , Li Tonghua 
Published: May 2018

Abstract

Motivation
MicroRNAs (miRNAs) are small non-coding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates.

Results
In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance.

Availability and implementation
DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bochner-type Formulas for the Weyl Tensor on Four-dimensional Einstein Manifolds
Authors: Catino Giovanni , Mastrolia Paolo 
Published: May 2018

Abstract
The very definition of an Einstein metric implies that all its geometry is encoded in the Weyl tensor. With this in mind, in this paper we derive higher-order Bochner-type formulas for the Weyl tensor on a four-dimensional Einstein manifold. In particular, we prove a 2nd Bochner-type formula that, formally, extends to the covariant derivative level the classical one for the Weyl tensor obtained by Derdziński in 1983. As a consequence, we deduce new integral identities involving the Weyl tensor and its derivatives on a compact four-dimensional Einstein manifold and we derive a new rigidity result.
Operational locality in global theories
Authors: Krämer Lea , del Rio Lídia 
Published: May 2018

Within a global physical theory, a notion of locality allows us to find and justify information-processing primitives, like non-signalling between distant agents. Here, we propose exploring the opposite direction: to take agents as the basic building blocks through which we test a physical theory, and recover operational notions of locality from signalling conditions. First, we introduce an operational model for the effective state spaces of individual agents, as well as the range of their actions. We then formulate natural secrecy conditions between agents and identify the aspects of locality relevant for signalling. We discuss the possibility of taking commutation of transformations as a primitive of physical theories, as well as applications to quantum theory and generalized probability frameworks. This ‘it from bit’ approach establishes an operational connection between local actions and local observations, and gives a global interpretation to concepts like discarding a subsystem or composing local functions.This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
What is quantum in quantum randomness?
Authors: Grangier P. , Auffèves A. 
Published: May 2018

It is often said that quantum and classical randomness are of different nature, the former being ontological and the latter epistemological. However, so far the question of ‘What is quantum in quantum randomness?’, i.e. what is the impact of quantization and discreteness on the nature of randomness, remains to be answered. In a first part, we make explicit the differences between quantum and classical randomness within a recently proposed ontology for quantum mechanics based on contextual objectivity. In this view, quantum randomness is the result of contextuality and quantization. We show that this approach strongly impacts the purposes of quantum theory as well as its areas of application. In particular, it challenges current programmes inspired by classical reductionism, aiming at the emergence of the classical world from a large number of quantum systems. In a second part, we analyse quantum physics and thermodynamics as theories of randomness, unveiling their mutual influences. We finally consider new technological applications of quantum randomness that have opened up in the emerging field of quantum thermodynamics.
This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
The small stellated dodecahedron code and friends
Authors: Conrad J. , Chamberland C. , Breuckmann N. P. , Terhal B. M. 
Published: May 2018

We explore a distance-3 homological CSS quantum code, namely the small stellated dodecahedron code, for dense storage of quantum information and we compare its performance with the distance-3 surface code. The data and ancilla qubits of the small stellated dodecahedron code can be located on the edges respectively vertices of a small stellated dodecahedron, making this code suitable for three-dimensional connectivity. This code encodes eight logical qubits into 30 physical qubits (plus 22 ancilla qubits for parity check measurements) in contrast with one logical qubit into nine physical qubits (plus eight ancilla qubits) for the surface code. We develop fault-tolerant parity check circuits and a decoder for this code, allowing us to numerically assess the circuit-based pseudo-threshold.
This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Quantum reference frames and their applications to thermodynamics
Authors: Popescu Sandu , Sainz Ana Belén , Short Anthony J. , Winter Andreas 
Published: May 2018

We construct a quantum reference frame, which can be used to approximately implement arbitrary unitary transformations on a system in the presence of any number of extensive conserved quantities, by absorbing any back action provided by the conservation laws. Thus, the reference frame at the same time acts as a battery for the conserved quantities. Our construction features a physically intuitive, clear and implementation-friendly realization. Indeed, the reference system is composed of the same types of subsystems as the original system and is finite for any desired accuracy. In addition, the interaction with the reference frame can be broken down into two-body terms coupling the system to one of the reference frame subsystems at a time. We apply this construction to quantum thermodynamic set-ups with multiple, possibly non-commuting conserved quantities, which allows for the definition of explicit batteries in such cases.
This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Machine characterization of rat toxin responses identifies disease states, tolerance mechanisms and organ to whole-body communication
Authors: Shimada Kenichi , Mitchison Timothy J. 
Published: May 2018

AbstractBackgroundLiving organisms are constantly exposed to toxic xenobiotics and have therefore evolved protective responses. In mammals, the liver and kidney play central roles in protecting the organism from xenobiotics, and are at high risk of xenobiotic-induced injury. Liver and kidney damage by drugs and industrial toxins have been extensively studied from both classical histopathologic and biochemical perspectives.Methods and FindingsWe introduce a machine learning approach for the analysis of toxicological response. Unsupervised characterization of physiological and histological changes in a large toxicogenomic dataset revealed nine discrete toxin-induced disease states. Transcriptome analysis showed that some of the machine-identified disease states correspond to known pathology, and to known effects of certain toxin classes, but others were novel. Analysis of dynamics revealed transitions between disease states at constant toxin exposure, mostly in the direction of decreased pathology, which implies induction of tolerance. Tolerance correlated with induction of known xenobiotic defense genes and novel decreased ferroptosis sensitivity biomarkers. These data reinforce emerging evidence that ferroptosis drives organ pathology, and suggest that its downreagulation may promote tolerance and recovery. Lastly, mechanism of body weight decrease, a known primary marker for toxicity, was investigated. Combined analysis of food consumption, body weight, and molecular biomarkers indicated that organ disease states promote cachexia by whole-body signaling through Gdf15 and Igf1, suggesting strategies for therapeutic intervention that may be broadly relevant to human disease.ConclusionsApplication of machine learning to systematic data collection of physiology, histopathology, transcriptome reveals multiple disease states, tolerance mechanisms and organ to whole-body communication.
Physiological predictors of reproductive performance in the European Starling (Sturnus vulgaris): II. Multivariate Analysis
Authors: Cohen Alan A. , Paquet Mélissa , Fowler Melinda A. , Legault Véronique , Williams Tony D. 
Published: May 2018

AbstractPhysiological variation is generally thought or supposed to underlie variation in fitness related traits in wild animals, including reproductive effort, reproductive success, and survival. However, physiological markers of individual quality have proven elusive. In this paper and its companion, we use data on 14 physiological parameters measured in 152 observations of 93 individual European starlings (Sturnus vulgaris) over 2 years in an attempt to understand how physiological variation relates to variation in current breeding productivity, future fecundity, and survival. The companion paper, focusing on univariate analysis, showed that individual physiological parameters have little relationship with these performance measures. Here, we used more sophisticated statistical approaches in an attempt to extract a multivariate signal from the biomarkers – physiological dysregulation as calculated via statistical distance, and a number of principal components analysis approaches. Broadly speaking, there was a surprising lack of association between physiology and performance: while some physiological summary measures were associated with some performance measures, the associations were not particularly strong or robust given the large number of statistical tests conducted. This implies either that there are relatively few links between physiology and performance, or, more likely, that the complexity of these relationships exceeds our ability to measure and model it, even using state-of-the-art statistical approaches. This is likely particularly true because our population was quite heterogeneous; we nonetheless urge caution regarding the over-interpretation of isolated significant findings in the literature.
EROS is required for phagocyte NADPH oxidase function in humans and its deficiency causes Chronic Granulomatous Disease
Authors: Thomas David C. , Charbonnier Louis-Marie , Schejtman Andrea , Aldhekri Hasan , Coomber Eve , Dufficy Elizabeth R. , Beenken Anne E. , Lee James C. , Clare Simon , Speak Annaliese O. , Thrasher Adrian J. , Santilli Giorgia , Al-Mousa Hamoud , Alkuraya Fowzan S. , Chatila Talal A. , Smith Kenneth G.C. 
Published: May 2018

AbstractThe phagocyte respiratory burst is mediated by the phagocyte NADPH oxidase, a multi-protein subunit complex that facilitates production of reactive oxygen species and which is essential for host defence. Monogenic deficiency of individual subunits leads to chronic granulomatous disease (CGD), which is characterized by an inability to make reactive oxygen species, leading to severe opportunistic infections and auto-inflammation. However, not all cases of CGD are due to mutations in previously identified subunits. We recently showed that Eros, a novel and highly conserved ER-resident transmembrane protein, is essential for the phagocyte respiratory burst in mice because it is required for expression of gp91phox-p22phox heterodimer, which are the membrane bound components of the phagocyte NADPH oxidase. We now show that the function of EROS is conserved in human cells and describe a case of CGD secondary to a homozygous EROS mutation that abolishes EROS protein expression. This work demonstrates the fundamental importance of EROS in human immunity and describes a novel cause of CGD.Clinical ImplicationsChronic granulomatous disease is caused by an inability to make reactive oxygen species via the phagocyte NADPH oxidase. Mutations in C17ORF62/EROS, which controls gp91phox- p22phox abundance, are a novel cause of chronic granulomatous disease.Key MessagesThe murine gene, Eros, is known to regulate abundance of gp91phox-p22phox heterodimer and Eros deficient mice are susceptible to infectionWe show that the function of EROS is conserved in human cells and that a homozygous mutation in EROS causes chronic granulomatous disease
Identifying Plasmids in Bacterial Genome Assemblies
Authors: Hall Barry G. 
Published: May 2018

AbstractDespite their importance to bacterial pathogenesis, plasmids are rarely identified in incomplete genome sequences. The free FindPlasmids (FP) package for Windows, Mac OS X, and Linux facilitates identification of plasmids in incomplete genome sequences. FP found plasmids in 98.8% of complete genomes in which they were present, correctly identifying plasmids ranging in number from 1 to 10 plasmids. In a sample of 50 E. coli genome assemblies it has identified from zero to three plasmids ranging in size from 1,549 to 133,843 bp and present in 42% of the assemblies examined.