bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metaphor variation of spatial conceptualizations in Irish English
Authors: Lucek Stephen 
Published: May 2017

Abstract
The current paper offers a novel methodological approach to gathering rich spatial data from Irish English speakers, showing variation in the cognition of physical and conceptual space. A mixed method study was conducted to gather conceptual and sociolinguistic data. This includes the first part of the data gathering: a structured interview, focusing on geographic aspects of the town and two wayfinding exercises. I then describe the second part of the study: twenty cloze procedure questions relating to a written example, followed by questions relating to seventeen hand-drawn images. I take as a baseline the instruments used by, inter alia, Levinson and Wilkins (2006a) and apply them to a within-culture study. I conclude this paper by discussing replicability and future studies. While Conceptual Metaphor Theory (CMT) offers researchers a model to connect physical and conceptual elements of space, we have not seen a large-scale study of how CMT affects the language of space in varieties of English.
‘Idioms in the making’ and variation in conceptual metaphor
Authors: Callies Marcus 
Published: May 2017

AbstractThis paper discusses the culture-specificity of figurative language use in varieties of English. Idioms as a special type of figurative language are understood as being conceptually motivated by underlying metaphorical mappings, also reflecting the nexus of language and culture. On the basis of data from large-scale web corpora of varieties of English, the paper examines the lexico-grammatical and conceptual variability of selected idiomatic expressions related to the source domainsfoodandeating. The results show patterns of lexico-grammatical variation and innovation of idioms in (West) African Englishes and confirm previous research that points towards the high salience and frequency of food and related concepts of eating as source domains in conceptual metaphorical mappings in West African cultures. The paper concludes thatfoodandeatingseem fruitful points of departure for further studies on culture- and variety-specific “linguistic markers” across varieties of English.
Emotion metaphors in new Englishes
Authors: Güldenring Barbara Ann 
Published: May 2017

AbstractResearch into emotion concepts has become an established part of the cognitive-linguistic research agenda and has often revolved around the competing notions of universality (from the perspective of embodied cognition) and (cross- and within-cultural) variation (seeKövecses 2005). At the same time, a relatively recent approach to socio-variational aspects of language in the form of Cognitive Sociolinguistics has created an ideal platform for the study of variation in institutionalized second-language varieties of English, often referred to as new Englishes (seeKristiansen & Dirven 2008;Wolf & Polzenhagen 2009). This paper aims at bringing together these two research strands in a study devoted to variation on the level of metaphor in new Englishes, specifically involved in the conceptualization of emotion. While metaphor is theoretically understood within the framework of Conceptual Metaphor Theory (Lakoff & Johnson 1980), this study will make use of a corpus-based method of metaphor retrieval and identification informed by Stefanowitsch’s (2004,2006) Metaphorical Pattern Analysis (MPA) andSteen et al.’s (2010)method for linguistic metaphor identification (MIPVU).angermetaphors will be examined for four second-language varieties of English, namely those spoken in Nigeria, Kenya, India, and Singapore, which are represented in theGlobal Web-based Englishcorpus (GloWbE;Davies 2013).With the assumption that metaphor variation emerges in a variety’s preference for certain source domains in emotion-based mappings vis-à-vis other varieties, the main questions at the core of the analysis are: (1) Which source domains are employed in a respective variety to conceptualizeanger? and (2) To what extent are the source domain preferences of new Englishes similar to a norm-providing variety, namely British English? Although initial results reveal much similarity, some differences in the data are highlighted at a deeper level of analysis. Thus, a discussion of the results provides a basis for inter-variety comparison ofangermetaphors and, thus, contribute to the universality / variation debate.
Cultural conceptualizations of gender and homosexuality in BrE, IndE, and NigE
Authors: Finzel Anna , Wolf Hans-Georg 
Published: May 2017

AbstractWith the spread of English in many parts of the world, numerous local varieties have emerged, shaped by the sociocultural contexts in which they are embedded. Hence, although English is a unifying element, these varieties express different conceptualizations that are deeply rooted in culture. For the most part, these conceptualizations come in the form of conceptual metaphors, which not only influence our perception of the world (Lakoff & Johnson 1980), but also reveal cultural specifics of a particular society.One of the latest approaches in the field of conceptual metaphor research suggests that conceptual metaphors are actually multimodal, i.e., that they are expressed not only in language, but also, e.g., in gestures, facial expressions, sounds or images (Forceville 2009). Films are an ideal source of data for such multimodal metaphors.In the form of a pilot study, this paper applies this novel approach to metaphor to the field of World Englishes. While adding to the range of research that has already used the methodological toolbox of Cognitive Linguistics or its cognate discipline Cultural Linguistics in the investigation of the cultural dimension of varieties of English (e.g.,Kövecses 1995;Liu 2002;Malcolm & Rochecouste 2000;Sharifian 2006;Wolf 2001;Wolf & Polzenhagen 2009), we provide a new exploratory angle to that investigation by using cinematic material for the analysis. Specifically, this study focuses on conceptualizations pertaining to the target domainswomanandhomosexuality. The data we have selected are from Great Britain, India and Nigeria, because these countries have important film industries, and British English, Indian English and Nigerian English constitute culturally distinct varieties.
Physiological functions of pyruvate:NADP+ oxidoreductase and 2-oxoglutarate decarboxylase in Euglena gracilis under aerobic and anaerobic conditions
Authors: Nakazawa Masami , Hayashi Ryuta , Takenaka Shigeo , Inui Hiroshi , Ishikawa Takahiro , Ueda Mitsuhiro , Sakamoto Tatsuji , Nakano Yoshihisa , Miyatake Kazutaka 
Published: May 2017

Abstract
In Euglena gracilis, pyruvate:NADP+ oxidoreductase, in addition to the pyruvate dehydrogenase complex, functions for the oxidative decarboxylation of pyruvate in the mitochondria. Furthermore, the 2-oxoglutarate dehydrogenase complex is absent, and instead 2-oxoglutarate decarboxylase is found in the mitochondria. To elucidate the central carbon and energy metabolisms in Euglena under aerobic and anaerobic conditions, physiological significances of these enzymes involved in 2-oxoacid metabolism were examined by gene silencing experiments. The pyruvate dehydrogenase complex was indispensable for aerobic cell growth in a glucose medium, although its activity was less than 1% of that of pyruvate:NADP+ oxidoreductase. In contrast, pyruvate:NADP+ oxidoreductase was only involved in the anaerobic energy metabolism (wax ester fermentation). Aerobic cell growth was almost completely suppressed when the 2-oxoglutarate decarboxylase gene was silenced, suggesting that the tricarboxylic acid cycle is modified in Euglena and 2-oxoglutarate decarboxylase takes the place of the 2-oxoglutarate dehydrogenase complex in the aerobic respiratory metabolism.
Production of d-lactate using a pyruvate-producing Escherichia coli strain
Authors: Akita Hironaga , Nakashima Nobutaka , Hoshino Tamotsu 
Published: May 2017

Abstract
To generate an organism capable of producing d-lactate, NAD+-dependent d-lactate dehydrogenase was expressed in our pyruvate-producing strain, Escherichia coli strain LAFCPCPt-accBC-aceE. After determining the optimal culture conditions for d-lactate production, 18.4 mM d-lactate was produced from biomass-based medium without supplemental mineral or nitrogen sources. Our results show that d-lactate can be produced in simple batch fermentation processes.
OMSim: a simulator for optical map data
Authors: Miclotte Giles , Plaisance Stéphane , Rombauts Stephane , Van de Peer Yves , Audenaert Pieter , Fostier Jan 
Published: May 2017

Abstract

Motivation
The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire genome. In turn, these optical maps can be used to validate or improve de novo genome assembly projects or to detect large-scale structural variation in genomes. Simulated optical map data can assist in the development and benchmarking of tools that operate on those data, such as alignment and assembly software. Additionally, it can help to optimize the experimental setup for a genome of interest. Such a simulator is currently not available.

Results
We have developed a simulator, OMSim, that produces synthetic optical map data that mimics real Bionano Genomics data. These simulated data have been tested for compatibility with the Bionano Genomics Irys software system and the Irys-scaffolding scripts. OMSim is capable of handling very large genomes (over 30 Gbp) with high throughput and low memory requirements.

Availability and implementation
The Python simulation tool and a cross-platform graphical user interface are available as open source software under the GNU GPL v2 license (http://www.bioinformatics.intec.ugent.be/omsim).

Supplementary information
Supplementary data are available at Bioinformatics online.
A deep learning framework for improving long-range residue–residue contact prediction using a hierarchical strategy
Authors: Xiong Dapeng , Zeng Jianyang , Gong Haipeng 
Published: May 2017

Abstract

Motivation
Residue–residue contacts are of great value for protein structure prediction, since contact information, especially from those long-range residue pairs, can significantly reduce the complexity of conformational sampling for protein structure prediction in practice. Despite progresses in the past decade on protein targets with abundant homologous sequences, accurate contact prediction for proteins with limited sequence information is still far from satisfaction. Methodologies for these hard targets still need further improvement.

Results
We presented a computational program DeepConPred, which includes a pipeline of two novel deep-learning-based methods (DeepCCon and DeepRCon) as well as a contact refinement step, to improve the prediction of long-range residue contacts from primary sequences. When compared with previous prediction approaches, our framework employed an effective scheme to identify optimal and important features for contact prediction, and was only trained with coevolutionary information derived from a limited number of homologous sequences to ensure robustness and usefulness for hard targets. Independent tests showed that 59.33%/49.97%, 64.39%/54.01% and 70.00%/59.81% of the top L/5, top L/10 and top 5 predictions were correct for CASP10/CASP11 proteins, respectively. In general, our algorithm ranked as one of the best methods for CASP targets.

Availability and implementation
All source data and codes are available at http://166.111.152.91/Downloads.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
PopFly: the Drosophila population genomics browser
Authors: Hervas Sergi , Sanz Esteve , Casillas Sònia , Pool John E , Barbadilla Antonio 
Published: May 2017

Abstract

Summary
The recent compilation of over 1100 worldwide wild-derived Drosophila melanogaster genome sequences reassembled using a standardized pipeline provides a unique resource for population genomic studies (Drosophila Genome Nexus, DGN). A visual display of the estimated metrics describing genome-wide variation and selection patterns would allow gaining a global view and understanding of the evolutionary forces shaping genome variation.

Availability and implementation
Here, we present PopFly, a population genomics-oriented genome browser, based on JBrowse software, that contains a complete inventory of population genomic parameters estimated from DGN data. This browser is designed for the automatic analysis and display of genetic variation data within and between populations along the D. melanogaster genome. PopFly allows the visualization and retrieval of functional annotations, estimates of nucleotide diversity metrics, linkage disequilibrium statistics, recombination rates, a battery of neutrality tests, and population differentiation parameters at different window sizes through the euchromatic chromosomes. PopFly is open and freely available at site http://popfly.uab.cat.
An analysis of sailfish daily activity in the Eastern Pacific Ocean using satellite tagging and recreational fisheries data
Authors: Pohlot Bruce G , Ehrhardt Nelson 
Published: May 2017

AbstractAnalysing hourly behavioural patterns of Pacific sailfish, Istiophorus platypterus, provide an ecological perspective relative to their exploitation. In the Pacific off Central America, sailfish sustain important recreational fisheries while impacted as bycatch in commercial tuna fisheries. Given their susceptibility and potential for overexploitation, it is important to define their behavioural activity to better regulate exploitation patterns. In this study, we discuss concepts of sailfish vision related to light availability and its role on successful foraging patterns. For this purpose, activity patterns were analysed using data collected by satellite tags equipped with accelerometers and, separately, recreational fishery statistics from the region. Data are incorporated with physical and ecological information to offer a means of analysing hourly habitat use. The results reveal a positive photokinetic response to sunlight in both sailfish acceleration activity and recreational fishery statistics. Tagged sailfish also showed this activity increase as a response to full moon light. Such information is further integrated with knowledge of intra-species relationships and other key species within the pelagic fish community. Findings on daily behaviour allow the drawing of some generic conceptualizations that aid understanding of sailfish community dynamics in the region.
The Certainty, Modality, and Grounding of Newton’s Laws
Authors: Biener Zvi , Schliesser Eric 
Published: May 2017

AbstractNewton began his Principia with three Axiomata sive Leges Motus. We offer an interpretation of Newton’s dual label and investigate two tensions inherent in his account of laws. The first arises from the juxtaposition of Newton’s confidence in the certainty of his laws and his commitment to their variability and contingency. The second arises because Newton ascribes fundamental status both to the laws and to the bodies and forces they govern. We argue the first is resolvable, but the second is not. However, the second tension shows that Newton conceives laws as formal causes of bodies and forces. This neo-Aristotelian conception goes missing in Kantian accounts of laws, as well as accounts that stress laws’ grounding in powers and capacities.
Prognostic Factors for Satisfaction After Decompression Surgery for Lumbar Spinal Stenosis
Authors: Paulsen Rune Tendal , Bouknaitir Jamal Bech , Fruensgaard Søren , Carreon Leah , Andersen Mikkel 
Published: May 2017

Abstract

BACKGROUND
Surgical treatment for lumbar spinal stenosis is associated with both short- and long-term benefits with improvements in patient function and pain. Even though most patients are satisfied postoperatively, some studies report that up to one-third of patients are dissatisfied.

OBJECTIVE
To present clinical outcome data and identify prognostic factors related to patient satisfaction 1 yr after posterior decompression surgery for lumbar spinal stenosis.

METHODS
This multicenter register study included 2562 patients. Patients were treated with various types of posterior decompression. Patients with previous spine surgery or concomitant fusion were excluded. Patient satisfaction was analyzed for associations with age, sex, body mass index, smoking status, duration of pain, number of decompressed vertebral levels, comorbidities, and patient-reported outcome measures, which were used to quantify the effect of the surgical intervention.

RESULTS
At 1-yr follow-up, 62.4% of patients were satisfied but 15.1% reported dissatisfaction. The satisfied patients showed significantly greater improvement in all outcome measures compared to the dissatisfied patients. The outcome scores for the dissatisfied patients were relatively unchanged or worse compared to baseline. Association was seen between dissatisfaction, duration of leg pain, smoking status, and patient comorbidities. Patients with good walking capacity at baseline were less prone to be dissatisfied compared to patients with poor walking capacity.

CONCLUSION
This study found smoking, long duration of leg pain, and cancerous and neurological disease to be associated with patient dissatisfaction, whereas good walking capacity at baseline was positively associated with satisfaction after 1 yr.
Ceftaroline for Severe Methicillin-Resistant Staphylococcus aureus Infections: A Systematic Review
Authors: Cosimi Reese A. , Beik Nahal , Kubiak David W. , Johnson Jennifer A. 
Published: May 2017

Abstract
Ceftaroline is approved by the Food and Drug Administration for acute bacterial skin and skin-structure infections and community-acquired bacterial pneumonia, including cases with concurrent bacteremia. Use for serious methicillin-resistant Staphylococcus aureus (MRSA) infections has risen for a multitude of reasons. The aim of this article is to review the literature evaluating clinical outcomes and safety of ceftaroline prescribed for serious MRSA infections. We conducted a literature search in Ovid (Medline) and PubMed for reputable case reports, clinical trials, and reviews focusing on the use of ceftaroline for treatment of MRSA infections. Twenty-two manuscripts published between 2010 and 2016 met inclusion criteria. Mean clinical cure was 74% across 379 patients treated with ceftaroline for severe MRSA infections. Toxicities were infrequent. Ceftaroline treatment resulted in clinical and microbiologic cure for severe MRSA infections. Close monitoring of hematological parameters is necessary with prolonged courses of ceftaroline.
Controversies about fertility and pregnancy issues in young breast cancer patients: current state of the art
Authors: Lambertini Matteo , Goldrat Oranite , Clatot Florian , Demeestere Isabelle , Awada Ahmad 
Published: May 2017

Purpose of review
For trying to help physicians in counseling their young patients with breast cancer interested in fertility preservation and future reproductive plans, this manuscript aims to perform an overview of the main available data on 10 controversies in this field.

Recent findings
Thanks to the improvement in patients’ prognosis, a growing attention towards fertility and pregnancy issues has been given over the past years and is currently provided to young breast cancer patients. However, several grey zones persist in many domains of this field and some physicians are still uncomfortable to deal with these issues.

Summary
Despite the great number of breast cancer patients experiencing fertility and pregnancy concerns at the time of diagnosis, the pursuit of fertility preserving strategies is realized only for a small proportion of them. The lack of adequate oncofertility counseling at the time of anticancer treatment decisions and the high costs of fertility preserving procedures can be considered the main explanations for these findings. The several ongoing registries and prospective studies investigating fertility and pregnancy issues in young breast cancer patients are crucial to acquire more robust data and try to address and solve the still unmet controversies in this field.
Immunogenicity of Therapeutic Antibodies: Monitoring Antidrug Antibodies in a Clinical Context
Authors: Bloem Karien , Hernández-Breijo Borja , Martínez-Feito Ana , Rispens Theo 
Published: May 2017

Abstract:
One of the factors that may impact drug levels of therapeutic antibodies in patients is immunogenicity, with potential loss of efficacy. Nowadays, many immunogenicity assays are available for testing antidrug antibodies (ADA). In this article, we discuss different types of immunogenicity assays and their clinical relevance in terms of drug tolerance, relation with pharmacokinetics (PK), neutralizing antibodies, potential adverse events associated with ADA, and prediction of ADA production. Drug-tolerant assays can provide insight into the process of immunogenicity, but for clinical management, these assays do not necessarily outperform drug-sensitive assays. The usefulness of any ADA assay for clinical decision making will be larger when drug concentrations are also measured, and this is true, in particular, for drug-tolerant assays.
Time to transient and stable reductions in hot flush frequency in postmenopausal women using conjugated estrogens/bazedoxifene
Authors: Pinkerton JoAnn V. , Bushmakin Andrew G. , Abraham Lucy , Komm Barry S. , Bobula Joel 
Published: May 2017

Abstract

Objective:
This post hoc analysis estimates time to transient and stable reductions in hot flush frequency in postmenopausal women using conjugated estrogens/bazedoxifene.

Methods:
In the 12-week Selective estrogens, Menopause, And Response to Therapy (SMART)-2 trial of conjugated estrogens/bazedoxifene 0.45 mg/20 mg and 0.625 mg/20 mg, women with at least seven moderate/severe hot flushes per day or 50 per week at screening recorded frequency of moderate/severe hot flushes in diaries. Nonparametric models and SAS Proc Lifetest were used to estimate median times to various degrees of transient reductions (first day with improvement) and stable reductions (first day with improvement maintained through study's end) in hot flush frequency.

Results:
Treatment produced transient hot flush reductions of 40% to 100% and stable reductions of 30% to 100% significantly faster than placebo. Median time to a transient 50% reduction was 8 days for conjugated estrogens/bazedoxifene 0.45 mg/20 mg, 9.5 for 0.625 mg/20 mg, and 10 for placebo; median time to a stable 50% reduction was 9, 10, and 38 days. Median time to a transient 90% reduction was 32 and 22.5 days for 0.45 mg/20 mg and 0.625 mg/20 mg, and median time to a stable 90% reduction was 83 and 29 days, respectively; median times to transient/stable 90% reductions were not reached during the 12-week study in the placebo group.

Conclusions:
Although not all women using conjugated estrogens/bazedoxifene achieve permanent elimination of hot flushes, the frequency is likely to be substantially reduced during the first week to month. Women can expect approximately 50% reduction in hot flush frequency after about 8 to 10 days, and sustained improvement with continued treatment.