bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dacarbazine depletes the ovarian reserve in mice and depletion is enhanced with age
Authors: Winship Amy L. , Bakai Monika , Sarma Urooza , Liew Seng H. , Hutt Karla J. 
Published: April 2018

AbstractDacarbazine is commonly administered for the treatment of cancers prevalent in reproductive age females. However, investigations of off-target effects of dacarbazine on the ovary are limited. We assessed the impact of dacarbazine on the ovarian reserve of primordial follicles, essential for fertility. Eight week and 6 month old C57BL/6 J mice were administered with dacarbazine or saline on day (d)0 and d7, then sacrificed after 12 hours (h), or 14d (n = 4–5/group). Follicle numbers, follicle density, serum AMH and corpora lutea were quantified and estrous cyclicity monitored. In reproductively young mice, dacarbazine did not affect primordial follicle numbers at 12 h, but resulted in a 36% reduction at 14d (p < 0.05). Dacarbazine-mediated primordial follicle depletion was accelerated with age, with a 24% (p < 0.05) and 36% (p < 0.01) reduction at 12 h and 14d. Follicle density remained unchanged between treatment groups at either age. Dacarbazine depleted antral follicles at 14d (p < 0.05), at both ages. Despite partial reduction of antral follicles, serum AMH, estrous cyclicity and corpora lutea (indicative of ovulation) remained unchanged between treatment groups, at both ages. Importantly, diminished ovarian reserve can result in premature ovarian insufficiency and infertility, thus, fertility preservation options should be considered for young female patients prior to dacarbazine treatment.
Is Putting SUGAR (Sampling Utterances of Grammatical Analysis Revised) Into Language Sample Analysis a Good Thing? A Response to Pavelko and Owens (2017)
Authors: Guo Ling-Yu , Eisenberg Sarita , Ratner Nan Bernstein , MacWhinney Brian 
Published: April 2018

PurposeIn this letter, the authors respond to Pavelko and Owens' (2017) newly advanced set of procedures for language sample analysis: Sampling Utterances and Grammatical Analysis Revised (SUGAR).MethodThe authors contrast some of the new guidelines for transcription, morpheme segmentation, and language sample elicitation in SUGAR with traditional conventions for language sample analysis (LSA). They address the potential impact of the new guidelines on some of the target measures in SUGAR—mean length of utterances in morphemes (MLUm), words per sentence (WPS), and clauses per sentence (CPS)—and provide their suggestions.ResultsInclusion of partially intelligible utterances in SUGAR may over- or underestimate children's MLUmand reduce the reliability of computing WPS. Counting derivational morphemes and the component morphemes of catenatives (e.g.,gonna) may result in overestimation of children's morphosyntactic skills.ConclusionFurther data are needed to determine whether MLUmincluding derivational morphemes and the component morphemes of catenatives is a better measure of children's morphosyntactic skills than MLUmexcluding those morphemes. Pending such data, the authors recommend maintaining traditional LSA conventions and measures. Furthermore, free, fast automated utilities already exist that reduce barriers for clinicians to conduct informative, in-depth LSA.
Auswirkung der Kodierung der Mangelernährung im SwissDRG-System
Authors: Aeberhard Carla , Abt Mirjam , Endrich Olga , Aubry Emilie , Leuenberger Michèle , Schütz Philipp , Sterchi Anna-Barbara , Stanga Zeno 
Published: April 2018

Zusammenfassung
Hintergrund Die krankheitsassoziierte Mangelernährung (KAM) ist in Krankenhäusern ein häufiges Problem mit medizinischen und ökonomischen Folgen. Die vorliegende Vier-Jahres-Analyse soll zeigen, ob die Aufwände für die Ernährungstherapien der mangelernährten Patienten durch den Mehrertrag, der durch die Kodierung der KAM im SwissDRG-System erreicht wird, gedeckt werden.
Material und Methodik In dieser Datenerhebung (2013 – 2016) wurden alle stationären Patienten mit einer E4-Diagnose im Universitätsspital Bern analysiert. Betrachtet wurden die E-Diagnose, Hauptdiagnose, Spitalaufenthaltsdauer, Alter, Art der Ernährungstherapie, Mehrertrag und Kosten, welche durch die ernährungstherapeutischen Behandlungen generiert wurden. Der Aufwand für die Ernährungsberatung, daas Pflegefachpersonal und die Ernährungstherapien wurde hochgerechnet. Zudem wurden die Patienten aufgrund ihrer Hauptdiagnose in 12 Gruppen eingeteilt (beruhend auf der WHO ICD-10-Klassifikation).
Ergebnisse Von den stationären Patienten (n = 169 515) wurden insgesamt 5442 Fälle (3,2 %) in den betrachteten 4 Jahren mit einer KAM kodiert. Davon waren 462 Fälle (8,5 %) erlösrelevant. Von den 5442 Patienten erhielten 3211 (59 %) orale Trinknahrungen, 1578 (29 %) eine enterale Ernährung per Sonde und 653 (12 %) eine parenterale Ernährung. Die Kodierung der KAM ergab einen Mehrertrag von insgesamt CHF 3 494 081 und einen Aufwand von hochgerechnet CHF 2 803 432. Am häufigsten wurden onkologische Patienten mit einer KAM kodiert (n = 1708; 31,4 %), gefolgt von Patienten mit Krankheiten des Verdauungssystems (n = 671; 12,3 %) und des Kreislaufsystems (n = 609; 11,2 %).
Schlussfolgerung Diese Analyse zeigt, dass der Mehrertrag durch die Kodierung der KAM im SwissDRG-System den finanziellen Aufwand für die Ernährungstherapien deckt. Die konsequente und frühzeitige Erfassung, Behandlung und Kodierung der KAM führt zu einer hohen Behandlungsqualität und -sicherheit für die Patienten und ist kostendeckend für das Krankenhaus.
Conventionality and linguistic domain(s) involved in the characterization of metonymies (for the creation of a detailed typology of metonymy)
Authors: Blanco-Carrión Olga 
Published: April 2018

Abstract
This is the second of three chapters devoted to the presentation of a set of criteria included in a database resulting from a project on the characterization of conceptual metonymy. It discusses Fields 5 and 7 of the database entry model, concerning conventionality, either conceptual or conceptual and linguistic, and the linguistic levels where metonymies operate (grammatical rank, meaning, form, grammatical process, and function).
What kind of reasoning mode is metonymy?
Authors: Panther Klaus-Uwe , Thornburg Linda L. 
Published: April 2018

Abstract
In this chapter we present new arguments for a conception of metonymy as a contingent, i.e. defeasible, inferential relation between a source and a target sense within the same conceptual frame. Some scholars have raised objections against our approach to metonymy, claiming that there exist entailment-based metonymies. We demonstrate that the “counterexamples” in support of this thesis are in fact not entailments but cancelable inferences based on encyclopedic knowledge. We develop an account of metonymy inspired by the Peircean concept of abduction, a mode of reasoning that is pervasive in both scientific and everyday inferencing. Finally, we propose a distinction between default and incongruence-based metonymies and point out some parallelisms between metonymies and Gricean conversational implicatures.
Molly married money
Authors: Radden Günter 
Published: April 2018

Abstract
This chapter is concerned with the conceptual basis of metonymy. Particular attention is devoted to properties that are considered crucial to conceptual metonymy. The metonymic source has received little attention. However, it plays an important role as an element of the target and is given due attention. The notion of association is applied to metonymic interconnections, inference, and strength of association. A central element of metonymy is the notion of relation: However, neither contiguity nor indexicality adequately covers the range of metonymic relations. The paper argues that two more properties are pertinent to conceptual metonymy: a metonymic shift from a source concept to a complex metonymic target, and the conceptual

integration of source and target and its resulting emergent meanings.
The mouth of the speaker
Authors: Pannain Rossella 
Published: April 2018

Abstract
Among body parts, speech organs are a default source of metonymic mapping towards the domain of linguistic action. In Italian this conceptual metonymy is responsible for several representations of types of speaker and linguistic behavior, and may be encoded in nominal modification and in word formation by compounding or evaluative suffixation. Within these construction schemas, the semantics of the lexical bases and of the additional lexical/morphological elements interact in conjuring the metonymic (-metaphoric) denotations of the four Italian linguistic items analyzed in the chapter. Their semantics involves value judgment, which partly depends on the target domain, and the contribution of scalar dimensional notions such as size and quantity. The data are primarily drawn from two corpora of contemporary written Italian.
Newt cells secrete extracellular vesicles with therapeutic bioactivity in mammalian cardiomyocytes
Authors: Middleton Ryan C. , Rogers Russell G. , De Couto Geoffrey , Tseliou Eleni , Luther Kristin , Holewinski Ronald , Soetkamp Daniel , Van Eyk Jennifer E. , Antes Travis J. , Marbán Eduardo 
Published: April 2018

ABSTRACTNewts can regenerate amputated limbs and cardiac tissue, unlike mammals which lack broad regenerative capacity. Several signaling pathways involved in cell proliferation, differentiation and survival during newt tissue regeneration have been elucidated, however the factors that coordinate signaling between cells, as well as the conservation of these factors in other animals, are not well defined. Here we report that media conditioned by newt limb explant cells (A1 cells) protect mammalian cardiomyocytes from oxidative stress‐induced apoptosis. The cytoprotective effect of A1‐conditioned media was negated by exposing A1 cells to GW4869, which suppresses the generation of extracellular vesicles (EVs). A1‐EVs are similar in diameter (~100–150 nm), structure, and share several membrane surface and cargo proteins with mammalian exosomes. However, isolated A1‐EVs contain significantly higher levels of both RNA and protein per particle than mammalian EVs. Additionally, numerous cargo RNAs and proteins are unique to A1‐EVs. Of particular note, A1‐EVs contain numerous mRNAs encoding nuclear receptors, membrane ligands, as well as transcription factors. Mammalian cardiomyocytes treated with A1‐EVs showed increased expression of genes in the PI3K/AKT pathway, a pivotal player in survival signaling. We conclude that newt cells secrete EVs with diverse, distinctive RNA and protein contents. Despite ~300 million years of evolutionary divergence between newts and mammals, newt EVs confer cytoprotective effects on mammalian cardiomyocytes.
Predicting novel microRNA: a comprehensive comparison of machine learning approaches
Authors: Stegmayer Georgina , Di Persia Leandro E , Rubiolo Mariano , Gerard Matias , Pividori Milton , Yones Cristian , Bugnon Leandro A , Rodriguez Tadeo , Raad Jonathan , Milone Diego H 
Published: April 2018

Abstract

Motivation
The importance of microRNAs (miRNAs) is widely recognized in the community nowadays because these short segments of RNA can play several roles in almost all biological processes. The computational prediction of novel miRNAs involves training a classifier for identifying sequences having the highest chance of being precursors of miRNAs (pre-miRNAs). The big issue with this task is that well-known pre-miRNAs are usually few in comparison with the hundreds of thousands of candidate sequences in a genome, which results in high class imbalance. This imbalance has a strong influence on most standard classifiers, and if not properly addressed in the model and the experiments, not only performance reported can be completely unrealistic but also the classifier will not be able to work properly for pre-miRNA prediction. Besides, another important issue is that for most of the machine learning (ML) approaches already used (supervised methods), it is necessary to have both positive and negative examples. The selection of positive examples is straightforward (well-known pre-miRNAs). However, it is difficult to build a representative set of negative examples because they should be sequences with hairpin structure that do not contain a pre-miRNA.

Results
This review provides a comprehensive study and comparative assessment of methods from these two ML approaches for dealing with the prediction of novel pre-miRNAs: supervised and unsupervised training. We present and analyze the ML proposals that have appeared during the past 10 years in literature. They have been compared in several prediction tasks involving two model genomes and increasing imbalance levels. This work provides a review of existing ML approaches for pre-miRNA prediction and fair comparisons of the classifiers with same features and data sets, instead of just a revision of published software tools. The results and the discussion can help the community to select the most adequate bioinformatics approach according to the prediction task at hand. The comparative results obtained suggest that from low to mid-imbalance levels between classes, supervised methods can be the best. However, at very high imbalance levels, closer to real case scenarios, models including unsupervised and deep learning can provide better performance.
An optimization framework for network annotation
Authors: Patkar Sushant , Sharan Roded 
Published: April 2018

Abstract

Motivation
A chief goal of systems biology is the reconstruction of large-scale executable models of cellular processes of interest. While accurate continuous models are still beyond reach, a powerful alternative is to learn a logical model of the processes under study, which predicts the logical state of any node of the model as a Boolean function of its incoming nodes. Key to learning such models is the functional annotation of the underlying physical interactions with activation/repression (sign) effects. Such annotations are pretty common for a few well-studied biological pathways.

Results
Here we present a novel optimization framework for large-scale sign annotation that employs different plausible models of signaling and combines them in a rigorous manner. We apply our framework to two large-scale knockout datasets in yeast and evaluate its different components as well as the combined model to predict signs of different subsets of physical interactions. Overall, we obtain an accurate predictor that outperforms previous work by a considerable margin.

Availability and implementation
The code is publicly available at https://github.com/spatkar94/NetworkAnnotation.git.
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood
Authors: Zhu Jiafan , Nakhleh Luay 
Published: April 2018

AbstractMotivationPhylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses data that consist of bi-allelic markers (e.g. single nucleotide polymorphism data) and allows for exact likelihood computations of phylogenetic networks while numerically integrating over all possible gene trees per marker. While the approach has good accuracy in terms of estimating the network and its parameters, likelihood computations remain a major computational bottleneck and limit the method’s applicability.ResultsIn this article, we first demonstrate why likelihood computations of networks take orders of magnitude more time when compared to trees. We then propose an approach for inference of phylogenetic networks based on pseudo-likelihood using bi-allelic markers. We demonstrate the scalability and accuracy of phylogenetic network inference via pseudo-likelihood computations on simulated data. Furthermore, we demonstrate aspects of robustness of the method to violations in the underlying assumptions of the employed statistical model. Finally, we demonstrate the application of the method to biological data. The proposed method allows for analyzing larger datasets in terms of the numbers of taxa and reticulation events. While pseudo-likelihood had been proposed before for data consisting of gene trees, the work here uses sequence data directly, offering several advantages as we discuss.Availability and implementationThe methods have been implemented in PhyloNet (http://bioinfocs.rice.edu/phylonet).
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples
Authors: Asgari Ehsaneddin , Garakani Kiavash , McHardy Alice C , Mofrad Mohammad R K 
Published: April 2018

Abstract

Motivation
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment. A major challenge in microbiome research is the classification of microbial communities of different environments or host phenotypes. The most common and cost-effective approach for such studies to date is 16S rRNA gene sequencing. Recent falls in sequencing costs have increased the demand for simple, efficient and accurate methods for rapid detection or diagnosis with proved applications in medicine, agriculture and forensic science. We describe a reference- and alignment-free approach for predicting environments and host phenotypes from 16S rRNA gene sequencing based on k-mer representations that benefits from a bootstrapping framework for investigating the sufficiency of shallow sub-samples. Deep learning methods as well as classical approaches were explored for predicting environments and host phenotypes.

Results
A k-mer distribution of shallow sub-samples outperformed Operational Taxonomic Unit (OTU) features in the tasks of body-site identification and Crohn’s disease prediction. Aside from being more accurate, using k-mer features in shallow sub-samples allows (i) skipping computationally costly sequence alignments required in OTU-picking and (ii) provided a proof of concept for the sufficiency of shallow and short-length 16S rRNA sequencing for phenotype prediction. In addition, k-mer features predicted representative 16S rRNA gene sequences of 18 ecological environments, and 5 organismal environments with high macro-F1 scores of 0.88 and 0.87. For large datasets, deep learning outperformed classical methods such as Random Forest and Support Vector Machine.

Availability and implementation
The software and datasets are available at https://llp.berkeley.edu/micropheno.

Supplementary information
Supplementary data are available at Bioinformatics online.
Comment to Hansson, S. et al. (2017): “Competition for the fish – fish extraction from the Baltic Sea by humans, aquatic mammals, and birds”, with special reference to cormorants, perch, and pikeperch
Authors: Heikinheimo Outi , Lehtonen Hannu , Lehikoinen Aleksi 
Published: April 2018

Abstract
Hansson et al. (2017) concluded that competition between fisheries and piscivorous mammals and birds exists in the Baltic Sea, based on the estimation of biomass of the fish species consumed in the ICES subdivisions. We compared their results to the data and scientific knowledge from the coastal waters of Finland and show that local differences in fisheries, fish assemblages and abundance of predators should be taken into account to reliably assess potential competition. Hansson et al. (2017) did not include the piscivorous fish in their analysis, but these may be the most important predators. In the Archipelago Sea, for instance, the consumption by fish predators is considerably larger than that of cormorants.
Constraining the H2 column density distribution at z ∼ 3 from composite DLA spectra
Authors: Balashev S A , Noterdaeme P 
Published: April 2018

Abstract
We present the detection of the average H2 absorption signal in the overall population of neutral gas absorption systems at z∼ 3 using composite absorption spectra built from the Sloan Digital Sky Survey-III damped Lyman α catalogue. We present a new technique to directly measure the H2 column density distribution function $f_{\rm H_2}(N)$ from the average H2 absorption signal. Assuming a power-law column density distribution, we obtain a slope $\beta = -1.29 \pm 0.06(\rm stat) \pm 0.10 (\rm sys)$ and an incidence rate of strong H2 absorptions [with N(H2) ≳ 1018 cm−2] to be $4.0 \pm 0.5(\rm stat) \pm 1.0 (\rm sys)\, \hbox{ per cent}$ in H i absorption systems with N(H i) ≥1020 cm−2. Assuming the same inflexion point where $f_{\rm H_2}(N)$ steepens as at z = 0, we estimate that the cosmological density of H2 in the column density range $\log N(\rm H_2) ({\rm cm}^{-2})= 18{\text{--}}22$ is ${\sim } 15\hbox{ per cent}$ of the total. We find one order of magnitude higher H2 incident rate in a sub-sample of extremely strong damped Lyman α absorption systems (DLAs) [$\log N(\rm{H\,\small {I}}) ({\rm cm}^{-2}) \ge 21.7$], which, together with the derived shape of $f_{\rm H_2}(N)$, suggests that the typical H i–H2 transition column density in DLAs is log N(H)(cm−2) ≳ 22.3 in agreement with theoretical expectations for the average (low) metallicity of DLAs at high-z.
El Niño–Southern Oscillation and its impact in the changing climate
Authors: Yang Song , Li Zhenning , Yu Jin-Yi , Hu Xiaoming , Dong Wenjie , He Shan 
Published: April 2018

AbstractExtensive research has improved our understanding and forecast of the occurrence, evolution and global impacts of the El Niño–Southern Oscillation (ENSO). However, ENSO changes as the global climate warms up and it exhibits different characteristics and climate impacts in the twenty-first century from the twentieth century. Climate models project that ENSO will also change in the warming future and have not reached an agreement about the flavor, as to the intensity and the frequency, of future ENSO conditions. This article presents the conventional view of ENSO properties, dynamics and teleconnections, and reviews the emerging understanding of the diversity and associated climate impacts of ENSO. It also reviews the results from investigations into the possible changes in ENSO under the future global-warming scenarios.
Global Prevalence of Fetal Alcohol Spectrum Disorder Among Children and Youth: A Systematic Review and Meta-analysis
Authors: Lange Shannon , Probst Charlotte , Gmel Gerrit , Rehm Jürgen , Burd Larry , Popova Svetlana 
Published: April 2018

(Abstracted from JAMA Pediatr 2017;171(10):948–956)
Fetal alcohol spectrum disorder (FASD) is an umbrella term for the wide range of adverse effects to the developing fetus when exposed to alcohol during pregnancy, some of which are lifelong. The severity and type of defects induced by FASD are affected by the age of embryo at exposure, pattern of exposure, and dose; however, other factors including genetic background, maternal age, and environmental influences also appear to impact susceptibility.