bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lions, Bylaws, and Conservation Metrics
Authors: Mulder Monique Borgerhoff , Kwiyega Jonathan Lucas , Beccaria Simone , Bwasama Sylvester Sadock , Fitzherbert Emily , Genda Peter , Caro Tim 
Published: September 2019

Abstract
African lions are a significant threat to pastoralists, triggering both retaliatory and nonretaliatory killings that represent a high-profile example of human–wildlife conflict. In the present article, we report on a grassroots campaign to reduce such conflict by shifting agropastoralists’ attitudes toward lion killing and the central role of bylaws in its apparent success. Insofar as all of East Africa's principal protected areas still harboring lions are surrounded by pastoralist populations, the vast majority of which persecute lions, this novel strategy is of considerable wide-scale and practical significance. We report on an estimated 59%–69% reduction in the number of lions killed since the implementation of bylaws and use our experiences to highlight the need for fresh dialog among project managers, conservation organizations, and their funders in crafting appropriate conservation success metrics. In the context of human–wildlife conflict, changes in peoples’ norms and attitudes are of greater significance over the long term than simplistic tabulations of the number of individuals saved.
CRY2 suppresses trophoblast migration and invasion in recurrent spontaneous abortion
Authors: Wu Lianzhi , Cheng Biheng , Liu Qian , Jiang Ping , Yang Jing 
Published: September 2019

AbstractDisruption of circadian rhythms is associated with aberrant trophoblast migration and invasion in recurrent spontaneous abortion (RSA). This study aims to explore the functional role and the mechanisms of cryptochrome 2 (CRY2), a fundamental component of the circadian clock, in regulating trophoblast migration and invasion. Human extravillous trophoblast cell line HTR-8/SVneo was used as a cell model. Cell migration and invasion were examined using wound healing assay and Transwell assay, respectively. The mRNA and protein levels were determined using quantitative real-time polymerase chain reaction and western blot, respectively. Luciferase reporter assay and chromatin immunoprecipitation assay were performed to explore the interaction between c-Myc to the brain and muscle ARNT-like protein 1 (BMAL1) promoter. CRY2 was highly expressed in human villous specimens of RSA. Furthermore, CRY2 overexpression impaired migration and invasion in HTR-8/SVneo cells, whereas CRY2 knockdown yielded the opposite results. Mechanistically, c-Myc bound to the BMAL1 promoter and induced BMAL1 transcription, both of which further activated matrix metalloproteinase 2/9 (MMP2/9) and facilitated migration and invasion in HTR-8/SVneo cells. CRY2 inhibited c-Myc-BMAL1 pathway and impaired migration and invasion of HTR-8/SVneo cells. Collectively, these findings demonstrate that CRY2 suppresses trophoblast migration and invasion via inhibiting c-Myc-BMAL1-MMP2/9 pathway.
Acute fulminant necrotizing mesenteric lymphadenitis causing bowel ischemia
Authors: Carr John Alfred 
Published: September 2019

Abstract
This case report documents the medical progression of a 56-year-old man who presented with a small bowel obstruction and was found to have acute fulminant necrotizing mesenteric lymphadenitis causing small intestinal ischemia. A large portion of the proximal jejunal mesentery was necrotic with vascular thrombosis leading to small bowel ischemia and obstruction. He was successfully managed surgically and survived. The evaluation and possible aetiologies are discussed.
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Disrupts Control of Cell Proliferation and Apoptosis in a Human Model of Adult Liver Progenitors
Authors: Svobodová Jana , Procházková Jiřina , Kabátková Markéta , Krkoška Martin , Šmerdová Lenka , Líbalová Helena , Topinka Jan , Kléma Jiří , Kozubík Alois , Machala Miroslav , Vondráček Jan 
Published: September 2019

Abstract
The aryl hydrocarbon receptor (AhR) activation has been shown to alter proliferation, apoptosis, or differentiation of adult rat liver progenitors. Here, we investigated the impact of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-mediated AhR activation on a human model of bipotent liver progenitors, undifferentiated HepaRG cells. We used both intact undifferentiated HepaRG cells, and the cells with silenced Hippo pathway effectors, yes-associated protein 1 (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), which play key role(s) in tissue-specific progenitor cell self-renewal and expansion, such as in liver, cardiac, or respiratory progenitors. TCDD induced cell proliferation in confluent undifferentiated HepaRG cells; however, following YAP, and, in particular, double YAP/TAZ knockdown, TCDD promoted induction of apoptosis. These results suggested that, unlike in mature hepatocytes, or hepatocyte-like cells, activation of the AhR may sensitize undifferentiated HepaRG cells to apoptotic stimuli. Induction of apoptosis in cells with silenced YAP/TAZ was associated with upregulation of death ligand TRAIL, and seemed to involve both extrinsic and mitochondrial apoptosis pathways. Global gene expression analysis further suggested that TCDD significantly altered expression of constituents and/or transcriptional targets of signaling pathways participating in control of expansion or differentiation of liver progenitors, including EGFR, Wnt/β-catenin, or tumor growth factor-β signaling pathways. TCDD significantly upregulated cytosolic proapoptotic protein BMF (Bcl-2 modifying factor) in HepaRG cells, which could be linked with an enhanced sensitivity of TCDD-treated cells to apoptosis. Our results suggest that, in addition to promotion of cell proliferation and alteration of signaling pathways controlling expansion of human adult liver progenitors, AhR ligands may also sensitize human liver progenitor cells to apoptosis.
Switching from branched-chain amino acid granules to branched-chain amino acid-enriched nutrient improves the branched-chain amino acid-to-tyrosine ratio in patients with cirrhosis with hypoalbuminemia: a prospective study
Authors: Fukui Aiko , Kawabe Naoto , Hashimoto Senju , Kamei Hiroyuki , Yoshioka Kentaro 
Published: September 2019

Objective:
The present study aimed to elucidate the effect of switching from branched-chain amino acid granules to branched-chain amino acid-enriched nutrient in patients with cirrhosis with hypoalbuminemia.

Methods:
Twenty-six patients with cirrhosis with hypoalbuminemia despite treatment with branched-chain amino acid granules containing 12 g of branched-chain amino acid were enrolled in the prospective study. The branched-chain amino acid-enriched nutrient and control groups were composed of 16 and 10 patients, respectively. The patients in branched-chain amino acid-enriched nutrient group switched to branched-chain amino acid-enriched nutrient mixture containing 12.2 g of branched-chain amino acid and 410 kcal with a half of it consumed as a late evening snack, and the patients in the control group continued branched-chain amino acid granules. Laboratory data related to nutrition parameter were assessed at baseline, 3 months after baseline, and at 6 months after baseline.

Results:
Two patients were withdrawn; hence, nine and 15 patients in the branched-chain amino acid granules and branched-chain amino acid-enriched nutrient groups, respectively, were subjected to full analysis. Serum albumin levels and total lymphocyte counts in both groups did not change in the study period. The branched-chain amino acid-to-tyrosine ratio in the branched-chain amino acid-enriched nutrient group significantly increased from baseline to 6 months after baseline (P = 0.030), whereas that in the control group did not increase.

Conclusion:
Switching from branched-chain amino acid granules to branched-chain amino acid-enriched nutrients improves branched-chain amino acid-to-tyrosine ratio in patients with cirrhosis with hypoalbuminemia.
What Does Reduced FDG Uptake Mean in High-Grade Gliomas?
Authors: Bund Caroline , Lhermitte Benoît , Cicek A. Ercument , Ruhland Elisa , Proust François , Namer Izzie Jacques 
Published: September 2019

Purpose
As well as in many others cancers, FDG uptake is correlated with the degree of malignancy in gliomas, that is, commonly high FDG uptake in high-grade gliomas. However, in clinical practice, it is not uncommon to observe high-grade gliomas with low FDG uptake. Our aim was to explore the tumor metabolism in 2 populations of high-grade gliomas presenting high or low FDG uptake.

Methods
High-resolution magic-angle spinning nuclear magnetic resonance spectroscopy was realized on tissue samples from 7 high-grade glioma patients with high FDG uptake and 5 high-grade glioma patients with low FDG uptake. Tumor metabolomics was evaluated from 42 quantified metabolites and compared by network analysis.

Results
Whether originating from astrocytes or oligodendrocytes, the high-grade gliomas with low FDG avidity represent a subgroup of high-grade gliomas presenting common characteristics: low aspartate, glutamate, and creatine levels, which are probably related to the impaired electron transport chain in mitochondria; high serine/glycine metabolism and so one-carbon metabolism; low glycerophosphocholine-phosphocholine ratio in membrane metabolism, which is associated with tumor aggressiveness; and finally negative MGMT methylation status.

Conclusions
It seems imperative to identify this subgroup of high-grade gliomas with low FDG avidity, which is especially aggressive. Their identification could be important for early detection for a possible personalized treatment, such as antifolate treatment.
Resource theory of contextuality
Authors: Amaral Barbara 
Published: September 2019

In addition to the important role of contextuality in foundations of quantum theory, this intrinsically quantum property has been identified as a potential resource for quantum advantage in different tasks. It is thus of fundamental importance to study contextuality from the point of view of resource theories, which provide a powerful framework for the formal treatment of a property as an operational resource. In this contribution, we review recent developments towards a resource theory of contextuality and connections with operational applications of this property.
This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Generalized Fock space and contextuality
Authors: Rashkovskiy Sergey , Khrennikov Andrei 
Published: September 2019

This paper is devoted to linear space representations of contextual probabilities—in generalized Fock space. This gives the possibility to use the calculus of creation and annihilation operators to express probabilistic dynamics in the Fock space (in particular, the wide class of classical kinetic equations). In this way, we reproduce the Doi–Peliti formalism. The context-dependence of probabilities can be quantified with the aid of the generalized formula of total probability—by the magnitude of the interference term.This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond'.
Contextuality, memory cost and non-classicality for sequential measurements
Authors: Budroni Costantino 
Published: September 2019

The Kochen–Specker theorem, and the associated notion of quantum contextuality, can be considered as the starting point for the development of a notion of non-classical correlations for single systems. The subsequent debate around the possibility of an experimental test of Kochen–Specker-type contradiction stimulated the development of different theoretical frameworks to interpret experimental results. Starting from the approach based on sequential measurements, we will discuss a generalization of the notion of non-classical temporal correlations that goes beyond the contextuality approach and related ones based on Leggett and Garg's notion of macrorealism, and it is based on the notion of memory cost of generating correlations. Finally, we will review recent results on the memory cost for generating temporal correlations in classical and quantum systems. The present work is based on the talk given at the Purdue Winer Memorial Lectures 2018: probability and contextuality.
This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
On joint distributions, counterfactual values and hidden variables in understanding contextuality
Authors: Dzhafarov Ehtibar N. 
Published: September 2019

This paper deals with three traditional ways of defining contextuality: (C1) in terms of (non)existence of certain joint distributions involving measurements made in several mutually exclusive contexts; (C2) in terms of relationship between factual measurements in a given context and counterfactual measurements that could be made if one used other contexts; and (C3) in terms of (non)existence of ‘hidden variables’ that determine the outcomes of all factually performed measurements. It is generally believed that the three meanings are equivalent, but the issues involved are not entirely transparent. Thus, arguments have been offered that C2 may have nothing to do with C1, and the traditional formulation of C1 itself encounters difficulties when measurement outcomes in a contextual system are treated as random variables. I show that if C1 is formulated within the framework of the Contextuality-by-Default (CbD) theory, the notion of a probabilistic coupling, the core mathematical tool of CbD, subsumes both counterfactual values and ‘hidden variables’. In the latter case, a coupling itself can be viewed as a maximally parsimonious choice of a hidden variable.
This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
On measures and measurements: a fibre bundle approach to contextuality
Authors: Terra Cunha Marcelo 
Published: September 2019

Contextuality is the failure of ‘local’ probabilistic models to become global ones. In this paper, we introduce the notions ofmeasurable fibre bundle,probability fibre bundleandsample fibre bundlewhich capture and make precise the former statement. The central notions of contextuality are discussed under this formalism, examples worked out, and some new aspects pointed out.This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Measures of contextuality and non-contextuality
Authors: Kujala Janne V. , Dzhafarov Ehtibar N. 
Published: September 2019

We discuss three measures of the degree of contextuality in contextual systems of dichotomous random variables. These measures are developed within the framework of the Contextuality-by-Default (CbD) theory, and apply to inconsistently connected systems (those with ‘disturbance’ allowed). For one of these measures of contextuality, presented here for the first time, we construct a corresponding measure of the degree of non-contextuality in non-contextual systems. The other two CbD-based measures do not suggest ways in which degree of non-contextuality of a non-contextual system can be quantified. We find the same to be true for the contextual fraction measure developed by Abramsky, Barbosa and Mansfield. This measure of contextuality is confined to consistently connected systems, but CbD allows one to generalize it to arbitrary systems.This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Indistinguishability and the origins of contextuality in physics
Authors: de Barros J. Acacio , Holik Federico , Krause Décio 
Published: September 2019

In this work, we discuss a formal way of dealing with the properties of contextual systems. Our approach is to assume that properties describing the same physical quantity, but belonging to different measurement contexts, are indistinguishable in a strong sense. To construct the formal theoretical structure, we develop a description using quasi-set theory, which is a set-theoretical framework built to describe collections of elements that violate Leibnitz's principle of identity of indiscernibles. This framework allows us to consider a new ontology in order to study the properties of quantum systems.
This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Evidence of multifaceted functions of codon usage in translation within the model beetleTribolium castaneum
Authors: Whittle Carrie A. , Kulkarni Arpita , Extavour Cassandra G. 
Published: September 2019

AbstractSynonymous codon use is non-random. Codons most used in highly transcribed genes, often called optimal codons, typically have high gene counts of matching tRNA genes (tRNA abundance) and promote accurate and/or efficient translation. Non-optimal codons, those least used in highly expressed genes, may also affect translation. In multicellular organisms, codon optimality may vary among tissues. At present however, codon use remains poorly understood in multicellular organisms. Here, we studied codon usage of genes highly transcribed in germ line (testis, ovary) and somatic tissues (gonadectomized males and females) of the beetleTribolium castaneum. The results demonstrate that: 1) the majority of optimal codons were organism-wide, the same in all tissues, and had numerous matching tRNA gene copies (Opt-codon↑tRNAs), consistent with translational selection; 2) some optimal codons varied among tissues, suggesting tissue-specific tRNA populations; 3) wobble tRNA were required for translation of certain optimal codons (Opt-codonwobble), possibly allowing precise translation and/or protein folding; and 4) remarkably, some non-optimal codons had abundant tRNA genes (Nonopt-codon↑tRNAs), and genes using those codons were tightly linked to ribosomal and stress-response functions. Thus, Nonopt-codon↑tRNAscodons may regulate translation of specific genes. Together, the evidence suggests that codon use and tRNA genes regulate multiple translational processes inT. castaneum.
A new GABAergic projection from the BNST onto accumbal parvalbumin neurons controls anxiety
Authors: Xiao Qian , Zhou Xinyi , Wei Pengfei , Xie Li , Han Yaning , Wu Bifeng , Wang Jie , Cai Aoling , Xu Fuqiang , Lu Yi , Tu Jie , Wang Liping 
Published: September 2019

AbstractThe prevailing view is that parvalbumin (PV) interneurons play modulatory roles in emotional response through local medium spiny projection neurons (MSNs). Here, we show that PV activity within the nucleus accumbens shell (sNAc) is required for producing anxiety-related avoidance when mice are under anxiogenic situations; sNAcPV neurons exhibited high excitability in chronically stressed mice model, which generated excessive maladaptive avoidance behavior in an anxiogenic context. We also discovered a novel GABAergic projections from the anterior dorsal bed nuclei of stria terminalis (adBNST) to sNAcPV neurons; optogenetic activation of these afferent terminals in sNAc produced an anxiolytic effect via GABA transmission. Next, we further demonstrated that chronic stressors attenuated the inhibitory synaptic transmission at adBNSTGABA sNAcPV synapses, which in turn explains the hyperexcitability of sNAcPV neurons on stressed models; therefore, activation of these GABAergic afferents in sNAc rescued the excessive avoidance behavior related to anxious state.Our findings reveal the coordination between BNST and NAc through an inhibitory architecture in controlling of anxiety-related response and provide a neurobiological basis for therapeutic interventions in pathological anxiety.
Hormones as adaptive control systems in juvenile fish
Authors: Weidner Jacqueline , Jensen Camilla Håkonsrud , Giske Jarl , Eliassen Sigrunn , Jørgensen Christian 
Published: September 2019

AbstractGrowth is an important theme in many biological disciplines. Physiologists often relate growth rates to hormonal control of essential processes. Ecologists often study growth as function of gradients or combinations of environmental factors. Fewer studies have investigated the combined effects of environmental and hormonal control on growth. Here, we present an evolutionary optimization model of fish growth that combines internal regulation of growth by hormone levels with the external influence of food availability and predation risk. Hormones are represented by growth hormone, thyroid hormone and orexin functions. By studying a range from poor to rich environments, we find that the level of food availability in the environment results in different evolutionarily optimal strategies of hormone levels. With more food available, higher levels of hormones are optimal, resulting in higher food uptake and growth. By using this fitness-based approach we also find a consequence of evolutionary optimization of survival on optimal hormone use. Where foraging is risky, aerobic scope can be used strategically to increase the chance of escaping from predators. By comparing model results to empirical observations, many mechanisms can be recognized, for instance a change in pace-of-life due to resource availability, and reduced emphasis on reserves in more stable environments.Summary statementWe combine physiological, environmental and evolutionary aspects of fish growth in a state-dependent model where the optimal regulation of growth and survival is achieved through hormonal regulation of behaviour.
Arabidopsis thaliana natural variation in temperature-modulated immunity uncovers transcription factor UNE12 as a thermoresponsive regulator
Authors: Bruessow Friederike , Bautor Jaqueline , Hoffmann Gesa , Parker Jane E. 
Published: September 2019

AbstractTemperature impacts plant immunity and growth but how temperature intersects with endogenous pathways remains unclear. Here we uncover variation between Arabidopsis thaliana natural accessions in response to two non-stress temperatures (22°C and 16°C) affecting accumulation of the thermoresponsive stress hormone salicylic acid (SA) and plant growth. Analysis of differentially responding A. thaliana accessions shows that pre-existing SA provides a benefit in limiting bacterial pathogen infection at both temperatures. Several A. thaliana genotypes display a capacity to mitigate negative effects of high SA on growth, indicating within-species plasticity in SA - growth tradeoffs. An association study of temperature x SA variation, followed by physiological and immunity phenotyping of mutant and over-expression lines, identifies the transcription factor unfertilized embryo sac 12 (UNE12) as a temperature-responsive SA immunity regulator. Here we reveal previously untapped diversity in plant responses to temperature and a way forward in understanding the genetic architecture of plant adaptation to changing environments.