bluuebunny/crossref_metadata_2025 huggingface dataset:
Moving at the speed of flight: dabbling duck-movement rates and the relationship with electronic tracking interval
Authors: McDuie Fiona , Casazza Michael L. , Keiter David , Overton Cory T. , Herzog Mark P. , Feldheim Cliff L. , Ackerman Joshua T.
Published: September 2019

Abstract Context Effective wildlife management requires information on habitat and resource needs, which can be estimated with movement information and modelling energetics. One necessary component of avian models is flight speeds at multiple temporal scales. Technology has limited the ability to accurately assess flight speeds, leading to estimates of questionable accuracy, many of which have not been updated in almost a century. Aims We aimed to update flight speeds of ducks, and differentiate between migratory and non-migratory flight speeds, a detail that was unclear in previous estimates. We also analysed the difference in speeds of migratory and non-migratory flights, and quantified how data collected at different temporal intervals affected estimates of flight speed. Methods We tracked six California dabbling duck species with high spatio-temporal resolution GPS–GSM transmitters, calculated speeds of different flight types, and modelled how estimates varied by flight and data interval (30min to 6h). Key results Median migratory speeds were faster (but non-significant) for the larger mallard (Anas platyrhynchos; 82.5kmh–1), northern pintail (Anas acuta; 79.0kmh–1) and gadwall (Mareca strepera; 70.6kmh–1), than the smaller-bodied northern shoveler (Spatula clypeata; 65.7kmh–1), cinnamon teal (Spatula cyanoptera; 63.5kmh–1) and American wigeon (Mareca Americana; 52kmh–1). Migratory flights were faster than non-migratory flights for all species and speeds were consistently slower with an increasing data interval. Implications The need to balance time and energy requirements may drive different speeds for migratory and non-migratory flights. Lower speeds at longer intervals are likely to be due to a greater proportion of ‘loafing’ time included in flighted segments, demonstrating that data acquired at different intervals provide a means to evaluate and estimate behaviours that influence speed estimation. Shorter-interval data should be the most accurate, but longer-interval data may be easier to collect over lengthier timeframes, so it may be expedient to trade-off a degree of accuracy in broad-scale studies for the larger dataset. Our updated flight speeds for dabbling duck species can be used to parameterise and validate energetics models, guide management decisions regarding optimal habitat distribution, and, ultimately, improve conservation management of wetlands for waterfowl.
Preliminary investigation of the effect of oral supplementation of Lactobacillus plantarum strain SNK12 on mRNA levels of neurotrophic factors and GABA receptors in the hippocampus of mice under stress-free and sub-chronic mild social defeat-stressing conditions
Authors: Tsukahara Takamitsu , Kawase Takahiro , Yoshida Hiroya , Bukawa Wakoto , Kan Tatsuhiko , Toyoda Atsushi
Published: September 2019

The effect of Lactobacillus plantarum SNK12 (CPLP) supplementation on mRNA levels of hippocampal neurotrophic factors and gamma aminobutyric acid receptors (GABAR) was tested. In Experiment 1, stress-free, unsupplemented and CPLP (4 × 108 cells/head)-supplemented male C57BL/6J (B6) mice were the experimental animals. In Experiment 2, intruder (male, B6) mice [negative control; unsupplemented, sub-chronic mild social defeat stress (sCSDS)-induced; and CPLP-supplemented, sCSDS-induced] were exposed to aggressor mice (adult male Slc:ICR). mRNA levels of neurotrophic factors and GABAR in hippocampal samples of these mice were analyzed. In CPLP-supplemented mice of both experiments, mRNA levels of bdnf, nt-3, and GABAR were upregulated. Moreover, a tendency toward the improvement of habituation ability (Experiment 1) and behavior (Experiment 2) was observed in mice, which may be associated with upregulated neurotrophic factors and GABAR. We demonstrated that oral supplementation of CPLP to stress-free and stress-induced mice upregulated mRNA levels of hippocampal neurotrophic factors and GABAR.
Characterization of Activated Carbon Prepared From Banana Peels: Effect of Chemical Activators on the Adsorption of Gas Emissions
Authors: Viena V , Elvitriana  , Nizar M.
Published: September 2019

The aims of the study were to investigate characteristics of activated carbon prepared from banana peels as adsorbent for the removal gasesemission from motorcycles. The effect of differents chemocalactivators and contact time were studied on the characteristics of banana peels raw carbon (RC) and chemically activated carbon (CAC) such as moisture content, ash content, volatile matter. The best ofIodine adsorption capacity of CAC H2SO4 3N 3 hour contact, was obtained at 913,68 mg/g adsorbent. Structure and morphology ofRC and CAC were characterized by Fourier transform infrared (FTIR) and field emission scanning electron microscopy (SEM). The results showed that RC and CAC could significantly adsorbed the CO and SO2gasesemissions from motorcycles, but not applicable for NO, NOx gases. After 10 minutes analysis using gas emission Analyzer, CO gas could be removed, from initial 16014 ppm to 3578 ppm using CAC H2SO4 adsorbent, while SO2 gas could also be partly removed from 217 ppm to 19 ppm using CAC ZnCl2 adsorbent.Banana peels carbon produced was suitable for application in removing CO and SO2gases emissions from motorcycles and it helps to reduce the green house gas effects of fossil fuel usage to the environment.
The effect of Acetic Acid Ratio in The Electrodeposition Process of Chitosan/ZnO
Authors: Saisa  , Agusnar Harry , Alfian Zul , Nainggolan Irwana
Published: September 2019

Chitosan is a material that sensitive to the environmental changes and has been used in the developing of sensor. The fabrication of chitosan/ZnO composite was prepared using the electrodeposition method over PCB plate. ZnO content was variated to be 10, 20 and 30 wt.% also the composite was prepared in acetic acid 2 and 5%. The aim of the present study is to evaluate the preparation process of chitosan/ZnO composite with acetic acid concentration as the independent variable in this research. The XRD data showed a peak at 2θ; 30.8° that confirmed the presence of ZnO in the composite. The FTIR spectra showed the presence of ZnO can be found at 550 cm−1 and the acetic acid concentration influenced the intensities of the composites. The surface morphology of composite that prepared using acetic acid 2% has a smoother surface than the composite that prepared using acetic acid 5%. The voltage response of chitosan/ZnO composite that prepared using acetic acid 5% showed the highest value (0,1525 V) than the composite that prepared using acetic acid 2% (0,0581 V).
Proximate and Amino Acid Composition of DengkeNaniura Prepared from Carp (Cyprinuscarpio) of Lake Toba Indonesia
Authors: Manik Maria , Kaban Jamaran , Silalahi Jansen , Ginting Mimpin
Published: September 2019

Dengkenaniurais a traditional Batak Toba dish processed from carp (Cyprinus carpio) marinated with lime juice and spices and consumed without cooking.Dengkenaniura in this research was prepared with carp taken from Haranggaol village, Lake Toba area, marinated with jungga lime (Citrus jambhiri Lush) juice and various spices for 7 hours. This research was conducted to analyze the proximate nutritional valuesand amino acid composition of freshcarpmeat and after the carp meat was processed as dengkenaniura. The research was done experimentally in a laboratory by acquiring data descriptively. The results of proximate analysis of dengkenaniurashow the moisture content decreased from 74.6% to 69.26%; the fat content decreased from 5.74% to 4.35% and the protein content decreased from 18.3% to 17.09%, while the ash content increased from 1.13% to 2.69% and the carbohydrate content proximately increased from 0,23% to 6.61%.The results of amino acid analysis with HPLC show the largest amino acids in fresh meat and dengkenaniuraare lysine (4.5% and 4.55%), leucine (4.04% and 4.48%) and arginine (3.09% and 3.46%), glutamic acid (7.94% and 8.69%) and aspartic acid (5.07% and 5.54%).
Temperature Control System Design Chicken Coop Using Gateway SMS
Authors: Sulistiyowati Indah , Haris Rosy Akhmad , Suprayitno Eko Agus , Jamaaluddin
Published: September 2019

This research will be made a special chicken coop that works automatically. This chicken coop works based on the temperature in the cage. To know the temperature value in the enclosure is used temperature sensor LM35. From LM35 temperature sensor then processed to activate the relay module, where the relay works turn on the DC fan motor and the DC water pump. Here SMS Gateway serves as a warning alarm when there is a target temperature problem . In testing this system the cage can work well, it is shown that the system can stabilize the temperature inside the chicken coop as desired. With this research is expected to change from open cage into a closed cage in order to improve the production of chicken pieces.
Evaluation of the Implementation of Basic Literacy Education Program in Bogor Regency, Indonesia
Authors: Oktapiani Marliza , Akbar Ma’ruf , Karnati Neti
Published: September 2019

The purpose of this research is to evaluate the implementation of basic literacy educational program in Bogor regency. This research used discrepancy evaluation model which includes four aspects: (1) design, (2) installation, (3) process, and (4) product. The data werecollected through interview, observation, and documentation. The interviewwas conducted to the chief of development division for non-formal education, implementing officer of curriculum and assessment for nonformal education, head of curriculum and assessmentsection for non-formal education, head of community learning center, tutors and illiterate learners. The data wereanalyzed qualitatively, displayed in narrative text, reducing data, and drawing conclusion. The results showed that all aspects of basic literacy educationprogram were less appropriate than the standard evaluation. Thus,the collaboration among the government, local government, and society are needed to support the development of basic literacy education program next year, in order to bring Indonesia to lifelong literacy.
Improving Motivation and Learning Outcomes of MTsN 2 the Great Aceh Students in Vocational Processing Subject Through the Cooperative Learning Model Think Pair and Share
Authors: Mahyiddin Zuraini
Published: September 2019

One learning strategy that can be used to increase motivation and learning outcomes is by using cooperative pair think and share models. This research was carried out on the material of vocational processing with the subject matter “Processing healthy food from fresh vegetables” in class VII (2) MTsN 2 The Great Aceh aimed at seeing the improvement of students’ motivation and learning outcomes by using this learning model. The research subjects were students of class VII (2) MTsN 2 The Great Aceh, amounting to 32 people, consisting of 14 men and 18 women. The approach taken in this study was a quantitative descriptive approach and the type of research used was Classroom Action Research (CAR). Research data collection instruments are learning implementation plans (RPP), observation sheets of teacher and student activities, student worksheets, student motivation sheets for processing vocational subject matter by applying think pair and share cooperative learning models where learning outcomes are analyzed using percentage test and student motivation by referring to the criteria of analysis results of learning motivation level. Based on the results of the data analysis, it can be concluded that: (1) There is an increase in motivation and learning outcomes in class VII (2) MTsN 2 The Great Aceh, as seen from (1) the results of classical learning completeness of 37.5% in the cycle I became 875% in cycle II with an increase of 50%, (2) Student motivation scores also increased from “high” to “very high” categories. The average motivation score obtained when filling out the questionnaire in cycle I was followed by 32 students, namely 65.625% classified as “High”, while the average score of motivation in cycle II was 81.25%, which was classified as “Very High” with an increase 15.62%.
TiO2 Hybridized with Natural Ilmenite Nanocomposites for Enhanced Visible Light Photocatalytic Activity
Authors: Chongsri K. , Phoohinkong W. , Pavasupree S. , Mekprasart W. , Boonyarattanakalin K. , Pecharapa W.
Published: September 2019

The activated ilmenite nanocomposite of TiO2 hybridized were prepared by natural ilmenite and commercial TiO2 anatase assembled using sugar as cross-link agents and carbon source. The heterostructure interface of anatase-ilmenite junction, crystallinity and chemical state were characterized by X-ray diffraction (XRD), UV-Vis diffuse reflectance spectroscopy and X-ray photoelectron spectroscopy (XPS). Composite morphologies and structures were investigated by scanning electron microscope (SEM). Synergistic of low energy gap in range of visible light and interfacial charge separate from TiO2 to ilmenite junction was evaluated in photocatalytic degradation of organic dye. The result from visible light catalytic dye degradation suggests that narrow bandgap energy is associated to ilmenite phase and sensitization by carbon with low recombination rate of generated electron-hole pair transfer. This mechanism occurred by multiphase junction could enhance visible light photocatalytic activity.
Fabricating Piezoelectric Tape of PZT-SKN
Authors: Hemadhulin O. , Kongphimai J. , Photankham W. , Srinuanlae P. , Wattanasarn H.
Published: September 2019

Tape ceramics are widely used in the sensor and electronic industries. In this work, we studied the ferroelectric properties of the 0.975Pb(Zr0.52Ti0.48)O3-0.025Sr(K0.25Nb0.75)O3 tape ceramic; (PZT-SKN). We fabricated the PZT-SKN using doctor blade technique with the slurry, obtained from the calcined of PZT-SKN mixing with organic solution. The crystalline structure was investigated by using X-ray diffraction, relative density, and Vickers Hardness technique. We also determined the dielectric properties and polarization electric field loops. The results of crystalline structure show that the percentage of perovskite is 97.57 %, the relative density is 98.4 %, and Vickers Hardness is 107 MPa. At the thickness 0.89 mm, the dielectric constant temperature is 1499 at 532 °C, the remnant polarization is 17 μC cm−2, Currie temperature is 552 °C, and piezoelectric coefficient is 235 pC N−1. The PZT-SKN tape ceramic has the ferroelectric properties better than tablet ceramic.
Biomass derived carbon materials for electrochemical energy storage devices
Authors: Kasian P. , Nilmoung S. , Pukird S.
Published: September 2019

This paper presents water hyacinth and sensitive plant derived carbon as a biomass carbon with utility for electrochemical energy storage. The prepared samples were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM). Electrochemical properties of the carbon materials were investigated by using cyclic voltammetry and galvanostatic charge-discharge. The specific capacitance value of 38 and 16 F g-1 were observed for biomass carbon of water hyacinth and sensitive, respectively.
Optical Gas Sensor based on Al-doped ZnO/ZnTPP hybrid thin film
Authors: Lorwongtragool P , Boonyopakorn N , Kladsomboon S
Published: September 2019

Hybrid optical gas sensors based on Al-doped ZnO/Zinc porphyrin (AZO/ZnTPP) thin films have been fabricated and demonstrated to detect ethanol vapor. Double-sensing layer of AZO and ZnTPP films were deposited on a cleaned glass substrate by RF magnetron sputtering and spin-coating techniques, respectively. We have investigated the influences of Al-doping concentration (0%, 2% and 3 wt% Al2O3) on ZnO structure with regarding to enhancing optical gas sensing properties when exposed the films to the volatile. Structural, electrical and optical properties of the AZO thin films were characterized and related to the optical gas sensing responses. It was found that an increase of Al-doped concentration in ZnO structure can also induce a potentially optical sensing response. These results were mentioned that an enhancement of carrier concentration due to Al3+ substitution in Zn2+ on ZnO structure can generate the adsorbed oxygen ion on the AZO surface as well. Absorption spectra of AZO thin films showed blue shift in near UV region due to releasing of electrons when the adsorbed oxygen ions were interacted with ethanol molecules. According to the introduced the AZO layer to form AZO/ZnTPP sensing film, the results could be demonstrated significantly enhanced the optical responses to the ethanol in broaden range of near UV-visible region at room temperature. Finally, the authors have suggest that the A3ZO/ZnTPP thin film exhibiting a good performance to detect ethanol vapor and overcome a conventional ZnTPP, ZnO/ZnTPP and A2ZO/ZnTPP thin films may be promoted as one of the optical gas sensor in an optoelectronic nose system due to broaden responses at room temperature.
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

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

Disruption 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

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

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.
CXCR4 inhibition modulates the tumor microenvironment and retards the growth of B16-OVA melanoma and Renca tumors
Authors: Saxena Ruchi , Wang Yan , Mier James W.
Published: September 2019

To determine whether blockade of the chemokine receptor CXCR4 might alter the tumor microenvironment and inhibit tumor growth, we tested the efficacy of the CXCR4 antagonist X4-136 as a single agent and in combination with various immune checkpoint inhibitors in the syngeneic murine melanoma model B16-OVA. We also tested its activity alone and in combination with axitinib in the renal cancer model Renca. We found that X4-136 exhibited potent single agent antitumor activity in the B16-OVA model that was additive to that of an anti-PDL1 antibody. The antitumor activities were associated with a reduction in the number of immunosuppressive regulatory T cells and myeloid-derived suppressor cells and an increase in the number of tumor-specific CD8+/perforin+ cells in the tumor-microenvironment. Apart from these immune effects, X4-136 alone and in combination with checkpoint inhibitors inhibited the Akt/FOXO-3a cell survival pathway in vitro and in vivo, suggesting that it might have antitumor activity independent of its effects on immune cell trafficking. Similar effects on tumor growth and cytotoxic T lymphocytes infiltration were observed in the Renca model. These studies show that the effects of CXCR4 blockade on immune cell trafficking might serve as a useful adjunct to immune checkpoint inhibitors and other therapies in the treatment of cancer.
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’.
Quantum contextuality in the Copenhagen approach
Authors: Jaeger Gregg
Published: September 2019

The origin and basis of the notion of quantum contextuality is identified in the Copenhagen approach to quantum mechanics, where context is automatically invoked by its requirement that the experimental arrangement involved in any measurements or set of measurements be taken into account while, in general, the outcome of a measurement may depend on other measurements immediately preceding or jointly performed on the same system. For Bohr, the specification of the experimental situation of any measurement is essential to its significance in light of complementarity and the omnipresence of the quantum of action in physics; for Heisenberg, the incompatibility of pairs of sharp measurements belonging to different situations coheres with both the completeness of the quantum state as an objective physical description and the principle of indeterminacy. Here, context in the Copenhagen approach is taken to be the equivalence class of experimental arrangements corresponding to a set of compatible measurements of quantum observables in standard quantum mechanics; the associated form of contextuality in quantum mechanics arises via the non-commutativity in general of sharp observables, proven by von Neumann, that can appear, providing
different
contexts. This notion is related to theoretical situations explored later by Bell, by Kochen and Specker, and by others in relation to the classification of hidden-variables theories and elsewhere in physics.

This article is part of the theme issue ‘Contextuality and probability in quantum mechanics and beyond’.
Non-locality, contextuality and valuation algebras: a general theory of disagreement
Authors: Abramsky Samson , Carù Giovanni
Published: September 2019

We establish a strong link between two apparently unrelated topics: the study of conflicting information in the formal framework of valuation algebras, and the phenomena of non-locality and contextuality. In particular, we show that these peculiar features of quantum theory are mathematically equivalent to a general notion of
disagreement
between information sources. This result vastly generalizes previously observed connections between contextuality, relat- ional databases, constraint satisfaction problems and logical paradoxes, and gives further proof that contextual behaviour is not a phenomenon limited to quantum physics, but pervades various domains of mathematics and computer science. The connection allows to translate theorems, methods and algorithms from one field to the other, and paves the way for the application of generic inference algorithms to study contextuality.

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

Synonymous 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

The 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

Growth 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 statement

We 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

Temperature 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.
Lipidomics analysis of juveniles’ blue mussels (Mytilus edulisL. 1758), a key economic and ecological species
Authors: Laudicella Vincenzo Alessandro , Beveridge Christine , Carboni Stefano , Franco Sofia Cota , Doherty Mary K. , Long Nina , Mitchell Elaine , Stanley Michelle S. , Whitfield Philip D. , Hughes Adam D.
Published: September 2019

Blue mussels (Mytilus edulisL.) are important components of coastal ecosystems functioning through benthopelagic coupling and ecosystem engineering. At the same time, mussel production is central in the economy of coastal areas. Therefore, understanding their nutritional, physiological and metabolic processes at key life stages is important for their management, both within food production systems and in wild populations.

Lipids are crucial molecules for bivalve growth, but their diversity and roles have been considered from fatty acid (FA) perspective. In this paper, we applied lipidomics to bivalve nutrition. Lipidomics provides a holistic perspective on lipid patterns; by examining the lipidome, important physiological information can be acquired. Here, we use controlled laboratory experiments to elucidate the responses to changes in the diet of newly settled mussels juveniles, one of the most critical life stages. The diets considered in this study are single strains diet ofCylindrotheca fusiformisCCAP 1017/2 – CYL,Isochrysis galbanaCCAP 927/1– ISO,Monodopsis subterraneanCCAP 848/1 – MONO,Nannochloropsis oceanicaCCAP 849/10– NANNO and a commercial algae paste –SP.

The diets had a significant effect on spat GR and WI, and according to their efficacy resulted ranked as follows: ISO>NANNO/CYL>SP>MONO. Spat FA composition and neutral lipid content (principally triacylglycerols - TG), were influenced by the diets. Furthermore, untargeted lipidomics also showed shifts in several phospholipid species, with changes related to the essential PUFA available from the diet. TG content, neutral lipids and several TG and FA species were correlated (Spearman R2>0.8 FDR p<0.05) with spat WI, suggesting their possible application as markers of mussel juvenile condition. The availability of dietary essential PUFA deeply modified the spat lipidome both for neutral and for polar lipids. This change in the lipidome could have major impacts on their ecology and their production for food.
ML-morph: A Fast, Accurate and General Approach for Automated Detection and Landmarking of Biological Structures in Images
Authors: Porto Arthur , Voje Kjetil L.
Published: September 2019

Morphometrics has become an indispensable component of the statistical analysis of size and shape variation in biological structures. Morphometric data has traditionally been gathered through low-throughput manual landmark annotation, which represents a significant bottleneck for morphometric-based phenomics. Here we propose a machine-learning-based high-throughput pipeline to collect high-dimensional morphometric data in images of semi rigid biological structures.

The proposed framework has four main strengths. First, it allows for dense phenotyping with minimal impact on specimens. Second, it presents landmarking accuracy comparable to manual annotators, when applied to standardized datasets. Third, it performs data collection at speeds several orders of magnitude higher than manual annotators. And finally, it is of general applicability (i.e., not tied to a specific study system).

State-of-the-art validation procedures show that the method achieves low error levels when applied to three morphometric datasets of increasing complexity, with error varying from 0.5% to 2% of the structure’s length in the automated placement of landmarks. As a benchmark for the speed of the entire automated landmarking pipeline, our framework places 23 landmarks on 13,686 objects (zooids) detected in 1684 pictures of fossil bryozoans in 3.12 minutes using a personal computer.

The proposed machine-learning-based phenotyping pipeline can greatly increase the scale, reproducibility and speed of data collection within biological research. To aid the use of the framework, we have developed a file conversion algorithm that can be used to leverage current morphometric datasets for automation, allowing the entire procedure, from model training all the way to prediction, to be performed in a matter of hours.