bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implicit food odour priming effects on reactivity and inhibitory control towards foods
Authors: Mas Marine , Brindisi Marie-Claude , Chabanet Claire , Chambaron Stéphanie 
Published: January 2020

AbstractThe food environment can interact with cognitive processing and influence eating behaviour. Our objective was to characterize the impact of implicit olfactory priming on inhibitory control towards food, in groups with different weight status. Ninety-two adults completed a modified Affective Shifting Task: they had to detect target stimuli and ignore distractor stimuli while being primed with non-attentively perceived odours. We measured reactivity and inhibitory control towards food pictures. Priming effects were observed on reactivity: participants with overweight and obesity were slower when primed with pear and pound cake odour respectively. Common inhibitory control patterns toward foods were observed between groups. We suggest that non-attentively perceived food cues influence bottom-up processing by activating distinguished mental representations according to weight status. Also, our data show that cognitive load influences inhibitory control toward foods. Those results contribute to understanding how the environment can influence eating behaviour in individuals with obesity.
MazeMaster: an open-source Python-based software package for controlling virtual reality experiments
Authors: Bexter Alexander , Kampa Björn M. 
Published: January 2020

AbstractIn the last 15 years, virtual realities have revolutionized behavior experiments in particular for rodents. In combination with treadmills, running wheels, or air-floating balls, the implementation of a virtual reality (VR) provides not only the opportunity to simultaneously explore behavior and neuronal activity in head-fixed animals under nearly natural conditions, but also allows full control over the visual sensory input presented to the animal. Furthermore, VRs can be combined with other sensory modalities such as auditory, tactile or olfactory stimuli. Despite the power of using VRs in animal experiments, available software packages are very limited, expensive and lack the required flexibility to design appropriate behavior and neurophysiology experiments. For this reason, we have developed the versatile, adaptable and easy to use VR environmentMazeMaster, an open-source, Python-based software package for controlling virtual reality setups and behavior experiments. The software package includes a graphical user interface (GUI) and can be integrated into standard electrophysiology and imaging setups even by non-programmers. Ready-made behavioral experiments such as multisensory discrimination in T-mazes are already implemented including full control for reward supply and bias correction. For more individual setup designs, the modularity ofMazeMasterallows more programming-affine users to extend the software with potentially missing features. WithMazeMaster, we offer a free and easy-to-use VR controller that will facilitate the implementation of VR setups in scientific laboratories. In addition,MazeMasterallows the design and control of common head-fixed rodent behavior paradigms with extensive acquisition of meta-data required for reproducible VR experiments. TheMazeMasterVR package, therefore, offers a collaboration tool for reproducible research within and across neuroscience laboratories according to the FAIR principles.
Polymorphisms in immunoglobulin heavy chain variable genes and their upstream regions
Authors: Mikocziova Ivana , Gidoni Moriah , Lindeman Ida , Peres Ayelet , Snir Omri , Yaari Gur , Sollid Ludvig M. 
Published: January 2020

ABSTRACTGermline variations in immunoglobulin genes influence the repertoire of B cell receptors and antibodies, and such polymorphisms may impact disease susceptibility. However, the knowledge of the genomic variation of the immunoglobulin loci is scarce. Here, we report 25 novel germlineIGHValleles as inferred from rearranged naïve B cell cDNA repertoires of 98 individuals. Thirteen novel alleles were selected for validation, out of which ten were successfully confirmed by targeted amplification and Sanger sequencing of non-B cell DNA. Moreover, we detected a high degree of variability upstream of the V-region in the 5’UTR, leader 1, and leader 2 sequences, and found that identical V-region alleles can differ in upstream sequences. Thus, we have identified a large genetic variation not only in the V-region but also in the upstream sequences ofIGHVgenes. Our findings challenge current approaches used for annotating immunoglobulin repertoire sequencing data.
PathWalks: Identifying pathway communities using a disease-related map of integrated information
Authors: Karatzas Evangelos , Zachariou Margarita , Bourdakou Marilena , Minadakis George , Oulas Anastasios , Kolios George , Delis Alex , Spyrou George M. 
Published: January 2020

AbstractUnderstanding disease underlying biological mechanisms and respective interactions remains an elusive, time consuming and costly task. The realization of computational methodologies that can propose pathway/mechanism communities and reveal respective relationships can be of great value as it can help expedite the process of identifying how perturbations in a single pathway can affect other pathways.Random walks is a stochastic approach that can be used for both efficient discovery of strong connections and identification of communities formed in networks. The approach has grown in popularity as it efficiently exposes key network components and reveals strong interactions among genes, proteins, metabolites, pathways and drugs. Using random walks in biology, we need to overcome two key challenges: 1) construct disease-specific biological networks by integrating information from available data sources as they become available, and 2) provide guidance to the walker so as it can follow plausible trajectories that comply with inherent biological constraints.In this work, we present a methodology called PathWalks, where a random walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study. We present maps forAlzheimer’s DiseaseandIdiopathic Pulmonary Fibrosisand we use them as case-studies for identifying pathway communities through the application of PathWalks.In the case ofAlzheimer’s Disease, the most visited pathways are the “Alzheimer’s disease” and the “Calcium signaling” pathways which have indeed the strongest association withAlzheimer’s Disease. Interestingly however, in the top-20 visited pathways we identify the “Kaposi sarcoma-associated herpesvirus infection” (HHV-8) and the “Human papillomavirus infection” (HPV) pathways suggesting that viruses may be involved in the development and progression ofAlzheimer’s. Similarly, most of the highlighted pathways inIdiopathic Pulmonary Fibrosisare backed by the bibliography. We establish that “MAPK signaling” and “Cytokine-cytokine receptor interaction” pathways are the most visited. However, the “NOD receptor signaling” pathway is also in the top-40 edges. InIdiopathic Pulmonary Fibrosissamples, increased NOD receptor signaling has been associated with augmented concentrations of certain strains of Streptococcus. Additional experimental evidence is required however to further explore and ascertain the above indications.
A novel metabarcoding strategy for studying nematode communities
Authors: Sikder Md. Maniruzzaman , Vestergård Mette , Sapkota Rumakanta , Kyndt Tina , Nicolaisen Mogens 
Published: January 2020

AbstractNematodes are widely abundant soil metazoa and often referred to as indicators of soil health. While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the ecology of nematodes remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. Objectives of the present study were (i) to compare commonly used primer sets and to identify the most suitable primer set for metabarcoding of nematodes; (ii) to establish and validate a high-throughput sequencing strategy for nematodes using Illumina paired-end sequencing. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition); SSU_04F/SSU_22R (18S rRNA, V1-V2 region); Nemf/18Sr2b (18S rRNA, V6-V8 region) from earlier studies; and MMSF/MMSR (18S rRNA, V4-V5 region), a newly developed primer set from this study. In order to test the primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 spiked soil samples (mock communities in soil), and 4 root/rhizosphere soil samples. We successfully amplified the target regions (I3-M11 partition of the COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were efficient in detecting nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets are suggested for studies of nematode communities in agricultural environments.
Testing of the survivin suppressant YM155 in a large panel of drug-resistant neuroblastoma cell lines
Authors: Michaelis Martin , Voges Yvonne , Rothweiler Florian , Weipert Fabian , Zia-Ahmad Amara , Cinatl Jaroslav , von Deimling Andreas , Westermann Frank , Rödel Franz , Wass Mark N. , Cinatl Jindrich 
Published: January 2020

AbstractThe survivin suppressant YM155 is a drug candidate for neuroblastoma. Here, we tested YM155 in 101 neuroblastoma cell lines (19 parental cell lines, 82 drug-adapted sublines). 77 cell lines displayed YM155 IC50s in the range of clinical YM155 concentrations. ABCB1 was an important determinant of YM155 resistance. The activity of the ABCB1 inhibitor zosuquidar ranged from being similar to that of the structurally different ABCB1 inhibitor verapamil to being 65-fold higher. ABCB1 sequence variations may be responsible for this, suggesting that the design of variant-specific ABCB1 inhibitors may be possible. Further, we showed that ABCC1 confers YM155 resistance. Previously, p53 depletion had resulted in decreased YM155 sensitivity. However,TP53-mutant cells were not generally less sensitive to YM155 thanTP53wild-type cells in this study. Finally, YM155 cross-resistance profiles differed between cells adapted to drugs as similar as cisplatin and carboplatin. In conclusion, the large cell line panel was necessary to reveal an unanticipated complexity of the YM155 response in neuroblastoma cell lines with acquired drug resistance. Novel findings include that ABCC1 mediates YM155 resistance and that YM155 cross-resistance profiles differ between cell lines adapted to drugs as similar as cisplatin and carboplatin.
Negative Overgeneralization is Associated with Anxiety and Mechanisms of Pattern Completion in Peripubertal Youth
Authors: McMakin Dana L. , Kimbler Adam , Tustison Nicholas J. , Pettit Jeremy W. , Mattfeld Aaron T. 
Published: January 2020

ABSTRACTBACKGROUNDThis study examines neural mechanisms of negative overgeneralization in peri-puberty to identify potential contributors to escalating anxiety during this sensitive period. Theories suggest that weakpattern separation(a neurocomputational process by which overlapping representations are made distinct, indexed by DG/CA3 hippocampal subfields) is a major contributor to negative overgeneralization. We alternatively propose that neuromaturation related to generalization and anxiety-related pathology in peri-puberty predicts contributions from strongpattern completion(a partial match of cues reinstates stored representations, indexed by CA1) and related modulatory mechanisms (amygdala, medial prefrontal cortices [mPFC]).METHODSYouth (N=34, 9-14 years) recruited from community and clinic settings participated in an emotional mnemonic similarity task while undergoing MRI. At Study, participants indicated the valence of images; at Test, participants made an ‘old/new’ recognition memory judgment. Critical lure stimuli, that were similar but not the same as images from Study, were presented at Test, and errors (“false alarms”) to negative relative to neutral stimuli reflected negative overgeneralization. Univariate, multivariate, and functional connectivity analyses were performed to evaluate mechanisms of negative overgeneralization.RESULTSNegative overgeneralization was related to greater and more similar patterns of activation in CA1 and both dorsal and ventral mPFC for negative relative to neutral stimuli. At Study, amygdala increased functional coupling with CA1 and dorsal mPFC during negative items that were later generalized.CONCLUSIONSNegative overgeneralization is rooted in amygdala and mPFC modulation at encoding and pattern completion at retrieval. These mechanisms could prove to reflect etiological roots of anxiety that precede symptom escalation across adolescence.
Constitutive Steroidal Glycoalkaloid Biosynthesis in Tomato is Regulated by the Clade IIIe Basic Helix-Loop-Helix Transcription Factors MYC1 and MYC2
Authors: Swinnen Gwen , De Meyer Margaux , Pollier Jacob , Molina-Hidalgo Francisco Javier , Ceulemans Evi , De Clercq Rebecca , Bossche Robin Vanden , Fernández-Calvo Patricia , Ron Mily , Pauwels Laurens , Goossens Alain 
Published: January 2020

ABSTRACTSpecialized metabolites are produced by plants to fend off biotic enemies. Across the plant kingdom, the biosynthesis of these defense compounds is promoted by jasmonate signaling in which clade IIIe basic helix-loop-helix (bHLH) transcription factors take on a central role. Tomato (Solanum lycopersicum) produces cholesterol-derived steroidal glycoalkaloids (SGAs) that act as phytoanticipins against a broad variety of herbivores and pathogens. The biosynthesis of SGAs from cholesterol occurs constitutively in tomato plants and can be further stimulated by jasmonates. Here, we demonstrate that the two tomato clade IIIe bHLH transcription factors, MYC1 and MYC2, redundantly and specifically control the constitutive biosynthesis of SGAs. Doublemyc1 myc2loss-of-function tomato hairy roots displayed suppressed constitutive expression of cholesterol and SGA biosynthesis genes, and consequently severely reduced levels of the main tomato SGAs α-tomatine and dehydrotomatine. In contrast, basal expression of genes involved in canonical jasmonate signaling or in the biosynthesis of highly jasmonate-inducible phenylpropanoid-polyamine conjugates was not affected. Furthermore, CRISPR-Cas9(VQR)-mediated genome editing of a specificcis-regulatory element, targeted by MYC1/2, in the promoter of a cholesterol biosynthesis gene led to decreased constitutive expression of this gene, but did not affect its jasmonate inducibility. Our results demonstrate that clade IIIe bHLH transcriptional regulators might have evolved to regulate the biosynthesis of specific constitutively accumulating specialized metabolites independent of jasmonate signaling.One sentence summaryThe clade IIIe basic helix-loop-helix transcription factors MYC1 and MYC2 control the constitutive biosynthesis of tomato steroidal glycoalkaloids and might do so independently of jasmonate signaling.
Behavioral recovery after a spinal deafferentation injury in monkeys does not correlate with corticospinal sprouting
Authors: Crowley Matthew , Lilak Alayna , Garner Joseph , Darian-Smith Corinna 
Published: January 2020

AbstractA long held view in the spinal cord injury field is that corticospinal terminal sprouting is needed for new connections to form that then mediate behavioral recovery. The inference is that more extensive sprouting predicts greater recovery, though there is little evidence to support this. Here we compare behavioral data from two established deafferentation injury models in monkeys, to provide a clear example that sprouting does not track with behavioral recovery.
A derivation error that affects carbon balance models exists in the current implementation of the modified Arrhenius function
Authors: Murphy Bridget , Stinziano Joseph R. 
Published: January 2020

SummaryUnderstanding biological temperature responses is crucial to predicting global carbon fluxes. The current approach to modelling temperature responses of photosynthetic capacity in large scale modelling efforts uses a modified Arrhenius equation.We rederived the modified Arrhenius equation from the source publication from 1942 and uncovered a missing term that was dropped by 2002. We compare fitted temperature response parameters between the correct and incorrect derivation of the modified Arrhenius equation.We find that most parameters are minimally affected, though activation energy is impacted quite substantially. We then scaled the impact of these small errors to whole plant carbon balance and found that the impact of the rederivation of the modified Arrhenius equation on modelled daily carbon gain causes a meaningful deviation of ~18% day−1.This suggests that the error in the derivation of the modified Arrhenius equation has impacted the accuracy of predictions of carbon fluxes at larger scales since >40% of Earth System Models contain the erroneous derivation. We recommend that the derivation error be corrected in modelling efforts moving forward.
Assesssing the role of humans in Greater Antillean land vertebrate extinctions: new insights from Cuba
Authors: Orihuela Johanset , Viñola Lázaro W. , Vázquez Osvaldo Jiménez , Mychajliw Alexis M. , de Lara Odlanyer Hernández , Lorenzo Logel , Soto-Centeno J. Angel 
Published: January 2020

ABSTRACTThe Caribbean archipelago is a hotspot of biodiversity characterized by a high rate of extinction. Recent studies have examined these losses, but the causes of the Antillean Late Quaternary vertebrate extinctions, and especially the role of humans, are still unclear. Current results provide support for climate-related and human-induced extinctions, but often downplaying other complex bio-ecological factors that are difficult to model or to detect from the fossil and archaeological record. Here, we discuss Caribbean vertebrate extinctions and the potential role of humans derived from new and existing fossil and archaeological data from Cuba. Our results indicate that losses of Cuba’s native fauna occurred in three waves: one during the late Pleistocene and early Holocene, a second during the middle Holocene, and a third one during the last 2 ka, coinciding with the arrival of agroceramists and the early Europeans. The coexistence of now-extinct species with multiple cultural groups in Cuba for over 4 ka implies that Cuban indigenous non-ceramic cultures exerted far fewer extinction pressures to native fauna than the later agroceramists and Europeans that followed. This suggests a determinant value to increased technological sophistication and demographics as the most plausible effective extinction drivers.
Expression Atlas ofSelaginella moellendorffiiProvides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots
Authors: Ferrari Camilla , Shivhare Devendra , Hansen Bjoern Oest , Pasha Asher , Esteban Eddi , Provart Nicholas J. , Kragler Friedrich , Fernie Alisdair , Tohge Takayuki , Mutwil Marek 
Published: January 2020

AbstractSelaginella moellendorffii is a representative of the lycophyte lineage that is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only a few studies have investigated the expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of the transcriptional programs behind these traits. We present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles for S. moellendorffii. We show that the transcriptional gene module responsible for the biosynthesis of lignocellulose evolved in the ancestor of vascular plants and pinpoint the duplication and subfunctionalization events that generated multiple gene modules involved in the biosynthesis of various cell wall types. We demonstrate how secondary metabolism is transcriptionally coordinated and integrated with other cellular pathways. Finally, we identify root-specific genes and show that the evolution of roots did not coincide with an increased appearance of gene families, suggesting that the development of new organs does not coincide with increased fixation of new gene functions. Our updated database at conekt.plant.tools represents a valuable resource for studying the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom.
Attitude towards entrepreneurship: a study among Asnaf Millennials in Malaysia
Authors: Mahmood Tengku Mohd Azizuddin Tuan , Mamun Abdullah Al , Ibrahim Mohamed Dahlan 
Published: January 2020

Purpose
This study intended to determine the effect of selected entrepreneurial traits on the attitude of Asnaf Millennials in Malaysia towards entrepreneurship.

Design/methodology/approach
This is a cross-sectional study that collected the quantitative data via structured interviews from 310 randomly selected Asnaf Millennials from Kelantan, Malaysia.

Findings
The findings confirmed the positive and statistically significant effect of innovativeness, internal locus of control, need for achievement and proactive personality on the attitude of Asnaf Millennials on entrepreneurship.

Originality/value
This study focussed on the development of non-cognitive skills for individual characteristics regarding entrepreneurship for the benefit of development practitioners and policymakers. The government and development organisations should focus on developing entrepreneurial traits that are expected to improve the attitude towards entrepreneurship and increase the entrepreneurial activities in Malaysia. This initiative can improve the socio-economic condition of Asnaf Millennials with low income.
Coffee brews composition from coffea canephora cultivars with different fruit-ripening seasons
Authors: Mori Andre Luiz Buzzo , Viegas Marcelo Caldeira , Ferrão Maria Amélia Gava , Fonseca Aymbiré Francisco , Ferrão Romário Gava , Benassi Marta Toledo 
Published: January 2020

PurposeThe purpose of this paper is to evaluate the contents of bioactive compounds and/or that of interest for the brew quality (trigonelline, caffeine, total chlorogenic acids and melanoidins), acidity and antioxidant activity (AA) of roasted coffee brews produced with Coffea canephora.Design/methodology/approachCoffee samples corresponded to three cultivars – Diamante ES8112, ES8122 “Jequitibá,” and Centenária ES8132 – with different fruit-ripening seasons (early, medium and late, respectively). The study evaluated five genotypes from each cultivar and coffees were cultivated in two sites, a total of 30 samples.FindingsThe average contents on the coffee brews varied from 1,176 to 1,452 µg mL−1 for caffeine; from 206 to 413 µg mL−1 for trigonelline; from 528 to 942 µg mL−1 for total chlorogenic acids; from 6.8 to 7.8 mg mL−1 for melanoidins; showing total titratable acidity between 1.15 and 1.79 mL of NaOH 0.1 mol L−1 by 20 mL of the brew. AA varied from 6.78 to 8.80 mg of TROLOX mL−1, correlating positively with the contents of caffeine, total chlorogenic acids, melanoidins. Fruit-ripening seasons had no effect on coffee brew composition and AA.Originality/valueThe results presented provide not only a unique analysis of coffee brew from genotypes developed to improve the good agricultural practice and brew quality, but also relevant information that can be extended for research in coffee composition and for the coffee industry.