bluuebunny/crossref_metadata_2025_split huggingface dataset:
A descending dopamine pathway conserved from basal vertebrates to mammals
Authors: Ryczko Dimitri , Cone Jackson J. , Alpert Michael H. , Goetz Laurent , Auclair François , Dubé Catherine , Parent Martin , Roitman Mitchell F. , Alford Simon , Dubuc Réjean 
Published: April 2016

Significance
In vertebrates, the contribution of dopamine neurons to locomotor control is traditionally attributed to their ascending projections to the basal ganglia that, in turn, project down to brainstem locomotor networks. We recently discovered in lampreys that brainstem networks receive a direct descending dopaminergic input that increases locomotor output. Here, we show that this descending dopaminergic pathway is conserved in higher vertebrates. We found that dopamine is released in salamander brainstem locomotor networks, together with reticulospinal cell activation, known to trigger locomotion. Dopamine is released in rat brainstem locomotor networks, and amphetamine potentiates dopamine release in vivo. Finally, brainstem locomotor networks in human tissue contain dopaminergic terminals. Our findings have important implications for understanding the locomotor role of dopamine in vertebrates.
Anthropogenic disturbances jeopardize biodiversity conservation within tropical rainforest reserves
Authors: Martínez-Ramos Miguel , Ortiz-Rodríguez Iván A. , Piñero Daniel , Dirzo Rodolfo , Sarukhán José 
Published: April 2016

Significance
Human activities disrupt ecosystem functioning and jeopardize biodiversity, especially in the tropics. Increasing evidence shows this disturbance is happening even within reserves, but the underlying causative mechanisms are unclear. This paper provides a unique long-term (four decades) empirical, experimental, and modeling study showing how cascading effects of human disturbances affect the structure, dynamics, and functioning of a tropical rainforest reserve. In particular, we provide evidence of how fragmentation and defaunation, operating in synergy, stimulated the population explosion of a long-lived understory palm that, in turn, was followed by reductions in biodiversity and changes in some ecosystem properties.
Origins of the brain networks for advanced mathematics in expert mathematicians
Authors: Amalric Marie , Dehaene Stanislas 
Published: April 2016

Significance
Our work addresses the long-standing issue of the relationship between mathematics and language. By scanning professional mathematicians, we show that high-level mathematical reasoning rests on a set of brain areas that do not overlap with the classical left-hemisphere regions involved in language processing or verbal semantics. Instead, all domains of mathematics we tested (algebra, analysis, geometry, and topology) recruit a bilateral network, of prefrontal, parietal, and inferior temporal regions, which is also activated when mathematicians or nonmathematicians recognize and manipulate numbers mentally. Our results suggest that high-level mathematical thinking makes minimal use of language areas and instead recruits circuits initially involved in space and number. This result may explain why knowledge of number and space, during early childhood, predicts mathematical achievement.
Molecular convergence of clock and photosensory pathways through PIF3–TOC1 interaction and co-occupancy of target promoters
Authors: Soy Judit , Leivar Pablo , González-Schain Nahuel , Martín Guiomar , Diaz Céline , Sentandreu Maria , Al-Sady Bassem , Quail Peter H. , Monte Elena 
Published: April 2016

SignificanceThis study defines a molecular mechanism by which clock- and light-signaling pathways converge in Arabidopsis. The data reveal that Timing of CAB expression 1 (TOC1), an essential core component of the central oscillator, binds to and represses Phytochrome-interacting factor (PIF) transcriptional activators, which also are the direct molecular signaling partners of the phytochrome photosensory receptors. This finding shows that TOC1 functions as a clock output transducer, directly linking the core oscillator to a pleiotropically acting transcriptional network through repression of target genes. Collectively, in the plant, these components comprise a transcriptionally centered signaling hub that provides clock-imposed gating of PIF-mediated, photosensory-regulated diurnal growth patterns. These results provide a framework for future research aimed at understanding how circadian dynamics are integrated with other plant physiological processes important for optimal plant fitness.
Dual Cannabis and Alcohol use Disorders in Young Adults: Problems Magnified
Authors: Hayaki Jumi , Anderson Bradley J. , Stein Michael D. 
Published: April 2016

Background: Alcohol and marijuana are the 2 most commonly used substances among young adults. The present study examines whether having 2 DSM-5 ( Diagnostic and Statistical Manual of Mental Disorders, 5th Edition) diagnoses (alcohol and cannabis) is associated with greater problems than having 1 (alcohol or cannabis) diagnosis. Methods: Participants were 307 young adults (18–25 years) from the community who met criteria for DSM-5 alcohol use disorder (AUD), cannabis use disorder (CUD), or both (dual use disorder [DUD]). Participants reported alcohol and marijuana use in the past 90 days (Timeline Follow-Back), alcohol problems (Short Inventory of Problems), and marijuana problems (Marijuana Problems Scale). Results: Eighty-four participants (27.4%) met criteria for AUD, 107 (34.9%) met criteria for CUD, and 116 (37.8%) met criteria for DUD. In multivariate analyses, the DUD group reported greater alcohol use frequency and more alcohol problems than the CUD-only group but not the AUD-only group. However, DUD individuals reported greater drinking intensity than singly diagnosed individuals. Those with DUD reported a greater proportion of marijuana consumption days than the AUD-only group but not the CUD-only group. However, DUD individuals reported more marijuana problems than both singly diagnosed groups. Conclusions: Results show that the concurrent presence of both DSM-5 AUD and CUD is associated with heavier drinking patterns and greater marijuana problems than disordered use of either substance alone, thus affirming the magnified severity of alcohol and marijuana use that accompanies dual DSM-5 alcohol and marijuana use disorders.
Generating hESCs with reduced immunogenicity by disrupting TAP1 or TAPBP
Authors: Cui Di , Wang Jinping , Zeng Yelin , Rao Lingjun , Chen Haide , Li Wenling , Li Yang , Li Hui , Cui Chun , Xiao Lei 
Published: April 2016

Abstract
Human embryonic stem cells (hESCs) are thought to be a promising resource for cell therapy, while it has to face the major problem of graft immunological rejection. Major histocompatibility complex (MHC) class I expressed on the cell surface is the major cause of graft rejection. Transporter associated with antigen presentation 1 (TAP1) and TAP-associated glycoprotein (TAPBP) play important roles in regulating MHC class I expression. In this study, we generated TAP1- and TAPBP-deficient hESC lines, respectively, using transcription activator-like effector nucleases technique. These cells showed deficient expression of MHC class I on the cell surface and reduced immunogenicity compared with wild types, but maintained normal pluripotency, karyotypes, and differentiation ability. Thus, our findings are instrumental in developing a universal cell resource with both pluripotency and hypo-immunogenicity for transplantation therapy in the future.
Anti-inflammatory activity of myricetin from Diospyros lotus through suppression of NF-κB and STAT1 activation and Nrf2-mediated HO-1 induction in lipopolysaccharide-stimulated RAW264.7 macrophages
Authors: Cho Byoung Ok , Yin Hong Hua , Park Sang Hyun , Byun Eui Baek , Ha Hun Yong , Jang Seon Il 
Published: April 2016

Abstract
Diospyros lotus is traditionally used for the treatment of diabetes, diarrhea, tumor, and hypertension. The purpose of this study was to investigate the anti-inflammatory effect and underlying molecular mechanisms of myricetin in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. Myricetin dose-dependently suppressed the production of pro-inflammatory mediators (NO, iNOS, PGE2, and COX-2) in LPS-stimulated RAW264.7 macrophages. Myricetin administration decreased the production of NO, iNOS, TNF-α, IL-6, and IL-12 in mice. Myricetin decreased NF-κB activation by suppressing the degradation of IκBα, nuclear translocation of p65 subunit of NF-κB, and NF-κB DNA binding activity in LPS-stimulated RAW264.7 macrophages. Moreover, myricetin attenuated the phosphorylation of STAT1 and the production of IFN-β in LPS-stimulated RAW264.7 macrophages. Furthermore, myricetin induced the expression of HO-1 through Nrf2 translocation. In conclusion, these results suggest that myricetin inhibits the production of pro-inflammatory mediators through the suppression of NF-κB and STAT1 activation and induction of Nrf2-mediated HO-1 expression in LPS-stimulated RAW264.7 macrophages.
Increasing school autonomy in Western Europe: a comparative analysis of its causes and forms
Authors: Christ Claudia , Dobbins Michael 
Published: April 2016

ABSTRACT
This article comparatively explores the driving forces behind and variations in the trend toward increasing school autonomy in England, Germany, Italy and Sweden. In a first step, we focus on the impact of processes of internationalization and the spread of post-materialist values. We hypothesize, on the one hand, that school autonomy may be a direct result of international policy promotion by transnational organizations and, on the other hand, that post-materialist values may lead to either an increase or decrease of school autonomy, depending on the specific form of school governance. In a second step, we examine the impact of partisan factors and explore the hypothesis that center-right and center-left parties pursue different objectives when introducing school autonomy policies. We assume that conservative parties will grant more extensive decision-making autonomy to schools in order to promote competition, accountability and efficiency, while leftist governments will use increased school autonomy as means of promoting political participation and democracy. In the empirical case studies we thus examine whether the partisan orientation of governing coalitions has brought about different school autonomy models in the four countries.
R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter
Authors: Yang Jing , Jin Qi-Yu , Zhang Biao , Shen Hong-Bin 
Published: April 2016

Abstract
Motivation: Inter-residue contacts in proteins dictate the topology of protein structures. They are crucial for protein folding and structural stability. Accurate prediction of residue contacts especially for long-range contacts is important to the quality of ab inito structure modeling since they can enforce strong restraints to structure assembly.
Results: In this paper, we present a new Residue-Residue Contact predictor called R2C that combines machine learning-based and correlated mutation analysis-based methods, together with a two-dimensional Gaussian noise filter to enhance the long-range residue contact prediction. Our results show that the outputs from the machine learning-based method are concentrated with better performance on short-range contacts; while for correlated mutation analysis-based approach, the predictions are widespread with higher accuracy on long-range contacts. An effective query-driven dynamic fusion strategy proposed here takes full advantages of the two different methods, resulting in an impressive overall accuracy improvement. We also show that the contact map directly from the prediction model contains the interesting Gaussian noise, which has not been discovered before. Different from recent studies that tried to further enhance the quality of contact map by removing its transitive noise, we designed a new two-dimensional Gaussian noise filter, which was especially helpful for reinforcing the long-range residue contact prediction. Tested on recent CASP10/11 datasets, the overall top L/5 accuracy of our final R2C predictor is 17.6%/15.5% higher than the pure machine learning-based method and 7.8%/8.3% higher than the correlated mutation analysis-based approach for the long-range residue contact prediction.
Availability and Implementation: http://www.csbio.sjtu.edu.cn/bioinf/R2C/
Contact: hbshen@sjtu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Phylogeographic assessment of the northern pygmy mouse, Baiomys taylori
Authors: Light Jessica E. , Ostroff Marcy O. , Hafner David J. 
Published: April 2016

AbstractThe northern pygmy mouse, Baiomys taylori, occurs throughout the Trans-Mexican Volcanic Belt and southern Altiplano of central Mexico and extends northward in 3 projections into northern Mexico and the United States. We used mitochondrial DNA (from the cytochrome-b and NADH dehydrogenase 2 genes) and morphological data to assess diversity within B. taylori across its geographic range in relation to recognized subspecies and putative physiographic filter-barriers. Our results indicate 5 distinct mitochondrial clades despite little morphological variation across the species’ geographic range. The Sierra Madre Oriental and Sierra Madre Occidental separate clades representing the eastern (Gulf coastal lowlands), central (Altiplano), and Pacific coastal lowlands, which appear to be divided into 3 major mitochondrial clades. Based on a preliminary analysis of cranial morphology, we are able to reject the Balcones Escarpment of Texas as an impediment to the well-documented recent northern expansion of the species, while we are unable to reject a causal role of filter-barriers elsewhere in subspecific differentiation. Revision of subspecific taxonomy must await further genetic sampling, particularly along the western and southeastern portions of the species’ distribution.El ratón pigmeo norteño, Baiomys taylori, se distribuye a través del Eje Volcánico Transmexicano y la parte sur del Altiplano del centro de México y se extiende hacia el norte de México y los Estados Unidos en tres direcciones. Utilizamos ADN mitocondrial (del citocromo-b y del gen NADH deshidrogenasa) y datos morfológicos para evaluar la diversidad dentro de B. taylori a través de su rango geográfico en relación con las subespecies reconocidas y las supuestas barreras-filtro fisiográficas. Nuestros resultados indican 5 clados mitocondriales distintos a pesar de la escasa variación morfológica a lo largo de su rango geográfico. La Sierra Madre Oriental y la Sierra Madre Occidental separan los clados representantes de las tierras bajas del este (tierras bajas del Golfo), del centro (Altiplano), y las tierras bajas del Pacífico, que parecen estar divididas en 3 clados mitocondriales principales. Basados en un análisis preliminar de la morfología craneal, pudimos rechazar el Escarpe de Balcones de Texas como un impedimento a la bien documentada expansión norteña de la especie, mientras que no fue posible rechazar el rol causal de las otras barreras-filtro en la diferenciación subespecífica. La revisión de la taxonomía subespecífica deberá esperar un mayor muestreo genético, en particular a lo largo de las porciones oeste y sureste de la distribución de la especie.
DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context
Authors: Pisareva Vera P. , Pisarev Andrey V. 
Published: April 2016

Abstract
During eukaryotic translation initiation, the 43S preinitiation complex (43S PIC), consisting of the 40S ribosomal subunit, eukaryotic initiation factors (eIFs) and initiator tRNA scans mRNA to find an appropriate start codon. Key roles in the accuracy of initiation codon selection belong to eIF1 and eIF1A, whereas the mammalian-specific DHX29 helicase substantially contributes to ribosomal scanning of structured mRNAs. Here, we show that DHX29 stimulates the recognition of the AUG codon but not the near-cognate CUG codon regardless of its nucleotide context during ribosomal scanning. The stimulatory effect depends on the contact between DHX29 and eIF1A. The unique DHX29 N-terminal domain binds to the ribosomal site near the mRNA entrance, where it contacts the eIF1A OB domain. UV crosslinking assays revealed that DHX29 may rearrange eIF1A and eIF2α in key nucleotide context positions of ribosomal complexes. Interestingly, DHX29 impedes the 48S initiation complex formation in the absence of eIF1A perhaps due to forming a physical barrier that prevents the 43S PIC from loading onto mRNA. Mutational analysis allowed us to split the mRNA unwinding and codon selection activities of DHX29. Thus, DHX29 is another example of an initiation factor contributing to start codon selection.
Re-evaluation of MelCast for Fungicide Scheduling in Mid-Atlantic Watermelon
Authors: Everts Kathryne L. , Korir Robert C. , Newark Mason J. 
Published: April 2016

MelCast was originally tested in the mid-Atlantic production region from 1996 to 2000. Scheduling using MelCast reduced applications in comparison to weekly fungicide applications without a loss of efficacy or yield. The reduction in fungicide applications was seen as a success. The objective of this research, conducted in 2012-2014, was to determine whether the disease management and yields continued to be similar in watermelon crops managed with MelCast where fungicide applications were reduced, in comparison to a weekly schedule. Accepted for publication 14 March 2016. Published 29 March 2016.
A Quantifiable Disease Severity Rating Scale for Frogeye Leaf Spot of Soybean
Authors: Price Trey , Purvis Myra , Pruitt Hunter 
Published: April 2016

A quantifiable rating scale based on disease severity was developed for frogeye leaf spot (FLS) using image analysis software. The scale may be useful for estimating FLS severity in producer fields, which may aid in management decisions. Other applications of the scale include quantifying FLS severity in cultivar evaluations and foliar fungicide efficacy trials. Accepted for publication 17 February 2016. Published 22 February 2016.
Susceptibility of Hop Cultivars to Downy Mildew: Associations with Chemical Characteristics and Region of Origin
Authors: Woods Joanna L. , Gent David H. 
Published: April 2016

Hop downy mildew (caused by Pseudoperonospora humuli) is a yield-limiting disease in many hop-production regions of the world. In this research, 110 cultivars that are or were widely grown in the United States, Europe, or Australasia were evaluated in western Oregon over three years for their reaction to the shoot infection phase of downy mildew and vigor. There was a large range of downy mildew susceptibility and vigor amongst commercial cultivars, with some cultivars possessing a very high level of resistance. Overall, however, disease resistance and vigor were significantly greater in cultivars originating from Europe than those originating from the United States, Japan, and Australia/New Zealand. Amongst a subset of 79 cultivars, vigor was negatively correlated with levels, in cones, of cohumulone, a chemical constitute of bittering acids typically found in germplasm derived from North America. The generally poor vigor observed in cultivars derived outside of Europe likely is indicative of a lack of tolerance to the crown infection phase of the disease. Thus, the best sources of downy mildew resistance seems to be found in cultivars from the United Kingdom and continental Europe, and such cultivars are typically lower yielding and lack distinctive aroma and flavor characteristics presently desired by craft brewers. Introgression of downy mildew resistance into North American germplasm with high yield and desirable brewing characteristics is needed. Accepted for publication 3 March 2016. Published 7 March 2016.
Distribution and Abundance of Heterodera glycines and Macrophomina phaseolina in Ohio
Authors: Lopez-Nicora Horacio D. , Simon Abasola C. M. , Dossman Bryant C. , Paul Pierce A. , Dorrance Anne E. , Lindsey Laura E. , Niblack Terry L. 
Published: April 2016

Soybean and corn are grown on more than 60% of the arable land in Ohio. The soybean cyst nematode (SCN) is responsible for significant losses incurred by soybean growers every year. The fungus that causes charcoal rot, Macrophomina phaseolina, causes significant yield loss in soybeans worldwide and can also affect corn. Both organisms are soil-borne pathogens. The objective of this study was to determine the presence, distribution, and abundance of both SCN and M. phaseolina in soybean and corn fields across Ohio. During 2013 and 2014, composite soil samples were collected from 370 corn and soybean fields. Samples were processed for SCN eggs/100 cm3 and M. phaseolina colony forming units (CFU)/g soil with standard techniques. Results from this study revealed a widespread distribution of SCN and M. phaseolina in both soybean and corn fields. This study represents the first survey on the distribution of M. phaseolina in Ohio and the findings will be used to educate producers on the potential risks posed by both SCN and M. phaseolina. Accepted for publication 19 February 2016. Published 3 March 2016.
Functional enrichments of disease variants across thousands of independent loci in eight diseases
Authors: Sarkar Abhishek K. , Ward Lucas D. , Kellis Manolis 
Published: April 2016

AbstractFor most complex traits, known genetic associations only explain a small fraction of the narrow sense heritability prompting intense debate on the genetic basis of complex traits. Joint analysis of all common variants together explains much of this missing heritability and reveals that large numbers of weakly associated loci are enriched in regulatory regions, but fails to identify specific regions or biological pathways. Here, we use epigenomic annotations across 127 tissues and cell types to investigate weak regulatory associations, the specific enhancers they reside in, their downstream target genes, their upstream regulators, and the biological pathways they disrupt in eight common diseases. We show weak associations are significantly enriched in disease-relevant regulatory regions across thousands of independent loci. We develop methods to control for LD between weak associations and overlap between annotations. We show that weak non-coding associations are additionally enriched in relevant biological pathways implicating additional downstream target genes and upstream disease-specific master regulators. Our results can help guide the discovery of biologically meaningful, but currently undetectable regulatory loci underlying a number of common diseases.
The contribution of alternative splicing probability to the coding expansion of the genome
Authors: Oesterreich Fernando Carrillo , Bowne-Anderson Hugo , Howard Jonathon 
Published: April 2016

AbstractAlternative splicing results in the inclusion or exclusion of exons in an RNA, thereby allowing a single gene to code for multiple RNA isoforms. Genes are often composed of many exons, allowing combinatorial choice to significantly expand the coding potential of the genome. How much coding potential is gained by alternative splicing and what is the main contributor: alternative-splicing-depth or exon-count? Here we develop a splice-site-centric quantification method, allowing us to characterize transcriptome-wide alternative splicing with a simple probabilistic model, enabling species-wide comparison. We use information theory to quantify the coding potential gain and show that an increase in alternative splicing probability contributes more to transcriptome expansion than exon-count. Our results suggest that dominant isoforms are co-expressed alongside many minor isoforms. We propose that this solves two problems simultaneously, that is, expression of functional isoforms and expansion of the transcriptome landscape potentially without a direct function, but available for evolution.