bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telepsychiatry in Asperger’s syndrome
Authors: Clarke C. S. 
Published: July 2017

BackgroundInternet technology offers psychiatrists new opportunities for remote interaction with patients. It also raises issues regarding therapeutic effectiveness, safety, technical problems and possibilities for overcoming them, and matters related to specific mental health problems such as autism. The case presented concerns an adolescent male with severe social impairment and isolation as manifestations of Aspergers syndrome.MethodsThe patient was accepted contact with psychiatric services through telepsychiatry, which enabled initial assessment and the development of a therapeutic relationship.ResultsIn due course the patient was able to attend the clinic in person. He became somewhat reconciled to his family. With appropriate adaptations he was able to resume his education and career.ConclusionsTelepsychiatry shows promise in engaging with patients with autism spectrum disorders. As experience accrues, there is some evidence that it is safe and effective. Adaptations to traditional clinical psychotherapy may be required.
Late Tortonian–Quaternary tectonic evolution of central Sicily: the major role of the strike-slip deformation
Authors: CATALANO STEFANO , PAVANO FRANCESCO , ROMAGNOLI GINO , TORTORICI GIUSEPPE , TORTORICI LUIGI 
Published: July 2017

AbstractWe here propose a new kinematic picture of central Sicily based on the results of detailed field mapping of the region, combined with structural analyses and the interpretation of the available literature subsurface data. Our study focused on the tectonic boundary of a structural depression, the Caltanissetta Trough, which is now filled with allochthonous terrains resting on the deep-seated inverted African palaeomargin units. Our data refer to the tectonosedimentary evolution of the thrust-top basins, from Late Tortonian to Quaternary times. The study points out the occurrence of regional E–W-oriented dextral shear zones, cutting the NE-oriented trends of the thrust belt. This new evidence would confirm the major role of the E–W trend in the tectonic inversion of the external portions of the Africa palaeomargin in Sicily. Our results could contribute to a better understanding of the location in Sicily of the tectonic lineaments accommodating the hundreds of kilometres of lateral displacement, caused by the Late Miocene–Quaternary Tyrrhenian Basin opening to the north of the island.
An assessment of Irish farmers’ knowledge of the risk of spread of infection from animals to humans and their transmission prevention practices
Authors: MAHON M. M. , SHEEHAN M. C. , KELLEHER P. F. , JOHNSON A. J. , DOYLE S. M. 
Published: July 2017

SUMMARYThe aim of this study was to ascertain farmers’ knowledge of the risk of spread of infection from animals to humans, and their transmission prevention practices. This was a survey of farmers who submitted material to Ireland's Regional Veterinary Laboratories in 2015. There was an 84% response rate (1044 farmers). Ninety per cent of farmers were not aware that infection can be acquired from apparently healthy animals. Over half were not aware that disease could be contracted from sick poultry or pets. Conversely, the knowledge of the risk to pregnant women of infection from birthing animals was high (88%). Four-fifths of farmers sourced drinking water from a private well, and of these, 62% tested their water less frequently than once a year. Of dairy farmers, 39% drank unpasteurised milk once a week or more frequently. Veterinarians were the most commonly cited information source for diseases on farms. The survey findings indicate that the level of farmers’ knowledge and awareness of the spread of infection from animals to humans is a concern. Further education of the farming community is needed to increase awareness of both the potential biohazards present on farms and the practical measures that can be taken to mitigate the risk of zoonoses.
Corporate political activity of the dairy industry in France: an analysis of publicly available information
Authors: Mialon Melissa , Mialon Jonathan 
Published: July 2017

AbstractObjectiveIn the present study, we used a structured approach based on publicly available information to identify the corporate political activity (CPA) strategies of three major actors in the dairy industry in France.DesignWe collected publicly available information from the industry, government and other sources over a 6-month period, from March to August 2015. Data collection and analysis were informed by an existing framework for classifying the CPA of the food industry.Setting/SubjectsOur study included three major actors in the dairy industry in France: Danone, Lactalis and the Centre National Interprofessionnel de l’Economie Laitière (CNIEL), a trade association.ResultsDuring the period of data collection, the dairy industry employed CPA practices on numerous occasions by using three strategies: the ‘information and messaging’, the ‘constituency building’ and the ‘policy substitution’ strategies. The most common practice was the shaping of evidence in ways that suited the industry. The industry also sought involvement in the community, establishing relationships with public health professionals, academics and the government.ConclusionsOur study shows that the dairy industry used several CPA practices, even during periods when there was no specific policy debate on the role of dairy products in dietary guidelines. The information provided here could inform public health advocates and policy makers and help them ensure that commercial interests of industry do not impede public health policies and programmes.
A shower before bedtime may improve the sleep onset latency of youth soccer players
Authors: Whitworth‐Turner Craig , Di Michele Rocco , Muir Ian , Gregson Warren , Drust Barry 
Published: July 2017

AbstractDuring the competitive season, soccer players are likely exposed to numerous factors that may disrupt the process of sleep. The current investigation looked to evaluate a practical sleep hygiene strategy (10‐min showering at ∼40°C before lights out), within a group of 11 youth soccer players in comparison to normal sleeping conditions (control). Each condition consisted of three days within a randomised crossover trial design. Sleep information was collected using a commercial wireless bedside sleep monitor. Measures of skin temperature were evaluated using iButton skin thermistors to establish both distal and proximal skin temperatures and distal to proximal gradient. The shower intervention elevated distal skin temperature by 1.1°C (95% CI: 0.1–2.1°C, p = .04) on average prior to lights out. The elevation in distal temperature was also present during the first 30‐min following lights out (1.0°C, 95% CI: 0.4–1.6°C, p < .01). The distal to proximal gradient also showed a significant effect between the conditions within the first 30‐min after lights out (0.7°C, 95% CI: 0.3–1.2°C, p < .01). On average the sleep latency of the youth soccer players was −7‐min lower (95% CI: −13 to −2 min, p < .01) and sleep efficiency +2% higher (95% CI: 1–3%; p < .01) in the shower condition. These findings demonstrate that a warm shower performed before lights out may offer a practical strategy to promote thermoregulatory changes that may advance sleep onset latency and improve sleep efficiency in athletes.
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential
Authors: Meng Xianwen , Chen Qi , Zhang Peijing , Chen Ming 
Published: July 2017

Abstract

Summary
Circular RNAs (circRNAs), a novel class of endogenous RNAs, are widespread in eukaryotic cells. Emerging roles in diverse biological processes suggest that circRNA is a promising key player in RNA world. Most circRNAs are generated through back-splicing of pre-mRNAs, forming a covalently closed loop structure with no 5’ caps or 3’ polyadenylated tails. In addition, most circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome. To gain insights into the new area of circRNA translation, we introduce an integrated tool capable of detecting circRNAs with protein-coding potential from high-throughput sequencing data.

Availability and implementation
CircPro is available at http://bis.zju.edu.cn/CircPro.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improving Designer Glycan Production inEscherichia colithrough Model-Guided Metabolic Engineering
Authors: Wayman Joseph A. , Glasscock Cameron , Mansell Thomas J. , DeLisa Matthew P. , Varner Jeffrey D. 
Published: July 2017

AbstractAsparagine-linked (N-linked) glycosylation is the most common protein modification in eukaryotes, affecting over two-thirds of the proteome. Glycosylation is also critical to the pharmacokinetic activity and immunogenicity of many therapeutic proteins currently produced in complex eukaryotic hosts. The discovery of a protein glycosylation pathway in the pathogenCampylobacter jejuniand its subsequent transfer into laboratory strains ofEscherichia colihas spurred great interest in glycoprotein production in prokaryotes. However, prokaryotic glycoprotein production has several drawbacks, including insufficient availability of non-native glycan precursors. To address this limitation, we used a constraint-based model ofE. colimetabolism in combination with heuristic optimization to design gene knockout strains that overproduced glycan precursors. First, we incorporated reactions associated withC. jejuniglycan assembly into a genome-scale model ofE. colimetabolism. We then identified gene knockout strains that coupled optimal growth to glycan synthesis. Simulations suggested that these growth-coupled glycan overproducing strains had metabolic imbalances that rerouted flux toward glycan precursor synthesis. We then validated the model-identified knockout strains experimentally by measuring glycan expression using a flow cytometric-based assay involving fluorescent labeling of cell surface-displayed glycans. Overall, this study demonstrates the promising role that metabolic modeling can play in optimizing the performance of a next-generation microbial glycosylation platform.
Translational and HIF1α-dependent metabolic reprograming underpin oncometabolome plasticity and synergy between oncogenic kinase inhibitors and biguanides
Authors: Hulea Laura , Gravel Simon-Pierre , Morita Masahiro , Cargnello Marie , Uchenunu Oro , Im Young Kyuen , McLaughlan Shannon , Larsson Ola , Ohh Michael , Ferreira Tiago , Greenwood Celia , Bridon Gaëlle , Avizonis Daina , Ursini-Siegel Josie , St-Pierre Julie , Pollak Michael , Topisirovic Ivan 
Published: July 2017

AbstractThere is heightened interest to devise therapies that target the oncometabolome. We show that kinase inhibitors (KIs) and biguanides synergistically target melanoma, leukemia, and breast, colon and renal cancer cells, but not non-transformed cells. Metabolic profiling confirmed opposing effects of KIs and biguanides on glycolysis, but this was insufficient to explain the observed synergy between the drugs. Rather, we define a critical role for the synthesis of non-essential amino acids (NEAA) aspartate, asparagine and serine as well as reductive glutamine metabolism, in determining the sensitivity of cancer cells to KI - biguanide combinations. The mTORC1/4E-BP axis regulates aspartate, asparagine and serine synthesis by modulating translation of mRNAs encoding PC, ASNS, PHGDH and PSAT1. Ablation of 4E-BP1 and 2 results in a dramatic increase in serine, aspartate and asparagine levels and a substantial decrease in sensitivity of breast cancer and melanoma cells to KI - biguanide combinations. In turn, efficacy of KI – biguanide combinations is impeded by HIF1α and sustained reductive glutamine metabolism. These findings identify hitherto unappreciated translational reprograming of NEAA synthesis and HIF1α-dependent stimulation of reductive glutamine metabolism as critical metabolic vulnerabilities of cancer that underpin synergy between KIs and biguanides.
A random-matrix theory of the number sense
Authors: Hannagan T. , Nieder A. , Viswanathan P. , Dehaene S. 
Published: July 2017

AbstractNumber sense, a spontaneous ability to process approximate numbers, has been documented in human adults, infants and newborns, and many other animals. Species as distant as monkeys and crows exhibit number-selective neuronal activity. How number sense can emerge in the absence of learning or fine tuning is currently unknown. We introduce a random matrix theory of self-organised neural states where numbers are coded by vectors of activation across multiple units, and where the vector codes for successive integers are obtained through multiplication by a fixed but random matrix. This cortical implementation of the “von Mises” algorithm explains many otherwise disconnected observations ranging from neural tuning curves in monkeys to looking times in neonates and cortical numerotopy in adults. The theory clarifies the origin of Weber-Fechner’s law and yields a novel and empirically validated prediction of multi-peak number neurons. Random matrices constitute a novel mechanism for the emergence of brain states coding for quantity.
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions
Authors: Choi Kyuha , Zhao Xiaohui , Lambing Christophe , Underwood Charles J. , Hardcastle Thomas J. , Serra Heïdi , Tock Andrew J. , Ziolkowski Piotr A. , Yelina Nataliya E. , Martienssen Robert A. , Henderson Ian R. 
Published: July 2017

AbstractMeiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleotides. DSB hotspots occurred in gene promoters, terminators and introns, driven by AT-sequence richness, which excludes nucleosomes and allows SPO11-1 access. A strong positive relationship was observed between SPO11-1 DSBs and final crossover levels. Euchromatic marks promote recombination in fungi and mammals, and consistently we observe H3K4me3enrichment in proximity to DSB hotspots at gene 5’-ends. Repetitive transposons are thought to be recombination-silenced during meiosis, in order to prevent non-allelic interactions and genome instability. Unexpectedly, we found strong DSB hotspots in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. Hotspot transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination-enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used themet1DNA methyltransferase mutant to investigate the role of heterochromatin on the DSB landscape. Epigenetic activation of transposon meiotic DSBs occurred inmet1mutants, coincident with reduced nucleosome occupancy, gain of transcription and H3K4me3. Increasedmet1SPO11-1 DSBs occurred most strongly within centromeres and Gypsy and CACTA/EnSpm coldspot transposons. Together, our work reveals complex interactions between chromatin and meiotic DSBs within genes and transposons, with significance for the diversity and evolution of plant genomes.
Epigenetic activation of meiotic recombination in Arabidopsis centromeres via loss of H3K9me2 and non-CG DNA methylation
Authors: Underwood Charles J. , Choi Kyuha , Lambing Christophe , Zhao Xiaohui , Serra Heïdi , Borges Filipe , Simorowski Joe , Ernst Evan , Jacob Yannick , Henderson Ian R. , Martienssen Robert A. 
Published: July 2017

AbstractEukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis centromeres are suppressed for crossovers, as recombination in these regions can cause chromosome mis-segregation. Plant centromeres are surrounded by repetitive, transposon-dense heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. Here we show that disruption of Arabidopsis H3K9me2 and non-CG DNA methylation pathways increases meiotic DNA double strand breaks (DSBs) within centromeres, whereas crossovers increase within pericentromeric heterochromatin. Increased pericentromeric crossovers in H3K9me2/non-CG mutants occurs in both inbred and hybrid backgrounds, and involves the interfering crossover repair pathway. Epigenetic activation of recombination may also account for the curious tendency of maize transposonDsto disruptCHROMOMETHYLASE3when launched from proximal loci. Thus H3K9me2 and non-CG DNA methylation exert differential control of meiotic DSB and crossover formation in centromeric and pericentromeric heterochromatin.
Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation
Authors: Xue Zhuyi , Warren René L , Gibb Ewan A , MacMillan Daniel , Wong Johnathan , Chiu Readman , Hammond S Austin , Ennis Catherine A , Hahn Abigail , Reynolds Sheila , Birol Inanc 
Published: July 2017

AbstractAlternative polyadenylation (APA) of 3’ untranslated regions (3’ UTRs) has been implicated in cancer development. Earlier reports on APA in cancer primarily focused on 3’ UTR length modifications, and the conventional wisdom is that tumor cells preferentially express transcripts with shorter 3’ UTRs. Here, we analyzed the APA patterns of 114 genes, a select list of oncogenes and tumor suppressors, in 9,939 tumor and 729 normal tissue samples across 33 cancer types using RNA-Seq data from The Cancer Genome Atlas, and we found that the APA regulation machinery is much more complicated than what was previously thought. We report 77 cases (gene-cancer type pairs) of differential 3’ UTR cleavage patterns between normal and tumor tissues, involving 33 genes in 13 cancer types. For 15 genes, the tumor-specific cleavage patterns are recurrent across multiple cancer types. While the cleavage patterns in certain genes indicate apparent trends of 3’ UTR shortening in tumor samples, over half of the 77 cases imply 3’ UTR length change trends in cancer that are more complex than simple shortening or lengthening. This work extends the current understanding of APA regulation in cancer, and demonstrates how large volumes of RNA-seq data generated for characterizing cancer cohorts can be mined to investigate this process.
No cause for pause: new analyses of ramping and stepping dynamics in LIP (Rebuttal to Response to Reply to Comment on Latimer et al 2015)
Authors: Latimer Kenneth W. , Huk Alexander C. , Pillow Jonathan W. 
Published: July 2017

AbstractWe recently presented a statistical comparison between two models of latent dynamics in macaque lateral intraparietal (LIP) area spike trains—a continuous ‘ramping’ (diffusion-to-bound) model, and a discrete ‘stepping’ model—and found that a substantial fraction of neurons (recorded in two different studies) were better supported by the stepping model (Latimer et al., 2015). Here, we respond to a recent challenge to the validity of these findings that focuses primarily on the possibility of a lower bound on LIP firing rates (Zylberberg & Shadlen, 2016). The paper in question proposed alternate formulations of the ramping model, and argued (via indirect analyses) that half the neurons in the population were better explained by the new model; if correct, this would lead to an even split in the number of neurons better explained by each model. These analyses, while interesting, do not alter the conclusions of our original paper. Here, we review the criticisms raised by Zylberberg & Shadlen and report several new analyses using models with lower bounds. First, we show that the stepping model continued to provide a better description of LIP spike trains when fit using only an early period of each trial. Second, we performed a direct model comparison between our stepping model and a ramping-with-baseline model proposed by Zylberberg & Shadlen; we found that (in a pleasing moment of agreement) roughly half the neurons were better explained by each model. Interestingly, inspection of the cells that switched classifications revealed that many did not strictly exhibit the classical ramping PSTHs that motivated these analyses in the first place. We also examined two other issues raised in recent discussions of LIP: (1) We show that a non-integrating model is consistent with some core aspects of behavioral data previously offered as evidence for continuous integration; and (2) We examine analyses based on the response covariance (“CorCE”), and show that it does not reliably distinguish ramping and stepping dynamics for our dataset. Taken together, these discussions highlight the value of data-driven characterizations of both neural and behavioral dynamics with appropriate statistical tools.
SMELL-S and SMELL-R: olfactory tests not influenced by odor-specific insensitivity or prior olfactory experience
Authors: Hsieh Julien W. , Keller Andreas , Wong Michele , Jiang Rong-San , Vosshall Leslie B. 
Published: July 2017

AbstractSmell dysfunction is a common and underdiagnosed medical condition that can have serious consequences. It is also an early biomarker of Alzheimer’s disease that precedes detectable memory loss. Clinical tests that evaluate the sense of smell face two major challenges. First, human sensitivity to individual odorants varies significantly, leading to potential misdiagnosis of people with an otherwise normal sense of smell but insensitivity to the test odorant. Second, prior familiarity with odor stimuli can bias smell test performance. We have developed new non- semantic tests for olfactory sensitivity (SMELL-S) and olfactory resolution (SMELL-R) that overcome these challenges by using mixtures of odorants that have unfamiliar smells. The tests can be self-administered with minimal training and showed high test-retest reliability. Because SMELL-S uses odor mixtures rather than a single molecule, odor-specific insensitivity is averaged out. Indeed, SMELL-S accurately distinguished people with normal and dysfunctional smell. SMELL-R is a discrimination test in which the difference between two stimulus mixtures can be altered stepwise. This is an advance over current discrimination tests, which ask subjects to discriminate monomolecular odorants whose difference cannot be objectively calculated. SMELL-R showed significantly less bias in scores between North American and Taiwanese subjects than conventional semantically-based smell tests that need to be adapted and translated to different populations. We predict that SMELL-S and SMELL-R will be broadly effective in diagnosing smell dysfunction, including that associated with the earliest signs of memory loss in Alzheimer’s disease.Significance statementCurrently available smell testing methods can misdiagnose subjects with lack of prior experience or insensitivity to the odorants used in the test. This introduces a source of bias into clinical tests aimed at detecting patients with olfactory dysfunction. We have developed smell tests that use mixtures of 30 molecules that average out the variability in sensitivity to individual molecules. Because these mixtures have unfamiliar odors, and the tests are non-semantic, their use eliminates differences in test performance due to the familiarity with the smells or the words used to describe them. The SMELL-S and SMELL-R tests facilitate smell testing of diverse populations, without the need to adapt the test stimuli.