bluuebunny/crossref_metadata_2025_split huggingface dataset:
RAI1 Overexpression Promotes Altered Circadian Gene Expression and Dyssomnia in Potocki–Lupski Syndrome
Authors: Mullegama Sureni , Alaimo Joseph , Fountain Michael , Burns Brooke , Balog Amanda , Chen Li , Elsea Sarah 
Published: March 2017

Abstract
Retinoic acid induced 1 (RAI1) encodes a dosage-sensitive gene that when haploinsufficient results in Smith–Magenis syndrome (SMS) and when overexpressed results in Potocki–Lupski syndrome (PTLS). Phenotypic and molecular evidence illustrates that haploinsufficiency of RAI1 disrupts circadian rhythm through the dysregulation of the master circadian regulator, circadian locomotor output cycles kaput (CLOCK), and other core circadian components, contributing to prominent sleep disturbances in SMS. However, the phenotypic and molecular characterization of sleep features in PTLS has not been elucidated. Using the Pittsburgh Sleep Quality Index (PSQI), caregivers of 15 school-aged children with PTLS reported difficulties in initiating sleep. Indeed, more than 70% of individuals manifested moderate to severe sleep latency, as defined by the PSQI. Moreover, these individuals manifested difficulties in sleep maintenance, with middle of the night and early morning awakenings. When assessing daytime sleepiness through the Epworth Sleepiness Scale, approximately 21% of the individuals manifested excessive daytime somnolence. This indicates that mild dyssomnia characterizes the majority of the sleep phenotype, with occasionally problematic daytime somnolence, a phenotype different than that expressed by individuals with SMS, where daytime sleepiness is a chronic problem. Gene expression analysis of the core circadian machinery in the hypothalamus of the PTLS mouse model (Rai1-Tg) found significant dysregulation of the transcriptional activators, Clock and Arntl, and the transcriptional repressors, Per1–3 and Cry1/2, during both light and dark phases. These findings suggest a partial loss of circadian entrainment typically evoked by environmental photic cues. Examination of circadian clock gene expression in the Rai1-Tg mouse heart, liver, and kidney found unchanged expression of Clock and most of its downstream targets during both light and dark phases, suggesting an asynchronized circadian rhythm. Furthermore, examination of circadian gene expression in synchronized PTLS lymphoblasts revealed reduced transcripts of the Period (PER1–3) family and normal expression of CRY1/2. The finding that central circadian gene expression was altered while many peripheral circadian components were intact suggests a tissue-specific circadian uncoupling of the circadian machinery due to Rai1 overexpression. Overall, our results demonstrate that overexpression of RAI1 results in sleep deficiencies in individuals with PTLS due to a lack of properly regulated circadian machinery gene expression and highlight the importance of evaluating sleep concerns in individuals with PTLS.
Hollow Fiber Oxygenator Composition Has a Significant Impact on Failure Rates in Neonates on Extracorporeal Membrane Oxygenation: A Retrospective Analysis
Authors: Bernard Philip , Skinner Sean , Bhandary Prasad , Ruzic Ana , Bacon Matthew , Ballard Hubert , Daniel John 
Published: March 2017

AbstractIn extracorporeal life support (ECLS), there are two main types of oxygenators in clinical use for neonates: polymethylpentene (PMP) hollow fiber and polypropylene (PP) hollow fiber. A retrospective study was performed on neonates (n = 44) who had undergone ECLS for noncardiac indications from 2009 to 2015. Between the two groups (PMP n = 21, PP n = 23), the PP oxygenators failed 91% of the time, whereas the PMP oxygenators failed 43% of the time (p < 0.05). Analysis suggests PMP oxygenators are less prone to failure than PP oxygenators, and they require fewer number of oxygenator changes during a neonatal ECLS.
Unusual de novo Partial Trisomy 17p12p11.2 due to Unbalanced Insertion into 5p13.1 in a Severely Affected Boy
Authors: Mendez-Rosado Luis , Lantigua Araceli , Galarza Juan , Hamid Al-Rikabi Ahmed , Ziegler Monika , Liehr Thomas 
Published: March 2017

AbstractGain of copy numbers can be due to different chromosomal rearrangements such as direct or indirect duplications, translocations, small supernumerary marker chromosomes, or insertions. In a 3-year-old boy with dysmorphic features and developmental delay, chromosome analyses revealed a derivative chromosome 5. Microdissection and reverse fluorescence in situ hybridization identified the in 5p13.1 inserted part as 17p12-p11.2 material. Thus the patient suffered from a rare combination of genomic disorder, that is, Charcot-Marie-Tooth disease type 1A and Potocki-Lupski syndrome. Parental studies indicated that the abnormality was de novo in origin. As the question how this rearrangement arose cannot be answered conclusively, formal genetic counseling is warranted, which includes a discussion regarding the possibility of gonadal mosaicism. In conclusion, this case highlights that chromosome 17p is genetically relatively instable, and thus it can lead to rare chromosomal conditions.
Neural basis of impaired safety signaling in Obsessive Compulsive Disorder
Authors: Apergis-Schoute Annemieke M. , Gillan Claire M. , Fineberg Naomi A. , Fernandez-Egea Emilio , Sahakian Barbara J. , Robbins Trevor W. 
Published: March 2017

Significance
Assigning safety to stimuli and situations forms an important part of everyday functioning. Obsessive Compulsive Disorder (OCD) is a prototypical disorder of inflexible behavior influenced by anxiety. Here we show, using neuroimaging of fear reversal learning, which involves a previously threatening stimulus becoming safe while a previously safe stimulus becomes threatening, that OCD patients fail to differentiate a safe from a threatening stimulus only after such a reversal, as measured by skin conductance responses. This OCD impairment in safety signaling, a likely prominent component of successful exposure therapy, is predicted and mediated by altered activity in a neural salience network including the ventromedial prefrontal cortex.
Higher-than-ballistic conduction of viscous electron flows
Authors: Guo Haoyu , Ilseven Ekin , Falkovich Gregory , Levitov Leonid S. 
Published: March 2017

Significance
Free electron flows through constrictions in metals are often regarded as an ultimate high-conduction charge transfer. We predict that electron fluids can flow with a resistance that is much smaller than the fundamental quantum mechanical ballistic limit for nanoscale electronics. The “superballistic” low-dissipation transport is particularly striking for the flow through a viscous point contact, a constriction exhibiting the quantum mechanical ballistic transport at zero temperature but governed by viscous electron hydrodynamics at a higher temperature. Unlike other mechanisms of low-dissipation transport, for example, superconductivity, the viscous electron flows can be realized at elevated temperatures, granting a new route for the low-power electronics research.
Yellow taxis have fewer accidents than blue taxis because yellow is more visible than blue
Authors: Ho Teck-Hua , Chong Juin Kuan , Xia Xiaoyu 
Published: March 2017

Significance
This paper examines the phenomenon that yellow taxis have fewer accidents than blue taxis. Statistical analysis of a unique and comprehensive dataset suggests that the higher visibility of the color yellow makes it easier for other drivers to avoid getting into accidents with yellow taxis, leading to a lower accident rate. This suggests that color visibility should play a major role in determining the colors used for public transport vehicles.
Amyotrophic lateral sclerosis-linked mutations increase the viscosity of liquid-like TDP-43 RNP granules in neurons
Authors: Gopal Pallavi P. , Nirschl Jeffrey J. , Klinman Eva , Holzbaur Erika L. F. 
Published: March 2017

Significance
Mutations in TAR-DNA binding protein 43 (TDP-43), an RNA-binding protein (RBP) with multiple functions in RNA metabolism, cause amyotrophic lateral sclerosis (ALS), but it is uncertain how defects in RNA biology cause disease. Purified RNA-binding protein FUS and heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) form liquid droplets in vitro through liquid–liquid phase separation. However, the biophysical properties of ribonucleoprotein (RNP) granules composed of wild-type (WT) or ALS-linked TDP-43 have not been studied in primary neurons. We show that TDP-43 WT RNP granules exhibit distinct biophysical properties depending on their axonal location, whereas granules formed by ALS-linked mutant TDP-43 are more viscous and show disrupted axonal transport dynamics. We propose the distinct biophysical properties of these neuronal RNP granules may reflect different maturational states and differential propensity for pathological transformation.
Determining climate effects on US total agricultural productivity
Authors: Liang Xin-Zhong , Wu You , Chambers Robert G. , Schmoldt Daniel L. , Gao Wei , Liu Chaoshun , Liu Yan-An , Sun Chao , Kennedy Jennifer A. 
Published: March 2017

Significance
Projections of the economic consequences of climate change are valuable for policy making but generally rely on integrated assessments that cannot account for highly localized climate effects. Most agricultural climate impact studies focus on local effects or partial productivity measures insufficient to capture national economic outcomes. Here, we directly link climate variables in specific US regions to total factor productivity (TFP). We quantify the national economic consequences of past climate variations, identify critical agricultural regions with national significance, and project future changes in TFP under different climate scenarios. We provide a physical understanding of these climate−economic links, show that the agricultural economy is becoming increasingly sensitive to climate, and lay a more concrete foundation for informed decision-making.
Spatial confinement of active microtubule networks induces large-scale rotational cytoplasmic flow
Authors: Suzuki Kazuya , Miyazaki Makito , Takagi Jun , Itabashi Takeshi , Ishiwata Shin’ichi 
Published: March 2017

Significance
At the microscopic scale, collective behaviors of motile units can induce directed fluid flow on a larger length scale than individual units based on their hydrodynamic interactions. Here, we found that the motor-driven extensile behaviors of microtubule bundles in the cytoplasm induce rotational flow in a cell-sized confined space on length scale and timescale that were 10- to 100-fold longer than the vortex flows emerging in the bulk space. These scale differences were derived from mechanical force generation by microtubule bundle elongation near the physical boundary and the transmission of this force over the microtubule network. These findings suggest that the microtubule cytoskeleton utilizes not only hydrodynamic interactions but also mechanical interactions to induce large-scale cytoplasmic flow.
Arsenic trioxide targets MTHFD1 and SUMO-dependent nuclear de novo thymidylate biosynthesis
Authors: Kamynina Elena , Lachenauer Erica R. , DiRisio Aislyn C. , Liebenthal Rebecca P. , Field Martha S. , Stover Patrick J. 
Published: March 2017

Significance
We have identified de novo thymidylate biosynthesis as a target of arsenic at exposure levels observed in human populations. Arsenic enhances methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) small ubiquitin-like modifier (SUMO)-ylation and subsequent proteolytic degradation of MTHFD1 and serine hydroxymethyltransferase (SHMT), resulting in depressed rates of de novo thymidylate synthesis, elevated uracil levels in nuclear DNA, and increased genome instability. These findings provide a molecular mechanism linking clastogenic and teratogenic effects of arsenic to impaired de novo thymidylate synthesis.
Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor
Authors: Salvi Michele , Schomburg Benjamin , Giller Karin , Graf Sabrina , Unden Gottfried , Becker Stefan , Lange Adam , Griesinger Christian 
Published: March 2017

Significance
Histidine kinases are key players in prokaryotic environment sensing. Citrate binding to the extracytoplasmic sensing domain of histidine kinase CitA triggers a contraction of the domain, resulting in a pull on the C-terminal β-strand. By a combination of liquid- and solid-state NMR spectroscopy, structural alterations observed for the isolated domain can be confirmed in context of its native environment as part of a membrane-embedded receptor. Our results demonstrate that the mechanistic model derived from the isolated ligand-sensing domain is compatible with the sensor in a native-like membrane environment and allows transfer of the model to transmembrane signaling by this class of sensor kinases.
The presumed ginkgophyteUmaltolepishas seed-bearing structures resembling those of Peltaspermales and Umkomasiales
Authors: Herrera Fabiany , Shi Gongle , Ichinnorov Niiden , Takahashi Masamichi , Bugdaeva Eugenia V. , Herendeen Patrick S. , Crane Peter R. 
Published: March 2017

SignificanceUnderstanding the origins of the five groups of living seed plants requires well-supported hypotheses of their relationships to extinct groups, many of which are poorly understood. New information from the Early Cretaceous of Mongolia on the enigmatic extinct plantUmaltolepisshows that its leaves are similar to those ofGinkgo, but its seed-bearing structures are unique, and more comparable to those of certain extinct Peltaspermales and Umkomasiales.Umaltolepisprovides new data for understanding relationships among living and fossil seed plants and supports previous ideas thatGinkgo bilobamay be the sole surviving relict of a once very diverse group of Mesozoic seed plants.
Effects of language impairment and bilingualism across domains
Authors: Blom Elma , Boerma Tessel 
Published: March 2017

Abstract
Purpose: This study examined the effects of language impairment (LI) and bilingualism across vocabulary, morphology and verbal memory in a sample of children learning Dutch. Methods: Children (MAGE = 71 months) were assigned to a monolingual group with typical development (TD) (n = 30), bilingual TD (n = 30), monolingual LI (n = 30) or bilingual LI group (n = 30). Vocabulary was measured with the Peabody Picture Vocabulary Test, morphology with the Taaltoets Alle Kinderen, verbal short-term (VSTM) and working memory (VWM) with forward and backward digit span tasks. Results: Language knowledge (vocabulary, morphology) was affected by LI and bilingualism. Language processing (VSTM, VWM) was influenced by LI only. When language knowledge was controlled, the bilinguals outperformed the monolinguals on VSTM and VWM when TD and LI were collapsed. Bilingualism aggravated the effects of LI for vocabulary. Conclusions: Bilingualism may create a risk for the vocabulary knowledge of children with LI, but might be beneficial for their verbal memory.
Recent progress in microstructural hydrogen mapping in steels: Quantification, kinetic analysis, and multi-scale characterisation
Authors: Koyama Motomichi , Rohwerder Michael , Tasan Cemal Cem , Bashir Asif , Akiyama Eiji , Takai Kenichi , Raabe Dierk , Tsuzaki Kaneaki 
Published: March 2017

This paper gives an overview of recent progress in microstructure-specific hydrogen mapping techniques. The challenging nature of mapping hydrogen with high spatial resolution, i.e. at the scale of finest microstructural features, led to the development of various methodologies: thermal desorption spectrometry, silver decoration, the hydrogen microprint technique, secondary ion mass spectroscopy, atom probe tomography, neutron radiography, and the scanning Kelvin probe. These techniques have different characteristics regarding spatial and temporal resolution associated with microstructure-sensitive hydrogen detection. Employing these techniques in a site-specific manner together with other microstructure probing methods enables multi-scale, quantitative, three-dimensional, high spatial, and kinetic resolution hydrogen mapping, depending on the specific multi-probe approaches used. Here, we present a brief overview of the specific characteristics of each method and the progress resulting from their combined application to the field of hydrogen embrittlement. This paper is part of a thematic issue on Hydrogen in Metallic Alloys
Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions
Authors: Wu Steven H , Schwartz Rachel S , Winter David J , Conrad Donald F , Cartwright Reed A 
Published: March 2017

Abstract

Motivation
Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error and reference-mapping biases, among others.

Results
We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity regions, which can produce erroneous genotype calls. By removing sites that do not fit the major component, we can improve the accuracy of genotype calls.

Availability and Implementation
Methods and data files are available at https://github.com/CartwrightLab/WuEtAl2017/ (doi:10.5281/zenodo.256858).

Supplementary information
Supplementary data is available at Bioinformatics online.
Science in the cloud (SIC): A use case in MRI connectomics
Authors: Kiar Gregory , Gorgolewski Krzysztof J. , Kleissas Dean , Roncal William Gray , Litt Brian , Wandell Brian , Poldrack Russel A. , Wiener Martin , Vogelstein R. Jacob , Burns Randal , Vogelstein Joshua T. 
Published: March 2017

Abstract
Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called ‘science in the cloud' (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended.
Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity
Authors: Christie Mark R. , Meirmans Patrick G. , Gaggiotti Oscar E. , Toonen Robert J. , White Crow 
Published: March 2017

AbstractAccurately estimating patterns of population connectivity in marine systems remains an elusive goal. Current genetic approaches have focused on assigning individuals back to their natal populations using one of two methods: parentage analyses and assignment tests. Each of these approaches has their relative merits and weaknesses. Here, we illustrate these tradeoffs using a forward-time agent-based model that incorporates relevant natural history and physical oceanography for 135 Kellet’s whelk (Kelletia kelletii) populations from Southern California. Like most marine organisms, Kellet’s whelks live in large meta-populations where local populations are connected by dispersive larvae. For estimating population connectivity, we found parentage analyses to be relatively insensitive to the amount of genetic differentiation among local populations, but highly sensitive to the proportion of the meta-population sampled. Assignment tests, on the other hand, were relatively insensitive to the proportion of the meta-population sampled, but highly sensitive to the amount of genetic differentiation found among local populations. Comparisons between the true connectivity matrices (generated by using the true origin of all sampled individuals) and those obtained via parentage analyses and assignment tests reveal that neither approach can explain &gt;26% of the variation in true connectivity. Furthermore, even with perfect assignment of all sampled individuals, sampling error alone can introduce noise into the estimated population connectivity matrix. Future work should aim to improve the number of correct assignments without the expense of additional incorrect assignments, perhaps by using dispersal information obtained from related individuals as priors in a Bayesian framework. These analyses dispel a number of common misconceptions in the field and highlight areas for both future research and methodological improvements.
Quality Programs in Neurosurgery: The Memorial Hermann/University of Texas Experience
Authors: Kim Dong H. , Morales Miriam , Tai Rahil , Hergenroeder Georgene , Shah Chirag , O’Leary Joanna , Harrison Nicole , Edquilang Gabrielle , Paisley Emily , Allen-McBride Enedra , Murphy Allison , Smith Justin , Gormley William , Spielman Amanda 
Published: March 2017

Abstract
The importance of outcome measures is steadily increasing due to the rise of “pay for performance” and the advent of population health. In 2007, a quality initiative was started due to poor performance on rankings such as the University Health Consortium (UHC) report card. Inherent to all such efforts are common challenges: how to engage the providers; how to gather and ensure the accuracy of the data; how to attribute results to individuals; how to ensure permanent improvements. After analysis, a strategy was developed that included an initial focus on 3 metrics (mortality, infection rates, and complications), leadership from practicing neurosurgeons, protocol development and adherence, and subspecialization. In addition, it was decided that the metrics would initially apply to attending physicians only, but that the entire team would need to be involved. Once the fundamental elements were established, the process could be extended to other measures and providers. To support this effort, special information system tools were developed and a support team formed. As the program matured, measured outcomes improved and more metrics were added (to a current total of 48). For example, UHC mortality ratios (observed over expected) decreased by 75%. Infection rates decreased 80%. The program now involves all trainee physicians, advanced practice providers, nurses, and other staff. This paper describes the design, implementation, and results of this effort, and provides a practical guide that may be useful to other groups undertaking similar initiatives.