bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of Myocardial Extracellular Volume Fraction From Iodine Density Images Using Single-Source, Dual-Energy Computed Tomography: A Feasibility Study
Authors: Ohta Yasutoshi , Kitao Shinichiro , Watanabe Tomomi , Mukai Natsuko , Kishimoto Junichi , Yamamoto Kazuhiro , Ogawa Toshihide 
Published: February 2017

Objective
The aims of this study were to develop and validate an iodine density method for the quantification of myocardial extracellular volume (ECV) fraction using single-source, dual-energy computed tomography.

Methods
Extracellular volume measurements were carried out in 40 subjects (20 patients with heart failure, 20 control subjects) using single-source, dual-energy computed tomography. Subtraction-derived ECVs (subECVs) were computed by subtracting precontrast from delayed images. Iodine density-derived ECVs (iECVs) were calculated from iodine density images obtained from delayed images. Iodine density-derived ECVs were compared with reference subECVs.

Results
A strong correlation (r = 0.896, P < 0.0001) and a small bias (−0.06%) were determined between subECV and iECV with high interobserver concordances (0.915 and 0.906, respectively). Extracellular volume measurements in patients with heart failure were higher in both subECV and iECV compared with control subjects (34.6% [SD, 5.0%] vs 29.5% [SD, 3.6%], P = 0.001, for subECV; 34.9% [SD, 4.5%] vs 29.2% [SD, 2.6%], P < 0.0001, for iECV).

Conclusions
Extracellular volume analysis using iodine density is a useful tool for the noninvasive quantification of ECV in myocardial diseases.
Diaphragmatic Hernia After Living-Donor Right Hepatectomy: An Important Late Donor Complication
Authors: Oh Ji-Won , Oh Soon Nam , Jung Seung Eun , Byun Jae Young 
Published: February 2017

Objective
This study was performed to evaluate the incidence and clinical outcome of diaphragmatic hernia after living-donor right hepatectomy.

Methods
Three hundred thirty-six patients (202 men, 134 women; mean age, 37.6 years) who underwent abdominal computed tomography (CT) after right donor hepatectomy were enrolled in this study. The CT images and the electronic medical records were reviewed. We evaluated the associations between diaphragmatic hernia and patient characteristics.

Results
Diaphragmatic hernia developed in 9 (2.7%) of 336 patients at a median time interval of 173 days (range, 98–488 days) after hepatectomy. In all 6 patients with available follow-up CT images, diaphragmatic hernia increased in size. Three patients presented with abdominal pain and underwent diaphragmatic repair. Diaphragmatic hernia was associated with older age but not with body mass index or sex.

Conclusions
Clinicians and radiologists should not overlook the possibility of diaphragmatic hernia after living-donor right hepatectomy, especially in old liver donors.
Comparison of 270 Versus 320 mg I/mL of Iodixanol in 1 Image Assessment of Both Renal Arteries and Veins With Dual-Energy Spectral CT Imaging in Late Arterial Phase and Their Influence on Renal Function
Authors: Zhou Kefeng , He Jian , Qu Feng , Fan Haijian , Ma Yi , Shi Tingting , Zhou Zhengyang , Zhu Bin 
Published: February 2017

Objective
The objective of this study was to compare the image quality of renal arteries and veins with dual-energy spectral computed tomography (CT) imaging in late arterial phase using 270 and 320 mg I/mL of iodixanol and their influence on renal function.

Methods
A total of 1062 patients underwent renal CT angiography with 270 or 320 mg I/mL of iodixanol with dual-energy spectral CT imaging in late arterial phase. Image quality and their influence on renal function were compared.

Results
There were no significant differences of CT value, signal-to-noise ratio, contrast-to-noise ratio, and subjective score of renal vessels between 2 groups (all P > 0.05). The incidence of contrast-induced nephropathy in patients with abnormal renal function using 320 mg I/mL of iodixanol was significantly higher than using 270 mg I/mL of iodixanol (P = 0.043).

Conclusions
The renal arteries and veins can be fully assessed in late arterial phase with 270 mg I/mL of iodixanol using dual-energy spectral CT scan with better preserved renal function.
Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans
Authors: Lee Julie J. , Keramati Mehdi 
Published: February 2017

AbstractDecision-making in the real world presents the challenge of requiring flexible yet prompt behavior, a balance that has been characterized in terms of a trade-off between a slower, prospective goal-directed model-based (MB) strategy and a fast, retrospective habitual model-free (MF) strategy. Theory predicts that flexibility to changes in both reward values and transition contingencies can determine the relative influence of the two systems in reinforcement learning, but few studies have manipulated the latter. Therefore, we developed a novel two-level contingency change task in which transition contingencies between states change every few trials; MB and MF control predict different responses following these contingency changes, allowing their relative influence to be inferred. Additionally, we manipulated the rate of contingency changes in order to determine whether contingency change volatility would play a role in shifting subjects between a MB and MF strategy. We found that human subjects employed a hybrid MB/MF strategy on the task, corroborating the parallel contribution of MB and MF systems in reinforcement learning. Further, subjects did not remain at one level of MB/MF behavior but rather displayed a shift towards more MB behavior over the first two blocks that was not attributable to the rate of contingency changes but rather to the extent of training. We demonstrate that flexibility to contingency changes can distinguish MB and MF strategies, with human subjects utilizing a hybrid strategy that shifts towards more MB behavior over blocks, consequently corresponding to a higher payoff.Author SummaryTo make good decisions, we must learn to associate actions with their true outcomes. Flexibility to changes in action/outcome relationships, therefore, is essential for optimal decision-making. For example, actions can lead to outcomes that change in value – one day, your favorite food is poorly made and thus less pleasant. Alternatively, changes can occur in terms of contingencies – ordering a dish of one kind and instead receiving another. How we respond to such changes is indicative of our decision-making strategy; habitual learners will continue to choose their favorite food even if the quality has gone down, whereas goal-directed learners will soon learn it is better to choose another dish. A popular paradigm probes the effect of value changes on decision making, but the effect of contingency changes is still unexplored. Therefore, we developed a novel task to study the latter. We find that humans used a mixed habitual/goal-directed strategy in which they became more goal-directed over the course of the task, and also earned more rewards with increasing goal-directed behavior. This shows that flexibility to contingency changes is adaptive for learning from rewards, and indicates that flexibility to contingency changes can reveal which decision-making strategy is used.
Poly(A)-ClickSeq: click-chemistry for next-generation 3´-end sequencing without RNA enrichment or fragmentation
Authors: Routh Andrew , Ji Ping , Jaworski Elizabeth , Xia Zheng , Li Wei , Wagner Eric J. 
Published: February 2017

AbstractThe recent emergence of alternative polyadenylation (APA) as an engine driving transcriptomic diversity has stimulated the development of sequencing methodologies designed to assess genome-wide polyadenylation events. The goal of these approaches is to enrich, partition, capture, and ultimately sequence poly(A) site junctions. However, these methods often require poly(A) enrichment, 3´ linker ligation steps, and RNA fragmentation, which can necessitate higher levels of starting RNA, increase experimental error, and potentially introduce bias. We recently reported a click-chemistry based method for generating RNAseq libraries called “ClickSeq”. Here, we adapt this method to direct the cDNA synthesis specifically toward the 3´ UTR/poly(A) tail junction of cellular RNA. With this novel approach, we demonstrate sensitive and specific enrichment for poly(A) site junctions without the need for complex sample preparation, fragmentation or purification. Poly(A)-ClickSeq (PAC-seq) is therefore a simple procedure that generates high-quality RNA-seq poly(A) libraries. As a proof-of-principle, we utilized PAC-seq to explore the poly(A) landscape of both human and Drosophila cells in culture and observed outstanding overlap with existing poly(A) databases and also identified previously unannotated poly(A) sites. Moreover, we utilize PAC-seq to quantify and analyze APA events regulated by CFIm25 illustrating how this technology can be harnessed to identify alternatively polyadenylated RNA.
Oxygen consumption rate inGasterosteus aculeatus-Schistocephalus solidussystem from a non-migratory naturally infected population
Authors: Andrea Tarallo , Giuseppe D’Onofrio , Claudio Agnisola 
Published: February 2017

AbstractThe three spine sticklebackGasterosteus aculeatusis a specific obligatory intermediate host for the cestode wormSchistocephalus solidus. This system is commonly used to investigate the host-parasite interaction in fishes. Despite the interesting attempts which have been made to quantify the impact of the parasite over the respiration rate of the host fish, none of the previous reports took in consideration that stickleback is diversified in different ecotypes according to its ability to made reproductive migration, from and to the sea. Here the oxygen consumption rate in specimens of three-spine stickleback collected from a non-migratory population was quantified with the aim to test if theS. solidusinfection drives a change in the oxygen consumption level of the host fish. The results showed that the infected fishes have a higher rate of oxygen consumption compared with the uninfected one. The differences were due to a direct effect of the parasite, not merely to its contribution to the whole oxygen consumption rate. The data were compared with previous reports, showing that the non-migratory population was characterized by a different level of oxygen consumption rate. The differences were interpreted in terms of divergence in physiological adaptations which had to be appeared in different populations.
Controlling cell shape on hydrogels using lift-off patterning
Authors: Moeller Jens , Denisin Aleksandra K. , Sim Joo Yong , Wilson Robin E. , Ribeiro Alexandre J.S. , Pruitt Beth L. 
Published: February 2017

AbstractPolyacrylamide gels functionalized with extracellular matrix proteins are commonly used as cell culture platforms to evaluate the combined effects of extracellular matrix composition, cell geometry and substrate rigidity on cell physiology. For this purpose, protein transfer onto the surface of polyacrylamide hydrogels must result in geometrically well-resolved micropatterns with homogeneous protein distribution. Yet the outcomes of micropatterning methods have not been pairwise evaluated against these criteria. We report a high-fidelity photoresist lift-off patterning method to pattern ECM proteins on polyacrylamide hydrogels ranging from 5 to 25 kPa. We directly compare the protein transfer efficiency and pattern geometrical accuracy of this protocol to the widely used microcontact printing method. Lift-off patterning achieves higher protein transfer efficiency, increases pattern accuracy, increases pattern yield, and reduces variability of these factors within arrays of patterns as it bypasses the drying and transfer steps of microcontact printing. We demonstrate that lift-off patterned hydrogels successfully control cell size and shape and enable long-term imaging of actin intracellular structure and lamellipodia dynamics when we culture epithelial cells on these substrates.
RNA Stores Tau Reversibly in Complex Coacervates
Authors: Zhang Xuemei , Lin Yanxian , Eschmann Neil A. , Zhou Hongjun , Rauch Jennifer , Hernandez Israel , Guzman Elmer , Kosik Kenneth S. , Han Songi 
Published: February 2017

AbstractNon-membrane-bound organelles that behave like liquid droplets are widespread among eukaryotic cells. Their dysregulation appears to be a critical step in several neurodegenerative conditions. Here we report that tau protein, the primary constituent of Alzheimer neurofibrillary tangles, can form liquid droplets and therefore has the necessary biophysical properties to undergo liquid-liquid phase separation (LLPS) in cells. Consonant with the factors that induce LLPS, tau is an intrinsically disordered protein that complexes with RNA to form droplets. Uniquely, the pool of RNAs to which tau binds in living cells are tRNAs. This phase state of tau is held in an approximately 1:1 charge balance across the protein and the nucleic acid constituents, and can thus be maximal at different RNA:tau mass ratios depending on the biopolymer constituents involved. This feature is characteristic of complex coacervation. We furthermore show that the LLPS process is directly and sensitively tuned by salt concentration and temperature, implying it is modulated by both electrostatic interactions between the involved protein and nucleic acid constituents, as well as net changes in entropy. Despite the high protein concentration within the complex coacervate phase, tau is locally freely tumbling and capable of diffusing through the droplet interior. In fact, tau in the condensed phase state does not reveal any immediate changes in local protein packing, local conformations and local protein dynamics from that of tau in the dilute solution state. In contrast, the population of aggregation-prone tau as induced by the complexation with heparin is accompanied by large changes in local tau conformations and irreversible aggregation. However, prolonged residency within the droplet state eventually results in the emergence of detectable β-sheet structures according to thioflavin-T assay. These findings suggest that the droplet state can incubate tau and pre-dispose the protein toward the formation of insoluble fibrils.
Accumulation of sensory evidence is impaired in Parkinson’s disease with visual hallucinations
Authors: O’Callaghan Claire , Hall Julie M. , Tomassini Alessandro , Muller Alana J. , Walpola Ishan C. , Moustafa Ahmed A. , Shine James M. , Lewis Simon J. G. 
Published: February 2017

AbstractModels of hallucinations across disorders emphasise an imbalance between sensory input and top-down influences over perception. However, the psychological and mechanistic correlates of this imbalance remain underspecified. Visual hallucinations in Parkinson’s disease (PD) are associated with impairments in lower level visual processes and attention, accompanied by over activity and connectivity in higher-order association brain networks. PD therefore provides an attractive framework to explore the relative contributions of bottom-up versus top-down disturbances in hallucinations. Here, we characterised sensory processing in PD patients with and without visual hallucinations, and in healthy controls, by fitting a hierarchical drift diffusion model (hDDM) to an attentional task. The hDDM uses Bayesian estimates to decompose reaction time and response output into parameters reflecting drift rates of evidence accumulation, decision thresholds and non-decision time. We observed slower drift rates in PD patients with hallucinations, which were insensitive to changes in task demand. In contrast, wider decision boundaries and shorter non-decision times relative to controls were found in PD regardless of hallucinator status. Inefficient and less flexible sensory evidence accumulation emerge as unique features of PD hallucinators. We integrate these results with current models of hallucinations, suggesting that slow and inefficient sensory input in PD is less informative, and may therefore be down-weighted leading to an over reliance on top-down influences. Our findings provide a novel computational framework to better specify the impairments in dynamic sensory processing that are a risk factor for visual hallucinations.
MRIQC: Advancing the Automatic Prediction of Image Quality in MRI from Unseen Sites
Authors: Esteban Oscar , Birman Daniel , Schaer Marie , Koyejo Oluwasanmi O. , Poldrack Russell A. , Gorgolewski Krzysztof J. 
Published: February 2017

AbstractQuality control of MRI is essential for excluding problematic acquisitions and avoiding bias in subsequent image processing and analysis. Visual inspection is subjective and impractical for large scale datasets. Although automated quality assessments have been demonstrated on single-site datasets, it is unclear that solutions can generalize to unseen data acquired at new sites. Here, we introduce the MRI Quality Control tool (MRIQC), a tool for extracting quality measures and fitting a binary (accept/exclude) classifier. Our tool can be run both locally and as a free online service via the OpenNeuro.org portal. The classifier is trained on a publicly available, multi-site dataset (17 sites, N=1102). We perform model selection evaluating different normalization and feature exclusion approaches aimed at maximizing across-site generalization and estimate an accuracy of 76%±13% on new sites, using leave-one-site-out cross-validation. We confirm that result on a held-out dataset (2 sites, N=265) also obtaining a 76% accuracy. Even though the performance of the trained classifier is statistically above chance, we show that it is susceptible to site effects and unable to account for artifacts specific to new sites. MRIQC performs with high accuracy in intra-site prediction, but performance on unseen sites leaves space for improvement which might require more labeled data and new approaches to the between-site variability. Overcoming these limitations is crucial for a more objective quality assessment of neuroimaging data, and to enable the analysis of extremely large and multi-site samples.
Evolutionary dynamics of male reproductive genes in theDrosophila virilissubgroup
Authors: Ahmed-Braimah Yasir H. , Unckless Robert L. , Clark Andrew G. 
Published: February 2017

AbstractPostcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and likely the main targets of PCSS in males. The virilis subgroup ofDrosophilaexhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we use short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup:D. americana, D. lummei, D. novamexicana, andD. virilis.For each of the three male reproductive organs (accessory glands, ejaculatory bulb, and testes), we identify genes that show strong expression bias in a given tissue relative to the remaining tissues. We find that the majority of male reproductive transcripts are testes-biased, accounting for ~15% of all annotated genes. Ejaculatory bulb-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of theD. melanogasterejaculatory bulb protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this set of genes has the highest rate of nonsynonymous codon substitution relative to testes- and ejaculatory bulb-biased genes. Furthermore, these SFPs are underrepresented on the X chromosome and are enriched for proteolytic enzymes, which is consistent with SFPs in other insect species. Surprisingly, we find 35D. melanogasterSFPs with conserved accessory gland expression in the virilis group, suggesting these genes may have conserved reproductive roles inDrosophila.Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitutions reside on the centromeric half of chromosome 2, which contributes to paternal gametic incompatibility between species. Our results suggest that SFPs are under strong selection in the virilis group, and likely play a major role in PCSS and/or gametic isolation.
A genome-wide interactome of DNA-associated proteins in the human liver
Authors: Ramaker Ryne C. , Savic Daniel , Hardigan Andrew A. , Newberry Kimberly , Cooper Gregory M. , Myers Richard M. , Cooper Sara J. 
Published: February 2017

AbstractLarge-scale efforts like the Encyclopedia of DNA Elements (ENCODE) Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology deviate in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation. Here we analyze ChIP-seq data for 20 DAPs assayed in two healthy human liver tissue samples, identifying more than 450,000 binding sites. We integrated binding data with transcriptome and phased whole genome data to investigate allelic DAP interactions and the impact of heterozygous sequence variation on the expression of neighboring genes. We find our tissue-based dataset demonstrates binding patterns more consistent with liver biology than cell lines, and describe uses of these data to better prioritize impactful non-coding variation. Collectively, our rich dataset offers novel insights into genome function in healthy liver tissue and provides a valuable research resource for assessing disease-related disruptions.
16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
Authors: Luo Ruibang , Schatz Michael C. , Salzberg Steven L. 
Published: February 2017

AbstractSummary16GT is a variant caller for Illumina WGS and WES germline data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT ran faster and demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy in calling indels as compared to the GATK HaplotypeCaller.Availability and implementationhttps://github.com/aquaskyline/16GTContactrluo5@jhu.eduSupplementary informationSupplementary tables and notes are available atBioinformaticsonline.
Beyond the limitation of randomized controlled trials (RCTs)-current drug repositioning by using human induced pluripotent stem (iPS) cells technology-
Authors: Midori Okabe M.D. 
Published: February 2017

AbstractTo ensure the clinical value of medical interventions, randomized controlled trials (RCTs) are necessary. However, the results of conventional RCTs cannot show individual therapeutic efficacy and safety for medical intervention to a targeted patient. It is the most important weak point of conventional RCTs. Here I show that the new clinical research method by using human induced pluripotent stem (iPS) cells technology will be able to complement the most important weak point of conventional RCTs.As the representative examples, I show the new clinical values of statins (inhibitors of 3-hydroxy-3-methylglutaryl-coenzyme A reductase) found by using human iPS cells technology in achondroplasia or hanatophoric dysplasia (type 1) case and hepatitis C virus (HCV) infection case. Furthermore, they are also important examples for drug repositioning.Therefore, my article would be valuable as a scientific communication for physicians and/or scientists.