bluuebunny/crossref_metadata_2025_split huggingface dataset:
PIK3R1 negatively regulates the epithelial-mesenchymal transition and stem-like phenotype of renal cancer cells through the AKT/GSK3β/CTNNB1 signaling pathway
Authors: Lin Youcheng , Yang Zhao , Xu Abai , Dong Pei , Huang Yi , Liu Huan , Li Feida , Wang Haifeng , Xu Qian , Wang Yongqiang , Sun Da , Zou Yong , Zou Xiaowen , Wang Yu , Zhang Duo , Liu Hongjie , Wu Xun , Zhang Meng , Fu Yu , Cai Zhiming , Liu Chunxiao , Wu Song 
Published: March 2015

AbstractThe phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) pathway has been identified as an important pathway in renal cell carcinoma (RCC). We have reported a nonsense mutation in PIK3R1, which encodes the regulatory subunit of PI3K, in a metastatic RCC (mRCC), while the mutation was absent in the corresponding primary RCC (pRCC). To identify the function of PIK3R1 in RCC, we examined its expression in normal kidney, pRCC and mRCC by immunohistochemistry and real-time polymerase chain reaction. The expression of PIK3R1 significantly decreased in pRCC and was further reduced in mRCC compared with normal tissue. Besides, its expression levels were negatively correlated with T-category of tumor stage. Additionally, 786-O and A-704 cells with PIK3R1 depletion introduced by CRISPR/Cas9 system displayed enhanced proliferation, migration and epithelial-mesenchymal transition (EMT) and acquired a stem-like phenotype. Moreover, the PIK3R1 depletion promoted the phosphorylation of AKT in the cells. The knockdown of AKT by shRNA reduced p-GSK3β and CTNNB1 expression in the cells, while the depletion of CTNNB1 impaired stem-like phenotype of the cells. Overall, PIK3R1 down-regulation in RCC promotes propagation, migration, EMT and stem-like phenotype in renal cancer cells through the AKT/GSK3β/CTNNB1 pathway and may contribute to progression and metastasis of RCC.
Carbon p Electron Ferromagnetism in Silicon Carbide
Authors: Wang Yutian , Liu Yu , Wang Gang , Anwand Wolfgang , Jenkins Catherine A. , Arenholz Elke , Munnik Frans , Gordan Ovidiu D. , Salvan Georgeta , Zahn Dietrich R. T. , Chen Xiaolong , Gemming Sibylle , Helm Manfred , Zhou Shengqiang 
Published: March 2015

AbstractFerromagnetism can occur in wide-band gap semiconductors as well as in carbon-based materials when specific defects are introduced. It is thus desirable to establish a direct relation between the defects and the resulting ferromagnetism. Here, we contribute to revealing the origin of defect-induced ferromagnetism using SiC as a prototypical example. We show that the long-range ferromagnetic coupling can be attributed to the p electrons of the nearest-neighbor carbon atoms around the VSiVC divacancies. Thus, the ferromagnetism is traced down to its microscopic electronic origin.
Amphiphilic p-Sulfonatocalix[4]arene as “Drug Chaperone” for Escorting Anticancer Drugs
Authors: Wang Yi-Xuan , Guo Dong-Sheng , Duan Yong-Chao , Wang Yong-Jian , Liu Yu 
Published: March 2015

AbstractSupramolecularly constructing multifunctional platform for drug delivery is a challenging task. In this work, we propose a novel supramolecular strategy “drug chaperone”, in which macrocyclic amphiphiles directly coassemble with cationic drugs into a multifunctional platform and its surface is further decorated with targeting ligands through host–guest recognition. The coassembling and hierarchical decoration processes were monitored by optical transmittance measurements and the size and morphology of amphiphilic coassemblies were identified by dynamic light scattering and high-resolution transmission electron microscopy. In cell experiments to validate the drug chaperone strategy, the anticancer activities of free drugs were pronouncedly improved by coassembling with amphiphilic chaperone and further functionalization with targeting ligand.
Active link selection for efficient semi-supervised community detection
Authors: Yang Liang , Jin Di , Wang Xiao , Cao Xiaochun 
Published: March 2015

AbstractSeveral semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches.
Asking the Stakeholders: Perspectives of Individuals With Aphasia, Their Family Members, and Physicians Regarding Communication in Medical Interactions
Authors: Burns Michael , Baylor Carolyn , Dudgeon Brian J. , Starks Helene , Yorkston Kathryn 
Published: March 2015

Purpose
The purpose of this study was to explore the experiences of patients with aphasia, their family members, and physicians related to communication during medical interactions.

Method
Face-to-face, semistructured interviews were conducted with 18 participants—6 patients with aphasia, 6 family members involved in patient care, and 6 practicing physicians. A qualitative description approach was used to collect and summarize narratives from participants' perspectives and experiences. Participants were asked about experiences with communication during medical interactions in which the family member accompanied the patient. Interviews were audio- and/or video-recorded, transcribed, and then coded to identify main themes.

Results
Patients and family members generally described their communication experiences as positive, yet all participants discussed challenges and frustrations. Three themes emerged: (a) patients and family members work as a team, (b) patients and family members want physicians to “just try” to communicate with the patient, and (c) physicians want to interact with patients but may not know how.

Conclusions
Participants discussed the need for successful accommodation, or changing how one communicates, to help facilitate the patients' increased understanding and ability to express themselves. Over- and underaccommodation with communication were commonly reported as problems. Speech-language pathologists have a role to play in helping to improve communication during medical interactions. Implications for current speech-language pathologist practice and future directions of research are discussed.

Supplemental Material

https://doi.org/10.23641/asha.6170237
A Sex‐Determining Gene (sdY) Assay Shows Discordance between Phenotypic and Genotypic Sex in Wild Populations of Chinook Salmon
Authors: Cavileer Timothy D. , Hunter Samuel S. , Olsen Jeffery , Wenburg John , Nagler James J. 
Published: March 2015

AbstractSex is determined genetically in most fishes, but the gene responsible for sex determination is not known for the vast majority of fish species, including Chinook Salmon Oncorhynchus tshawytscha. The purpose of this study was to characterize a putative sex‐determining gene (“sexually dimorphic on the Y‐chromosome” [sdY] gene) in Chinook Salmon and develop a method to test genomic DNA (gDNA) samples for genetic sex assignment. Using next‐generation sequencing and salmonid DNA sequence data from GenBank, the entire genomic organization of Chinook Salmon sdY was described. The corresponding full‐length complementary DNA (cDNA) sequence generated from total RNA was determined by using a combination of genomic‐based primers and “rapid amplification of cDNA ends” (RACE) PCR assays. A phylogenic analysis was conducted by comparing the Chinook Salmon sdY cDNA sequence with sdY sequences (GenBank) from 10 other teleost species. A multisequence alignment was performed, and a phylogenetic tree was inferred from the alignment, providing evidence for sdY identity. Based upon a TaqMan real‐time PCR assay, a genetic test for male sex using sdY was developed and tested on gDNA isolated from phenotypic female and male Chinook Salmon representing populations in Alaska, Idaho, and Washington. The results provide compelling evidence that sdY is the sex‐determining gene in Chinook Salmon. We developed a reliable assay for sdY that can be used for genetic sex assignment in this species. However, discordance between phenotype and genotype was noted in 13 of 107 phenotypic female Chinook Salmon from Alaska and Washington. Several explanations for this discordance are discussed.Received January 14, 2014; accepted November 25, 2014
Estimating Sturgeon Abundance in the Carolinas Using Side-Scan Sonar
Authors: Flowers H. Jared , Hightower Joseph E. 
Published: March 2015

Abstract
Sturgeons (Acipenseridae) are one of the most threatened taxa worldwide, including species in North Carolina and South Carolina. Populations of Atlantic Sturgeon Acipenser oxyrinchus in the Carolinas have been significantly reduced from historical levels by a combination of intense fishing and habitat loss. There is a need for estimates of current abundance, to describe status, and for estimates of historical abundance in order to provide realistic recovery goals. In this study we used N-mixture and distance models with data acquired from side-scan sonar surveys to estimate abundance of sturgeon in six major sturgeon rivers in North Carolina and South Carolina. Estimated abundances of sturgeon greater than 1 m TL in the Carolina distinct population segment (DPS) were 2,031 using the count model and 1,912 via the distance model. The Pee Dee River had the highest overall abundance of any river at 1,944 (count model) or 1,823 (distance model). These estimates do not account for sturgeon less than 1 m TL or occurring in riverine reaches not surveyed or in marine waters. Comparing the two models, the N-mixture model produced similar estimates using less data than the distance model with only a slight reduction of estimated precision.
Received May 3, 2014; accepted October 14, 2014
Video capture of crustacean fisheries data as an alternative to on-board observers
Authors: Hold Natalie , Murray Lee G. , Pantin Julia R. , Haig Jodie A. , Hinz Hilmar , Kaiser Michel J. 
Published: March 2015

AbstractFor EU member states to meet the requirements of the Marine Strategy Framework Directive and the reformed Common Fisheries Policy, it will be necessary to improve data collection related to many fisheries that are at present subject to relatively little monitoring or scientific research. This study evaluated the use of on-board camera systems to collect data from Cancer pagurus and Homarus gammarus fisheries. We evaluated the reliability of the hardware and its ability to collect images of sufficient accuracy and precision compared with using on-board observers. Fishers and on-board observers passed animals removed from traps across a defined area. The relationship between the in situ and predicted measurements of carapace length of lobsters or carapace width (CW) of crabs was investigated. The mean difference between the predicted and real crab measurements was −0.853 mm with a standard error of 0.378 mm. Suggesting that the model tends to underestimate the real CW slightly. The mean difference between predicted and real data for lobsters was 0.085 mm with a standard error of 0.208 mm. Sex allocation for crabs based on video images was 100% accurate. All male lobsters were correctly assigned. For lobsters &gt;86 mm in length, the correct female sex allocation was 100% accurate. For smaller lobsters, the accuracy of sex allocation decreased to a low of 51% in lobsters &lt;70 mm. Camera systems were found to be a suitable method for collecting data on the size and sex of crabs and lobsters. The error attributable to using video data rather than manual measurement was less than 3 mm, which is sufficient to detect growth increments in these species. The requirements to collect basic species data are increasing and the ability to do so without on-board observers will reduce the cost implications of these requirements. Future computer automation of image extraction and measurements will increase the application of video systems for data collection.
Prior Opioid Use Does Not Impact the Response to Pregabalin in Patients With Fibromyalgia
Authors: Argoff Charles E. , Clair Andrew , Emir Birol , Whalen Ed , Ortiz Marie , Pauer Lynne 
Published: March 2015

Objective:
Fibromyalgia (FM) is a chronic pain disorder for which pregabalin is an approved treatment in the United States. Although opioids are not a recommended treatment option, they continue to be used by many FM patients. The impact of patients’ prior opioid use on their subsequent response to pregabalin has not been assessed.

Methods:
This was a pooled analysis of 4 clinical trials to assess the efficacy of pregabalin in FM patients both with and without prior opioid use. Patients were divided into those using opioids prior to the trial and those who were not. The change in least squares mean pain score (assessed by 0 to 10 numeric rating scale) with pregabalin compared with placebo was assessed together with FM symptoms, anxiety, and depression.

Results:
There were 2062 patients in the analysis set, including 371 patients with prior opioid use. Equal numbers of patients were treated with placebo, pregabalin 300 mg/d, and pregabalin 450 mg/d. Pregabalin significantly improved the least squares mean (95% confidence interval) difference in pain score compared with placebo in patients both with and without prior opioid use 0.87 (0.34-1.41) and 0.41 (0.17-0.65), respectively, at 300 mg/d and 0.91 (0.39-1.44) and 0.72 (0.48-0.96) at 450 mg/d (P≤0.001 for all). FM symptoms, anxiety, and depression were also improved with pregabalin compared with placebo, regardless of prior opioid use.

Discussion:
FM patients respond to treatment with pregabalin with significant improvements in pain scores irrespective of prior opioid use. These data could inform treatment decisions for FM patients with prior use of opioids.
The importance of picking Porter: the Royal Institution, George Porter and the two cultures, 1959–64
Authors: Cole Rupert 
Published: March 2015

This paper examines the cultural reasons why in 1964 the Royal Institution (RI) selected George Porter, who became the only person so far to have been Director of the Royal Institution (1966–85), President of the Royal Society (1985–90) and President of the British Association (1985–86) at the same time, to succeed William Lawrence Bragg as the institution's scientific director and resident professor. Porter was established as first choice by an inner group of RI Managers before the formal selection process began. In this article I argue that Porter won their favour by presenting himself, during his tenure as the RI's Professor of Chemistry (1963–66), as a candidate who fitted well with the Managers' ideas about the future role of the RI—ideas that were deeply influenced by the prevailing technocratic visions of ‘science and society’, particularly C. P. Snow's writings on the ‘two cultures’.
svviz: a read viewer for validating structural variants
Authors: Spies Noah , Zook Justin M. , Salit Marc , Sidow Arend 
Published: March 2015

AbstractVisualizing read alignments is the most effective way to validate candidate SVs with existing data. We present svviz, a sequencing read visualizer for structural variants (SVs) that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele, and identifying reads that match one allele better than the other. Reads are assigned to the proper allele based on alignment score, read pair orientation and insert size. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared to the single reference genome-based view common to most current read browsers. The web view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations, and manual refinement of breakpoints. An optional command-line-only interface allows summary statistics and graphics to be exported directly to standard graphics file formats. svviz is open source and freely available from github, and requires as input only structural variant coordinates (called using any other software package), reads in bam format, and a reference genome. Reads from any high-throughput sequencing platform are supported, including Illumina short-read, mate-pair, synthetic long-read (assembled), Pacific Biosciences, and Oxford Nanopore. svviz is open source and freely available fromhttps://github.com/svviz/svviz.
Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Authors: Harry Chen Hung-I , Liu Yuanhang , Zou Yi , Lai Zhao , Sarkar Devanand , Huang Yufei , Chen Yidong 
Published: March 2015

AbstractBackgroundRNA sequencing (RNA-seq) is a powerful tool for genome-wide expression profiling of biological samples with the advantage of high-throughput and high resolution. There are many existing algorithms nowadays for quantifying expression levels and detecting differential gene expression, but none of them takes the misaligned reads that are mapped to non-exonic regions into account. We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.ResultsWe implemented our novel XBSeq algorithm and evaluated it by using a set of simulated expression datasets under different conditions, using a combination of negative binomial and Poisson distributions with parameters derived from real RNA-seq data. We compared the performance of our method with other commonly used differential expression analysis algorithms. We also evaluated the changes in true and false positive rates with variations in biological replicates, differential fold changes, and expression levels in non-exonic regions. We also tested the algorithm on a set of real RNA-seq data where the common and different detection results from different algorithms were reported.ConclusionsIn this paper, we proposed a novel XBSeq, a differential expression analysis algorithm for RNA-seq data that takes non-exonic mapped reads into consideration. When background noise is at baseline level, the performance of XBSeq and DESeq are mostly equivalent. However, our method surpasses DESeq and other algorithms with the increase of non-exonic mapped reads. Only in very low read count condition XBSeq had a slightly higher false discovery rate, which may be improved by adjusting the background noise effect in this situation. Taken together, by considering non-exonic mapped reads, XBSeq can provide accurate expression measurement and thus detect differential expressed genes even in noisy conditions.
Mutational oncogenic signatures on structurally resolved protein interacting interfaces
Authors: Garcia-Alonso Luz , Dopazo Joaquin 
Published: March 2015

AbstractThe importance of the context of interactions in the proteins mutated in cancer is long known. However, our knowledge on how mutations affecting to protein-protein interactions (PPIs) are related to cancer occurrence and progression is still poor. Here, we extracted the missense somatic mutations from 5920 cancer patients of 33 different cancer types, taken from the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), and mapped them onto a structurally resolved interactome, which integrates three-dimensional atomic-level models of domain-domain interactions with experimentally determined PPIs, involving a total of 7580 unique interacting domains that participate in 13160 interactions connecting 4996 proteins. We observed that somatic nonsynonymous mutations tend to concentrate in ordered regions of the affected proteins and, within these, they have a clear preference for the interacting interfaces. Also, we have identified more than 250 interacting interfaces candidate to drive cancer. Examples demonstrate how mutations in the interacting interfaces are strongly associated with patient survival time, while similar mutations in other areas of the same proteins lack this association. Our results suggest that the perturbation caused by cancer mutations in protein interactions is an important factor in explaining the heterogeneity between cancer patients.
Different Coupling Modes Mediate Cortical Cross-Frequency Interactions
Authors: Helfrich Randolph F. , Herrmann Christoph S. , Engel Andreas K. , Schneider Till R. 
Published: March 2015

AbstractCross-frequency coupling (CFC) has been suggested to constitute a highly flexible mechanism for cortical information gating and processing, giving rise to conscious perception and various higher cognitive functions in humans. In particular, it might provide an elegant tool for information integration across several spatiotemporal scales within nested or coupled neuronal networks. However, it is currently unknown whether low frequency (theta/alpha) or high frequency gamma oscillations orchestrate cross-frequency interactions, raising the question of who is master and who is slave. While correlative evidence suggested that at least two distinct CFC modes exist, namely phase-amplitude-coupling (PAC) and amplitude-envelope-correlations (AEC), it is currently unknown whether they subserve distinct cortical functions. Novel non-invasive brain stimulation tools, such as transcranial alternating current stimulation (tACS), now provide the unique opportunity to selectively entrain the low or high frequency component and study subsequent effects on CFC. Here, we demonstrate the differential modulation of CFC during selective entrainment of alpha or gamma oscillations. Our results reveal that entrainment of the low frequency component increased PAC, where gamma power became preferentially locked to the trough of the alpha oscillation, while gamma-band entrainment reduced alpha power through enhanced AECs. These results provide causal evidence for the functional role of coupled alpha and gamma oscillations for visual processing.