bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional profiling of dividing tumor cells detects intratumor heterogeneity linked to cell proliferation in a brain tumor model
Authors: Endaya Berwini B. , Lam Paula Y.P. , Meedeniya Adrian C.B. , Neuzil Jiri 
Published: September 2015

Intratumor heterogeneity is a primary feature of high‐grade gliomas, complicating their therapy. As accumulating evidence suggests that intratumor heterogeneity is a consequence of cellular subsets with different cycling frequencies, we developed a method for transcriptional profiling of gliomas, using a novel technique to dissect the tumors into two fundamental cellular subsets, namely, the proliferating and non‐proliferating cell fractions. The tumor fractions were sorted whilst maintaining their molecular integrity, by incorporating the thymidine analog 5‐ethynyl‐2′‐deoxyuridine into actively dividing cells. We sorted the actively dividing versus non‐dividing cells from cultured glioma cells, and parental and clonally derived orthotopic tumors, and analyzed them for a number of transcripts. While there was no significant difference in the transcriptional profiles between the two cellular subsets in cultured glioma cells, we demonstrate ∼2–6 fold increase in transcripts of cancer and neuronal stem cell and tumor cell migration/invasion markers, and ∼2‐fold decrease in transcripts of markers of hypoxia and their target genes, in the dividing tumor cells of the orthotopic glioma when compared to their non‐proliferative counterparts. This suggests the influence of the brain microenvironment in transcriptional regulation and, thereby, the physiology of glioma cells in vivo. When clonal glioma cells were derived from a parental glioma and the resultant orthotopic tumors were compared, their transcriptional profiles were closely correlated to tumor aggression and consequently, survival of the experimental animals. This study demonstrates the resolution of intratumor heterogeneity for profiling studies based on cell proliferation, a defining feature of cancers, with implications for treatment design.
Bank leverage and profitability: Evidence from a sample of international banks
Authors: Beltratti Andrea , Paladino Giovanna 
Published: September 2015

AbstractWe examine the relationship between leverage and residual income for a sample of international banks using an unbalanced panel over the period 2005–2011. Our GMM‐based econometric model considers both bank‐level and country‐level variables to control for several other factors aside from equity capital and allows for endogeneity and unobservable heterogeneity. We document a significant positive non‐monotonic link between the capital ratio and residual income for the international banking industry. These results are robust to a number of different model specifications.
Perspectives of Clinicians Involved in the RESTART-Study: Outcomes of a Focus Group
Authors: de Sonneville-Koedoot Caroline , Adams Samantha A. , Stolk Elly A. , Franken Marie-Christine 
Published: September 2015

Purpose
The purpose of this study was to explore the attitudes and beliefs of speech-language pathologists (SLPs) with regard to the Lidcombe Program and Demands and Capacities–based treatment and to examine how these attitudes and beliefs might have changed as a result of participating in the RESTART-study.

Method
A focus group meeting with 13 SLPs was organized. The discussion was structured using questions on therapy preference, attitudes about and explicit comparison of both treatments and treatment manuals, and learnings of trial participation.

Results
Four main themes were identified. First, a change in attitude toward treatment choice was observed. Second, this change was related to a change in beliefs about the potential of both treatments. Third, aspects of the treatments regarded as success factors were considered. Last, learning outcomes and increased professionalism as a result of participating in the RESTART-trial were discussed.

Conclusions
This study showed how attitudes and beliefs of SLPs with regard to the Lidcombe Program and Demands and Capacities–based treatment evolved during a randomized trial. This work increases our understanding of the role of attitudes and beliefs in the uptake and utilization of therapies and demonstrates the importance of collecting qualitative data. Results and recommendations should prove of value in implementing the RESTART-trial results and in training SLPs.
Comparison of Psychophysiological and Dual-Task Measures of Listening Effort
Authors: Seeman Scott , Sims Rebecca 
Published: September 2015

Purpose
We wished to make a comparison of psychophysiological measures of listening effort with subjective and dual-task measures of listening effort for a diotic-dichotic-digits and a sentences-in-noise task.

Method

Three groups of young adults (18–38 years old) with normal hearing participated in three experiments: two psychophysiological studies for two different listening tasks and a dual-task measure for a sentences-in-noise task. Psychophysiological variables included skin conductance, heart-rate variability, and heart rate; the dual-task measure was a letter-identification task. Heart-rate variability was quantified with the difference from baseline for the normalized standard deviation of
R
to
R
.

Results
Heart-rate variability differences from baseline were greater for increased task complexity and for poorer signal-to-noise ratios (SNRs). The dual-task measure of listening effort also increased for sentences presented at a +5 dB SNR compared with a +15 dB SNR. Skin conductance was elevated for greater task complexity only, and similar across noise conditions. None of these measures were significantly correlated with subjective measures of listening effort.

Conclusions
Heart-rate variability appears to be a robust psychophysiological indicator of listening effort, sensitive to both task complexity and SNR. This sensitivity to SNR was similar to a dual-task measure of listening effort.
An Open Conversation on Using Eye-Gaze Methods in Studies of Neurodevelopmental Disorders
Authors: Venker Courtney E. , Kover Sara T. 
Published: September 2015

Purpose
Eye-gaze methods have the potential to advance the study of neurodevelopmental disorders. Despite their increasing use, challenges arise in using these methods with individuals with neurodevelopmental disorders and in reporting sufficient methodological detail such that the resulting research is replicable and interpretable.

Method
This tutorial presents key considerations involved in designing and conducting eye-gaze studies for individuals with neurodevelopmental disorders and proposes conventions for reporting the results of such studies.

Results
Methodological decisions (e.g., whether to use automated eye tracking or manual coding, implementing strategies to scaffold children's performance, defining valid trials) have cascading effects on the conclusions drawn from eye-gaze data. Research reports that include specific information about procedures, missing data, and selection of participants will facilitate interpretation and replication.

Conclusions
Eye-gaze methods provide exciting opportunities for studying neurodevelopmental disorders. Open discussion of the issues presented in this tutorial will improve the pace of productivity and the impact of advances in research on neurodevelopmental disorders.
Auditory Masking Effects on Speech Fluency in Apraxia of Speech and Aphasia: Comparison to Altered Auditory Feedback
Authors: Jacks Adam , Haley Katarina L. 
Published: September 2015

Purpose
To study the effects of masked auditory feedback (MAF) on speech fluency in adults with aphasia and/or apraxia of speech (APH/AOS). We hypothesized that adults with AOS would increase speech fluency when speaking with noise. Altered auditory feedback (AAF; i.e., delayed/frequency-shifted feedback) was included as a control condition not expected to improve speech fluency.

Method
Ten participants with APH/AOS and 10 neurologically healthy (NH) participants were studied under both feedback conditions. To allow examination of individual responses, we used an ABACA design. Effects were examined on syllable rate, disfluency duration, and vocal intensity.

Results
Seven of 10 APH/AOS participants increased fluency with masking by increasing rate, decreasing disfluency duration, or both. In contrast, none of the NH participants increased speaking rate with MAF. In the AAF condition, only 1 APH/AOS participant increased fluency. Four APH/AOS participants and 8 NH participants slowed their rate with AAF.

Conclusions
Speaking with MAF appears to increase fluency in a subset of individuals with APH/AOS, indicating that overreliance on auditory feedback monitoring may contribute to their disorder presentation. The distinction between responders and nonresponders was not linked to AOS diagnosis, so additional work is needed to develop hypotheses for candidacy and underlying control mechanisms.

Supplemental Material

https://doi.org/10.23641/asha.14963628
Effects of flavonol-rich green tea cultivar (Camellia sinensis L.) on plasma oxidized LDL levels in hypercholesterolemic mice
Authors: Nomura Sachiko , Monobe Manami , Ema Kaori , Matsunaga Akiko , Maeda-Yamamoto Mari , Horie Hideki 
Published: September 2015

Abstract
To examine the possible benefits of tea flavonols, we compared anti-atherogenic effects between common and flavonol-rich tea cultivars. The tea infusion made from a flavonol-rich cultivar, but not a common cultivar, significantly decreased the plasma oxidized low-density lipoprotein level in mice fed a high-cholesterol diet. The result suggests that tea flavonols have the potential to protect against cardiovascular diseases.
A robust AMMI model for the analysis of genotype-by-environment data
Authors: Rodrigues Paulo C. , Monteiro Andreia , Lourenço Vanda M. 
Published: September 2015

Abstract
Motivation: One of the most widely used models to analyse genotype-by-environment data is the additive main effects and multiplicative interaction (AMMI) model. Genotype-by-environment data resulting from multi-location trials are usually organized in two-way tables with genotypes in the rows and environments (location-year combinations) in the columns. The AMMI model applies singular value decomposition (SVD) to the residuals of a specific linear model, to decompose the genotype-by-environment interaction (GEI) into a sum of multiplicative terms. However, SVD, being a least squares method, is highly sensitive to contamination and the presence of even a single outlier, if extreme, may draw the leading principal component towards itself resulting in possible misinterpretations and in turn lead to bad practical decisions. Since, as in many other real-life studies the distribution of these data is usually not normal due to the presence of outlying observations, either resulting from measurement errors or sometimes from individual intrinsic characteristics, robust SVD methods have been suggested to help overcome this handicap.
Results: We propose a robust generalization of the AMMI model (the R-AMMI model) that overcomes the fragility of its classical version when the data are contaminated. Here, robust statistical methods replace the classic ones to model, structure and analyse GEI. The performance of the robust extensions of the AMMI model is assessed through a Monte Carlo simulation study where several contamination schemes are considered. Applications to two real plant datasets are also presented to illustrate the benefits of the proposed methodology, which can be broadened to both animal and human genetics studies.
Availability and implementation: Source code implemented in R is available in the supplementary material under the function r-AMMI.
Contact: paulocanas@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
BamHash: a checksum program for verifying the integrity of sequence data
Authors: Óskarsdóttir Arna , Másson Gísli , Melsted Páll 
Published: September 2015

Abstract
Summary: Large resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Because the raw sequences are redundant once the alignment has been generated, it is possible to keep only the alignment files. We present BamHash, a checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity of the files stored and discover any discrepancies. Thus, BamHash can be used to determine if it is safe to delete the FASTQ files storing raw sequencing read after alignment, without the loss of data.
Availability and implementation: The software is implemented in C++, GPL licensed and available at https://github.com/DecodeGenetics/BamHash
Contact: pmelsted@hi.is
Navigating by the Stars: Investigating the Actual and Perceived Validity of Online User Ratings
Authors: de Langhe Bart , Fernbach Philip M. , Lichtenstein Donald R. 
Published: September 2015

Abstract
This research documents a substantial disconnect between the objective quality information that online user ratings actually convey and the extent to which consumers trust them as indicators of objective quality. Analyses of a data set covering 1272 products across 120 vertically differentiated product categories reveal that average user ratings (1) lack convergence with Consumer Reports scores, the most commonly used measure of objective quality in the consumer behavior literature, (2) are often based on insufficient sample sizes which limits their informativeness, (3) do not predict resale prices in the used-product marketplace, and (4) are higher for more expensive products and premium brands, controlling for Consumer Reports scores. However, when forming quality inferences and purchase intentions, consumers heavily weight the average rating compared to other cues for quality like price and the number of ratings. They also fail to moderate their reliance on the average user rating as a function of sample size sufficiency. Consumers’ trust in the average user rating as a cue for objective quality appears to be based on an “illusion of validity.”
Remifentanil Requirement for Inhibiting Responses to Tracheal Intubation and Skin Incision Is Reduced in Patients With Parkinson's Disease Undergoing Deep Brain Stimulator Implantation
Authors: Wang Jia-Feng , Xu Xiao-Ping , Yu Xi-Ya , Li Jin-Bao , Wu Xi , Chen Jian-Chun , Hu Xiao-Wu , Deng Xiao-Ming 
Published: September 2015

Background:Parkinson’s disease (PD) is a common neurodegenerative disease affecting the quality of life in the elderly. We speculated that PD patients might have abnormal pharmacodynamics due to the degenerative neural system, and the present study was performed to investigate the pharmacodynamics of remifentanil in PD patients.Materials and Methods:Two arms of patients were recruited, including 31 PD patients undergoing pulse generator placement after deep brain stimulator implantation and 31 pair-controlled patients undergoing intracranial surgery without PD (NPD). Patients were anesthetized with target-controlled infusion of propofol and remifentanil. The effective concentration of remifentanil to inhibit responses to intubation and skin incision in 50% and 95% patients (EC50and EC95) was determined by the up and down method.Results:Demographic data, bispectral index, and hemodynamic values were similar between the PD and the NPD groups. The average remifentanil concentration used in the PD group for tracheal intubation is significantly lower than in the NPD group (P<0.001). The EC50for inhibiting the response to tracheal intubation were 1.86 ng/mL (95% confidential interval [CI], 1.77-1.96 ng/mL) in the PD group and 3.20 ng/mL (95% CI, 3.13-3.27 ng/mL) in the NPD group. The average remifentanil concentration used in the PD group for skin incision is significantly lower than in the NPD group (P<0.001). EC50for inhibiting the response to skin incision were 2.17 ng/mL (95% CI, 2.09-2.25 ng/mL) in the PD group and 3.09 ng/mL (95% CI, 3.02-3.17 ng/mL) in the NPD group.Conclusions:The remifentanil concentrations required for inhibiting responses to tracheal intubation and skin incision are reduced markedly in PD patients undergoing pulse generator placement (NCT01992692).
A Modification to the McHale Procedure Reduces Operative Time and Blood Loss
Authors: Godfrey Jenna , McGraw Jessica , Kallur Antony , Silva Selina , Szalay Elizabeth 
Published: September 2015

Background:
Treatment of symptomatic spastic hip dislocations in adolescent patients with cerebral palsy includes a variety of described salvage type procedures. In 1990, McHale and colleagues described a technique involving a femoral head resection, valgus-producing proximal femoral osteotomy, and advancement of the lesser trochanter into the acetabulum. We have modified this technique in 3 ways by: performing it in the lateral position with a more posterior approach, not advancing the lesser trochanter into the acetabulum, and closing the capsule over the acetabulum. The purpose of this paper is to describe our technique and to compare the results to Castle type procedures and McHale procedures performed as originally described.

Methods:
We retrospectively reviewed all salvage type procedures performed at our institution for spastic hip dislocations in children with cerebral palsy from 2003 to 2013. Preoperative and postoperative pain, estimated blood loss, operative time, length of stay in the hospital, and postoperative pelvis radiographs were reviewed for heterotopic ossification formation and proximal femoral migration.

Results:
Twenty-six patients with 30 hip procedures were reviewed. The modified McHale technique had shorter operative times when compared with the supine McHale technique and the Castle procedure (134, 171, and 139 min, respectively). There was a trend toward less blood loss in the modified McHale technique, but this was not significant. There was no difference in length of stay in the hospital. The majority of McHale patients (>63%) had pain relief postoperatively, where half of the Castle patients required a revision surgery for pain (4 of 8). There was less heterotopic ossification seen in the modified McHale technique (6.25%) when compared with supine McHale and Castle techniques (both 50%). However, there was more proximal femoral migration in the modified McHale group.

Conclusions:
The modified McHale technique is faster with otherwise equivocal results in the immediate operative periods. There is less heterotopic bone formation but more proximal femoral migration with this new technique.

Level of Evidence:
Level IV—case series.
Transfer of Pectoralis Major to Subscapularis in the Management of Brachial Plexus Birth Palsy Sequels
Authors: Lahiji Faryvar A. , Tahririan Mohammad A. , Karami Mohsen , Madadi Firooz , Emami Mohammad , Maleki Arash 
Published: September 2015

Background:
Limitations in abduction and external rotation are the sequel of brachial palsy. The purpose of this study was to evaluate functional outcomes of modified L’Episcopo procedure in children with brachial palsy who do not have gross shoulder joint subluxation.

Methods:
From 2002 to 2012, a continuous series of 22 patients with brachial plexus birth palsy underwent a modified L’Episcopo procedure. Through an axillary approach, subscapularis release with latissimus dorsi rerouting and transfer of pectoralis major to subscapularis footprint was performed.

Results:
The mean age of patients at surgery was 49 months. The mean follow-up time was 51 months (range, 24 to 90 mo). Preoperatively, the mean active abduction and external rotation were 77.5 and 2.5 degrees, respectively. The mean active abduction and external rotation were 135.6 and 32 degrees, respectively, at the final follow-up (P<0.001).

Conclusions:
This modified L’Episcopo technique is an effective and reproducible procedure that improves shoulder function significantly.

Level of Evidence:
Level III.
Transthoracic Extracorporeal Gastric Conduit Preparation for Minimally Invasive Ivor-Lewis Esophagectomy
Authors: McGuire Anna L. , Gilbert Sebastien 
Published: September 2015

Objective During totally minimally invasive esophagectomy (MIE), the gastric conduit is typically constructed via laparoscopy. Trauma from laparoscopic instruments, inability to palpate the gastroepiploic arcade, and challenges in optimal positioning of the stomach for intra-abdominal stapling have led to the widespread use of laparotomy as part of hybrid MIE procedures. Our objective was to evaluate the safety of transthoracic extracorporeal gastric conduit preparation. We hypothesize that this alternative technique is equivalent in safety to the laparoscopic approach. Methods This is a retrospective comparison of laparoscopic and transthoracic extracorporeal gastric conduit preparation with regard to anastomotic and respiratory outcomes. Results During a 3-year period, 30 patients underwent MIE with a right intrathoracic anastomosis (extracorporeal conduit, 15; laparoscopic conduit, 15). Mean age (58.6 vs 67 years, P = 0.59), tumor location (gastroesophageal junction vs middle and lower esophageal, P = 0.27), and histology (adenocarcinoma vs other 26.7%, P = 0.68) were similar between groups. Anastomotic technique and operating surgeon were the same for all patients. Patients in the laparoscopic gastric conduit group were more likely to have undergone induction chemoradiotherapy (40% vs 80%, P = 0.030). There was no significant difference between groups with respect to anastomotic complications, including anastomotic leak and anastomotic stricture (20% vs 13.3%, P = 0.70). Transthoracic gastric conduit preparation was not associated with increased respiratory complications (8% vs 12%, P = 0.09). Conclusions Transthoracic gastric conduit preparation is a simple, minimally invasive alternative laparotomy for gastric conduit preparation during MIE. No additional incision is required. The technique may help surgeons overcome shortcomings of the laparoscopic approach without impacting perioperative risk.
Early and Midterm Results of No-Touch Aorta Multivessel Small Thoracotomy Coronary Artery Bypass Grafting: A Propensity Score-Matched Study
Authors: Ziankou Aliaksandr , Ostrovsky Yuri 
Published: September 2015

Objective To carry out the comparative analysis of early and midterm results of no-touch aorta multivessel small thoracotomy coronary artery bypass grafting (MVST CABG), conventional off-pump (OPCABG) and on-pump CABG (ONCABG). Methods From 2007 to 2014, 537 consecutive patients underwent CABG by the same surgeon. Propensity score computer matching was performed, and a total of 453 patients were successfully matched in 3 groups of 151 patients. Results Significant differences were found in the intraoperative blood loss: 220 (180; 300) mL in MVST CABG versus 400 (300; 550) mL in OPCABG vs 350 (250; 435) mL in ONCABG group; first 24-hour postoperative blood loss: 170 (100; 280), 320 (200; 470), and 380 (200; 500)mL, respectively; operation time: 352.4 ± 74.4,289.3 ± 55.0, and 280.4 ± 56.4 minutes, respectively; median time to return to full physical activity: 14, 56, and 56 days, respectively (P < 0.05); rate of deep wound infection: 0.0%, 2.0%, and 2.0%, respectively; and postoperative length of stay (surgical department): 4.5, 7.0, and 7.5 days, respectively (P < 0.1). No significant differences were observed in rates of severe in-hospital events (P > 0.05), cumulative midterm survival, and freedom from major adverse cardiac and cerebrovascular events (P > 0.05). Conclusions The MVST CABG seems as safe as OPCABG and ONCABG and is associated with less wound infections, perioperative blood loss, shorter hospital length of stay and time to return to full physical activity. Multivessel small thoracotomy CABG can be applied to most patients with coronary heart disease saving the effectiveness during midterm follow-up. The MVST CABG can be introduced avoiding a prolonged learning curve.