bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Authors: Bi Ran , Liu Peng 
Published: March 2016

AbstractBackgroundRNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of differential expression analysis with RNA-seq data. One challenge is that there are no closed-form formulae to calculate power for the popularly applied tests for differential expression analysis. In addition, false discovery rate (FDR), instead of family-wise type I error rate, is controlled for the multiple testing error in RNA-seq data analysis. So far, there are very few proposals on sample size calculation for RNA-seq experiments.ResultsIn this paper, we propose a procedure for sample size calculation while controlling FDR for RNA-seq experimental design. Our procedure is based on the weighted linear model analysis facilitated by thevoommethod which has been shown to have competitive performance in terms of power and FDR control for RNA-seq differential expression analysis. We derive a method that approximates the average power across the differentially expressed genes, and then calculate the sample size to achieve a desired average power while controlling FDR. Simulation results demonstrate that the actual power of several popularly applied tests for differential expression is achieved and is close to the desired power for RNA-seq data with sample size calculated based on our method.ConclusionsOur proposed method provides an efficient algorithm to calculate sample size while controlling FDR for RNA-seq experimental design. We also provide an R packagessizeRNAthat implements our proposed method and can be downloaded from the Comprehensive R Archive Network (http://cran.r-project.org).
Association between tensin 1 and p130Cas at focal adhesions links actin inward flux to cell migration
Authors: Zhao Zhihai , Tan Song Hui , Machiyama Hiroaki , Kawauchi Keiko , Araki Keigo , Hirata Hiroaki , Sawada Yasuhiro 
Published: March 2016

ABSTRACT
Cell migration is a highly dynamic process that plays pivotal roles in both physiological and pathological processes. We have previously reported that p130Cas supports cell migration through the binding to Src as well as phosphorylation-dependent association with actin retrograde flow at focal adhesions. However, it remains elusive how phosphorylated Cas interacts with actin cytoskeletons. We observe that the actin-binding protein, tensin 1, co-localizes with Cas, but not with its phosphorylation-defective mutant, at focal adhesions in leading regions of migrating cells. While a truncation mutant of tensin 1 that lacks the phosphotyrosine-binding PTB and SH2 domains (tensin 1-SH2PTB) poorly co-localizes or co-immunoprecitates with Cas, bacterially expressed recombinant tensin 1-SH2PTB protein binds to Cas in vitro in a Cas phosphorylation-dependent manner. Furthermore, exogenous expression of tensin 1-SH2PTB, which is devoid of the actin-interacting motifs, interferes with the Cas-driven cell migration, slows down the inward flux of Cas molecules, and impedes the displacement of Cas molecules from focal adhesions. Taken together, our results show that tensin 1 links inwardly moving actin cytoskeletons to phosphorylated Cas at focal adhesions, thereby driving cell migration.
Sticking to the story: outstanding challenges in gecko-inspired adhesives
Authors: Niewiarowski Peter H. , Stark Alyssa Y. , Dhinojwala Ali 
Published: March 2016

ABSTRACT
The natural clinging ability of geckos has inspired hundreds of studies seeking design principles that could be applied to creating synthetic adhesives with the same performance capabilities as the gecko: adhesives that use no glue, are self-cleaning and reusable, and are insensitive to a wide range of surface chemistries and roughness. Important progress has been made, and the basic mechanics of how ‘hairy’ adhesives work have been faithfully reproduced, advancing theory in surface science and portending diverse practical applications. However, after 15 years, no synthetic mimic can yet perform as well as a gecko and simultaneously meet of all the criteria listed above. Moreover, processes for the production of inexpensive and scalable products are still not clearly in view. Here, we discuss our perspective on some of the gaps in understanding that still remain; these gaps in our knowledge should stimulate us to turn to deeper study of the way in which free-ranging geckos stick to the variety of surfaces found in their natural environments and to a more complete analysis of the materials composing the gecko toe pads.
Mechanical responses of rat vibrissae to airflow
Authors: Yu Yan S. W. , Graff Matthew M. , Hartmann Mitra J. Z. 
Published: March 2016

ABSTRACT
The survival of many animals depends in part on their ability to sense the flow of the surrounding fluid medium. To date, however, little is known about how terrestrial mammals sense airflow direction or speed. The present work analyzes the mechanical response of isolated rat macrovibrissae (whiskers) to airflow to assess their viability as flow sensors. Results show that the whisker bends primarily in the direction of airflow and vibrates around a new average position at frequencies related to its resonant modes. The bending direction is not affected by airflow speed or by geometric properties of the whisker. In contrast, the bending magnitude increases strongly with airflow speed and with the ratio of the whisker's arc length to base diameter. To a much smaller degree, the bending magnitude also varies with the orientation of the whisker's intrinsic curvature relative to the direction of airflow. These results are used to predict the mechanical responses of vibrissae to airflow across the entire array, and to show that the rat could actively adjust the airflow data that the vibrissae acquire by changing the orientation of its whiskers. We suggest that, like the whiskers of pinnipeds, the macrovibrissae of terrestrial mammals are multimodal sensors – able to sense both airflow and touch – and that they may play a particularly important role in anemotaxis.
Epidemiology and health care situation of chronic wounds in Germany
Authors: Protz K. , Augustin M. , Herberger K. , Heyer K. 
Published: March 2016

SummaryChronic wounds are of great socioeconomic importance. Usually they are associated with a long, complicated and burdensome course of disease and require high nursing and medical expenses. The quality of life of patients with chronic wounds is substantially impaired. This article provides a systematic overview of current studies on the morbidity and the health care situation of patients with chronic wounds, especially in patients with leg ulcers in Germany.Analyses based on routine data of statutory health insurances show higher incidence and prevalence rates, for example of patients with leg ulcers, compared with previously regional surveys. The quality of care is inadequate, particularly in diagnostics and therapy of patients with leg ulcers. To date, there is undersupply and a lack of execution and deficient knowledge about the compression treatment in patients with venous leg ulcers.Thus, there is need for further action in order to establish better implementation of guidelines in the management of patients with chronic wounds.
The review of crimes against foreign tourists: The case of Marmaris<p>Yabancı turistlere yönelik işlenen suçların incelenmesi: Marmaris Örneği
Authors: Ayazlar Gökhan , Işık Taylan 
Published: March 2016

The relationship between tourism and crime has long been interested by researchers from various points of views. The present study addresses the crimes committed against tourists from overseas and aims to investigate based on the questions prepared with regard to the relevant literature. Study data, on the special permission issued by the Marmaris Chief Public Prosecutor Office, was collected in Marmaris County through document review method. Collected research data includes crimes committed against tourists in the period between 2011 and 2014. According to research findings covering tourists visiting Marmaris County from foreign countries, it was determined that females, 25-59 age group, employed ones, singles, and Britons were in higher risk group compared with other classification groups. Moreover, whereas these findings suggest that the most frequently crimes committed against tourists are robbery, injury, violation of immunity of residence and sexual assault, they are mostly experienced in June, July, August, and September months. The relationship between number of crimes committed against tourists and number of incoming tourists was investigated. It is expected that study results will be beneficent for destination managers and marketing professionals. Finally, theoretical and practical consequences of findings obtained in the study were discussed. ÖzetTurizm ve suç arasındaki ilişki, sunduğu farklı bakış açıları ile uzun bir süredir araştırmacıların ilgi alanı içerisindedir. Bu çalışmanın amacı yabancı turistlere yönelik olarak işlenen suçları, literatüre bağlı olarak oluşturulan sorular kapsamında incelemektir. Çalışma verileri Marmaris Cumhuriyet Başsavcılığından alınan özel izinle, doküman inceleme yöntemiyle Marmaris’te toplanmıştır. Veriler 2011-2014 yıllarına ait turistlere yönelik olarak işlenen suçları içermektedir. Araştırma bulgularına göre Marmaris’e gelen yabancı turistlerden kadınların, 25-59 yaş aralığındakilerin, çalışanların, bekâr olanların ve İngilizlerin suçla karşılaşma olasılıkları karşılaştırıldıkları diğer gruplara göre daha yüksektir. Ayrıca araştırma kapsamında elde edilen bulgulara göre turistlere yönelik en fazla işlenen suçlar hırsızlık, yaralama, konut dokunulmazlığının ihlali ve cinsel saldırı olarak belirlenmiştir. En fazla suç işlenen aylar ise Haziran, Temmuz, Ağustos ve Eylül ayları olmuştur. Turistlere yönelik işlenen suç sayısı ile gelen turist sayısı arasındaki ilişki elde edilen bulgular ve literatür ışığındadeğerlendirilmiştir. Çalışma sonuçlarının destinasyon yöneticileri ve pazarlama uzmanları için fayda sağlaması beklenmektedir. Çalışmada elde edilen bulguların teorik ve pratik sonuçları tartışılmaktadır.
The two faces of reactive oxygen species (ROS) in adipocyte function and dysfunction
Authors: Castro José Pedro , Grune Tilman , Speckmann Bodo 
Published: March 2016

AbstractWhite adipose tissue (WAT) is actively involved in the regulation of whole-body energy homeostasis via storage/release of lipids and adipokine secretion. Current research links WAT dysfunction to the development of metabolic syndrome (MetS) and type 2 diabetes (T2D). The expansion of WAT during oversupply of nutrients prevents ectopic fat accumulation and requires proper preadipocyte-to-adipocyte differentiation. An assumed link between excess levels of reactive oxygen species (ROS), WAT dysfunction and T2D has been discussed controversially. While oxidative stress conditions have conclusively been detected in WAT of T2D patients and related animal models, clinical trials with antioxidants failed to prevent T2D or to improve glucose homeostasis. Furthermore, animal studies yielded inconsistent results regarding the role of oxidative stress in the development of diabetes. Here, we discuss the contribution of ROS to the (patho)physiology of adipocyte function and differentiation, with particular emphasis on sources and nutritional modulators of adipocyte ROS and their functions in signaling mechanisms controlling adipogenesis and functions of mature fat cells. We propose a concept of ROS balance that is required for normal functioning of WAT. We explain how both excessive and diminished levels of ROS, e.g. resulting from over supplementation with antioxidants, contribute to WAT dysfunction and subsequently insulin resistance.
Altered Glycolysis and Mitochondrial Respiration in a Zebrafish Model of Dravet Syndrome
Authors: Kumar Maneesh G. , Rowley Shane , Fulton Ruth , Dinday Matthew T. , Baraban Scott C. , Patel Manisha 
Published: March 2016

AbstractAltered metabolism is an important feature of many epileptic syndromes but has not been reported in Dravet syndrome (DS), a catastrophic childhood epilepsy associated with mutations in a voltage-activated sodium channel, Nav1.1 (SCN1A). To address this, we developed novel methodology to assess real-time changes in bioenergetics in zebrafish larvae between 4 and 6 d postfertilization (dpf). Baseline and 4-aminopyridine (4-AP) stimulated glycolytic flux and mitochondrial respiration were simultaneously assessed using a Seahorse Biosciences extracellular flux analyzer.Scn1Labmutant zebrafish showed a decrease in baseline glycolytic rate and oxygen consumption rate (OCR) compared to controls. A ketogenic diet formulation rescued mutant zebrafish metabolism to control levels. Increasing neuronal excitability with 4-AP resulted in an immediate increase in glycolytic rates in wild-type zebrafish, whereas mitochondrial OCR increased slightly and quickly recovered to baseline values. In contrast,scn1Labmutant zebrafish showed a significantly slower and exaggerated increase of both glycolytic rates and OCR after 4-AP. The underlying mechanism of decreased baseline OCR inscn1Labmutants was not because of altered mitochondrial DNA content or dysfunction of enzymes in the electron transport chain or tricarboxylic acid cycle. Examination of glucose metabolism using a PCR array identified five glycolytic genes that were downregulated inscn1Labmutant zebrafish. Our findings inscn1Labmutant zebrafish suggest that glucose and mitochondrial hypometabolism contribute to the pathophysiology of DS.
Collaborative Control of Cell Cycle Progression by the RNA Exonuclease Dis3 and Ras Is Conserved Across Species
Authors: Snee Mark J , Wilson William C , Zhu Yi , Chen Shin-Yu , Wilson Beth A , Kseib Cedric , O’Neal Julie , Mahajan Nitin , Tomasson Michael H , Arur Swathi , Skeath James B 
Published: March 2016

Abstract
Dis3 encodes a conserved RNase that degrades or processes all RNA species via an N-terminal PilT N terminus (PIN) domain and C-terminal RNB domain that harbor, respectively, endonuclease activity and 3′–5′ exonuclease activity. In Schizosaccharomyces pombe, dis3 mutations cause chromosome missegregation and failure in mitosis, suggesting dis3 promotes cell division. In humans, apparently hypomorphic dis3 mutations are found recurrently in multiple myeloma, suggesting dis3 opposes cell division. Except for the observation that RNAi-mediated depletion of dis3 function drives larval arrest and reduces tissue growth in Drosophila, the role of dis3 has not been rigorously explored in higher eukaryotic systems. Using the Drosophila system and newly generated dis3 null alleles, we find that absence of dis3 activity inhibits cell division. We uncover a conserved CDK1 phosphorylation site that when phosphorylated inhibits Dis3’s exonuclease, but not endonuclease, activity. Leveraging this information, we show that Dis3’s exonuclease function is required for mitotic cell division: in its absence, cells are delayed in mitosis and exhibit aneuploidy and overcondensed chromosomes. In contrast, we find that modest reduction of dis3 function enhances cell proliferation in the presence of elevated Ras activity, apparently by accelerating cells through G2/M even though each insult by itself delays G2/M. Additionally, we find that dis3 and ras genetically interact in worms and that dis3 can enhance cell proliferation under growth stimulatory conditions in murine B cells. Thus, reduction, but not absence, of dis3 activity can enhance cell proliferation in higher organisms.
Role ofp53, Mitochondrial DNA Deletions, and Paternal Age in Autism: A Case-Control Study
Authors: Wong Sarah , Napoli Eleonora , Krakowiak Paula , Tassone Flora , Hertz-Picciotto Irva , Giulivi Cecilia 
Published: March 2016

BACKGROUND:The tumor suppressor p53 responds to a variety of environmental stressors by regulating cell cycle arrest, apoptosis, senescence, DNA repair, bioenergetics and mitochondrial DNA (mtDNA) copy number maintenance. Developmental abnormalities have been reported in p53-deficient mice, and altered p53 and p53-associated pathways in autism (AU). Furthermore, via the Pten-p53 crosstalk, Pten haploinsufficient-mice have autisticlike behavior accompanied by brain mitochondrial dysfunction with accumulation of mtDNA deletions.METHODS:mtDNA copy number and deletions, and p53 gene copy ratios were evaluated in peripheral blood monocytic cells from children aged 2–5 years with AU (n = 66), race-, gender-, and age-matched typically neurodeveloping children (n = 46), and both parents from each diagnostic group, recruited by the Childhood Autism Risk from Genes and Environment study at the University of California, Davis.RESULTS:mtDNA deletions and higher p53 gene copy ratios were more common in children with AU and their fathers. The incidence of mtDNA deletions in fathers of children with AU was increased 1.9-fold over fathers of typically neurodeveloping children, suggesting a role for deficient DNA repair capacity not driven by paternal age. Deletions in mtDNA and altered p53 gene copy ratios seem to result from genetics (children with severity scores ≥8) and/or act in concert with environmental factors (children with 6–7 severity scores).CONCLUSIONS:Given pro- and antioxidant activities of p53, and associations of genomic instability with disorders other than AU, our study suggests a link between DNA repair capacity, genomic instability in the 17p13.1 region influenced by environmental triggers, and AU diagnosis.
Cardiac size of high-volume resistance trained female athletes: shaping the body but not the heart
Authors: Venckunas T , Simonavicius J , Marcinkeviciene JE 
Published: March 2016

Introduction
Exercise training, besides many health benefits, may result in cardiac remodelling which is dependent on the type and amount of exercise performed. It is not clear, however, whether significant adaptation in cardiac structure is possible in females undergoing resistance type of exercise training. Rigorous high volume training of most muscle groups emphasising resistance exercises are being undertaken by athletes of some aesthetic sports such as female fitness (light bodybuilding). The impact of this type of training on cardiac adaptation has not been investigated until now. The aim of the current study was to disclose the effect of high volume resistance training on cardiac structure and function.

Methods
11 top-level female fitness athletes and 20 sedentary age-matched controls were recruited to undergo two-dimensional echocardiography.

Results
Cardiac structure did not differ between elite female fitness athletes and controls (p > 0.05), and fitness athletes had a tendency for a smaller (p = 0.07) left ventricular (LV) mass indexed to lean body mass. Doppler diastolic function index (E/A ratio) and LV ejection fraction were similar between the groups (p > 0.05).

Conclusions
Elite female fitness athletes have normal cardiac size and function that do not differ from matched sedentary controls. Consequently, as high volume resistance training has no easily observable effect on adaptation of cardiac structure, when cardiac hypertrophy is present in young resistance-trained lean female, other reasons such as inherited cardiac disease are to be considered carefully.
Protective effects of Quercetin and chronic moderate exercise (training) against oxidative stress in the liver tissue of streptozotocin-induced diabetic rats
Authors: Chiş IC , Mureşan A , Oros A , Nagy AL , Clichici S 
Published: March 2016

Background
To investigate the protective effects of Quercetin administration associated with chronic moderate exercise (training) on oxidative stress in the liver in streptozotocin-induced diabetic rats.

Methods
Diabetic rats that performed exercise training were subjected to a swimming training program (1 hour/day, 5 days/week, 4 weeks). The diabetic rats received natural antioxidant, Quercetin (20 mg/kg body weight/day) for 4 weeks. At the end of the study, all animals were sacrificed and liver samples were collected for estimation: some oxidative stress markers (malondialdehyde, MDA and protein carbonyls groups, PC), the activity of antioxidant enzymes (superoxide dismutase, SOD and catalase, CAT), reduced glutathione (GSH) level and reduced (GSH) and oxidized (GSSG) glutathione ratio.

Results
Diabetic rats submitted to exercise training showed significantly increased the oxidative stress markers (MDA and PC) and a reduction of antioxidant enzyme (SOD and CAT) activity, GSH level and GSH/ GSSG ratio in hepatic tissues. A decrease in the levels of oxidative stress markers associated with elevated activity of antioxidant enzymes, the GSH level and GSH/GSSG ratio in the hepatic tissue were observed in Quercetin-treated diabetic trained rats.

Conclusions
These findings suggest that Quercetin administration in association with chronic moderate exercise exerts a protective effect in diabetes by attenuating hyperglycemia-mediated oxidative stress in hepatic tissue.
Applying music as a supplemental treatment in cancer care
Authors: Kollár János 
Published: March 2016

Theoretical background
Applying music as a supplemental therapeutic method is a flexible, patient-directed and adaptable, non-invasive treatment. Several forms of musical interventions are able to reduce distress, chronic pain, anxiety and depression.

Aim
The purpose of this review was drawing attention to the possibility of applying music as a supplementary, supportive treatment for cancer patients. The article would like to give a broader view of different fields of applying music in cancer treatment.

Methods
A search was made in Journal of Music Therapy, Music Therapy and Music Therapy Perspectives. Besides PubMed and Web of Knowledge were used for searching relevant articles reported in English and containing the expressions “music” and “cancer” or “music” and “psychooncology”, or “music” and “oncology”, or “music “ and “tumor”, or “music” and “tumour” in their titles. The searching process was closed in 2013. The articles were filtered by relevant content regarding the application of music in cancer treatment. The articles were considered as relevant 1) if they were focusing on any application of music in cancer treatment and 2) if they reported about original research results, so the reviews were filtered out of our selection. 61 articles were found of which 25 were considered as relevant for the review. The analysis of data was based on the following criteria: a) the aim of applying music with cancer patients, b) the applied method and period of intervention, c) number of participants and d) results.

Results
There is a significant improvement in quality of life of cancer patients receiving music as a supportive treatment. Both active and receptive forms of music therapy can be applied successfully either independently or with other therapies as a part of the supportive care.

Conclusion
Music applied by qualified music therapists in therapeutic circumstances can be suggested as a supportive treatment for cancer patients.