bluuebunny/crossref_metadata_2025_split huggingface dataset:
KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis
Authors: Yang Pengyi , Patrick Ellis , Humphrey Sean J. , Ghazanfar Shila , James David E. , Jothi Raja , Yang Jean Yee Hwa 
Published: May 2016

Mass spectrometry (MS)‐based quantitative phosphoproteomics has become a key approach for proteome‐wide profiling of phosphorylation in tissues and cells. Traditional experimental design often compares a single treatment with a control, whereas increasingly more experiments are designed to compare multiple treatments with respect to a control. To this end, the development of bioinformatic tools that can integrate multiple treatments and visualise kinases and substrates under combinatorial perturbations is vital for dissecting concordant and/or independent effects of each treatment. Here, we propose a hypothesis driven kinase perturbation analysis (KinasePA) to annotate and visualise kinases and their substrates that are perturbed by various combinatorial effects of treatments in phosphoproteomics experiments. We demonstrate the utility of KinasePA through its application to two large‐scale phosphoproteomics datasets and show its effectiveness in dissecting kinases and substrates within signalling pathways driven by unique combinations of cellular stimuli and inhibitors. We implemented and incorporated KinasePA as part of the “directPA” R package available from the comprehensive R archive network (CRAN). Furthermore, KinasePA also has an interactive web interface that can be readily applied to annotate user provided phosphoproteomics data (http://kinasepa.pengyiyang.org).
Infancy and pediatric cancer: an exploratory study of parent psychological distress
Authors: Vernon L. , Eyles D. , Hulbert C. , Bretherton L. , McCarthy M. C. 
Published: May 2016

AbstractBackgroundResearch on the psychological experiences of parents of infants within pediatric oncology is sparse. This study examined rates and indicative risk factors for psychological distress in parents where there is either an infant patient or infant sibling of a patient.MethodsParticipants were mothers (n = 41) and fathers (n = 25) of infants under 2 years who either had a cancer diagnosis (n = 37; infant patients) or was an infant sibling of an older child with cancer (n = 29; infant siblings) recruited from a single oncology center. There were 21 couple dyads. Parents completed the Depression Anxiety Stress Scales short form and the Posttraumatic Stress Disorder Checklist.ResultsMothers (47.5%) and fathers (37.5%) reported elevated, cancer‐related posttraumatic stress symptoms. Rates of depression (12.2% of mothers and 12.0% of fathers) and anxiety symptoms (17.1% of mothers and 8.0% of fathers) were lower. Compared with parents of infant patients, parents of infant siblings reported significantly higher rates of depressive symptoms and trends toward higher rates of posttraumatic stress symptoms and anxiety symptoms. Parent anxiety was higher with increased time post diagnosis. No demographic or illness‐related variables were associated with psychological distress, with the exception of the number of children in the family.ConclusionsParent–child relationships are of fundamental importance during infancy. This study provides novel data highlighting the psychological impact for parents when a cancer diagnosis is made during this critical developmental period, including the contribution of family structure to parental distress. Results provide further support for applying a traumatic stress framework when exploring parent experiences of pediatric cancer. Copyright © 2016 John Wiley & Sons, Ltd.
Cognitive behavioral therapies for informal caregivers of patients with cancer and cancer survivors: a systematic review and meta‐analysis
Authors: O'Toole Mia S. , Zachariae Robert , Renna Megan E. , Mennin Douglas S. , Applebaum Allison 
Published: May 2016

AbstractObjectiveInformal caregivers (ICs) of patients with cancer and cancer survivors report a number of psychological and physical complaints because of the burden associated with providing care. Given the documented effect of Cognitive Behavioral Therapy (CBT) on ICs' common psychological complaints, such as anxiety and depression, the objective was to conduct a meta‐analysis on the effect of CBTs for adult ICs.MethodsA literature search was conducted in order to identify all intervention studies on adult ICs that employed at least one therapeutic component defined as a CBT component.ResultsLiterature searches revealed 36 unique records with sufficient data. These studies were subjected to meta‐analyses using random effects models. A small, statistically significant effect of CBTs (Hedge's g = 0.08, p = 0.014) was revealed, which disappeared when randomized controlled trials were evaluated alone (g = 0.04, p = 0.200). A number of variables were explored as moderators. Only the percentage of female participants was positively associated with the effect size.ConclusionsBased on the negligible effect of CBTs across outcomes, future studies should consider moving beyond traditional CBT methods as these do not appear efficacious. It is suggested that future interventions orient towards advances in the basic affective sciences and derived therapies in order to better understand and treat the emotional struggles experienced by ICs. © 2016 The Authors. Psycho‐Oncology published by John Wiley & Sons Ltd.
A systematic review of sleep in hospitalized pediatric cancer patients
Authors: Lee Soeun , Narendran Gaya , Tomfohr‐Madsen Lianne , Schulte Fiona 
Published: May 2016

AbstractObjectiveThe purpose of this systematic review was to describe the occurrence of sleep disruptions in pediatric cancer patients and to identify and discuss the factors related to the hospital sleep environment that may be associated with disturbed sleep.MethodsA total of 108 articles were located in five databases (PubMed, PsychINFO, Medline, CancerLit, and Google Scholar), and seven met our inclusion criteria and formed the basis of this review.ResultsParticipants ranged from 1 to 18 years (n = 147). Data from objective and subjective assessments of sleep showed that child sleep was disrupted in the hospital when compared to previously established age‐related norms. Noise, light levels, and staff room interruptions were associated with decreased total sleep minutes and increased nighttime awakenings. Methodological limitations of the current research as well as potential directions for future research are discussed.ConclusionsInvestigations into the sources of increased sleep difficulties can be used to inform hospital procedures to create a more supportive sleep environment and more effective screening tools for patients who may be at greater risk for sleep difficulties. This may help to minimize the role that hospitalization plays in precipitating and perpetuating chronic sleep disturbances in pediatric cancer patients.Copyright © 2016 John Wiley & Sons, Ltd.
Disciplinary literacy in the science classroom: Using adaptive primary literature
Authors: Koomen Michele Hollingsworth , Weaver Sarah , Blair Robert B. , Oberhauser Karen S. 
Published: May 2016

AbstractThis study reports on an innovative version of adaptive primary literature (APL) that we call Science Behind the Scenes used during a summer professional development (PD) program. Classroom teachers read and discussed papers from the primary literature, and created translations of these papers relevant to their own classroom needs. We randomly selected 31 teacher‐created Science behind the Scenes products for evaluation with a rubric that was aligned with the K‐12 Science Education Frameworks (2012). In addition, we interviewed groups of teachers at follow‐up sessions and individual teachers who used the APL in their classrooms. We used frameworks for grounded theory to sort the interview text and descriptive statistical measures for quantitative data. Our analysis reveals two key findings: (i) the teachers created respectable adaptations of primary scientific literature into APL; and (ii) the teachers used the APL products in their classrooms to support the discourse of science and disciplinary literacy, and to create a bridge to the scientific enterprise. Our findings have implications for instructional design, curricular materials, professional development, and science education. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 53: 847–894, 2016
Improved in vivo antitumor effect of a daunorubicin - GnRH-III bioconjugate modified by apoptosis inducing agent butyric acid on colorectal carcinoma bearing mice
Authors: Kapuvári Bence , Hegedüs Rózsa , Schulcz Ákos , Manea Marilena , Tóvári József , Gacs Alexandra , Vincze Borbála , Mező Gábor 
Published: May 2016

SummaryCompared to classical chemotherapy, peptide-based drug targeting is a promising therapeutic approach for cancer, which can provide increased selectivity and decreased side effects to anticancer drugs. Among various homing devices, gonadotropin-releasing hormone-III (GnRH-III) peptide represents a suitable targeting moiety, in particular in the treatment of hormone independent tumors that highly express GnRH receptors (e.g. colon carcinoma). We have previously shown that GnRH-III[4Lys(Ac),8Lys(Dau = Aoa)] bioconjugate, in which daunorubicin was attached via oxime linkage to the 8Lys of a GnRH-III derivative, exerted significant in vivo antitumor effect on subcutaneously developed HT-29 colon tumor. In contrast, results of the study reported here indicated that this compound was not active on an orthotopically developed tumor. However, if Lys in position 4 was acylated with butyric acid instead of acetic acid, the resulting bioconjugate GnRH-III[4Lys(Bu),8Lys(Dau = Aoa)] had significant tumor growth inhibitory effect. Furthermore, it prevented tumor neovascularization, without detectable side effects. Nevertheless, the development of metastases could not be inhibited by the bioconjugate; therefore, its application in combination with a metastasis preventive agent might be necessary in order to achieve complete tumor remission. In spite of this result, the treatment with GnRH-III[4Lys(Bu),8Lys(Dau = Aoa)] bioconjugate proved to have significant benefits over the administration of free daunorubicin, which was used at the maximum tolerated dose.
Quality of care from the perspective of women with gestational diabetes in China
Authors: Ge Li , Wikby Kerstin , Rask Mikael 
Published: May 2016

AbstractObjectiveTo explore the quality of gestational diabetes mellitus (GDM) care experienced by women in China and how it could be improved.MethodsA qualitative study was conducted at a municipal hospital in south east China. Women who had been diagnosed with GDM at 34–38 weeks of pregnancy were enrolled during two periods; between May 1 and July 31, 2012, and between April 1 and July 31, 2013. Data regarding patient‐perceived care quality were collected through semi‐structured individual interviews and were analyzed by qualitative content analysis.ResultsThe study enrolled 44 patients; the interviews recorded a lack of professional care resources for GDM, a lack of high‐quality personalized care for women with GDM, and patients' suggestions regarding how to improve GDM care.ConclusionThe participants reported a lack of high‐quality GDM care, describing the core problem as an imbalance between over‐stretched hospitals and low‐efficiency under‐utilized primary healthcare centers. Clinical‐practice reforms identified, particularly in primary healthcare settings, included improving services through increasing the number of health professionals and material resources to comply with diabetes guidelines, and incorporating a humanistic approach in the provision of care.
Maternal 25‐hydroxyvitamin D level and the occurrence of neural tube defects in Tunisia
Authors: Nasri Kaouther , Ben Fradj Mohamed K. , Feki Moncef , Kaabechi Naziha , Sahraoui Mariem , Masmoudi Aida , Marrakchi Raja , Gaigi Soumeya S. 
Published: May 2016

AbstractObjectiveTo determine whether low vitamin D levels in pregnant women are associated with the occurrence of neural tube defects (NTDs) in Tunisia.MethodsIn a prospective study, pregnant women were recruited at a center in Tunis between January 1, 2012, and December 30, 2013. Women carrying a fetus with a severe NTD were recruited before elective termination. Matched, healthy pregnancy women were enrolled into a control group. Plasma levels of 25‐hydroxyvitamin D were measured by a competitive chemiluminescence immunoassay.ResultsOverall, 68 women formed the NTD group and 64 the control group. The mean maternal vitamin D level was significantly lower in the NTD group (20.65 ± 10.25 nmol/L) than in the control group (28.30 ± 13.82 nmol/L;P< 0.001). Vitamin D deficiency was recorded for 53 (78%) women in the NTD group and 39 (61%) in the control group. Vitamin D insufficiency was recorded for 15 (22%) women in the NTD group and 20 (31%) in the control group. Vitamin D sufficiency was found only in the control group (n = 5 [8%];P< 0.001).ConclusionThe findings confirm an association between a decreased vitamin D level in pregnant women and the risk of fetal NTDs.
Biofilms in chronic rhinosinusitis: Pathophysiology and therapeutic strategies
Authors: Fastenberg Judd H. , Hsueh Wayne D. , Mustafa Ali , Akbar Nadeem A. , Abuzeid Waleed M. 
Published: May 2016

BackgroundThere is increasing evidence that biofilms are critical to the pathophysiology of chronic infections including chronic rhinosinusitis (CRS). Until relatively recently, our understanding of biofilms was limited. Recent advances in methods for biofilm identification and molecular biology have offered new insights into the role of biofilms in CRS. With these insights, investigators have begun to investigate novel therapeutic strategies that may disrupt or eradicate biofilms in CRS.ObjectiveThis review seeks to explore the evidence implicating biofilms in CRS, discuss potential anti‐biofilm therapeutic strategies, and suggest future directions for research.ResultsThe existing evidence strongly supports the role of biofilms in the pathogenesis of CRS. Several anti‐biofilm therapies have been investigated for use in CRS and these are at variable stages of development. Generally, these strategies: 1) neutralize biofilm microbes; 2) disperse existing biofilms; or 3) disrupt quorum sensing. Several of the most promising anti‐biofilm therapeutic strategies are reviewed.ConclusionsA better understanding of biofilm function and their contribution to the CRS disease process will be pivotal to the development of novel treatments that may augment and, potentially, redefine the CRS treatment paradigm. There is tremendous potential for future research.
After Obama
Authors: Singh Robert S. 
Published: May 2016

Barack Obama's foreign policy has failed but the American strategic mind has not yet closed. In After Obama, Robert Singh examines how and why US influence has weakened and contributed to the erosion of the world America made, endangering international order and liberal values. A well-intentioned but naive strategy of engagement has encouraged US adversaries such as Russia, China and Iran to assert themselves while allowing Western alliances to fray. But, challenging claims of an inevitable American decline, Singh argues that US leadership is a matter of will as much as wallet. Despite partisan polarization at home and the rise of the rest abroad, Washington can renew American leadership and, through a New American Internationalism, pave a path to the restoration of global order. Timely and provocative, the book offers a powerful critique of the Obama Doctrine and a call for strategic resolution in place of 'leading from behind'.
Particle based modelling and simulation of natural sand dynamics in the wave bottom boundary layer
Authors: Finn Justin R. , Li Ming , Apte Sourabh V. 
Published: May 2016

Sand transport and morphological change occur in the wave bottom boundary layer due to sand particle interactions with an oscillatory flow and granular interactions between particles. Although these interactions depend strongly on the characteristics of the particle population, i.e. size and shape, little is known about how natural sand particles behave under oscillatory conditions and how variations in particle size influence transport behaviour. To enable this to be studied numerically, an Euler–Lagrange point-particle model is developed which can capture the individual and collective dynamics of subaqueous natural sand grains. Special treatments for particle collision, friction and hydrodynamic interactions are included to take into account the wide size and shape variations in natural sands. The model is used to simulate sand particle dynamics in two asymmetric oscillatory flow conditions corresponding to the vortex ripple experiments of Van der Werfet al.(J. Geophys. Res., vol. 112, 2007, F02012) and the sheet-flow experiments of O’Donoghue & Wright (Coast. Engng, vol. 50, 2004, pp. 117–138). A comparison of the phase resolved velocity and concentration fields shows overall excellent agreement between simulation and experiments. The particle based datasets are used to investigate the spatio-temporal dynamics of the particle-size distribution and the influence of three-dimensional vortical features on particle entrainment and suspension processes. For the first time, it is demonstrated that even for the relatively well-sorted medium-size sands considered here, the characteristics of the local grain size population exhibit significant space–time variation. Both conditions demonstrate a distinct coarse-over-fine armouring at the bed surface during low-velocity phases, which restricts the vertical mobility of finer fractions in the bed, and also results in strong pickup events involving disproportionately coarse fractions. The near-bed layer composition is seen to be very dynamic in the sheet-flow condition, while it remains coarse through most of the cycle in the vortex ripple condition. Particles in suspension spend more time sampling the upward directed parts of these flows, especially the smaller fractions, which delays particle settling and enhances the vertical size sorting of grains in suspension. For the submillimetre grain sizes considered, most particle–particle collisions occur at low impact Stokes numbers and can be expected to have low rebound velocities. The results are considered to be fundamental to the understanding of particle sorting and transport mechanisms, and can help to improve current transport modelling approaches.
Dietary patterns in India: a systematic review
Authors: Green Rosemary , Milner James , Joy Edward J. M. , Agrawal Sutapa , Dangour Alan D. 
Published: May 2016

AbstractDietary patterns analysis is an emerging area of research. Identifying distinct patterns within a large dietary survey can give a more accurate representation of what people are eating. Furthermore, it allows researchers to analyse relationships between non-communicable diseases (NCD) and complete diets rather than individual food items or nutrients. However, few such studies have been conducted in developing countries including India, where the population has a high burden of diabetes and CVD. We undertook a systematic review of published and grey literature exploring dietary patterns and relationships with diet-related NCD in India. We identified eight studies, including eleven separate models of dietary patterns. Most dietary patterns were vegetarian with a predominance of fruit, vegetables and pulses, as well as cereals; dietary patterns based on high-fat, high-sugar foods and more meat were also identified. There was large variability between regions in dietary patterns, and there was some evidence of change in diets over time, although no evidence of different diets by sex or age was found. Consumers of high-fat dietary patterns were more likely to have greater BMI, and a dietary pattern high in sweets and snacks was associated with greater risk of diabetes compared with a traditional diet high in rice and pulses, but other relationships with NCD risk factors were less clear. This review shows that dietary pattern analyses can be highly valuable in assessing variability in national diets and diet–disease relationships. However, to date, most studies in India are limited by data and methodological shortcomings.
Antibiotic and metal resistance of cultivable bacteria in the Antarctic sea urchin
Authors: González-Aravena M. , Urtubia R. , Del Campo K. , Lavín P. , Wong C.M.V.L. , Cárdenas C.A. , González-Rocha G. 
Published: May 2016

AbstractIn this paper we report the first characterization of cultivable bacteria obtained from the Antarctic sea urchinSterechinus neumayeri. The coelomic fluid was obtained from a pool of sea urchins which was plated onto different media to isolate the bacteria. A total of 42 isolates of psychrotrophic and aerobic γ-Proteobacteria (59.5%), Flavobacteria (33.3%) and Actinomycetes (7.2%) were isolated and sequenced. These bacteria were exposed to heavy metals and antibiotics, where 38 strains were analysed by the minimal inhibitory concentration method. Antibiotic resistance was detected in 44% of cultivable strains, and a further 13% presented co-resistance to antibiotics and heavy metals. The genera of bacteria that showed an increased resistance and co-resistance to metals and antibiotics wereFlavobacterium,PsychrobacterandPseudomonas. Additionally, 30.9% of isolated bacterial strains contained plasmids, which are probably related to resistance and co-resistance to metals. These results indicate that sea urchin-associated bacteria could be reservoirs for antibiotic resistance genes.
Aberration-Corrected Scanning Transmission Electron Microscope (STEM) Through-Focus Imaging for Three-Dimensional Atomic Analysis of Bismuth Segregation on Copper [001]/33° Twist Bicrystal Grain Boundaries
Authors: Wade Charles Austin , McLean Mark J. , Vinci Richard P. , Watanabe Masashi 
Published: May 2016

AbstractScanning transmission electron microscope (STEM) through-focus imaging (TFI) has been used to determine the three-dimensional atomic structure of Bi segregation-induced brittle Cu grain boundaries (GBs). With TFI, it is possible to observe single Bi atom distributions along Cu [001] twist GBs using an aberration-corrected STEM operating at 200 kV. The depth resolution is ~5 nm. Specimens with GBs intentionally inclined with respect to the microscope’s optic axis were used to investigate Bi segregant atom distributions along and through the Cu GB. It was found that Bi atoms exist at most once per Cu unit cell along the GB, meaning that no continuous GB film is present. Therefore, the reduced fracture toughness of this particular Bi-doped Cu boundary would not be caused by fracture of Bi–Bi bonds.
Inhibition of HIF-prolyl-4-hydroxylases prevents mitochondrial impairment and cell death in a model of neuronal oxytosis
Authors: Neitemeier S , Dolga A M , Honrath B , Karuppagounder S S , Alim I , Ratan R R , Culmsee C 
Published: May 2016

AbstractMitochondrial impairment induced by oxidative stress is a main characteristic of intrinsic cell death pathways in neurons underlying the pathology of neurodegenerative diseases. Therefore, protection of mitochondrial integrity and function is emerging as a promising strategy to prevent neuronal damage. Here, we show that pharmacological inhibition of hypoxia-inducible factor prolyl-4-hydroxylases (HIF-PHDs) by adaptaquin inhibits lipid peroxidation and fully maintains mitochondrial function as indicated by restored mitochondrial membrane potential and ATP production, reduced formation of mitochondrial reactive oxygen species (ROS) and preserved mitochondrial respiration, thereby protecting neuronal HT-22 cells in a model of glutamate-induced oxytosis. Selective reduction of PHD1 protein using CRISPR/Cas9 technology also reduced both lipid peroxidation and mitochondrial impairment, and attenuated glutamate toxicity in the HT-22 cells. Regulation of activating transcription factor 4 (ATF4) expression levels and related target genes may mediate these beneficial effects. Overall, these results expose HIF-PHDs as promising targets to protect mitochondria and, thereby, neurons from oxidative cell death.