bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating Methods to Establish Habitat Suitability Criteria: A Case Study in the Upper Delaware River Basin, USA
Authors: Galbraith H. S. , Blakeslee C. J. , Cole J. C. , Talbert C. A. , Maloney K. O. 
Published: April 2016

AbstractDefining habitat suitability criteria (HSC) of aquatic biota can be a key component to environmental flow science. HSC can be developed through numerous methods; however, few studies have evaluated the consistency of HSC developed by different methodologies. We directly compared HSC for depth and velocity developed by the Delphi method (expert opinion) and by two primary literature meta‐analyses (literature‐derived range and interquartile range) to assess whether these independent methods produce analogous criteria for multiple species (rainbow trout, brown trout, American shad, and shallow fast guild) and life stages. We further evaluated how these two independently developed HSC affect calculations of habitat availability under three alternative reservoir management scenarios in the upper Delaware River at a mesohabitat (main channel, stream margins, and flood plain), reach, and basin scale. In general, literature‐derived HSC fell within the range of the Delphi HSC, with highest congruence for velocity habitat. Habitat area predicted using the Delphi HSC fell between the habitat area predicted using two literature‐derived HSC, both at the basin and the site scale. Predicted habitat increased in shallow regions (stream margins and flood plain) using literature‐derived HSC while Delphi‐derived HSC predicted increased channel habitat. HSC generally favoured the same reservoir management scenario; however, no favoured reservoir management scenario was the most common outcome when applying the literature range HSC. The differences found in this study lend insight into how different methodologies can shape HSC and their consequences for predicted habitat and water management decisions. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
Synthesis and Physico‐Chemical Properties of Sodium 3‐Oxo‐2‐(3‐(4‐sulphonatophenyl)triaz‐2‐enyl)octadecanoate Anionic Surfactant
Authors: El‐Sharkawy El‐Sayed A. , Mead Attia I. , Abdel Reheim Mohamed A. M. , Tolba Ahmed M. 
Published: April 2016

AbstractThe novel anionic surfactant sodium 3‐oxo‐2‐(3‐(4‐sulphonatophenyl)triaz‐2‐enyl)octadecanoate (SSTO) was prepared from renewable raw materials; glycine and palmitic acid. Surface and bulk properties of SSTO were investigated by surface tension and electrical conductivity techniques at 298, 308, 318 and 328 K. Surface properties including critical micelle concentration (CMC), maximum surface excess concentration (Γmax), minimum area per molecule (Amin), surface tension at CMC (γCMC), effectiveness of surface tension reduction (ΠCMC), efficiency of surface adsorption (pC20), and degree of counterion dissociation (α) were determined. The thermodynamic parameters of micellization (ΔG°mic, ΔH°mic and ΔS°mic) and adsorption (ΔG°ad, ΔH°ad and ΔS°ad) were also investigated at 298, 308, 318 and 328 K. The effect of 3 wt% n‐propanol, n‐butanol and n‐pentanol on surface tension and conductivity at 298 K was also determined.
Pathoconnectomics of cognitive impairment in small vessel disease: A systematic review
Authors: Dey Ayan K. , Stamenova Vessela , Turner Gary , Black Sandra E. , Levine Brian 
Published: April 2016

AbstractIntroductionCerebral small vessel disease (CSVD) is a highly prevalent condition associated with diffuse ischemic damage and cognitive dysfunction particularly in executive function and attention. Functional brain imaging studies can reveal mechanisms of cognitive impairment in CSVD, although findings are mixed.MethodsA systematic review integrating findings from functional magnetic resonance imaging and electroencephalography in CSVD is involved.ResultsCSVD damages long‐range white matter tracts connecting nodes within distributed brain networks. It also disrupts frontosubcortical circuits and cholinergic fiber tracts mediating attentional processes. These changes, illustrated within a model of network dynamics, synergistically relate to neurodegenerative pathology contributing to dementia.DiscussionThe effects of CSVD on attention and executive functioning are best understood within a network model of cognition as revealed by functional neuroimaging. Analysis of network function in CSVD can improve characterization of disease severity and treatment effects, and it can inform theoretical models of brain function.
2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity
Authors: Basu Subhadip , Plewczynski Dariusz , Saha Satadal , Roszkowska Matylda , Magnowska Marta , Baczynska Ewa , Wlodarczyk Jakub 
Published: April 2016

Abstract
Motivation: Accurate and effective dendritic spine segmentation from the dendrites remains as a challenge for current neuroimaging research community. In this article, we present a new method (2dSpAn) for 2-d segmentation, classification and analysis of structural/plastic changes of hippocampal dendritic spines. A user interactive segmentation method with convolution kernels is designed to segment the spines from the dendrites. Formal morphological definitions are presented to describe key attributes related to the shape of segmented spines. Spines are automatically classified into one of four classes: Stubby, Filopodia, Mushroom and Spine-head Protrusions.
Results: The developed method is validated using confocal light microscopy images of dendritic spines from dissociated hippocampal cultures for: (i) quantitative analysis of spine morphological changes, (ii) reproducibility analysis for assessment of user-independence of the developed software and (iii) accuracy analysis with respect to the manually labeled ground truth images, and also with respect to the available state of the art. The developed method is monitored and used to precisely describe the morphology of individual spines in real-time experiments, i.e. consequent images of the same dendritic fragment.
Availability and Implementation: The software and the source code are available at https://sites.google.com/site/2dspan/ under open-source license for non-commercial use.
Contact: subhadip@cse.jdvu.ac.in or j.wlodarczyk@nencki.gov.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
Inferring heterozygosity from ancient and low coverage genomes
Authors: Kousathanas Athanasios , Leuenberger Christoph , Link Vivian , Sell Christian , Burger Joachim , Wegmann Daniel 
Published: April 2016

ABSTRACTWhile genetic diversity can be quantified accurately from high coverage sequencing, it is often desirable to obtain such estimates from low coverage data, either to save costs or because of low DNA quality as observed for ancient samples. Here we introduce a method to accurately infer heterozygosity probabilistically from very low coverage sequences of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence and takes into account both variable sequencing errors and potential post-mortem damage. It is thus also applicable to non-model organisms and ancient genomes. Since error rates as reported by sequencing machines are generally distorted and require recalibration, we also introduce a method to infer accurately recalibration parameter in the presence of post-mortem damage. This method does also not require knowledge about the underlying genome sequence, but instead works from haploid data (e.g. from the X-chromosome from mammalian males) and integrates over the unknown genotypes. Using extensive simulations we show that a few Mb of haploid data is sufficient for accurate recalibration even at average coverages as low as 1-3x. At similar coverages, out method also produces very accurate estimates of heterozygosity down to 10−4within windows of about 1Mb. We further illustrate the usefulness of our approach by inferring genome-wide patterns of diversity for several ancient human samples and found that 3,000-5,000 samples showed diversity patterns comparable to modern humans. In contrast, two European hunter-gatherer samples exhibited not only considerably lower levels of diversity than modern samples, but also highly distinct distributions of diversity along their genomes. Interestingly, these distributions were also very differently between the two samples, supporting earlier conclusions of a highly diverse and structured population in Europe prior to the arrival of farming.
Developing consensus on hospital prescribing indicators of potential harm for infants and children
Authors: Fox Andy , Pontefract Sarah , Brown David , Portlock Jane , Coleman Jamie 
Published: April 2016

AimsThe aim of the study was to develop a list of hospital based paediatric prescribing indicators that can be used to assess the impact of electronic prescribing or clinical decision support tools on paediatric prescribing errors.MethodsTwo rounds of an electronic consensus method (eDelphi) were carried out with 21 expert panellists from the UK. Panellists were asked to score each prescribing indicator for its likelihood of occurrence and severity of outcome should the error occur. The scores were combined to produce a risk score and a median score for each indicator calculated. The degree of consensus between panellists was defined as the proportion that gave a risk score in the same category as the median. Indicators were included if a consensus of 80% or higher was achieved and were in the high risk categories.ResultsEach of the 21 panellists completed an exploratory round and two rounds of scoring. This identified 41 paediatric prescribing indicators with a high risk rating and greater than 80% consensus. The most common error type within the indicators was wrong dose (n = 19) and the most common drug classes were antimicrobials (n = 10) and cardiovascular (n = 7).ConclusionsA set of 41 paediatric prescribing indicators describing potential harm for the hospital setting has been identified by an expert panel. The indicators provide a standardized method of evaluation of prescribing data on both paper and electronic systems. They can also be used to assess implementation of clinical decision support systems or other quality improvement initiatives.
Bisphenol A Increases the Migration and Invasion of Triple‐Negative Breast Cancer Cells via Oestrogen‐related Receptor Gamma
Authors: Zhang Xiao‐Lin , Liu Na , Weng Shan‐Fan , Wang Hong‐Sheng 
Published: April 2016

AbstractTriple‐negative breast cancer (TNBC) is characterized by great metastasis and invasion capability. Our study revealed that nanomolar bisphenol A (BPA), one of the most ubiquitous endocrine disruptors, can increase wound closure and invasion of both MDA‐MB‐231 and BT‐549 cells. BPA treatment can increase protein and mRNA expression of matrix metalloproteinase‐2 (MMP‐2) and MMP‐9, while had no effect on the expression of vimentin (Vim) and fibronectin (FN) in TNBC cells. The expression of G‐protein‐coupled receptor (GPER), which has been suggested to mediate rapid oestrogenic signals, was not varied in BPA‐treated MDA‐MB‐231 and BT‐549 cells. Its inhibitor G15 also had no effect on BPA‐induced MMPs expression and cell invasion. Interestingly, BPA treatment can significantly increase the mRNA and protein expressions of oestrogen‐related receptor γ (ERRγ), but not ERRα or ERRβ, in both MDA‐MB‐231 and BT‐549 cells. The knock‐down of ERRγ can markedly attenuate BPA‐induced expression of MMP‐2 and MMP‐9 in TNBC cells. BPA treatment can activate both ERK1/2 and Akt in TNBC cells. Both inhibitors of ERK1/2 (PD98059) and Akt (LY294002) can attenuate BPA‐induced ERRγ expression and cell invasion of MDA‐MB‐231 cells. Collectively, our data revealed that BPA can increase the expression of MMPs and in vitro motility of TNBC cells via ERRγ. Both activation of ERK1/2 and Akt participated in this process. Our study suggests that more attention should be paid to the roles of xenoestrogens such as BPA in the development and progression of TNBC.
Comparing Biomarkers as Trial Level General Surrogates
Authors: Gabriel Erin E. , Daniels Michael J. , Halloran M. Elizabeth 
Published: April 2016

SummaryAn intermediate response measure that accurately predicts efficacy in a new setting can reduce trial cost and time to product licensure. In this article, we define a trial level general surrogate, which is an intermediate response that can be used to accurately predict efficacy in a new setting. Methods for evaluating general surrogates have been developed previously. Many methods in the literature use trial level intermediate responses for prediction. However, all existing methods focus on surrogate evaluation and prediction in new settings, rather than comparison of candidate general surrogates, and few formalize the use of cross validation to quantify the expected prediction error. Our proposed method uses Bayesian non-parametric modeling and cross-validation to estimate the absolute prediction error for use in evaluating and comparing candidate trial level general surrogates. Simulations show that our method performs well across a variety of scenarios. We use our method to evaluate and to compare candidate trial level general surrogates in several multi-national trials of a pentavalent rotavirus vaccine. We identify at least one immune measure that has potential value as a trial level general surrogate and use it to predict efficacy in a new trial where the clinical outcome was not measured.
Inhaled corticosteroids and HPA axis suppression: how important is it and how should it be managed?
Authors: Rao Bondugulapati L. N. , Rees D. A. 
Published: April 2016

SummaryInhaled corticosteroids (ICS) are established as a cornerstone of management for patients with bronchoconstrictive lung disease. However, systemic absorption may lead to suppression of the hypothalamic–pituitary–adrenal (HPA) axis in a significant minority of patients. This is more likely in ‘higher risk’ patients exposed to high cumulative ICS doses, and in those treated with frequent oral corticosteroids or drugs which inhibit cytochrome p450 3A4. Hypothalamic–pituitary–adrenal axis suppression is frequently unrecognized, such that some patients, notably children, only come to light when an adrenal crisis is precipitated by physical stress. To minimize this risk, ‘higher risk’ patients and those with previously identified suppressed cortisol responses to Synacthen testing should undergo an education programme to inform them about sick day rules. A review of ICS therapy should also be undertaken to ensure that the dose administered is the minimum required to control symptoms.
Insights into 6q21‐q22: Refinement of the critical region for acro‐cardio‐facial syndrome
Authors: Milani Donatella , Cagnoli Giulia Anna , Baccarin Marco , Alfei Enrico , Guerneri Silvana , Esposito Susanna 
Published: April 2016

AbstractDeletions on chromosome 6q are rarely reported in the literature, and genotype‐phenotype correlations are poorly understood. We report a child with a deletion of the 6q21‐q22 chromosomal region, providing some intriguing results about the correlation between this region and acro‐cardio‐facial syndrome, congenital heart disease, split hand and foot malformation, and epilepsy.
Benefit Sharing in a Global Context: Working Towards Solutions for Implementation
Authors: Hurst Daniel J. 
Published: April 2016

AbstractDue to the state of globalized clinical research, questions have been raised as to what, if any, benefits those who contribute to research should receive. One model for compensating research participants is “benefit sharing,” and the basic premise is that, as a matter of justice, those who contribute to scientific research should share in its benefits. While incorporated into several international documents for over two decades, benefit sharing has only been sparsely implemented. This analysis begins by addressing the concept of benefit sharing, its historical development, and how it has been applied in the context of virus sharing for influenza research. The second portion of this analysis presents recommendations for ensuring benefit sharing. These recommendations are threefold: 1) an emphasis on social pressure, 2) the revision of international documents as means to ensure benefit sharing, and 3) greater collaboration between sponsor IRB and host country IRB. Because clinical research is a globalized industry, a global model will be proposed in the second that focuses on collaboration between the sponsor and host country. This collaboration is vital in order to ensure that proper forms of benefit sharing are accomplished as a matter of justice.
Association between gross motor function and nutritional status in children with cerebral palsy: a cross‐sectional study from Colombia
Authors: Herrera‐Anaya Elizabeth , Angarita‐Fonseca Adriana , Herrera‐Galindo Víctor M , Martínez‐Marín Rocío D P , Rodríguez‐Bayona Cindy N 
Published: April 2016

AimTo determine the association between gross motor function and nutritional status in children with cerebral palsy (CP) residing in an urban area in a developing country.MethodWe conducted a cross‐sectional study in 177 children (ages 2–12y, 59.3% male) with a diagnosis of CP who were attending rehabilitation centres in Bucaramanga, Colombia (2012–2013). A physiotherapist evaluated patients using the Gross Motor Function Classification System (GMFCS, levels I to V). Nutritional status was evaluated by nutritionists and classified according to the World Health Organization growth charts. We used linear and multinomial logistic regression methods to determine the associations.ResultsThere were 39.5%, 6.8%, 5.6%, 16.4%, and 31.6% patients classified in levels I to V respectively. The mean adjusted differences for weight‐for‐age, height‐for‐age, BMI‐for‐age, and height‐for‐weight z‐scores were significantly larger for children classified in levels II to V compared with those in level I. The children classified in levels IV and V were more likely to have malnutrition (adjusted odds ratio [OR] 5.64; 95% confidence interval [CI] 2.27–14.0) and stunting (OR 8.42; 95% CI 2.90–24.4) than those classified in GMFCS levels I to III.InterpretationStunting and malnutrition are prevalent conditions among paediatric patients with CP, and both are directly associated with higher levels of gross motor dysfunction.
Epilepsy diagnostic and treatment needs identified with a collaborative database involving tertiary centers in France
Authors: Chipaux Mathilde , Szurhaj William , Vercueil Laurent , Milh Mathieu , Villeneuve Nathalie , Cances Claude , Auvin Stéphane , Chassagnon Serge , Napuri Sylvia , Allaire Catherine , Derambure Philippe , Marchal Cécile , Caubel Isabelle , Ricard‐Mousnier Brigitte , N'Guyen the Tich Sylvie , Pinard Jean‐Marc , Bahi‐Buisson Nadia , de Baracé Claire , Kahane Philippe , Gautier Agnès , Hamelin Sophie , Coste‐Zeitoun Delphine , Rosenberg Sarah‐Dominique , Clerson Pierre , Nabbout Rima , Kuchenbuch Mathieu , Picot Marie‐Christine , Kaminska Anna ,   the GRENAT Group
Published: April 2016

SummaryObjectiveTo obtain perspective on epilepsy in patients referred to tertiary centers in France, and describe etiology, epilepsy syndromes, and identify factors of drug resistance and comorbidities.MethodsWe performed a cross‐sectional analysis of the characteristics of 5,794 pediatric and adult patients with epilepsy included in a collaborative database in France between 2007 and 2013. Comparisons between groups used Student's t‐test or Fisher's exact test for binary or categorical variables. Factors associated with drug resistance and intellectual disability were evaluated in multi‐adjusted logistic regression models.ResultsMean age at inclusion was 17.9 years; children accounted for 67%. Epilepsy was unclassified in 20% of patients, and etiology was unknown in 65%, including those with idiopathic epilepsies. Etiologies differed significantly in adult‐ when compared to pediatric‐onset epilepsy; however, among focal structural epilepsies, mesial temporal lobe epilepsy with hippocampal sclerosis began as often in the pediatric as in adult age range. Drug resistance concerned 53% of 4,210 patients evaluable for seizure control and was highest in progressive myoclonic epilepsy (89%), metabolic diseases (84%), focal cortical dysplasia (70%), other cortical malformations (69%), and mesial temporal lobe epilepsy with hippocampal sclerosis (67%). Fifty‐nine percent of patients with focal structural epilepsy and 69% with epileptic encephalopathies were drug resistant; however, 40–50% of patients with West syndrome and epileptic encephalopathy with continuous spike‐and‐waves during sleep were seizure‐free. Ages at onset in infancy and in young adults shared the highest risk of drug resistance. Epilepsy onset in infancy comprised the highest risk of intellectual disability, whereas specific cognitive impairment affected 36% of children with idiopathic focal epilepsy.SignificanceOur study provides a snapshot on epilepsy in patients referred to tertiary centers and discloses needs for diagnosis and treatment. Large databases help identify patients with rare conditions that could benefit from specific prospective studies.
Double plate fixation for the management of proximal interphalangeal joint instability in 30 horses (1987–2015)
Authors: McCormick J. D. , Watkins J. P. 
Published: April 2016

SummaryReasons for performing studyDouble plate fixation has been reported in a small number of horses with comminuted fractures of the middle phalanx. There are no published reports using this technique in the management of other injuries that destabilise the proximal interphalangeal joint (PIJ), including biaxial palmar/plantar eminence fractures and disruption of the palmar/plantar soft tissue support structures of the PIJ. Furthermore, there is a paucity of information on the long‐term prognosis for horses undergoing double plate fixation to manage destabilising injuries of the PIJ.ObjectivesTo document further the clinical use of double plate fixation for management of injuries to the PIJ resulting in palmar/plantar instability and compare these results with other methods of management.Study designRetrospective case series.MethodsThe case records and radiographs of 30 horses with destabilising injuries to the PIJ treated by double plate fixation at Texas A&M University between 1987 and 2013 were analysed. Long‐term follow‐up information was obtained by telephone interview with the client or referring veterinarian.ResultsThirty‐one disruptive PIJ injuries were double plated in 30 cases. Twenty‐nine of 30 horses were discharged from the hospital. The medial time for post operative external coaptation was 41 days. Long‐term follow‐up (>2 years) was available for 25 horses, of which 15 (60%) returned to useful function. Radiographic evidence of fracture healing and arthrodesis of the PIJ was evident in 28 (90%) repairs at 6 months following repair.ConclusionsThe use of 2 abaxially placed dorsal plates for management of destabilising injuries to the PIJ results in a very good prognosis for survival and a reasonable prognosis for return to functional use.