bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Approaches to Smoothing and Comparing SELDI TOF Spectra
Authors: Meleth Sreelatha , Eltoum Isam-Eldin , Zhu Liu , Oelschlager Denise , Piyathilake Chandrika , Chhieng David , Grizzle William E. 
Published: October 2017

Background Most published literature using SELDI-TOF has used traditional techniques in Spectral Analysis such as Fourier transforms and wavelets for denoising. Most of these publications also compare spectra using their most prominent feature, ie, peaks or local maximums. Methods The maximum intensity value within each window of differentiable m/z values was used to represent the intensity level in that window. We also calculated the ‘Area under the Curve’ (AUC) spanned by each window. Results Keeping everything else constant, such as pre-processing of the data and the classifier used, the AUC performed much better as a metric of comparison than the peaks in two out of three data sets. In the third data set both metrics performed equivalently. Conclusions This study shows that the feature used to compare spectra can have an impact on the results of a study attempting to identify biomarkers using SELDI TOF data.
Merging Microarray Data, Robust Feature Selection, and Predicting Prognosis in Prostate Cancer
Authors: Wang Jing , Do Kim Anh , Wen Sijin , Tsavachidis Spyros , Mcdonnell Timothy J. , Logothetis Christopher J. , Coombes Kevin R. 
Published: October 2017

Motivation Individual microarray studies searching for prognostic biomarkers often have few samples and low statistical power; however, publicly accessible data sets make it possible to combine data across studies. Method We present a novel approach for combining microarray data across institutions and platforms. We introduce a new algorithm, robust greedy feature selection (RGFS), to select predictive genes. Results We combined two prostate cancer microarray data sets, confirmed the appropriateness of the approach with the Kolmogorov-Smirnov goodness-of-fit test, and built several predictive models. The best logistic regression model with stepwise forward selection used 7 genes and had a misclassification rate of 31%. Models that combined LDA with different feature selection algorithms had misclassification rates between 19% and 33%, and the sets of genes in the models varied substantially during cross-validation. When we combined RGFS with LDA, the best model used two genes and had a misclassification rate of 15%. Availability Affymetrix U95Av2 array data are available at http://www.broad.mit.edu/cgi-bin/cancer/datasets.cgi . The cDNA microarray data are available through the Stanford Microarray Database ( http://cmgm.stanford.edu/pbrown/ ). GeneLink software is freely available at http://bioinformatics.mdanderson.org/GeneLink/ . DNA-Chip Analyzer software is publicly available at http://biosun1.harvard.edu/complab/dchip/ .
An Empirical Study of Univariate and Genetic Algorithm-Based Feature Selection in Binary Classification with Microarray Data
Authors: Lecocke Michael , Hess Kenneth 
Published: October 2017

Background We consider both univariate- and multivariate-based feature selection for the problem of binary classification with microarray data. The idea is to determine whether the more sophisticated multivariate approach leads to better misclassification error rates because of the potential to consider jointly significant subsets of genes (but without overfitting the data). Methods We present an empirical study in which 10-fold cross-validation is applied externally to both a univariate-based and two multivariate- (genetic algorithm (GA)-) based feature selection processes. These procedures are applied with respect to three supervised learning algorithms and six published two-class microarray datasets. Results Considering all datasets, and learning algorithms, the average 10-fold external cross-validation error rates for the univariate-, single-stage GA-, and two-stage GA-based processes are 14.2%, 14.6%, and 14.2%, respectively. We also find that the optimism bias estimates from the GA analyses were half that of the univariate approach, but the selection bias estimates from the GA analyses were 2.5 times that of the univariate results. Conclusions We find that the 10-fold external cross-validation misclassification error rates were very comparable. Further, we find that a two-stage GA approach did not demonstrate a significant advantage over a 1-stage approach. We also find that the univariate approach had higher optimism bias and lower selection bias compared to both GA approaches.
Ovarian Cancer Classification Based on Mass Spectrometry Analysis of Sera
Authors: Wu Baolin , Abbott Tom , Fishman David , Mcmurray Walter , Mor Gil , Stone Kathryn , Ward David , Williams Kenneth , Zhao Hongyu 
Published: October 2017

In our previous study [ 1 ], we have compared the performance of a number of widely used discrimination methods for classifying ovarian cancer using Matrix Assisted Laser Desorption Ionization (MALDI) mass spectrometry data on serum samples obtained from Reflectron mode. Our results demonstrate good performance with a random forest classifier. In this follow-up study, to improve the molecular classification power of the MALDI platform for ovarian cancer disease, we expanded the mass range of the MS data by adding data acquired in Linear mode and evaluated the resultant decrease in classification error. A general statistical framework is proposed to obtain unbiased classification error estimates and to analyze the effects of sample size and number of selected m/z features on classification errors. We also emphasize the importance of combining biological knowledge and statistical analysis to obtain both biologically and statistically sound results. Our study shows improvement in classification accuracy upon expanding the mass range of the analysis. In order to obtain the best classification accuracies possible, we found that a relatively large training sample size is needed to obviate the sample variations. For the ovarian MS dataset that is the focus of the current study, our results show that approximately 20–40 m/z features are needed to achieve the best classification accuracy from MALDI-MS analysis of sera. Supplementary information can be found at http://bioinformatics.med.yale.edu/proteomics/BioSupp2.html .
Global Tumor RNA Expression in Early Establishment of Experimental Tumor Growth and Related Angiogenesis following Cox-Inhibition Evaluated by Microarray Analysis
Authors: Axelsson Hans , Lönnroth Christina , Andersson Marianne , Wang Wenhua , Lundholm Kent 
Published: October 2017

Altered expression of COX-2 and overproduction of prostaglandins, particularly prostaglandin E2, are common in malignant tumors. Consequently, non-steroidal anti-inflammatory drugs (NSAIDs) attenuate tumor net growth, tumor related cachexia, improve appetite and prolong survival. We have also reported that COX-inhibition (indomethacin) interfered with early onset of tumor endothelial cell growth, tumor cell proliferation and apoptosis. It is however still unclear whether such effects are restricted to metabolic alterations closely related to eicosanoid pathways and corresponding regulators, or whether a whole variety of gene products are involved both up- and downstream effects of eicosanoids. Therefore, present experiments were performed by the use of an in vivo, intravital chamber technique, where micro-tumor growth and related angiogenesis were analyzed by microarray to evaluate for changes in global RNA expression caused by indomethacin treatment.Indomethacin up-regulated 351 and down-regulated 1852 genes significantly (p < 0.01); 1066 of these genes had unknown biological function. Genes with altered expression occurred on all chromosomes.Our results demonstrate that indomethacin altered expression of a large number of genes distributed among a variety of processes in the carcinogenic progression involving angiogenesis, apoptosis, cell-cycling, cell adhesion, inflammation as well as fatty acid metabolism and proteolysis. It remains a challenge to distinguish primary key alterations from secondary adaptive changes in transcription of genes altered by cyclooxygenase inhibition.
Treatment of cranial dural arteriovenous fistulas with exclusive cortical venous drainage: A single-center cohort of 35 patients
Authors: Kortman HG , Bloemsma G , Boukrab I , Peluso JP , Sluzewski M , van der Pol B , Beute GN , Majoie CB , van Rooij WJ 
Published: October 2017

Background and purpose Dural arteriovenous fistulas (DAVFs) with cortical venous drainage often present with hemorrhage or neurological deficits and prompt treatment is indicated. Disconnection of the draining vein is considered curative. We present the multimodality treatment results of 35 patients with cranial DAVFs with exclusive cortical venous drainage. Materials and methods Between January 2010 and January 2017, 35 consecutive patients with cranial dural fistulas with exclusive cortical venous drainage were treated. There were 27 men and eight women, mean age 68 years (range 45–87). Clinical presentation was hemorrhage in 23 (66%), pulsatile bruit in two (6%), seizures in one (3%) and blurred vision in one (3%). In eight patients (22%), the DAVF was an incidental finding. Location of the DAVFs was convexity in 25 (71%), posterior fossa in eight (23%) and tentorium in two (6%). Results Surgery was performed in four patients with anterior cranial fossa fistulas and in one patient with a tentorial dural fistula. In 30 patients, embolization with Onyx via the arterial route was the primary treatment with complete obliteration in one session in 25 patients. Additional surgical or endovascular sessions were necessary in five patients after incomplete embolization and in one patient after incomplete surgery. Obliteration was confirmed with angiography after three months. There were no procedural complications. Conclusions Patients with dural fistulas with cortical venous drainage were cured with a strategy of arterial endovascular treatment with Onyx and surgery. These techniques were either primarily successful or complementary. There were no complications of treatment.
Ready or not? Pharmacist perceptions of a changing injection scope of practice before it happens
Authors: Foong Esther Ai-Leng , Edwards David J. , Houle Sherilyn , Grindrod Kelly A. 
Published: October 2017

Background: Since 2012, Ontario pharmacists have been authorized to administer the influenza vaccine. In April 2016, the Ontario College of Pharmacists (OCP) proposed to expand the Pharmacy Act to allow pharmacists to vaccinate against 13 additional conditions. The OCP held an online public consultation and invited pharmacists, members of the public and organizations to weigh in on the proposed changes. Our objective was to explore the factors influencing how Ontario pharmacists may adopt or reject an expanding scope of practice, using data from the public consultation. Methods: We coded the responses to the public consultation in 2 ways: 1) sentiment analysis and 2) an integrative approach to coding using Rogers’s diffusion of innovations theory across 5 domains: relative advantage, compatibility, complexity, trialability and observability. Results: Responses from pharmacists, the public and organizations were moderately positive on average. Pharmacists most commonly mentioned relative advantages, including benefits for patients, pharmacists, physicians and the health system. Positive responses focused on accessibility for patients, improved vaccine coverage, lower health care spending and freed physician time but cited lack of prescribing privileges as a barrier to the proposed changes. Negative responses focused on increased workload, patient safety concerns and the complexity of travel medicine. Conclusions: The expanded immunization services are likely to be well received by most pharmacists. Convenience and accessibility for patients were commonly cited benefits, but the changes will be only a slight improvement over the current system unless pharmacists can prescribe these vaccines. Although employers responded positively, the question remains whether they will support pharmacists in a way that aligns with pharmacists’ values and expectations. Decision makers must pay close attention to the pharmacy infrastructure and how this will affect uptake of these services. Recognition of this, combined with pharmacists’ positive perceptions of the expanded scope, will facilitate smooth integration of this legislation into Ontario pharmacy practice.
Food for Life: evaluation of the impact of the Hospital Food Programme in England using a case study approach
Authors: Gray Selena , Orme Judy , Pitt Hannah , Jones Matthew 
Published: October 2017

Objectives To evaluate the impact and challenges of implementing a Food for Life approach within three pilot NHS sites in 2014/2015 in England. Food for Life is an initiative led by the Soil Association, a non-governmental organisation in the UK that aims to encourage a healthy, sustainable food culture across communities. Design A case-study approach was undertaken using semi-structured interviews with staff and key stakeholders together with analysis of relevant documents such as meeting minutes, strategic plans and reports. Setting Three NHS Trusts in England. Participants Staff and key stakeholders. Main outcome measures Synthesis of key findings from semi-structured interviews and analysis of relevant documents. Results Key themes included the potential to influence contracting processes; measuring quality; food for staff and visitors; the role of food in hospitals, and longer term sustainability and impact. Participants reported that adopting the Food for Life approach had provided enormous scope to improve the quality of food in hospital settings and had provided levers and external benchmarks for use in contracting to help drive up standards of the food provided by external contractors for patients and staff. This was demonstrated by the achievement of an FFLCM for staff and visitor catering in all three organisations. Conclusions Participants all felt that the importance of food in hospitals is not always recognised. Engagement with Food for Life can produce a significant change in the focus on food within hospitals, and help to improve the quality of food and mealtime experience for staff, visitors and patients.
Annulo-Nucleoplasty Using Disc-Fx in the Management of Degenerative Lumbar Disc Pathology: How Long Can the Effect Last?
Authors: Kumar Naresh , Zaw Aye Sandar , Kumar Nishant , Sonawane Dhiraj , Hey Hwee Weng Dennis , Kumar Aravind 
Published: October 2017

Study Design: Prospective analysis. Objectives: To evaluate 2-year clinical outcomes in patients undergoing Disc-FX for the management of low back pain (LBP) due to degenerate disc (DD) or contained lumbar disc herniation (CLDH). To study salient factors that can potentially influence the clinical outcomes. Methods: We analyzed the prospectively collected data of 51 patients who underwent Disc-FX procedure for DD or CLDH, nonresponsive to 6 months of nonoperative treatment. Clinical outcome measures collected were visual analogue scale (VAS), Oswestry Disability Index (ODI), and MacNab scores. These preoperative values were compared with respective values at immediate, 6 months, 1 year, and 2 years postoperation. Minimum clinically important difference values for these outcomes in accordance with previously published data was used to evaluate the effectiveness of Disc-FX intervention. Results: Of 51 patients, 84% had DD and 16% had CLDH. Significant improvement ( P < .01) in VAS and ODI scores was observed at all assessment periods compared to the respective preoperative values. Based on the MacNab scores, there was significant increase ( P < .01) in the proportion of patients with excellent/good MacNab outcomes at each time point after the procedure; 78% achieving excellent/good outcomes at 2-year follow-up. Ease of access to the disc space was significantly influencing VAS, ODI, and MacNab scores at 1-year and 2-year follow-ups. VAS and MacNab scores were negatively influenced by high body mass index and smoking status at 6 and 12 months postoperation. Conclusions: Our data suggests that Disc-FX may be helpful in selected patients with symptomatic degenerative disc disease providing favorable outcomes lasting up to 2 years or more. The results were more favorable in patients with easier access to disc space.
Consistent Condom Use with Paying and Nonpaying Partners among Female Sex Workers in Iran: Findings of a National Biobehavioral Survey
Authors: Karamouzian Mohammad , Sadeghirad Behnam , Sharifi Hamid , Sedaghat Abbas , Haghdoost Ali Akbar , Mirzazadeh Ali 
Published: October 2017

Objectives: Little is known about the dynamics of condom use among female sex workers (FSWs) in Iran. We investigated the correlates of consistent condom use (CCU) among FSWs, using data from a national biobehavioral surveillance survey in 2010. Methods: A total of 872 FSWs were recruited using a facility-based sampling strategy from 21 sites in 13 cities in Iran. Data were collected through face-to-face interviews using a standardized questionnaire. Results: Overall, 33.6% and 17.3% of FSWs reported CCU with paying and nonpaying sex partners, respectively. Consistent condom use with paying partners was significantly associated with temporary marriage, accessing family planning services and history of working in brothels. Conversely, temporary marriage or married status, condom rupture/slippage, and HIV seropositivity remained independently significantly associated with CCU with nonpaying sex partners. Conclusion: Our findings indicated the urgent need for scaling up condom promotion interventions catered toward FSWs and their sex partners to practice safe sex consistently.
Applying a statistical method in transvaginal ultrasound training: lessons from the learning curve cumulative summation test (LC-CUSUM) for endometriosis mapping
Authors: Eisenberg Vered H. , Alcazar Juan L. , Arbib Nissim , Schiff Eyal , Achiron Reuven , Goldenberg Motti , Soriano David 
Published: October 2017

Abstract
Background
Methods available for assessing the learning curve, such as a predefined number of procedures or direct mentoring are lacking. Our aim was to describe the use of a statistical method to identify the minimal training length of an experienced sonographer, newly trained in deep infiltrating endometriosis (DIE) mapping by evaluating the learning curve of transvaginal ultrasound (TVUS) in the preoperative assessment of endometriosis.

Methods
A retrospective study in a tertiary referral center for endometriosis. Reports and stored data from TVUS scans performed by one operator with training in general gynecological ultrasound, but not in endometriosis mapping, were analyzed retrospectively for patients who subsequently underwent laparoscopy, which served as a reference standard. The performance of TVUS was assessed for the following sites: endometriomas, bladder, vagina, pouch of Douglas, bowel and uterosacral ligaments, and correlated with laparoscopic findings. Sensitivity, specificity, PPV, NPV, and accuracy were calculated, and the operator’s diagnostic performance was assessed using the learning curve cumulative summation test (LC-CUSUM).

Results
Data from 94 women were available for analysis. The learning curve using the LC-CUSUM graph showed that the sonographer reached the predefined level of proficiency in detecting endometriosis lesions after 20, 26, 32, 31, 38, and 44 examinations for endometriomas, bladder nodules, vaginal nodules, pouch of Douglas obliteration, bowel nodules, and uterosacral ligament nodules, respectively.

Conclusions
LC-CUSUM allows monitoring of individual performance during the learning process of new methodologies. This study shows that a sonographer trained in general gynecologic ultrasonography, who devotes time to learn TVUS for DIE mapping, can achieve proficiency for diagnosing the major types of endometriotic lesions after examining less than 50 patients who subsequently undergo surgery in a training setting.
Physiological mechanisms constraining ectotherm fright-dive performance at elevated temperatures
Authors: Rodgers Essie M. , Franklin Craig E. 
Published: October 2017

ABSTRACTSurvival of air-breathing, diving ectotherms is dependent on their capacity to optimise the time available for obligate underwater activities, such as predator avoidance. Submergence times are thermally sensitive, with dive durations significantly reduced by increases in water temperature, deeming these animals particularly vulnerable to the effects of climate change. The physiological mechanisms underlying this compromised performance are unclear but are hypothesised to be linked to increased oxygen demand and a reduced capacity for metabolic depression at elevated temperatures. Here, we investigated how water temperature (both acute and chronic exposures) affected the physiology of juvenile estuarine crocodiles (Crocodylus porosus) performing predator avoidance dives (i.e. fright-dives). Diving oxygen consumption, ‘fright’ bradycardia, haematocrit and haemoglobin (indicators of blood oxygen carrying capacity) were assessed at two test temperatures, reflective of different climate change scenarios (i.e. current summer water temperatures, 28°C, and ‘high’ climate warming, 34°C). Diving oxygen consumption rate increased threefold between 28 and 34°C (Q10=7.4). The capacity to depress oxygen demand was reduced at elevated temperatures, with animals lowering oxygen demand from surface levels by 52.9±27.8% and 27.8±16.5% (means±s.e.m.) at 28°C and 34°C, respectively. Resting and post-fright-dive haematocrit and haemoglobin were thermally insensitive. Together these findings suggest decrements in fright-dive performance at elevated temperatures stem from increased oxygen demand coupled with a reduced capacity for metabolic depression.
Molecular plasticity and functional enhancements of leg muscles in response to hypergravity in the fruit fly Drosophila melanogaster
Authors: Schilder Rudolf J. , Raynor Megan 
Published: October 2017

ABSTRACT
Studies of organismal and tissue biomechanics have clearly demonstrated that musculoskeletal design is strongly dependent on experienced loads, which can vary in the short term, as a result of growth during life history and during the evolution of animal body size. However, how animals actually perceive and make adjustments to their load-bearing musculoskeletal elements that accommodate variation in their body weight is poorly understood. We developed an experimental model system that can be used to start addressing these open questions, and uses hypergravity centrifugation to experimentally manipulate the loads experienced by Drosophila melanogaster. We examined effects of this manipulation on leg muscle alternative splicing of the sarcomere gene troponin T (Dmel\up; Fbgn0004169, herein referred to by its synonym TnT), a process that was previously demonstrated to precisely correlate with quantitative variation in body weight in Lepidoptera and rat. In a similar fashion, hypergravity centrifugation caused fast (i.e. within 24 h) changes to fly leg muscle TnT alternative splicing that correlated with body weight variation across eight D. melanogaster lines. Hypergravity treatment also appeared to enhance leg muscle function, as centrifuged flies showed an increased negative geotaxis response and jump ability. Although the identity and location of the sensors and effectors involved remains unknown, our results provide further support for the existence of an evolutionarily conserved mechanism that translates signals that encode body weight into appropriate skeletal muscle molecular and functional responses.