LLukas22/scidocs huggingface dataset:
Improving fatigue and depression in individuals with multiple sclerosis using telephone-administered physical activity counseling.

OBJECTIVE
To evaluate the impact of a physical activity intervention consisting of telephone counseling with home-based monitoring to improve fatigue and depression in individuals with multiple sclerosis (MS).


METHOD
Single-blind randomized controlled trial. Sixty-four individuals with MS received either telephone counseling (N = 31), or self-directed physical activity education (N = 33). The education condition (EC) consisted of advice to increase physical activity and a DVD with examples of in-home exercises for multiple physical ability levels. The telephone counseling condition (TC) included EC as well as mailed graphic feedback, 6 telephone counseling sessions using principles of motivational interviewing, and telehealth home monitoring to track progress on physical activity goals. Booster sessions were provided when participants indicated they did not meet their goals. Assessment was conducted at baseline, 3-month, and 6-month follow-up.


RESULTS
TC participants reported significantly reduced fatigue (d = -.70), reduced depression (d = -.72) and increased physical activity (d = .92) relative to EC participants. Of individuals receiving TC, 33.3% experienced clinically significant improvement in fatigue (vs. 18.2% in EC) and 53.3% experienced clinically significant improvement in depression (vs. 9.1% in EC). Improvements in physical activity mediated improvements in fatigue with a similar trend for depression. TC was highly feasible (participants completed 99.5% of schedule telephone sessions) and well tolerated (100% rated it highly successful).


CONCLUSION
Telephone-based counseling with home monitoring is a promising modality to improve physical activity and treat fatigue and depression.
Superficial dorsal penile vein thrombosis: a little-known complication of subinguinal varicocelectomy.

OBJECTIVE
To describe the symptomatology, diagnosis and treatment of superficial thrombosis of the dorsal penile vein - the most common complication of subinguinal varicocelectomy - and analyse the possible mechanisms involved in the development of the condition.


PATIENTS AND METHODS
The clinical records of 326 patients who underwent varicocele repair during the last 10 years was reviewed. The technique used was subinguinal varicocelectomy with arterial preservation. A mini-Doppler probe was used during surgery for artery identification. We report on the postoperative complications of varicocelectomy, with special attention to superficial dorsal penile vein thrombosis, and provide a detailed description of the anatomy of the superficial venous system of the penis.


RESULTS
Complications usually associated with varicocele surgery occurred in less than 1% of patients. However, the most common complication in our series was superficial dorsal penile vein thrombosis, which occurred in 2.1% of patients. The use of the mini-Doppler probe allowed us to identify and preserve the arteries in all 326 patients.


CONCLUSION
Subinguinal varicocelectomy with intra-operative use of a mini-Doppler probe is a rapid and safe technique. The outcomes and complications are similar to those reported for subinguinal microscopic varicocelectomy. Superficial dorsal penile vein thrombosis is a benign self-limited condition whose association with subinguinal varicocelectomy has not been previously reported.
The use of Talking Mats to support people with dementia and their carers to make decisions together.

Policy guidelines insist that people with dementia should be involved in decisions about key life choices and transitions. However, as dementia affects both cognitive and communication difficulties, it becomes increasingly difficult to do this, and innovative and effective ways to support people with dementia and their carers to interact with each other are needed. This project, funded by Joseph Rowntree Foundation, examined if Talking Mats, a low-tech communication framework, could support family carers and people with dementia to discuss issues around daily living with each other. The fieldwork phase took place from September 2008 to May 2009. Eighteen couples (person with dementia and their family carer) from Scotland and the North of England were involved. The couples were visited in their own homes and asked to discuss together four topics (Personal Care; Getting Around; Housework; Activities) under two different conditions: (i) using the Talking Mats framework and (ii) using their usual communication methods (UCMs). After the interviews, each participant was asked separately to complete a short questionnaire (Involvement Measure), which included five questions to evaluate how involved s/he felt in each type of discussion and a final question to measure satisfaction with the overall discussion. The findings show that both people with dementia and their carers feel more involved in discussions about how they are managing their daily living when using the Talking Mats framework, compared with their UCM. They also feel more satisfied with the outcome of those discussions. The use of Talking Mats could result in increased well-being and positive adjustment to accepting increasing levels of care for people with dementia. In addition, it could improve the relationship between the person with dementia and family carers, if all involved feel that the views of the person with dementia and the family carer have truly been acknowledged.
A scalable collaborative filtering framework based on co-clustering

Collaborative filtering-based recommender systems have become extremely popular due to the increase in Web-based activities such as e-commerce and online content distribution. Current collaborative filtering (CF) techniques such as correlation and SVD based methods provide good accuracy, but are computationally expensive and can be deployed only in static off-line settings. However, a number of practical scenarios require dynamic real-time collaborative filtering that can allow new users, items and ratings to enter the system at a rapid rate. In this paper, we consider a novel CF approach based on a proposed weighted co-clustering algorithm (Banerjee et al., 2004) that involves simultaneous clustering of users and items. We design incremental and parallel versions of the co-clustering algorithm and use it to build an efficient real-time CF framework. Empirical evaluation demonstrates that our approach provides an accuracy comparable to that of the correlation and matrix factorization based approaches at a much lower computational cost.
What outcomes from pharmacologic treatments are important to people with rheumatoid arthritis? Creating the basis of a patient core set.

OBJECTIVE
Function, patient global assessment, and pain are routinely measured in rheumatoid arthritis (RA) clinical trials. However, other patient-reported outcomes identified as important to patients in qualitative studies, such as fatigue and quality of life, are commonly not included, and modern treatment regimens may have changed patients' expectations of treatment outcomes. Our objective was to elicit patient priority treatment outcomes for pharmacologic interventions since the common use of anti-tumor necrosis factor (anti-TNF) therapy, which will form the basis of a core set of patient priorities to complement existing professional core sets.


METHODS
In-depth interviews were conducted with 23 RA patients, purposively sampled for age, sex, medication (anti-TNF or other disease-modifying antirheumatic drugs), disease severity, and work status. Grounded theory guided iterative data collection and analysis. Coding of the data was peer reviewed. A patient research partner collaborated in the research design and analysis.


RESULTS
Sixty-three different outcomes important to patients were generated from the interviews. Four major categories of patient outcomes from pharmacologic treatments were developed: "RA under control," "Doing things," "Emotional health," and "Coping with illness." The core category (or overall theme) was "Minimizing the personal impact of RA."


CONCLUSION
Although the routine outcomes of pain, function, and overall well-being were raised by the patients, they also generated a further 60 important outcomes that they look for from treatment. This difference in perspective may potentially influence treatment decisions. The next step is therefore to use these data to develop a patient core set.
Comparison of the photodynamic fungicidal efficacy of methylene blue, toluidine blue, malachite green and low-power laser irradiation alone against Candida albicans

This study was to evaluate specific effects of photodynamic therapy (energy density 15.8 J/cm2, 26.3 J/cm2 and 39.5 J/cm2) using methylene blue, toluidine blue and malachite green as photosensitizers and low-power laser irradiation on the viability of Candida albicans. Suspensions of C. albicans containing 106 cells/ml were standardized in a spectrophotometer. For each dye, 120 assays, divided into four groups according to the following experimental conditions, were carried out: laser irradiation in the presence of the photosensitizer; laser irradiation only; treatment with the photosensitizer only; no exposure to laser light or photosensitizer. Next, serial dilutions were prepared and seeded onto Sabouraud dextrose agar for the determination of the number of colony-forming units per milliliter (CFU/ml). The results were subjected to analysis of variance and the Tukey test (P < 0.05). Photodynamic therapy using the photosensitizers tested was effective in reducing the number of C. albicans.. The number of CFU/ml was reduced by between 0.54 log10 and 3.07 log10 and depended on the laser energy density used. Toluidine blue, methylene blue and malachite green were effective photosensitizers in antimicrobial photodynamic therapy against C. albicans, as was low-power laser irradiation alone.
Challenges of migrating to agile methodologies

Software development methodologies are constantly evolving due to changing technologies and new demands from users. Today's dynamic business environment has given rise to emergent organizations that continuously adapt their structures, strategies, and policies to suit the new environment [12]. Such organizations need information systems that constantly evolve to meet their changing requirements---but the traditional, plan-driven software development methodologies lack the flexibility to dynamically adjust the development process.
FCSE at Medical Tasks of ImageCLEF 2013

This paper presents the details of the participation of FCSE (Faculty of Computer Science and Engineering) research team in ImageCLEF 2013 medical tasks (modality classification, ad-hoc image retrieval and case-based retrieval). For the modality classification task we used SIFT descriptors and tf − idf weights of the surrounding text (image caption and paper title) as features. SVMs with χ kernel and one-vsall strategy were used as classifiers. For the ad-hoc image retrieval task and case-based retrieval we adopted a strategy which uses a combination of word-space and concept-space approaches. The word-space approach uses the Terrier IR search engine to index and retrieve the text associated with the images/cases. The concept-space approach uses Metamap to map the text data into a set of UMLS (Unified Medical Language System) concepts, which are later indexed and retrieved by the Terrier IR search engine. The results from the word-space and concept-space retrieval are fused using linear combination. For the compound figure separation task, we used unsupervised algorithm based on breadth-first search strategy using only visual information from the medical images. The selected algorithms were tuned and tested on the data from ImageCLEF 2012 medical task and based on the selected parameters we submitted the new experiments for ImageCLEF 2013 medical task. We achieved very good overall performance: the best run for the modality classification ranked 2nd in the overall score, the best run for the ad-hoc image retrieval ranked 3rd.
Bias and high-dimensional adjustment in observational studies of peer effects

Peer effects, in which the behavior of an individual is affected by the behavior of their peers, are posited by multiple theories in the social sciences. Other processes can also produce behaviors that are correlated in networks and groups, thereby generating debate about the credibility of observational (i.e. nonexperimental) studies of peer effects. Randomized field experiments that identify peer effects, however, are often expensive or infeasible. Thus, many studies of peer effects use observational data, and prior evaluations of causal inference methods for adjusting observational data to estimate peer effects have lacked an experimental “gold standard” for comparison. Here we show, in the context of information and media diffusion on Facebook, that high-dimensional adjustment of a nonexperimental control group (677 million observations) using propensity score models produces estimates of peer effects statistically indistinguishable from those from using a large randomized experiment (220 million observations). Naive observational estimators overstate peer effects by 320% and commonly used variables (e.g., demographics) offer little bias reduction, but adjusting for a measure of prior behaviors closely related to the focal behavior reduces bias by 91%. High-dimensional models adjusting for over 3,700 past behaviors provide additional bias reduction, such that the full model reduces bias by over 97%. This experimental evaluation demonstrates that detailed records of individuals’ past behavior can improve studies of social influence, information diffusion, and imitation; these results are encouraging for the credibility of some studies but also cautionary for studies of rare or new behaviors. More generally, these results show how large, high-dimensional data sets and statistical learning techniques can be used to improve causal inference in the behavioral sciences. * We are grateful to L. Adamic, S. Aral, J. Bailenson, J. H. Fowler, W. H. Hobbs, G. W. Imbens, S. Messing, C. Nass, M. Nowak, A. B. Owen, A. Peysakhovich, B. Reeves, D. Rogosa, J. Sekhon, A. C. Thomas, J. Ugander, and participants in seminars at New York University Stern School of Business, Stanford University Graduate School of Business, UC Berkeley Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, University of Chicago Booth School of Business, Columbia University Department of Statistics, and UC Davis Department of Statistics for comments on this work. D.E. was previously an employee of Facebook while contributing to this research and is a contractor with Facebook. D.E. and E.B. have significant financial interests in Facebook. 1 ar X iv :1 70 6. 04 69 2v 1 [ st at .M E ] 1 4 Ju n 20 17
Predicting change in academic abilities after conformal radiation therapy for localized ependymoma.

PURPOSE
Conformal radiation therapy (CRT) aims to limit the highest radiation dose to the tissue volume at risk while sparing surrounding normal tissues. This study investigated whether treatment of childhood ependymoma with CRT would preserve cognitive function. Academic competence was chosen as the primary outcome measure given it is a measure of applied cognitive abilities in a child's natural setting.


PATIENTS AND METHODS
Eighty-seven pediatric patients diagnosed with ependymoma received CRT in which doses ranging from 54.0 to 59.4 Gy were prescribed to the postoperative tumor bed with a 10-mm clinical target volume margin. Cognitive testing was conducted at the start of CRT, 6 months, and annually after the start of CRT. The median length of follow-up was 59.6 months. Academic testing included subtests from the Wechsler Individual Achievement Test (WIAT) and the Achenbach Child Behavior Checklist.


RESULTS
Linear mixed models with random coefficients revealed a modest but significant decline in reading scores during follow-up (WIAT slope estimate -0.064 +/- 0.028 points/month; P = .026). Math and spelling performance remained stable. Supratentorial tumor location and multiple surgeries were predictive of worse reading performance at CRT baseline. Male sex, longer symptomatic interval, pre-CRT chemotherapy, pre-existing endocrine deficiencies, hydrocephalus, and younger age at CRT (< 5 years) were predictive of a significant decline in reading scores over time.


CONCLUSION
CRT may result in better long-term cognitive outcomes when compared to conventional radiation therapy approaches. Reading appears more vulnerable than other academic skills and may decline over time despite stable intellectual functioning.
Additive glucose-lowering effects of glucagon-like peptide-1 and metformin in type 2 diabetes.

OBJECTIVE
The incretin hormone glucagon-like peptide-1 (GLP-1) reduces plasma glucose in type 2 diabetic patients by stimulating insulin secretion and inhibiting glucagon secretion. The biguanide metformin is believed to lower plasma glucose without affecting insulin secretion. We conducted this study to investigate the effect of a combination therapy with GLP-1 and metformin, which could theoretically be additive, in type 2 diabetic patients.


RESEARCH DESIGN AND METHODS
In a semiblinded randomized crossover study, seven patients received treatment with metformin (1,500 mg daily orally) alternating with GLP-1 (continuous subcutaneous infusion of 2.4 pmol x kg(-1) x min(-1)) alternating with a combination of metformin and GLP-1 for 48 h. Under fixed energy intake, we examined the effects on plasma glucose, insulin, C-peptide, glucagon, and appetite.


RESULTS
Fasting plasma glucose (day 2) decreased from 13.9 +/- 1 (no treatment) to 11.2 +/- 0.4 (metformin) and 11.5 +/- 0.5 (GLP-1) and further decreased to 9.4 +/- 0.7 (combination therapy) (P = 0.0005, no difference between monotherapy with GLP-1 and metformin). The 24-h mean plasma glucose (day 2) decreased from 11.8 +/- 0.5 (metformin) and 11.7 +/- 0.8 (GLP-1) to 9.8 +/- 0.5 (combination) (P = 0.02, no difference between GLP-1 and metformin). Insulin levels were similar between the three regimens, but glucagon levels were significantly reduced with GLP-1 compared with metformin (P = 0.0003). Combination therapy had no additional effect on appetite scores.


CONCLUSIONS
Monotherapy with GLP-1 and metformin have equal effects on plasma glucose and additive effects upon combination.
A Test Collection for Research on Depression and Language Use

Several studies in the literature have shown that the words people use are indicative of their psychological states. In particular, depression was found to be associated with distinctive linguistic patterns. In this talk, I will describe our first steps to try to identify as early as possible if the writer is developing a depressive state. I will detail the methodology we have adopted to build and make publicly available a test collection on depression and language use. The resulting corpus includes a series of textual interactions written by different subjects. The new collection not only encourages research on differences in language between depressed and non-depressed individuals, but also on the evolution of the language use of depressed individuals. I will also present the new CLEF lab that we will run next year on this topic (eRisk 2017), that includes a novel depression detection task and the proposal of effectiveness measure to systematically compare early detection algorithms and baseline results. Bio : Fabio Crestani est titulaire d'un diplôme en statistiques de l'Université de Padoue (Italie) et d'une maîtrise et d'un doctorat en sciences informatiques de l'Université de Glasgow (Royaume-Uni). Ses principaux domaines de recherche sont la recherche d'information, la fouille de textes et les bibliothèques numériques. Il a co-édité 10 livres et publié plus de 160 publications dans ces domaines de recherche. Il a été rédacteur en chef de Information Processing and Management (Elsevier) jusqu'en 2015 et membre du comité de rédaction de plusieurs revues. Ses travaux sur les réseaux sociaux sont particulièrement en phase avec les recherches menées par plusieurs équipes de l'IRIT.
Texture analysis on (18)F-FDG PET/CT images to differentiate malignant and benign bone and soft-tissue lesions.

OBJECTIVE
The purpose is to develop and evaluate the ability of the computer-aided diagnosis (CAD) methods that apply texture analysis and pattern classification to differentiate malignant and benign bone and soft-tissue lesions on 18F-fluorodeoxy-glucose positron emission tomography/computed tomography ((18)F-FDG PET/CT) images.


METHODS
Subjects were 103 patients with 59 malignant and 44 benign bone and soft tissue lesions larger than 25 mm in diameter. Variable texture parameters of standardized uptake values (SUV) and CT Hounsfield unit values were three-dimensionally calculated in lesional volumes-of-interest segmented on PET/CT images. After selection of a subset of the most optimal texture parameters, a support vector machine classifier was used to automatically differentiate malignant and benign lesions. We developed three kinds of CAD method. Two of them utilized only texture parameters calculated on either CT or PET images, and the other one adopted the combined PET and CT texture parameters. Their abilities of differential diagnosis were compared with the SUV method with an optimal cut-off value of the maximum SUV.


RESULTS
The CAD methods utilizing only optimal PET (or CT) texture parameters showed sensitivity of 83.05 % (81.35 %), specificity of 63.63 % (61.36 %), and accuracy of 74.76 % (72.82 %). Although the ability of differential diagnosis by PET or CT texture analysis alone was not significantly different from the SUV method whose sensitivity, specificity, and accuracy were 64.41, 61.36, and 63.11 % (the optimal cut-off SUVmax was 5.4 ± 0.9 in the 10-fold cross-validation test), the CAD method with the combined PET and CT optimal texture parameters (PET: entropy and coarseness, CT: entropy and correlation) exhibited significantly better performance compared with the SUV method (p = 0.0008), showing a sensitivity of 86.44 %, specificity of 77.27 %, and accuracy of 82.52 %.


CONCLUSIONS
The present CAD method using texture analysis to analyze the distribution/heterogeneity of SUV and CT values for malignant and benign bone and soft-tissue lesions improved the differential diagnosis on (18)F-FDG PET/CT images.