nils-herrmann/clean_scirepeval huggingface dataset:
Using augmented reality to treat phobias

Virtual reality (VR) is useful for treating several psychological problems, including phobias such as fear of flying, agoraphobia, claustrophobia, and phobia to insects and small animals. We believe that augmented reality (AR) could also be used to treat some psychological disorders. AR and VR share some advantages over traditional treatments. However, AR gives a greater feeling of presence (the sensation of being there) and reality judgment (judging an experience as real) than VR because the environment and the elements the patient uses to interact with the application are real. Moreover, in AR users see their own hands, feet, and so on, whereas VR only simulates this experience. With these differences in mind, the question arises as to the kinds of psychological treatments AR and VR are most suited for. In our system, patients see their own hands, feet, and so on. They can touch the table that animals are crossing or seeing their feet while the animals are running on the floor. They can also hold a marker with a dead spider or cockroach or pick up a flyswatter, a can of insecticide, or a dustpan.
Effects of home-based exercise training for patients with chronic heart failure and sleep apnoea: a randomized comparison of two different programmes.

To evaluate the effects of home-based exercise for patients with chronic heart failure and sleep apnoea and to compare two different training programmes.



A randomized, prospective controlled trial.



Department of Cardiology, University Hospital, Brazil.



Fifty chronic heart failure patients with sleep apnoea were randomized in three groups: Group 1 (aerobic training, n = 18), Group 2 (aerobic with strength training, n = 18), and Group 3 (untrained, n = 14).



The training programme for Groups 1 and 2 began with three supervised exercise sessions, after they underwent three months of home-based exercise. Patients were followed by weekly telephone call and were reviewed monthly. Group 3 had the status of physical activity evaluated weekly by interview to make sure they remained untrained.



At baseline and after three months: cardiopulmonary exercise testing, isokinetic strength and endurance, Minnesota living with heart failure questionnaire and polysomnography. Adherence was evaluated weekly.



Of the 50 patients enrolled in the study, 45 completed the programme.  Group 1 (one death), Group 2 (one myocardial infarction), Group 3 (one death and two strokes). None were training related. Training groups showed improvement in all outcomes evaluated and the adherence was an important factor (Group 1 = 98.5% and Group 2 = 100.2%, P = 0.743). Untrained Group 3 demonstrated significant decrease or no change on measurements after three months without training.



Home-based exercise training is an important therapeutic strategy in chronic heart failure patients with sleep apnoea, and strength training resulted in a higher increase in muscle strength and endurance.
Qualitative study of barriers to cervical cancer screening among Nigerian women

To explore the barriers to cervical cancer screening, focusing on religious and cultural factors, in order to inform group-specific interventions that may improve uptake of cervical cancer screening programmes.



We conducted four focus group discussions among Muslim and Christian women in Nigeria.



Discussions were conducted in two hospitals, one in the South West and the other in the North Central region of Nigeria.



27 Christian and 22 Muslim women over the age of 18, with no diagnosis of cancer.



Most participants in the focus group discussions had heard about cervical cancer except Muslim women in the South Western region who had never heard about cervical cancer. Participants believed that wizardry, multiple sexual partners and inserting herbs into the vagina cause cervical cancer. Only one participant knew about the human papillomavirus. Among the Christian women, the majority of respondents had heard about cervical cancer screening and believed that it could be used to prevent cervical cancer. Participants mentioned religious and cultural obligations of modesty, gender of healthcare providers, fear of disclosure of results, fear of nosocomial infections, lack of awareness, discrimination at hospitals, and need for spousal approval as barriers to uptake of screening. These barriers varied by religion across the geographical regions.



Barriers to cervical cancer screening vary by religious affiliations. Interventions to increase cervical cancer awareness and screening uptake in multicultural and multireligious communities need to take into consideration the varying cultural and religious beliefs in order to design and implement effective cervical cancer screening intervention programmes.
Mapping EORTC QLQ-C30 onto EQ-5D for the assessment of cancer patients

The European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 (EORTC QLQ-C30) is the instrument most frequently used to measure quality of life in cancer patients, whereas the EQ-5D is widely used to measure and evaluate general health status. Although the EORTC QLQ-C30 has been mapped to EQ-5D utilities, those studies were limited to patients with a single type of cancer. The present study aimed to develop a mapping relationship between the EORTC QLQ-C30 and EQ-5D-based utility values at the individual level.



The model was derived using patients with different types of cancer who were receiving chemotherapy. The external validation set comprised outpatients with colon cancer. Ordinary least squares regression was used to estimate the EQ-5D index from the EORTC QLQ-C30 results. The predictability, goodness of fit, and signs of the estimated coefficients of the model were assessed. Predictive ability was determined by calculating the mean absolute error, the estimated proportions with absolute errors > 0.05 and > 0.1, and the root-mean-squared error (RMSE).



A model that included global health, physical, role, emotional functions, and pain was optimal, with a mean absolute error of 0.069 and an RMSE of 0.095 (normalized RMSE, 8.1%). The explanatory power of this model was 51.6%. The mean absolute error was higher for modeled patients in poor health.



This mapping algorithm enabled the EORTC QLQ-C30 to be converted to the EQ-5D utility index to assess cancer patients in Korea.
Addressing health disparities in the mental health of refugee children and adolescents through community-based participatory research: a study in 2 communities.

We sought to understand the problems, strengths, and help-seeking behaviors of Somali Bantu and Bhutanese refugees and determine local expressions of mental health problems among youths in both communities.



We used qualitative research methods to develop community needs assessments and identify local terms for child mental health problems among Somali Bantu and Bhutanese refugees in Greater Boston and Springfield, Massachusetts, between 2011 and 2014. A total of 56 Somali Bantu and 93 Bhutanese refugees participated in free list and key informant interviews.



Financial and language barriers impeded the abilities of families to assist youths who were struggling academically and socially. Participants identified resources both within and outside the refugee community to help with these problems. Both communities identified areas of distress corresponding to Western concepts of conduct disorders, depression, and anxiety.



There are numerous challenges faced by Somali Bantu and Bhutanese youths, as well as strengths and resources that promote resilience. Future steps include using culturally informed methods for identifying those in need of services and developing community-based prevention programs.
Multi-view 3D human pose estimation combining single-frame recovery, temporal integration and model adaptation

We present a system for the estimation of unconstrained 3D human upper body movement from multiple cameras. Its main novelty lies in the integration of three components: single frame pose recovery, temporal integration and model adaptation. Single frame pose recovery consists of a hypothesis generation stage, where candidate 3D poses are generated based on hierarchical shape matching in the individual camera views. In the subsequent hypothesis verification stage, candidate 3D poses are reprojected to the other camera views and ranked according to a multiview matching score. Temporal integration consists of computing best trajectories combining a motion model and observations in a Viterbi style maximum likelihood approach. Poses that lie on the best trajectories are used to generate and adapt a texture model, which in turn enriches the shape component used for pose recovery. We demonstrate that our approach outperforms the state of the art in experiments with large and challenging real world data from an outdoor setting. The new data set is made public to facilitate benchmarking.
Angelix: Scalable Multiline Program Patch Synthesis via Symbolic Analysis

Since debugging is a time-consuming activity, automated program repair tools such as GenProg have garnered interest. A recent study revealed that the majority of GenProg repairs avoid bugs simply by deleting functionality. We found that SPR, a state-of-the-art repair tool proposed in 2015, still deletes functionality in their many "plausible" repairs. Unlike generate-and-validate systems such as GenProg and SPR, semantic analysis based repair techniques synthesize a repair based on semantic information of the program. While such semantics-based repair methods show promise in terms of quality of generated repairs, their scalability has been a concern so far. In this paper, we present Angelix, a novel semantics-based repair method that scales up to programs of similar size as are handled by search-based repair tools such as GenProg and SPR. This shows that Angelix is more scalable than previously proposed semantics based repair methods such as SemFix and DirectFix. Furthermore, our repair method can repair multiple buggy locations that are dependent on each other. Such repairs are hard to achieve using SPR and GenProg. In our experiments, Angelix generated repairs from large-scale real-world software such as wireshark and php, and these generated repairs include multi-location repairs. We also report our experience in automatically repairing the well-known Heartbleed vulnerability.
Exploring the pathophysiology of hypogonadism in men with type 2 diabetes: kisspeptin-10 stimulates serum testosterone and LH secretion in men with type 2 diabetes and mild biochemical hypogonadism.

Low serum testosterone is commonly observed in men with type 2 diabetes (T2DM), but the neuroendocrine pathophysiology remains to be elucidated.



The hypothalamic neuropeptide kisspeptin integrates metabolic signals with the reproductive axis in animal models. We hypothesized that administration of exogenous kisspeptin-10 will restore luteinizing hormone (LH) and testosterone secretion in hypotestosteronaemic men with T2DM.



Five hypotestosteronaemic men with T2DM (age 33·6 ± 3 years, BMI 40·6 ± 6·3, total testosterone 8·5 ± 1·0 nmol/l, LH 4·7 ± 0·7 IU/l, HbA1c 7·4±2%, duration of diabetes <5 years) and seven age-matched healthy men.  Mean LH increased in response to intravenous administration of kisspeptin-10 (0·3 mcg/kg bolus) both in healthy men (5·5 ± 0·8 to 13·9 ± 1·7 IU/l P < 0·001) and in men with T2DM (4·7 ± 0·7 to 10·7 ± 1·2 IU/l P = 0·02) with comparable ΔLH (P = 0·18). EXPERIMENT 2: Baseline 10-min serum sampling for LH and hourly testosterone measurements were performed in four T2DM men over 12 h. An intravenous infusion of kisspeptin-10 (4 mcg/kg/h) was administered for 11 h, 5 days later. There were increases in LH (3·9 ± 0·1 IU/l to 20·7 ± 1·1 IU/l P = 0·03) and testosterone (8·5 ± 1·0 to 11·4 ± 0·9 nmol/l, P = 0·002). LH pulse frequency increased from 0·6 ± 0·1 to 0·9 ± 0 pulses/h (P = 0·05) and pulsatile component of LH secretion from 32·1 ± 8·0 IU/l to 140·2 ± 23·0 IU/l (P = 0·007).



Kisspeptin-10 administration increased LH pulse frequency and LH secretion in hypotestosteronaemic men with T2DM in this proof-of-concept study, with associated increases in serum testosterone. These data suggest a potential novel therapeutic role for kisspeptin agonists in enhancing endogenous testosterone secretion in men with T2DM and central hypogonadism.
A pilot trial assessing the efficacy of paroxetine hydrochloride (Paxil) in controlling hot flashes in breast cancer survivors.

Many breast cancer survivors suffer debilitating hot flashes. Estrogen, the drug of choice in perimenopausal women, is generally not recommenced to breast cancer survivors. Nonhormonal treatments are mostly disappointing. Anecdotal reports in our institution suggested that the selective serotonin-reuptake inhibitor, paroxetine hydrochloride, might be efficacious in alleviating hot flashes.



Thirty women with prior breast cancer who were suffering at least two hot flashes a day entered a single institution pilot trial to evaluate paroxetine's efficacy in reducing the frequency and severity of hot flashes. After completing daily diaries for one week on no therapy, the women received open-label paroxetine, 10 mg daily for one week, followed by four weeks of paroxetine, 20 mg daily. The women completed hot-flash daily diaries throughout the study period, and a health-related symptom-assessment questionnaire and a quality-of-life rating scale in the first and sixth week of the study.



Twenty-seven women completed the six-week study period. The mean reduction of hot flash frequency was 67% (95% confidence interval (95% CI): 56%-79%). The mean reduction in hot flash severity score was 75% (95% CI: 66%-85%). There was a statistically significant improvement in depression, sleep, anxiety, and quality of life scores. Furthermore, 25 (83%) of the study participants chose to continue paroxetine therapy at the end of study. The most common adverse effect was somnolence, resulting in drug discontinuation in two women, and dose reduction in two women. One woman discontinued drug due to anxiety.



Paroxetine hydrochloride is a promising new treatment for hot flashes in breast cancer survivors, and warrants further evaluation in a double-blind randomized placebo-controlled trial.
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships.



We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.


AVAILABILITY
Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu
Silencing efficacy prediction: a retrospective study on target mRNA features

Post-transcriptional gene silencing is a widely used method to suppress gene expression. Unfortunately only a portion of siRNAs do successfully reduce gene expression. Target mRNA secondary structures and siRNA-mRNA thermodynamic features are believed to contribute to the silencing activity. However, there is still an open discussion as to what determines siRNA efficacy. In this retrospective study, we analysed the target accessibility comparing very high (VH) compared with low (L) efficacy siRNA sequences obtained from the siRecords Database. We determined the contribution of mRNA target local secondary structures on silencing efficacy. Both the univariable and the multivariable logistic regression evidenced no relationship between siRNA efficacy and mRNA target secondary structures. Moreover, none of the thermodynamic and sequence-base parameters taken into consideration (H-b index, ΔG°overall, ΔG°duplex, ΔG°break-target and GC%) was associated with siRNA efficacy. We found that features believed to be predictive of silencing efficacy are not confirmed to be so when externally evaluated in a large heterogeneous sample. Although it was proposed that silencing efficacy could be influenced by local target accessibility we show that this could be not generalizable because of the diversity of experimental setting that may not be representative of biological systems especially in view of the many local protein factors, usually not taken into consideration, which could hamper the silencing process.
Effects of lansoprazole plus amoxycillin on the cure of Helicobacter pylori infection in Japanese peptic ulcer patients.

The effect of lansoprazole plus amoxycillin on curing Helicobacter pylori infection and peptic ulcer recurrence was evaluated.



The study group was composed of 68 patients with gastric ulcers and 51 with duodenal ulcers, all were H. pylori-positive. The participants were assigned at random to the lansoprazole alone group (lansoprazole 30 mg o.m. for 6 or 8 weeks) or the lansoprazole plus amoxycillin group (lansoprazole alone regimen plus amoxycillin at 500 mg q.d.s. concomitantly for the first 2 weeks). Healed patients were not given maintenance treatment with acid secretion inhibitors. The cure rate for H. pylori infection and the ulcer recurrence rate after 1 year were investigated.



The cure rate for H. pylori infection was 4.2% in patients receiving lansoprazole alone and 38.5% in patients receiving lansoprazole plus amoxycillin (P < 0.01) for gastric ulcers, and 0% in patients receiving lansoprazole alone and 61.9% in patients receiving lansoprazole plus amoxycillin (P < 0.001) for duodenal ulcers. The recurrence rate was 42.3% in patients receiving lansoprazole alone and 28.6% in patients receiving lansoprazole plus amoxycillin for gastric ulcers, and 66.7% for patients receiving lansoprazole alone and 11.1% for patients receiving lansoprazole plus amoxycillin (P < 0.001) for duodenal ulcers. None of the patients with gastric or duodenal ulcers cured of H. pylori infection had a recurrence.



Concomitant use of lansoprazole and amoxycillin increased the curative effects on H. pylori infection. However, the cure rates with this regimen remained inadequate.
Effect of selective anthelmintic treatments on health and production parameters in Pelibuey ewes during lactation

A study was conducted from December to April 2013, with the aim of evaluating a system of selective antiparasitic treatments using the FAMACHA© color chart compared with a conventional suppressive deworming system every 30 days in Pelibuey ewes during lactation. For the study, 54 ewes were used. They were randomly divided into two groups: FAMACHA and chemical treatments. The ewes in the first group received selective treatment depending on the ocular mucosa coloration (FAMACHA) and body condition score (BCS), while in the second group (chemical) all the animals remained under routine deworming every 30 days. Fecal nematode egg counts, proportion of third-stage trichostrongylid larvae, body condition, coloration of the ocular mucosa, and packed cell volume in the ewes were determined, while in lambs only body weight (BW) was recorded. No significant differences (p > 0.05) were observed in any of the studied variables between groups; however, the use of antiparasitic drugs was reduced during the experimental period in the FAMACHA group and no deaths of lambs or ewes were recorded. The results indicate that during the lactation of ewes, a strategy of selective treatments can be implemented without showing deterioration in major health and productive parameters of these animals.
Multimodal analytics to study collaborative problem solving in pair programming

Collaborative problem solving (CPS) is seen as a key skill in K-12 education---in computer science as well as other subjects. Efforts to introduce children to computing rely on pair programming as a way of having young learners engage in CPS. Characteristics of quality collaboration are joint exploring or understanding, joint representation, and joint execution. We present a data driven approach to assessing and elucidating collaboration through modeling of multimodal student behavior and performance data.
Efficacy and safety of thrice weekly DOTS in tuberculosis patients with and without HIV co-infection: an observational study

Despite the latest World Health Organization guidelines advocating daily therapy in HIV-TB co-infected individuals, there are few recent studies comparing outcomes of thrice-weekly anti-tuberculosis treatment in HIV-positive and HIV-negative patients with TB. The present study sets out to compare TB treatment outcomes in these two groups in the Indian national programme, which currently involves thrice-weekly therapy for all, regardless of HIV status.



HIV-positive and HIV-negative were consecutively screened for enrolment into this prospective observational study, carried out at the All India Institute of Medical Sciences hospital, New Delhi, India, between 2006 and 2010. Patients were given short-course thrice-weekly rifampicin-based therapy, with all HIV-positive patients being started on highly active antiretroviral therapy at least 14 days after commencing TB treatment. Patients were regularly followed-up for 24 months after completion of treatment.



150 HIV-positive, 155 HIV-negative patients were enrolled consecutively for the study. Significantly higher treatment success (93.5% vs. 76.7% at end of treatment, p < 0.001) and lower mortality (2.8% vs. 21.6% on follow up, p < 0.001) were observed in HIV-negative patients. No significant difference was found in treatment failure (p = 0.16), sputum smear (p = 0.58) and culture conversion (p = 0.55), and non-serious adverse event incidence (p = 0.851) between the two groups. Low baseline CD4 cell count (<100 cells/ mm3) was the only predictor of mortality in HIV-TB patients (odds ratio 8 · 43, p = 0 · 013).



Thrice-weekly anti-tuberculosis therapy is more effective in HIV-negative than in HIV-positive patients. However, outcomes in this HIV co-infected cohort were found to be similar to those reported previously with daily therapy, with no safety concerns. This should prompt further study into whether intermittent or daily therapy should be used universally in resource-poor settings, using large well executed randomised controlled trials.