Miracle-dz/UniFAR-FTUs huggingface dataset:
A random forest approach for competing risks based on pseudo‐values

Random forest is a supervised learning method that combines many classification or regression trees for prediction. Here we describe an extension of the random forest method for building event risk prediction models in survival analysis with competing risks. In case of right‐censored data, the event status at the prediction horizon is unknown for some subjects. We propose to replace the censored event status by a jackknife pseudo‐value, and then to apply an implementation of random forests for uncensored data. Because the pseudo‐responses take on values on a continuous scale, the node variance is chosen as split criterion for growing regression trees. In a simulation study, the pseudo split criterion is compared with the Gini split criterion when the latter is applied to the uncensored event status. To investigate the resulting pseudo random forest method for building risk prediction models, we analyze it in a simulation study of predictive performance where we compare it to Cox regression and random survival forest. The method is further illustrated in two real data sets. Copyright © 2013 John Wiley & Sons, Ltd.
Upper limb training using Wii Sports Resort™ for children with hemiplegic cerebral palsy: a randomized, single-blind trial

Objective: To investigate whether Wii Sports Resort™ training is effective and if any benefits are maintained. Design: Randomized, single-blind trial. Participants: Sixty-two hemiplegic children with cerebral palsy (6–13 years). Intervention: Experimental group undertook six weeks of home-based Wii Sports Resort™ training plus usual therapy, while the control group received usual therapy. Main measures: Outcomes were coordination, strength, hand function, and carers’ perception of hand function, measured at baseline, six, and 12 weeks by a blinded assessor. Results: There was a trend of mean difference (MD) for the experimental group to have more grip strength by six (MD 4.0 N, 95% confidence interval (CI) −0.8 to 8.8, p = 0.10) and 12 (MD 4.1 N, 95% CI −2.1 to 10.3, p = 0.19) weeks, and to have a higher quantity of hand function according to carers’ perception by six (MD 4.5 N, 95% CI −0.7 to 9.7, p = 0.09) and strengthened by 12 (MD 6.4, 95% CI 0.6 to 12.3, p = 0.03) weeks than the control group. There was no difference between groups in coordination and hand function by six or 12 weeks. Conclusion: Wii™ training did not improve coordination, strength, or hand function. Beyond the intervention, carers perceived that the children used their hands more.
Fast distributed optimization over directed graphs

We develop a fast distributed algorithm, termed DEXTRA, to solve optimization problems when N agents reach agreement and collaboratively minimize the sum of their local objectives over the network, where the communications between agents are described by a directed graph. Existing algorithms, including Gradient-Push (GP) and Directed-Distributed Gradient Descent (D-DGD), solve this problem restricted to directed graphs with a convergence rate of O(ln k/√k). Our analysis shows that DEXTRA converges at a linear rate O(εk) for some constant ε <; 1, with the assumption that the objective functions are strongly convex. Simulation examples illustrate our findings.
A general framework for robust and efficient association analysis in family‐based designs: quantitative and dichotomous phenotypes

Although transmission disequilibrium tests (TDT) and the FBAT statistic are robust against population substructure, they have reduced statistical power, as compared with fully efficient tests that are not guarded against confounding because of population substructure. This has often limited the application of transmission disequilibrium tests/FBATs to candidate gene analysis, because, in a genome‐wide association study, population substructure can be adjusted by approaches such as genomic control and EIGENSTRAT. Here, we provide new statistical methods for the analysis of quantitative and dichotomous phenotypes in extended families. Although the approach utilizes the polygenic model to maximize the efficiency, it still preserves the robustness to non‐normality and misspecified covariance structures. In addition, the proposed method performs better than the existing methods for dichotomous phenotype, and the new transmission disequilibrium test for candidate gene analysis is more efficient than FBAT statistics. Copyright © 2013 John Wiley & Sons, Ltd.
Physiological and Biomechanical Responses to Prolonged Heavy Load Carriage During Level Treadmill Walking in Females.

Heavy load carriage has been identified as a main contributing factor to the high incidence of overuse injuries in soldiers. Peak vertical ground reaction force (VGRFMAX) and maximal vertical loading rates (VLRMAX) may increase during heavy prolonged load carriage with the development of muscular fatigue and reduced shock attenuation capabilities. The objectives of the current study were (1) to examine physiological and biomechanical changes that occur during a prolonged heavy load carriage task, and (2) to examine if this task induces neuromuscular fatigue and changes in muscle architecture. Eight inexperienced female participants walked on an instrumented treadmill carrying operational loads for 60 minutes at 5.4 km·h-1. Oxygen consumption ( V ˙ O 2 ), heart rate, rating of perceived exertion (RPE), trunk lean angle, and ground reaction forces were recorded continuously during task. Maximal force and in-vivo muscle architecture were assessed pre- and posttask. Significant increases were observed for VGRFMAX, VLRMAX, trunk lean angle, [Formula: see text], heart rate, and RPE during the task. Increased vastus lateralis fascicle length and decreased maximal force production were also observed posttask. Prolonged heavy load carriage, in an inexperienced population carrying operational loads, results in progressive increases in ground reaction force parameters that have been associated with overuse injury.
Data generation for the Cox proportional hazards model with time‐dependent covariates: a method for medical researchers

The proliferation of longitudinal studies has increased the importance of statistical methods for time‐to‐event data that can incorporate time‐dependent covariates. The Cox proportional hazards model is one such method that is widely used. As more extensions of the Cox model with time‐dependent covariates are developed, simulations studies will grow in importance as well. An essential starting point for simulation studies of time‐to‐event models is the ability to produce simulated survival times from a known data generating process. This paper develops a method for the generation of survival times that follow a Cox proportional hazards model with time‐dependent covariates. The method presented relies on a simple transformation of random variables generated according to a truncated piecewise exponential distribution and allows practitioners great flexibility and control over both the number of time‐dependent covariates and the number of time periods in the duration of follow‐up measurement. Within this framework, an additional argument is suggested that allows researchers to generate time‐to‐event data in which covariates change at integer‐valued steps of the time scale. The purpose of this approach is to produce data for simulation experiments that mimic the types of data structures applied that researchers encounter when using longitudinal biomedical data. Validity is assessed in a set of simulation experiments, and results indicate that the proposed procedure performs well in producing data that conform to the assumptions of the Cox proportional hazards model. Copyright © 2013 John Wiley & Sons, Ltd.
Some issues in predicting patient recruitment in multi‐centre clinical trials

A key paper in modelling patient recruitment in multi‐centre clinical trials is that of Anisimov and Fedorov. They assume that the distribution of the number of patients in a given centre in a completed trial follows a Poisson distribution. In a second stage, the unknown parameter is assumed to come from a Gamma distribution. As is well known, the overall Gamma‐Poisson mixture is a negative binomial. For forecasting time to completion, however, it is not the frequency domain that is important, but the time domain and that of Anisimov and Fedorov have also illustrated clearly the links between the two and the way in which a negative binomial in one corresponds to a type VI Pearson distribution in the other. They have also shown how one may use this to forecast time to completion in a trial in progress. However, it is not just necessary to forecast time to completion for trials in progress but also for trials that have yet to start. This suggests that what would be useful would be to add a higher level of the hierarchy: over all trials. We present one possible approach to doing this using an orthogonal parameterization of the Gamma distribution with parameters on the real line. The two parameters are modelled separately. This is illustrated using data from 18 trials. We make suggestions as to how this method could be applied in practice. Copyright © 2013 John Wiley & Sons, Ltd.
Effects of repetitive transcranial magnetic stimulation on arm function and decreasing unilateral spatial neglect in subacute stroke: a randomized controlled trial

Objective: The objective of this study is to investigate the effect of repetitive transcranial magnetic stimulation (rTMS) on the functional recovery of stroke patients with unilateral neglect. Design: Randomized controlled experimental study. Setting: Outpatient rehabilitation hospital. Subjects: Thirty patients with stroke were randomly assigned to two groups: an rTMS group (experimental) and a control group. Interventions: Stroke patients in the experimental group underwent comprehensive rehabilitation therapy and rTMS. Stroke patients in the control group underwent sham therapy and comprehensive rehabilitation therapy. Participants in both groups received therapy 5 days per week for 4 weeks. Main measures: Line bisection, Albert, Box and block and Grip strength tests were assessed before and after the four-week therapy period. Results: A significant difference in the post-training gains in Line bisection (16.53 SD 9.78 vs. 3.60 SD 5.02), Albert (14.13 SD 4.92 vs. 3.26 SD 2.01), Box and block (15.06 SD 9.68 vs. 6.93 SD 7.52), and Grip strength tests (3.60 SD 2.66 vs 0.80 SD 1.26) was observed between the experimental group and the control group (P<0.05). In addition, the effect size for gains in the experimental and control groups was very strong in AT, BBT (effect size=2.15, 0.77 respectively). Conclusion: We conclude that rTMS might be effective in improvement in reduction of the unilateral neglect and motor function.
Very early social support following mild stroke is associated with emotional and behavioral outcomes three months later

Objective: To investigate whether social contact and support received during hospitalization for acute ischemic stroke predict depression and daily life functioning three months later. Design: Prospective observational study using Ecological Momentary Assessments to evaluate the number of social contacts as well as social support received from family, friends and medical staff within 24 hours following admission for stroke. Patients also monitored depression symptoms and behavior in real-time and in daily life contexts three months later. Setting: A university hospital acute stroke unit. Subjects: Thirty-four mild ischemic stroke patients. Interventions: None. Main measures: One-day Ecological Momentary Assessments immediately following stroke collected information concerning perceived social support, number of social contacts and depression symptoms. Ecological Momentary Assessments was repeated three months later and addressed depression levels as well as activities of daily living, such as working, cooking, shopping and housework. Results: The number of social interactions received at hospitalization did not predict three-month outcomes. However, a better quality of moral support from friends and family immediately after stroke was associated with decreases in later depression levels (p = 0.041) and increases in activities of daily living (p = 0.011). Material support from friends and family was associated with increases in activities of daily living (p = 0.012). No effect was observed for support received from medical staff. Conclusions: Patient perceptions of better support quality, and not quantity, immediately following mild stroke, are associated with better behavioral and emotional outcomes three months later.
The effectiveness of pre-operative exercise physiotherapy rehabilitation on the outcomes of treatment following anterior cruciate ligament injury: a systematic review

Objective: To evaluate the effectiveness of pre-operative exercise physiotherapy rehabilitation on the outcomes of treatment following anterior cruciate ligament injury. Methods: The following databases were searched: PubMed, Ovid, The Cochrane Library and Web of Science. Studies published between the inception of the databases and December 2015 were sought using appropriate keywords in various combinations. This search was supplemented with a manual search of the references of selected studies. Studies were assessed for methodological quality using the Physiotherapy Evidence Database scale. Results: A total of 500 studies were identified, of which eight studies met the inclusion criteria and were included in the present review. The average Physiotherapy Evidence Database score for the studies included was 5.8, which reflects an overall moderate methodological quality. The eight studies investigated a total of 451 subjects of which 71% (n=319) were males. The age of the participants in the eight studies ranged from 15 to 57 years. The duration of the intervention in the studies ranged from 3 to 24 weeks. This review found that pre-operative physiotherapy rehabilitation is effective for improving the outcomes of treatment following anterior cruciate ligament injury, including increasing knee-related function and improving muscle strength. However, whilst there was a significant improvement in quality of life from baseline following intervention, no significant difference in quality of life was found between the control and intervention groups. Conclusions: There is evidence to suggest that pre-operative physiotherapy rehabilitation is beneficial to patients with anterior cruciate ligament injury.
Determining quality of public health care services in rural India

Purpose – This paper aims to measure the perception of patients towards quality of services in public health care centres in rural India.Design/methodology/approach – A 23‐item scale that tested well for reliability and construct validity was employed for the study. Mixed sampling technique was employed to select the sample. A total of 500 respondents from Eastern, Western and Central regions of Uttar Pradesh were surveyed.Findings – The survey instrument had an overall Cronbach's alpha value of 0.96 and was able to discern differences across various socio‐demographic characteristics of the respondents. The opinions of the respondents towards health care quality were not very favourable. Negative scores were obtained on items, “availability of adequate medical equipments” and “availability of doctors for women”. Education, gender and income were found to be significantly associated with user perception.Research limitations/implications – The current study was limited to measuring the perceived quality of .
The effectiveness of exercise therapy for temporomandibular dysfunction: a systematic review and meta-analysis

Objective: To investigate the effectiveness of exercise therapy on pain, function, and mobility outcomes in patients with temporomandibular joint dysfunction. Study design: Systematic review with meta-analysis. Methods: A systematic review and meta-analysis undertaken following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Studies that met the inclusion criteria: (1) randomized controlled trials; (2) a population with the diagnosis of temporomandibular joint dysfunction; and (3) interventions that included exercise therapy were considered for review. When studies demonstrated homogeneity on outcome measures, the mean differences or standardized mean differences with 95% confidence interval were calculated and pooled in a meta-analysis for pooled synthesis. Results: Six articles with a total of 419 participants were included in the review and only four studies were included in the meta-analysis. Mobility and mixed exercise therapy approaches appear to be the most common exercise approaches utilized for management of temporomandibular joint dysfunction. Exercise therapy and the associated dosage provide moderate short-term and varying long-term benefits in reduction of pain and improvement of range of motion of the in patients with temporomandibular joint dysfunction. Conclusion: Included studies suggest a mobility or a mixed approach to exercise therapies have impact on reducing pain, significant impact for increasing range of motion, but lack a significant impact for functional improvement. Level of evidence: Therapy, level 1a-.
A systematic review of peer mentoring interventions for people with traumatic brain injury

Objective: This systematic review sought evidence concerning the effectiveness of peer mentoring for people with traumatic brain injury. Data sources: Fourteen electronic databases were searched, including PsycINFO, MEDLINE, CINAHL, EMBASE and the Cochrane Library, from inception to September 21 2016. Ten grey literature databases, PROSPERO, two trials registers, reference lists and author citations were also searched. Review methods: Studies which employed a model of one-to-one peer mentoring between traumatic brain injury survivors were included. Two reviewers independently screened all titles and abstracts before screening full texts of shortlisted studies. A third reviewer resolved disagreements. Two reviewers independently extracted data and assessed studies for quality and risk of bias. Results: The search returned 753 records, including one identified through hand searching. 495 records remained after removal of duplicates and 459 were excluded after screening. Full texts were assessed for the remaining 36 studies and six met the inclusion criteria. All were conducted in the United States between 1996 and 2012 and employed a variety of designs including two randomised controlled trials. A total of 288 people with traumatic brain injury participated in the studies. No significant improvements in social activity level or social network size were found, but significant improvements were shown in areas including behavioural control, mood, coping and quality of life. Conclusion: There is limited evidence for the effectiveness of peer mentoring after traumatic brain injury. The available evidence comes from small-scale studies, of variable quality, without detailed information on the content of sessions or the ‘active ingredient’ of the interventions.
The Peto odds ratio viewed as a new effect measure

Meta‐analysis has generally been accepted as a fundamental tool for combining effect estimates from several studies. For binary studies with rare events, the Peto odds ratio (POR) method has become the relative effect estimator of choice. However, the POR leads to biased estimates for the OR when treatment effects are large or the group size ratio is not balanced. The aim of this work is to derive the limit of the POR estimator for increasing sample size, to investigate whether the POR limit is equal to the true OR and, if this is not the case, in which situations the POR limit is sufficiently close to the OR. It was found that the derived limit of the expected POR is not equivalent to the OR, because it depends on the group size ratio. Thus, the POR represents a different effect measure. We investigated in which situations the POR is reasonably close to the OR and found that this depends only slightly on the baseline risk within the range (0.001; 0.1) yet substantially on the group size ratio and the effect size itself. We derived the maximum effect size of the POR for different group size ratios and tolerated amounts of bias, for which the POR method results in an acceptable estimator of the OR. We conclude that the limit of the expected POR can be regarded as a new effect measure, which can be used in the presented situations as a valid estimate of the true OR. Copyright © 2014 John Wiley & Sons, Ltd.
Fifteen Years of Quantum LDPC Coding and Improved Decoding Strategies

The near-capacity performance of classical low-density parity check (LDPC) codes and their efficient iterative decoding makes quantum LDPC (QLPDC) codes a promising candidate for quantum error correction. In this paper, we present a comprehensive survey of QLDPC codes from the perspective of code design as well as in terms of their decoding algorithms. We also conceive a modified non-binary decoding algorithm for homogeneous Calderbank-Shor-Steane-type QLDPC codes, which is capable of alleviating the problems imposed by the unavoidable length-four cycles. Our modified decoder outperforms the state-of-the-art decoders in terms of their word error rate performance, despite imposing a reduced decoding complexity. Finally, we intricately amalgamate our modified decoder with the classic uniformly reweighted belief propagation for the sake of achieving an improved performance.
Stochastic Geometric Models for Green Networking

In this paper, we use a stochastic geometric approach in order to study the impact on energy consumption when base stations are switched OFF independently of each other. We present here both the uplink and downlink analysis based on the assumption that the base stations are distributed according to an independent stationary Poisson point process. This type of modeling allows us to make use of the property that the spatial distribution of the base stations after thinning (switching OFF) is still a Poisson process. This implies that the probability distribution of the signal to interference and noise ratio (SINR) can be kept unchanged when switching-OFF base stations provided that we scale up the transmission power of the remaining base stations. We then solve the problem of optimally selecting the switch-OFF probabilities so as to minimize the energy consumptions, while keeping unchanged the SINR probability distribution. We then study the tradeoff in the uplink performance involved in switching-OFF base stations. These include the energy consumption, the coverage and capacity, and the impact on amount of radiation absorbed by the transmitting user.