Sharing and Preserving Computational Analyses for Posterity with encapsulator

Open data and open-source software may be part of the solution to science's "reproducibility crisis", but they are insufficient to guarantee reproducibility. Requiring minimal end-user expertise, encapsulator creates a "time capsule" with reproducible code in a self-contained computational environment. encapsulator provides end-users with a fully-featured desktop environment for reproducible research.Comment: 11 pages, 6 figure

Assessment of Altmetrics and PlumX Metrics Scoring as Mechanisms to Evaluate the Top 100 Trending Hidradenitis Suppurativa Articles on Social Media: Cross-Sectional Study

Background: Dermatologists are increasingly utilizing social media platforms to disseminate scientific information. New tools, such as altmetrics and PlumX metrics, have been made available to rapidly capture the level of scientific article dissemination across social media platforms. However, no studies have been performed to assess the level of scientific article dissemination across social media regarding hidradenitis suppurativa, a disease that is still currently not well understood. Objective: The aim of our study was to evaluate the utility of altmetrics and PlumX metrics by characterizing the top 100 “trending” hidradenitis suppurativa articles in the altmetric database by the altmetric attention score and PlumX score. Methods: Altmetric data components of the top 100 hidradenitis suppurativa articles were extracted from the altmetric database. Article citation count was found using Web of Science. PlumX field-weighted impact scores for each article were collected from the Scopus database. Journal title, open-access status, article type, and study design of original articles were assessed. Additionally, the altmetric attention score, PlumX score, and citation count were log transformed and adjusted by +1 for linear regression, and Spearman correlation coefficients were utilized to determine correlations. Results: Most of the top 100 “trending” hidradenitis suppurativa articles were published in JAMA Dermatology (n=27, 27%). The median altmetric attention score, PlumX score, and citation count were 25.5, 3.7, and 10.5, respectively. The most mentions regarding social media platforms came from Twitter. Although no correlation was observed between the citation count and altmetric attention score (r 2 =0.019, P=.17), positive correlation was observed between the citation count and PlumX score (r 2 =0.469, P\u3c.001). Conclusions: Our research demonstrated that citation count is not correlated with the altmetric attention score, but is strongly correlated with the PlumX score regarding hidradenitis suppurativa articles at this point in time. With the continual increase of social media usage by medical professionals and researchers, this study can help investigators understand the best way to captivate their audience

KINEMATICS AND PHYSIOLOGICAL EFFECT OF A SYNCHRONIZED BIPEDAL “RISE-SIT-GO” CYCLING EXERCISE

This study demonstrated the kinematics and physiological effect of a synchronized bipedal cycling exercise. Fifteen male subjects performed a 30-minutes exercise on a synchronized bipedal stationary bike and a conventional stationary bike at same cycling speed. The performance was evaluated by a metabolic testing system, a subjective rating of perceived exertion, an electromyography system and a motion analysis system, and was compared by paired t-tests. Results showed significant increases in oxygen uptake, energy expenditure, rating of perceived exertion, muscle activity in triceps, biceps, rectus abdominis, left gluteus maximus, left medial gastrocnemius, right tibialis anterior and left tibialis anterior, and range of motion of left hip, left and right knees, shoulders, elbows and wrists. The synchronized bipedal cycling exercise was more physically demanding

A pilot study showing that repeated exposure to stress produces alterations in subsequent responses to anesthetics in rats

The repeated use of a drug frequently leads to alterations in the response to that drug. We undertook this study to determine whether multiple exposures to the general anesthetic produced alterations in subsequent exposures to this anesthetic. For this study, adult male rats were anesthetized with 2.5% isoflurane for one hour. The rats were divided into 4 groups of 8 rats each. Groups 1–3 were transported between their homeroom and the anesthesia testing room and were handled in an identical manner weekly for a period of 12 weeks, but were anesthetized on different schedules. Group 1 was anesthetized weekly for 12 weeks, Group 2 on either a 3 or 4 week schedule and Group 3 was anesthetized a single time, at the end of the 12 week period. To receive anesthesia multiple times, animals were transported from their homeroom to the anesthesia location and handled repeatedly. We took into consideration of the frequency of anesthesia exposure and the stress involved. Rats in groups 2 and 3 were placed in the anesthesia chamber, with O2 but with no anesthetic, every week when they were not scheduled to receive anesthesia. In Group 4, rats were not transported or handled in any way and stayed in the home room for a period of 12 weeks. Rats in this group were anesthetized once, at the very end of the study. Recovery of the rat’s righting reflex was used to assess the acceleration of recovery time from general anesthesia. Group 1 rats showed dramatically faster emergence from anesthesia after several rounds of anesthesia. Surprisingly, Groups 2 and 3 rats, treated in an identical manner as Group 1, but which were anesthetized on different schedules, also exhibited more rapid emergence from anesthesia, when compared to Group 4 rats, which were never handled or transported prior to a single anesthesia. These results suggest that the stress of transportation and handling altered responsiveness to anesthesia. Our results show that responsiveness to anesthetic agents can change over time outside of the normal developmental changes taking place in rats as they age

Common Metrics for Human-Robot Interaction

This paper describes an effort to identify common metrics for task-oriented human-robot interaction (HRI). We begin by discussing the need for a toolkit of HRI metrics. We then describe the framework of our work and identify important biasing factors that must be taken into consideration. Finally, we present suggested common metrics for standardization and a case study. Preparation of a larger, more detailed toolkit is in progress

Gait analysis for designing a new assistive knee brace

Assistive knee brace is a species of wearable lower extremity exoskeletons. In this research, an assistive knee brace was developed by integrating a multifunctional actuator with a custom-made knee-ankle-foot orthosis. In the study, the location of the actuator is moved up to the lateral side of the hip, instead of knee joint. Waist belt and shoulder belt are appended on the knee brace. This paper aimed to improve the design of the assistive knee braces through gait analysis. By walking with the knee braces, the spatial and temporal gait parameters, joint kinematics and joint kinetics parameters were evaluated, and the changes from normal walking were compared as well. The experimental results showed that walking with the developed knee brace provided minimal hindrance to the wearer. © 2011 IEEE

Experimental studies on kinematics and kinetics of walking with an assistive knee brace

Assistive knee brace is a species of wearable lower extremity exoskeletons. Such assistive equipment can enhance people's strength and provide desired locomotion to have advantages over wheelchairs, which are commonly used for patients with mobility disorders. However, the integration between the assistive knee brace and the user is challenging as inaccurate alignments may adversely affect the biomechanics of the knee joint. The goal of this study is to evaluate the changes between normal walking and walking with an assistive knee brace in "off" mode. The assistive knee brace was developed by integrating a multifunctional actuator with a custom-made knee-ankle-foot orthosis in order to minimize excessive shifting and to improve alignment to the knee joint. Spatial and temporal gait parameters, joint kinematics and joint kinetics parameters were compared. In general, the observed results showed that most of the gait parameters were not affected when walking with the knee brace. The only significant differences were found in knee flexion and knee rotational motions. These results indicated that walking with the developed knee brace provided minimal hindrance to the user and assured that assistive torque can be applied to the knee joint

sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline.

Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline-sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/

Evaluation of combined prescription of rocker sole shoes and custom-made foot orthoses for the treatment of plantar fasciitis

Background: It is a routine practice to prescribe a combination of rocker shoes and custom-made foot orthoses for patients with plantar fasciitis. Recently, there has been a debate on this practice, and studies have shown that the individual prescription of rocker shoes or custom-made foot orthoses is effective in treating plantar fasciitis. The aim of this study was to evaluate and compare the immediate therapeutic effects of individually prescribed rocker sole shoes and custom-made foot orthoses, and a combined prescription of them on plantar fasciitis. Methods: This was a cross-over study. Fifteen patients with unilateral plantar fasciitis were recruited; they were from both genders and aged between 40 and 65. Subjects performed walking trials which consisted of one 'unshod' condition and four 'shod' conditions while wearing baseline shoes, rocker shoes, baseline shoes with foot orthotics, and rocker shoes with foot orthotics. The study outcome measures were the immediate heel pain intensity levels as reflected by visual analog scale pain ratings and the corresponding dynamic plantar pressure redistribution patterns as evaluated by a pressure insole system. Results: The results showed that a combination of rocker shoes and foot orthoses produced a significantly lower visual analog scale pain score (9.7 mm) than rocker shoes (30.9 mm) and foot orthoses (29.5 mm). With regard to baseline shoes, it also significantly reduced the greatest amount of medial heel peak pressure (- 33.58%) without overloading other plantar regions when compared to rocker shoes (- 7.99%) and foot orthoses (- 28.82%). Discussion: The findings indicate that a combined prescription of rocker sole shoes and custom-made foot orthoses had greater immediate therapeutic effects compared to when each treatment had been individually prescribed

Picosecond electric-field-induced threshold switching in phase-change materials

Many chalcogenide glasses undergo a breakdown in electronic resistance above a critical field strength. Known as threshold switching, this mechanism enables field-induced crystallization in emerging phase-change memory. Purely electronic as well as crystal nucleation assisted models have been employed to explain the electronic breakdown. Here, picosecond electric pulses are used to excite amorphous Ag$_4$In$_3$Sb$_{67}$Te$_{26}$. Field-dependent reversible changes in conductivity and pulse-driven crystallization are observed. The present results show that threshold switching can take place within the electric pulse on sub-picosecond time-scales - faster than crystals can nucleate. This supports purely electronic models of threshold switching and reveals potential applications as an ultrafast electronic switch.Comment: 6 pages manuscript with 3 figures and 8 pages supplementary materia