Lower-limb amputee recovery response to an imposed error in mediolateral foot placement

Despite walking with a wider step width, amputees remain 20% more likely to fall than non-amputees. Since mediolateral (ML) balance is critical for ambulation and contingent on ML foot placement, we used a ML disturbance to perturb walking balance and explore the influence of prosthetic foot stiffness on balance recovery. Ten transtibial amputees were fit with two commonly prescribed prosthetic feet with differing stiffness characteristics; 12 non-amputees also participated. A perturbation device that released an air burst just before heel strike imposed a repeatable medial or lateral disturbance in foot placement. After a medial disturbance, the first recovery step width was narrowed (p<0.0001) for the prosthetic limb (−103%), the sound limb (−51%) and non-amputees (−41%) and more than twice as variable. The ML inclination angle remained reduced (−109%) for the prosthetic limb, while the sound limb and non-amputees approached undisturbed levels (p<0.0004). Amputees required five steps to return to undisturbed step width after a prosthetic medial disturbance versus two steps for the sound limb and for non-amputees. After a lateral disturbance, the first recovery step was widened for the prosthetic limb (+82%), sound limb (+75%), and wider than non-amputees (+51%; p<0.0001), with all participants requiring three steps to return to undisturbed step width. Amputees also exhibited a similar upper torso response compared to the non-amputees for both disturbances. Prosthetic feet with different stiffness properties did not have a significant effect. In conclusion, amputee balance was particularly challenged by medial disturbances to the prosthetic limb implying a need for improved interventions that address these balance deficits.     

SFESA: a web server for pairwise alignment refinement by secondary structure shifts

Background

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate.

Results

We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software.

Conclusions

SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.     

A collisional model of the energetic cost of support work qualitatively explains leg sequencing in walking and galloping, pseudo-elastic leg behavior in running and the walk-to-run transition

Terrestrial legged locomotion requires repeated support forces to redirect the body's vertical velocity component from down to up. We assume that the redirection is accomplished by impulsive leg forces that cause small-angle glancing collisions of a point-mass model of the animal. We estimate the energetic costs of these collisions by assuming a metabolic cost proportional to positive muscle work involved in generating the impulses. The cost of bipedal running estimated from this collisional model becomes less than that of walking at a Froude number (v2/gl) of about 0.7. Two strategies to reduce locomotion costs associated with the motion redirection are: (1) having legs simulate purely elastic springs, as is observed in human running; and (2) sequencing the leg forces during the redirection phase; examples of this sequencing are the ba-da-dump pattern of a horse gallop and having push-off followed by heel-strike in human walking.     

Optimal foot shape for a passive dynamic biped

Passive walking dynamics describe the motion of a biped that is able to "walk" down a shallow slope without any actuation or control. Instead, the walker relies on gravitational and inertial effects to propel itself forward, exhibiting a gait quite similar to that of humans. These purely passive models depend on potential energy to overcome the energy lost when the foot impacts the ground. Previous research has demonstrated that energy loss at heel-strike can vary widely for a given speed, depending on the nature of the collision. The point of foot contact with the ground (relative to the hip) can have a significant effect: semi-circular (round) feet soften the impact, resulting in much smaller losses than point-foot walkers. Collisional losses are also lower if a single impulse is broken up into a series of smaller impulses that gradually redirect the velocity of the center of mass rather than a single abrupt impulse. Using this principle, a model was created where foot-strike occurs over two impulses, "heel-strike" and "toe-strike," representative of the initial impact of the heel and the following impact as the ball of the foot strikes the ground. Having two collisions with the flat-foot model did improve efficiency over the point-foot model. Representation of the flat-foot walker as a rimless wheel helped to explain the optimal flat-foot shape, driven by symmetry of the virtual spoke angles. The optimal long period foot shape of the simple passive walking model was not very representative of the human foot shape, although a reasonably anthropometric foot shape was predicted by the short period solution.     

Olminska and colleagues’ study, “Conversion of the helical tomotherapy plans to the step-and-shoot IMRT plans for patients with hip prosthesis during radiotherapy for prostate cancer” was interesting to read

Olmińska and colleagues’ study, Olmińska et al. (2016) was interesting to read [1]. While prasining the authors for their great work, I want to emphasize e few points.In the recent years, with the development of new device technology, Intensity Modulated Radiotherapy (IMRT) and complex treatment modalities such as stereotactic radiosurgery and helical tomotherapy were started to be implemented. Thus, due to increased local control of tumor growth and reduction of dose received by surrounding critical organs, serious complications were avoided. In this new treatment modality, while calculating appropriate dose, all the parameters such as patient anatomy and characteristics of radiation should be taken into account. Besides, during conformal radiotherapy, if hip prosthesis is located around or in the clinical target volume (CTV), type, thickness and density of biomaterial should be considered to avoid dose differences.     

两个生物序列比对的个数的渐近值

利用发生函数给出了两个生物序列比对的个数的精确公式,并运用多元函数的渐近估计法计算它的渐近值.     

蛋白质结构成对比较的新方法

介绍一种蛋白质三维结构的快速比较方法.此方法毋需初始联配,而能自动寻找和智能迭代.利用本程序对珠蛋白、丝氨酸蛋白酶、天冬氨酸蛋白酶、钙结合蛋白和溶菌酶作了系统的结构比较,取得了满意的结果.本文也讨论了衡量联配结果好坏的要素问题.     

Effects of size on vervet (Cercopithecus aethiops) gait parameters: a longitudinal approach

Changes in the values of certain locomotor parameters were analyzed over a range of speeds for five immature vervet monkeys sampled at 6 month intervals over approximately a 3 year period. Lateral and diagonal sequence walking gaits and transverse and rotary gallops were commonly used. The monkeys switched from walking to galloping at long cycle durations for their mass, although, as a group, their transition speeds were in agreement with data from other mammals. However, for individual monkeys, transition speed was not consistently dependent on body mass. Cycle and stance durations generally increased with increasing size at each speed for each animal, with the greatest increases occurring at slower speeds. Swing durations increased slightly with size. For any particular individual, speed was highly predictable from cycle (or stance) duration and body mass (or age). However, the multiple regression equations for each animal were significantly different from each other, suggesting that no single equation is satisfactory for all of the individuals within a species.     

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Background

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it can take hours and days to map millions of reads even for bacteria genomes.

Results

We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to most programs MaxSSmap identifies a local region of the genome followed by exact alignment. Instead of using hash tables or Burrows-Wheeler in the first part, MaxSSmap calculates maximum scoring subsequence score between the read and disjoint fragments of the genome in parallel on a GPU and selects the highest scoring fragment for exact alignment. We evaluate MaxSSmap’s accuracy and runtime when mapping simulated Illumina E.coli and human chromosome one reads of different lengths and 10% to 30% mismatches with gaps to the E.coli genome and human chromosome one. We also demonstrate applications on real data by mapping ancient horse DNA reads to modern genomes and unmapped paired reads from NA12878 in 1000 genomes.

Conclusions

We show that MaxSSmap attains comparable high accuracy and low error to fast Smith-Waterman programs yet has much lower runtimes. We show that MaxSSmap can map reads rejected by BWA and NextGenMap with high accuracy and low error much faster than if Smith-Waterman were used. On short read lengths of 36 and 51 both MaxSSmap and Smith-Waterman have lower accuracy compared to at higher lengths. On real data MaxSSmap produces many alignments with high score and mapping quality that are not given by NextGenMap and BWA. The MaxSSmap source code in CUDA and OpenCL is freely available from http://www.cs.njit.edu/usman/MaxSSmap.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-969) contains supplementary material, which is available to authorized users.     

降钙素对去势兔的人工假体四周骨组织形态计量学的影响

目的探讨降钙素对去势兔的假体四周骨组织形态计量学的影响.方法将30只全髋置换(THA)模型的骨质疏松症雌兔随机分成实验组和对照组,实验组给予降钙素治疗,持续半年;所有动物术后24周处死,分别行假体四周骨组织形态计量学分析.结果假体四周骨组织形态计量学显示,实验组骨吸收指标Oc.No/Tb.Pm、ES/BS较对照组有显著下降(P<0.01);假体四周骨量参数BV/TV及Tb.Th,实验组明显较对照组增多(P<0.01);成骨参数OV/BV、成骨细胞数量参数OB%及OB/1cm均较对照组有明显升高(P<0.05);骨形成速率参数BFR(T)及%L.Pm较对照组有明显升高(P<0.05).两组间,矿化沉积率MAR及矿化延迟时间MLT均无显著性差异(P﹥0.05).结论鲑鱼降钙素能抑制假体四周骨质的骨吸收,减少骨丢失,降低骨转化率;促进假体四周骨形成,增加骨量;改善假体四周骨微结构,提高骨质量.有利于提高假体四周骨质的生物力学性能,防止假体松动.     

Analysis of a femoral hip prosthesis designed to reduce stress shielding

The natural stress distribution in the femur is significantly altered after total hip arthroplasty (THA). When an implant is introduced, it will carry a portion of the load, causing a reduction of stress in some regions of the remaining bone. This phenomenon is commonly known as stress shielding. In response to the changed mechanical environment the shielded bone will remodel according to Wolff's law, resulting in a loss of bone mass through the biological process called resorption. Resorption can, in turn, cause or contribute to loosening of the prosthesis. The problem is particularly common among younger THA recipients. This study explores the hypothesis that through redesign, a total hip prosthesis can be developed to substantially reduce stress shielding. First, we describe the development of a new femoral hip prosthesis designed to alleviate this problem through a new geometry and system of proximal fixation. A numerical comparison with a conventional intramedullary prosthesis as well as another proximally fixed prosthesis, recently developed by Munting and Verhelpen (1995. Journal of Biomechanics 28(8), 949–961) is presented. The results show that the new design produces a more physiological stress state in the proximal femur.     

Concurrent validity of the Microsoft Kinect for assessment of spatiotemporal gait variables

Spatiotemporal characteristics of gait such as step time and length are often associated with overall physical function in clinical populations, but can be difficult, time consuming and obtrusive to measure. This study assessed the concurrent validity of overground walking spatiotemporal data recorded using a criterion reference – a marker-based three-dimensional motion analysis (3DMA) system – and a low-cost, markerless alternative, the automated skeleton tracking output from the Microsoft Kinect™ (Kinect). Twenty-one healthy adults performed normal walking trials while being monitored using both systems. The outcome measures of gait speed, step length and time, stride length and time and peak foot swing velocity were derived using supervised automated analysis. To assess the agreement between the Kinect and 3DMA devices, Bland–Altman 95% bias and limits of agreement, percentage error, relative agreement (Pearson's correlation coefficients: r) overall agreement (concordance correlation coefficients: r_c) and landmark location linearity as a function of distance from the sensor were determined. Gait speed, step length and stride length from the two devices possessed excellent agreement (r and r_c values >0.90). Foot swing velocity possessed excellent relative (r=0.93) but only modest overall (r_c=0.54) agreement. Step time (r=0.82 and r_c=0.23) and stride time (r=0.69 and r_c=0.14) possessed excellent and modest relative agreement respectively but poor overall agreement. Landmark location linearity was excellent (R²=0.991). This widely available, low-cost and portable system could provide clinicians with significant advantages for assessing some spatiotemporal gait parameters. However, caution must be taken when choosing outcome variables as some commonly reported variables cannot be accurately measured.