Web-based home rehabilitation gaming system for balance training

Currently, most systems for virtual rehabilitation and motor training require quite complex and expensive hardware and can be used only in clinical settings. Now, a low-cost rehabilitation game training system has been developed for patients with movement disorders; it is suitable for home use under the distant supervision of a therapist. It consists of a patient-side application installed on a home computer and the virtual rehabilitation Game Server in the Internet. System can work with different input gaming devices connected through USB or Bluetooth, such as a Nintendo Wii balance board, a Nintendo Wii remote, a MS Kinect sensor, and custom made rehabilitation gaming devices based on a joystick. The same games can be used with all training devices. Assessment of the Home Rehabilitation Gaming System for balance training was performed on six patients with Cerebral Palsy, who went through daily training sessions for two weeks. Preliminary results showed balance improvement in patients with Cerebral Palsy after they had completed home training courses. Further studies are needed to establish medical requirements and evidence length.Peer Reviewe

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth

<p>Abstract</p> <p>Background</p> <p>Bifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding studies with exogenous bifidobacteria show they don't remain in the intestine, suggesting they may lose competitive fitness when grown outside the gut.</p> <p>Results</p> <p>To further the understanding of genetic attenuation that may be occurring in bifidobacteria cultures, we obtained the complete genome sequence of an intestinal isolate, <it>Bifidobacterium longum </it>DJO10A that was minimally cultured in the laboratory, and compared it to that of a culture collection strain, <it>B. longum </it>NCC2705. This comparison revealed colinear genomes that exhibited high sequence identity, except for the presence of 17 unique DNA regions in strain DJO10A and six in strain NCC2705. While the majority of these unique regions encoded proteins of diverse function, eight from the DJO10A genome and one from NCC2705, encoded gene clusters predicted to be involved in diverse traits pertinent to the human intestinal environment, specifically oligosaccharide and polyol utilization, arsenic resistance and lantibiotic production. Seven of these unique regions were suggested by a base deviation index analysis to have been precisely deleted from strain NCC2705 and this is substantiated by a DNA remnant from within one of the regions still remaining in the genome of NCC2705 at the same locus. This targeted loss of genomic regions was experimentally validated when growth of the intestinal <it>B. longum </it>in the laboratory for 1,000 generations resulted in two large deletions, one in a lantibiotic encoding region, analogous to a predicted deletion event for NCC2705. A simulated fecal growth study showed a significant reduced competitive ability of this deletion strain against <it>Clostridium difficile </it>and <it>E. coli</it>. The deleted region was between two IS<it>30 </it>elements which were experimentally demonstrated to be hyperactive within the genome. The other deleted region bordered a novel class of mobile elements, termed mobile integrase cassettes (MIC) substantiating the likely role of these elements in genome deletion events.</p> <p>Conclusion</p> <p>Deletion of genomic regions, often facilitated by mobile elements, allows bifidobacteria to adapt to fermentation environments in a very rapid manner (2 genome deletions per 1,000 generations) and the concomitant loss of possible competitive abilities in the gut.</p

Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays

Microarray experiments typically involve washing steps that remove hybridized nonspecific targets with the purpose of improving the signal-to-noise ratio. The quality of washing ultimately affects downstream analysis of the microarray and interpretation. The paucity of fundamental studies directed towards understanding the dissociation of mixed targets from microarrays makes the development of meaningful washing/dissociation protocols difficult. To fill the void, we examined activation energies and preexponential coefficients of 47 perfect match (PM) and double-mismatch (MM) duplex pairs to discover that there was no statistical difference between the kinetics of the PM and MM duplexes. Based on these findings, we evaluated the nonequilibrium thermal dissociation (NTD) approach, which has been used to identify specific microbial targets in mixed target samples. We found that the major premises for various washing protocols and the NTD approach might be seriously compromised because: (i) nonspecific duplexes do not always dissociate before specific ones, and (ii) the relationship between dissociation rates of the PM and MM duplexes depends on temperature and duplex sequence. Specifically for the NTD, we show that previously suggested use of reference curves, indices of curves and temperature ramps lead to erroneous conclusions

DNA supercoiling suppresses real-time PCR: a new approach to the quantification of mitochondrial DNA damage and repair

As a gold standard for quantification of starting amounts of nucleic acids, real-time PCR is increasingly used in quantitative analysis of mtDNA copy number in medical research. Using supercoiled plasmid DNA and mtDNA modified both in vitro and in cancer cells, we demonstrated that conformational changes in supercoiled DNA have profound influence on real-time PCR quantification. We showed that real-time PCR signal is a positive function of the relaxed forms (open circular and/or linear) rather than the supercoiled form of DNA, and that the conformation transitions mediated by DNA strand breaks are the main basis for sensitive detection of the relaxed DNA. This new finding was then used for sensitive detection of structure-mediated mtDNA damage and repair in stressed cancer cells, and for accurate quantification of total mtDNA copy number when all supercoiled DNA is converted into the relaxed forms using a prior heat-denaturation step. The new approach revealed a dynamic mtDNA response to oxidative stress in prostate cancer cells, which involves not only early structural damage and repair but also sustained copy number reduction induced by hydrogen peroxide. Finally, the supercoiling effect should raise caution in any DNA quantification using real-time PCR

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves.

To investigate the effects of heating rate on the DNA melting profile and to test the predictions of the theory of slow relaxation processes in DNA melting (1) concerning these effects, we obtained differential melting curves for the Bsp I C1 fragment of T7 DNA (1461 bp) and the Sma I-Eco RI fragment of Col E1 DNA (1291 bp) at heating rates of 0.05 and 0.5 deg/min. At low ionic strength (0.02 M Na+) the heating rate has been shown to affect the position of the third peak in melting curve for C1 fragment. According to the melting maps (2), this peak corresponds to the unwinding of the section between the end of the molecule and the region already melted. At high ionic strength (0.2 M Na+), when the melting of this DNA is reversible (3), the position of the peaks does not depend on the heating rate. In the case of the Col E1 DNA fragment the heating rate affects, as might be expected from the melting maps (4), only the last peak, as the melting of the last section is always nonequilibrium. The results of the study are in good qualitative agreement and in satisfactory quantitative agreement with the theoretical predictions (1)

Динаміка інтелектуальної продуктивності у дітей з аутизмом у системі інтенсивної нейрофізіологічної реабілітації

Objective: to evaluate the efficiency of INRS system for rehabilitation of children with autism based on the study of the dynamics of their intellectual performance.Patients and methods: The inclusion criteria in the sample at initial randomization were: the child's age from 5 to 9 years, accordance to diagnostic criteria for the diagnosis of «child autism» in ICD010, the presence of signs of autism using Childhood Autism Rating Scale (CARS) or Autism Spectrum Screening Questionnaire (ASSQ), a rehabilitation course at INRS. We examined 79 children diagnosed with child autism (F84.0). To assess the effectiveness of rehabilitation coloured Raven matrices were used.Results: The intellectual dynamics of indicators in different clinical groups of children with autism was unidirectional. The most pronounced positive changes in the level of intellectual development occurred in patients with low performance (after the rehabilitation course in the area of intellectual defect remained 30.5±5.5% of children compared to 39±6% before treatment, in the area of the limited intellectual abilities were 25.5±5.0% compared to 35,5±6,0% before treatment).Conclusions: the outcome analysis of the level of intellectual development of children using raven Matrices after the end of rehabilitation by INRS has detected the presence of the expressed positive changes in the level of their intellectual development. The treatment by INRS in patients with autism showed an increase in the level of cognitive performance.Key words: infantile autism, Kozyavkin method, INRS, treatment of autism, coloured Raven matrices.Цель: оценить эффективность реабилитации детей с аутизмом по системе интенсивной нейрофизиологической реабилитации (СИНР) на основании изучения динамики их интеллектуальных показателей.Пациенты и методы. Критериями включения в выборку при первичной рандомизации были: возраст ребенка от 5 до 9 лет, соответствие диагностическим критериям диагноза «Детский аутизм» по МКБ010, наличие признаков аутизма по Childhood Autism Rating Scale (CARS) или Autism Spectrum Screening Questionnaire (ASSQ), прохождения ребенком курса реабилитации по СИНР. Было обследовано 79 детей, больных детским аутизмом (F84.0). С целью оценки эффективности реабилитации использовались цветные матрицы Равена.Результаты. Динамика интеллектуальных показателей в различных клинических группах детей с аутизмом имела однонаправленный характер. Наиболее выраженные положительные изменения уровня интеллектуального развития происходили у больных с низкими его показателями (после курса реабилитации в зоне интеллектуального дефекта оставались 30,5±5,5% детей по сравнению с 39±6% до начала лечения, в зоне предельного состояния — 25,5±5,0% по сравнению с 35,5±6,0% до начала лечения).Выводы. В результате проведенного лечения по СИНР у больных аутизмом детей произошли выраженные положительные сдвиги в уровне интеллектуального развития и повышение уровня когнитивной производительности.Ключевые слова: детский аутизм, метод Козявкина, система интенсивной нейрофизиологической реабилитации, лечение аутизма, цветные матрицы Равена.Мета: оцінити ефективність реабілітації дітей з аутизмом за системою інтенсивної нейрофізіологічної реабілітації (СІНР) на підставі вивчення динаміки їх інтелектуальних показників.Пацієнти і методи. Критеріями включення у вибірку при первинній рандомізації були: вік дитини від 5 до 9 років, відповідність діагностичних критеріїв діагнозу «Дитячий аутизм» за МКХ'10, наявність ознак аутизму за Childhood Autism Rating Scale (CARS) або Autism Spectrum Screening Questionnaire (ASSQ), проходження дитиною курсу реабілітації за СІНР. Було обстежено 79 дітей, хворих на дитячий аутизм (F84.0). З метою оцінки ефективності реабілітації використовувалися кольорові прогресивні матриці Равена.Результати. Динаміка інтелектуальних показників у різних клінічних групах дітей з аутизмом мала односпрямований характер. Найбільш виразні позитивні зміни рівня інтелектуального розвитку відбувалися у хворих з низькими його показниками (після курсу реабілітації у зоні інтелектуального дефекту залишалися 30,5±5,5% дітей порівняно з 39±6% до початку лікування, в зоні граничного стану — 25,5±5,0% порівняно з 35,5±6,0% до початку лікування).Висновки. У результаті проведеного лікування за СІНР у хворих на аутизм дітей відбулися виразні позитивні зрушення у рівні інтелектуального розвитку та підвищення рівня когнітивної продуктивності.Ключові слова: дитячий аутизм, метод Козявкіна, система інтенсивної нейрофізіологічної реабілітації, лікуванн

Застосування крокових комп'ютерних ігор для тренування рухових функцій

Для тренировки равновесия и шаговых движений разработаны реабилитационные игры, которые управляются при помощи танцевального коврика. Для управления игрой необходимо наступать ногой на соответствующий сектор коврика, подключённого к компьютеру. Для каждого пациента индивидуально настраиваются параметры сложности игр. Оценка эффективности предложенных игр осуществлялась на пяти пациентах с детскими церебральными параличами, которые на протяжении двух недель занимались дома. Состояние пациентов оценивалась до и после курса с помощью таких тестов: детская шкала равновесия; тест «Встань и иди»; степ-тест «4-квадрата»; стабилометрия. Первые полученные результаты указывают на усовершенствование равновесия у пациентов с церебральными параличами после курса реабилитационных игр.Ключевые слова: виртуальная реабилитация, церебральный паралич, шаговые игры, тренировка равновесия.Для тренування рівноваги та крокових рухів розроблено реабілітаційні ігри, які керуються через танцювальний килимок. Для управління грою необхідно наступати ногою на відповідний сектор килимка, приєднаного до комп'ютера. Для кожного пацієнта індивідуально налаштовуються параметри складності ігор. Попередня оцінка реабілітаційних ігор була проведена на п'яти пацієнтах з дитячими церебральними паралічами, які щоденно тренувались вдома протягом двох тижнів. Стан пацієнтів оцінювався до та після курсу за допомогою таких тестів: дитяча шкала рівноваги; тест «Встань та йди»; степ-тест «4-квадрати»; стабілометрія. Попередні результати вказують на вдосконалення рівноваги у хворих з церебральним паралічем після курсу реабілітаційних ігор.Ключові слова: віртуальна реабілітація, церебральний параліч, крокові ігри, тренування рівноваги

Sequence Analysis of Leuconostoc Mesenteroides Bacteriophage Φ1-A4 Isolated from an Industrial Vegetable Fermentation

Vegetable fermentations rely on the proper succession of a variety of lactic acid bacteria (LAB) including Leuconostoc mesenteroides. L. mesenteroides initiates the fermentation, producing lactic and acetic acids, CO2, and many flavor compounds. As the fermentation proceeds, L. mesenteroides dies off and other LAB complete the fermentation. Phage infecting L. mesenteroides may significantly influence the die-off of L. mesenteroides. However, no L. mesenteroides phages have been previously sequenced and genetically characterized. Knowledge of more phage genome sequences may provide new insights into phage genomics and phage-host interactions. We have determined the complete genome sequence of L. mesenteroides phage (phi)1-A4, which was isolated from an industrial sauerkraut fermentation. The phage possesses a linear, double-stranded, DNA genome consisting of 29,508 bp with a G+C content of 36%. Fifty open reading frames (ORFs) were predicted. Based on N-terminal amino acid sequencing and bioinformatic analyses, putative functions were assigned to 26 ORFs (52%), including 5 ORFs of structural proteins. The phage genome was found to be modularly organized and consist of DNA replication, DNA packaging, head-and-tail morphogenesis, cell lysis, and DNA regulation/modification modules. In silico analyses supported the observation that (phi)1-A4 is a unique lytic phage. A large scale genome inversion (~30% of the genome) was identified by comparison with other phages. The genome inversion encompassed the lysis module, part of the structural protein module and a putative cos-site. Promoter structures were identified that may initiate the transcription of the inverted genome region. Interestingly, the lysin gene was found to be flanked by two holin genes. The tail morphogenesis module was interspersed by cell lysis genes and other genes with unknown functions. The predicted amino acid sequences of the phage proteins showed little similarity with other phages, but functional analyses showed that (phi)1-A4 clusters with several Lactococcus phages. To our knowledge, (phi)1-A4 is the first genetically characterized Leuconostoc mesenteroides phage