A simple exploratory algorithm for the accurate and fast detection of spontaneous synaptic events

We have developed a program for the fast and accurate detection of spontaneous synaptic events. The algorithm identifies each event of which the slope and amplitude which meet criteria. The significant feature of this algorithm is its stepwise and exploratory search for the onset and the peak points. During the first step, the program employing the algorithm makes a rough estimate of the candidate for a synaptic event, and determines a 'temporary' onset data point. The next step is the detection of the true onset data point and 'temporary' peak data point, which probably exist several points after the temporary onset data point. The third step is a backward search to detect the true peak data point. The final step is to check whether the amplitude of the detected event exceeds the threshold. This stepwise and shuttlewise search allows for the accurate detection of the peak points. Using this program, we succeeded in detecting an increased frequency and amplitude of spontaneous excitatory postsynaptic currents in chick cerebral neurons following the application of 12-O-tetradecanoyl-phorbol-13-acetate (TPA). In addition, we demonstrated that the program employing the algorithm was able to be used for the detection of extracellular action potentials.     

Regression imputation of missing values in longitudinal data sets

A stand-alone, menu-driven PC program, written in GAUSS, which can be used to estimate missing observations in longitudinal data sets is described and made available to interested readers. The program is limited to the situation in which we have complete data on N cases at each of the planned times of measurement t₁, t₂,…, t_T; and we wish to use this information, together with the non-missing values for n additional cases, to estimate the missing values for those cases. The augmented data matrix may be saved in an ASCII file and subsequently imported into programs requiring complete data. The use of the program is illustrated. Ten percent of the observations in a data set consisting of mandibular ramus height measurements for N = 12 young male rhesus monkeys measured at T = 5 time points are randomly discarded. The augmented data matrix is used to determine the lowest degree polynomial adequate to fit the average growth curve (AGC); the regression coefficients are estimated and confidence intervals for them are determined; and confidence bands for the AGC are constructed. The results are compared with those obtained when the original complete data set is used.     

SILMUT: a computer program for the identification of regions suitable for silent mutagenesis to introduce restriction enzyme recognition sequences.

We describe a set of IBM-compatible computer programs designed to selectively identify the potential sites for silent mutagenesis within a target DNA sequence. This program is based on a novel strategy of identifying amino acid motifs compatible with each restriction site (BioTechniques 12:382-384, 1991). The programs can be used to identify the suitability for the introduction of any 6-base nucleic acid sequences, such as restriction enzyme sites in cassette mutagenesis strategies. The Table program generates a table of multiple amino acid motifs for each restriction enzyme, obtained by translating each unique recognition sequence in all three reading frames. The Silmut program, which utilizes the features of Table, will further identify the presence of a match between any amino acid motif of each restriction enzyme and the input target sequence. Minor manipulations of the data base files will enable the individual researcher to identify the potential for introduction of any 6-base sequences by silent mutagenesis.     

Worker rehabilitation programs. Separating fact from fiction.

A few worker rehabilitation programs have had outstanding success in improving ability to function for persons with occupational back pain. Local programs must show that they have similar success. Because the definitions of terms such as "back school," "work hardening," and "functional restoration" are blurred at a local level, the choice of a program for an individual patient must depend primarily on the program''s demonstrated success rate with similar patients. The chances of returning to work decrease as a function of time after injury. Therefore, referring physicians, insurers, and employers must be provided with information regarding results in terms of acute (0 to 6 weeks), subacute (7 to 12 weeks), and chronic (more than 12 weeks) back pain. Other important variables include selection criteria, program cost, and dropout rate. We advocate standardized reporting of such data for all worker rehabilitation programs. A model "report to consumers," described here, is a minimal obligation. The validity of a number of important internal quality assurance issues is uncertain. Ethical and legal pressures must be recognized.     

The road will be mastered by the walker

Anonymous questioning by the distribution of questionnaires among 1,600 young people (68.9% of them were city dwellers, 31.1% were villagers) was carried out. The questioning covered 1,079 adolescents aged 12-16 years (67.3%), 501 young people aged 16-19 years (31.3%) and 20 respondents aged 19-23 years (1.4%). The analysis of answers to questionnaires indicated that all respondents had the same level of knowledge on the subject, but the information they possessed was not duly analyzed and had no influence on their own behavior. It should be pointed out that 1% of persons aged 12-19 years took drugs by intravenous injection. These data, as well as other materials, gave grounds for the development of a new educational program on the prophylaxis of HIV/AIDS/STD and its introduction in 1997. The program is intended for a school course of 6 years (forms 6-11) and must provide adolescents with reliable and comprehensible information, conductive to the formation of a healthy mode of life.     

Operant conditioning and behavioral analyses using a minicomputer.

An operant conditioning and data analysis software system was developed for use on a PDP-12A minicomputer. The operant software functions in quasi time-sharing fashion to control and acquire data from any peripheral device that operates in the binary mode. In addition to independently running different experiments in near simultaneous fashion, the program also provides information on the current status of each experiment using a cathode ray-tube display. Response data from each experimental subject is stored on magnetic tape and analyzed, off-line, by the data analysis portion of the software system. A discussion of the operation of this system is given for one possible application: visual discrimination training.     

1-Set vs. 3-set resistance training: a crossover study

This crossover study was conducted to investigate the effects of a 1-set and 3-set strength training program. The subjects were untrained men and women who were randomly signed into 1 of 3 groups: 10 subjects trained during the first 9 weeks (training period 1) with 1 set and 8-12 repetitions per set. After the break (9 weeks), they trained with 3 sets and 8-12 repetitions in training period 2. Twelve subjects started with the 3-set program and continued with the 1-set regime after the break. The control group (n = 7) did not train. The subjects were tested on 1 repetition maximum (1RM) for the biceps curl, leg press (unilateral: left and right), and bench press. Analysis of the data was done in a sampled manner for each strength training program (1-set and 3-set). The 1-set (n = 22) and 3-set (n = 22) programs led to significantly (p < 0.05) improved 1RM performances in every exercise. The relative improvements (%) for the 1RM were significantly higher during the 3-set program for the biceps curl and the bench press compared with the 1-set program. The control group exhibited no changes in any of the tested parameters over the course of this study. The design of this study allowed insight into the effects of different strength training volume without any genetical variations. The same subjects improved their 1RM during the 3-set program by 2.3 kg (biceps curl; corresponding effect size = 0.24), 8.9 kg (leg press right; 0.30), 10.9 kg (leg press left; 0.28), and 2.5 kg (bench press; 0.09) more than during the 1-set program. Depending on the goals of each trainee, these differences between the effects of different strength training volumes indicate that it may be worth spending more time on working out with a 3-set strength training regime.     

Linkage of Asthma to Markers on Chromosome 12 in a Sample of 240 Families Using Quantitative Phenotype Scores

We present evidence of linkage between markers on chromosome 12 and asthma using the BETA program for nonparametric single- and multipoint linkage analysis. We have used quantitative scores as our phenotypic variables, combining data into indices for asthma and atopy and maximizing heritability. The largest single-locus LODs were achieved for asthma: D12S342 and asthma score (LOD 2.255), D12S324 and asthma affection (LOD 2.214), and D12S366 and wheeze (LOD 3.307). The region of interest identified using multipoint analysis, with a maximum LOD of 2.29, centers around D12S97 at location 173.5 cM with a standard error of 6.5 for the asthma score and close agreement for asthma affection and wheeze. Such evidence merits further investigation of this area in an attempt to define the region with greater precision with a view to identifying candidate genes. We hope that the methods presented will encourage researchers to use phenotypic information in a way that encourages meta-analysis.     

A 12-week structured education and exercise program improved climacteric symptoms in middle-aged women

In the present study, 40- to 60-year-old women with climacteric symptoms were placed on a 12-week structured education and exercise program to ascertain the effects of this program on climacteric symptoms, quality of life (QOL), and attitude towards exercise. A total of 35 women served as subjects. Twenty women were enrolled in an educational and exercise program that involved learning about menopause and participating in physical activity at least three times a week (Group E). For comparison, the other 15 women did not participate in this program and were instructed to refrain from exercising during study period (Group C). The effects of the 12-week interventional program on climacteric symptoms, QOL, and attitude towards exercise were thereby investigated. The program demonstrated significant effects on climacteric symptoms in terms of Kupperman index and psychosomatic symptoms, especially paresthesia and nervousness. In other words, climacteric symptoms improved significantly in Group E. Furthermore, scores for QOL and attitude towards exercise improved in Group E after the 12-week program; however, these trends did not reach statistical significance. Hence, the 12-week structured education and exercise program was shown to be effective in alleviating climacteric symptoms.     

BmuG@Sbase--a microarray database and analysis tool

The manufacture and use of a whole-genome microarray is a complex process and it is essential that all data surrounding the process is stored, is accessible and can be easily associated with the data generated following hybridization and scanning. As part of a program funded by the Wellcome Trust, the Bacterial Microarray Group at St. George's Hospital Medical School (BmuG@S) will generate whole-genome microarrays for 12 bacterial pathogens for use in collaboration with specialist research groups. BmuG@S will collaborate with these groups at all levels, including the experimental design, methodology and analysis. In addition, we will provide informatic support in the form of a database system (BmuG@Sbase). BmuG@Sbase will provide access through a web interface to the microarray design data and will allow individual users to store their data in a searchable, secure manner. Tools developed by BmuG@S in collaboration with specific research groups investigating analysis methodology will also be made available to those groups using the arrays and submitting data to BmuG@Sbase.     

Computer modeling of nitroxide spin labels on proteins

Electron paramagnetic resonance using site‐directed spin labeling can be used as an approach for determination of protein structures that are difficult to solve by other methods. One important aspect of this approach is the measurement of interlabel distances using the double electron–electron resonance (DEER) method. Interpretation of experimental data could be facilitated by a computational approach to calculation of interlabel distances. We describe an algorithm, PRONOX, for rapid computation of interlabel distances based on calculation of spin label conformer distributions at any site of a protein. The program incorporates features of the label distribution established experimentally, including weighting of favorable conformers of the label. Distances calculated by PRONOX were compared with new DEER distances for amphiphysin and annexin B12 and with published data for FCHo2 (F‐BAR), endophilin, and α‐synuclein, a total of 44 interlabel distances. The program reproduced these distances accurately (r² = 0.94, slope = 0.98). For 9 of the 11 distances for amphiphysin, PRONOX reproduced the experimental data to within 2.5 Å. The speed and accuracy of PRONOX suggest that the algorithm can be used for fitting to DEER data for determination of protein tertiary structure. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 35–44, 2012.     

Analyzing Personalized Policies for Online Biometric Verification

Motivated by India’s nationwide biometric program for social inclusion, we analyze verification (i.e., one-to-one matching) in the case where we possess similarity scores for 10 fingerprints and two irises between a resident’s biometric images at enrollment and his biometric images during his first verification. At subsequent verifications, we allow individualized strategies based on these 12 scores: we acquire a subset of the 12 images, get new scores for this subset that quantify the similarity to the corresponding enrollment images, and use the likelihood ratio (i.e., the likelihood of observing these scores if the resident is genuine divided by the corresponding likelihood if the resident is an imposter) to decide whether a resident is genuine or an imposter. We also consider two-stage policies, where additional images are acquired in a second stage if the first-stage results are inconclusive. Using performance data from India’s program, we develop a new probabilistic model for the joint distribution of the 12 similarity scores and find near-optimal individualized strategies that minimize the false reject rate (FRR) subject to constraints on the false accept rate (FAR) and mean verification delay for each resident. Our individualized policies achieve the same FRR as a policy that acquires (and optimally fuses) 12 biometrics for each resident, which represents a five (four, respectively) log reduction in FRR relative to fingerprint (iris, respectively) policies previously proposed for India’s biometric program. The mean delay is sec for our proposed policy, compared to 30 sec for a policy that acquires one fingerprint and 107 sec for a policy that acquires all 12 biometrics. This policy acquires iris scans from 32–41% of residents (depending on the FAR) and acquires an average of 1.3 fingerprints per resident.     

Computer programs in nucleic acid synthesis: synthetic strategy development using solid-phase chemical techniques with data storage, retrieval and analysis capabilities.

A computer program has been designed to aid development of synthetic strategies for oligonucleotides produced by solid-phase chemical techniques. The program reduces the time required to develop a strategy and a data file from hours to minutes. The program contains inventories, provides cost analyses, and generates and stores other associated data. The program searches an inventory of sequences for that sequence to avoid duplicate synthesis. If the sequence is not in the inventory the program devises a synthetic strategy, calculates the amounts of reagents and labor costs necessary to complete the synthetic oligonucleotide. The program also deducts the reagents from inventory files. Physical data is also calculated. A file is generated in a sequence inventory for storage of the data as well as other data that will be generated during the purification processes. All variable parameters can be easily edited. The programs were designed to provide a cross-referencing feature for data analysis and can use several parameters as a constant.     

Oblong,a program to analyse phylogenomic data sets with millions of characters,requiring negligible amounts of RAM

Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.     

A nonlinear regression program for small computers

A BASIC computer program for performing weighted nonlinear regression is described and a listing of the program is given. The program, which is small and simple to use, has been designed to be run by users with little knowledge of mathematics or computers. Robust methods of analysis are described which may be applied to data in which experimental errors are not normally distributed, and the program incorporates one such method. It is shown that the program is useful for the analysis of data conforming to the Michaelis-Menten equation, a single exponential, and to binding equations, and other applications are discussed.     

PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes

MOTIVATION: In silico genome analysis of bacteriophage genomes focuses mainly on gene discovery and functional assignment. The search for regulatory elements contained within these genome sequences is often based on prior knowledge of other genomic elements or on learning algorithms of experimentally determined data, potentially leading to a biased prediction output. The PHage In silico Regulatory Elements (PHIRE) program is a standalone program in Visual Basic. It performs an algorithmic string-based search on bacteriophage genome sequences to uncover and extract subsequence alignments hinting at regulatory elements contained within these genomes, in a deterministic manner without any prior experimental or predictive knowledge. RESULTS: The PHIRE program was tested on known phage genomes with experimentally verified regulatory elements. PHIRE was able to extract phage regulatory sequences correctly for bacteriophages T7, T3, YeO3-12 and lambda, based solely on the genome sequence. For 11 bacteriophages, new predictions of conserved phage-specific putative regulatory elements were made, further corroborating this approach. AVAILABILITY: http://www.agr.kuleuven.ac.be/logt/PHIRE.htm. Freely available for academic use. Commercial users should contact the corresponding author.     

widgetcon: A website and program for quick conversion among common population genetic data formats

One of the most tedious steps in genetic data analyses is the reformatting data generated with one program for use with other applications. This conversion is necessary because comprehensive evaluation of the data may be based on different algorithms included in diverse software, each requiring a distinct input format. A platform‐independent and freely available program or a web‐based tool dedicated to such reformatting can save time and efforts in data processing. Here, we report widgetcon , a website and a program which has been developed to quickly and easily convert among various molecular data formats commonly used in phylogenetic analysis, population genetics, and other fields. The web‐based service is available at https://www.widgetcon.net . The program and the website convert the major data formats in four basic steps in less than a minute. The resource will be a useful tool for the research community and can be updated to include more formats and features in the future.     

Effect of rhythmic gymnastics on the rhythm perception of children with deafness

This study was designed to examine the effect of a rhythmic gymnastics program on the rhythm perception of children with deafness. Two groups--control and experiment--of 12 and 17 children, respectively, coming from the same school for the deaf participated in this study. The duration of the program for the individuals in the experiment group was 16 weeks (at a frequency of 3 lessons per week, for 40 minutes each lesson), while children of both groups adhered to their regular school schedules. Five rhythmic patterns in 3 speeds (tempi) were reproduced both by a metronome and each child's performance and were recorded on a digital disk before and after the application of the program. The rate of time deviation (in seconds) between the 2 beats represented the score for each child. The average rate of the 5 rhythmic patterns in each tempo was calculated separately, giving 3 scores (one for every tempo) for each child. Significance was set at p < or = 0.05. The data revealed significant postexercise differences in favor of the experiment group, an improvement of the experiment group in all pre-post values, as well as an improved medium tempo with relation to the control group. The findings show the effectiveness of the specific program in terms of improving rhythm ability, thus indicating its use in educating children with deafness on rhythm instead of preferring the routine of the adapted school program.     

Multiple cycles of constant infusion recombinant interleukin-2 in adoptive cellular therapy of metastatic renal carcinoma

Twenty patients were treated with metastatic renal cell cancer with 5-day cycles of constant infusion recombinant interleukin-2 (rIL-2) at 3 X 10(6) U/m2/day and with infusion of in vitro activated autologous mononuclear cells. The initial eight patients completed all rIL-2 and cellular therapy in a single 25-day treatment period. The subsequent 12 patients entered a 6-month treatment program involving two separate 15-day cycles of cellular therapy followed by four monthly cycles of maintenance rIL-2. Among eight patients in the 25-day treatment program, there were two with partial response (PR) and one with minor response (MR). None of these responses exceeded 2 months in duration. Among the 12 patients undergoing recycling of therapy, there were two with complete response (CR), two with PR, and one with MR. All four patients with CR or PR in this group demonstrated continuing response with recycling of treatment and none relapsed while receiving maintenance interleukin-2. Three remain in remission at 10, 11, and 12 months. These pilot data confirm that patients can tolerate multiple cycles of adoptive immunotherapy involving constant infusion rIL-2 and suggest that recycling of therapy is necessary to achieve clinically meaningful results.