Analysis of extracellular potentials using an IBM PC

1. A system has been developed for using IBM PC-compatible computers in combination with a Grafitek Data Logging Interface to record spike trains on magentic discs for later analysis. 2. The times and amplitudes of spikes detected on two input channels are recorded, together with a third channel containing information on computer-generated stimuli and keyboard-activated event markers. In excess of 50,000 spikes can be recorded with a computer having 640 k of Random Access Memory. 3. The recorded spike trains can be reconstructed on the computer monitor and keyboard-controlled window discriminators can be used to select the spikes for analysis by amplitude. 4. The same recorded data can be analysed to produce displays of spike count against time, amplitude histograms, inter-spike interval histograms, peri-stimulus time histograms(PSTH), raster displays and auto- and cross-correlations between activity on the two channels. Each spike is identified by number, allowing easy location of the start and finish of the section of data to be analysed, and the PSTH, raster and correlation analyses allow pretriggering to investigate event occurring before stimulation. 5. The axes of the displays histograms can be adjusted to produce optimum displays, and hard copy can be produced on dot matrix printers or digital plotters. 6. Quantitative analysis enables comparison between different recordings and treatments.     

A low-cost interface for multi-electrode array data acquisition systems

Multi-electrode array systems have enabled the in vitro electrophysiological study of neuronal networks. The data processing component of these systems consists of an advanced computer system and data acquisition electronics that collectively cost more than the multi-electrode arrays and amplifiers. Considering that these elaborate systems may be cost-prohibitive for many laboratories, we have developed a simple but novel method for recording groups of related multi-electrode array channels with a low-cost data acquisition system.     

Enabling High Grayscale Resolution Displays and Accurate Response Time Measurements on Conventional Computers

Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ ¹ and DataPixx ² use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher ³ described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network ⁴ and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements.Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect to external events. Both VideoSwitcher and RTbox are available for users to purchase. The relevant information and many demonstration programs can be found at http://lobes.usc.edu/.     

Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.     

Integrated Mapping Package—A Physical Mapping Software Tool Kit

We have developed an integrated physical mapping computer software package (IMP), originally designed to support the physical mapping of human chromosome 13 and expanded to support several gene-identification projects based on the positional candidate approach. IMP displays map data in a form that provides useful guidelines to the end users. An integrated map with high resolution and confidence is constructed from different types of mapping data, including hybridization experiments, STS-based PCR assays, genetic linkage mapping, cDNA localization, and FISH data. The map is also designed to provide suggestions for specific experiments that are required to obtain maps with even higher resolution and confidence. To this end, the optimization employs multiple constraints that take into account already established STS “scaffold” maps. This software thus serves as an important general tool kit for physical mapping, sequencing, and gene-hunting projects.     

基于数学优化的手术室调度研究

手术室是医院的重要医疗资源,通过有效流程优化及使用麻醉恢复室,其运转效率不断提高,但是仍然不能满足患者和临床科室日益增长的医疗服务需求,仍然存在手术室过度利用和利用不足的情况。人工手术资源调度一定程度提高手术资源利用效率,而借助计算机系统的数学协同优化的手术资源调度,能弥补人工调度的不足,实现系统资源匹配与动态实时优化,有效减少手术患者住院等待时间、提高手术资源利用效率。     

On-line data acquisition and evaluation of long-term measurements of circadian rhythms in individual cells of Acetabularia

A multitasking time-sharing computer system was implemented for studies of different circadian rhythms in individual cells of the unicellular green alga, Acetabularia. This fully automatized system allows simultaneous data acquisition and analysis. Graphical presentation of untreated and mathematically treated data is permanently available on three graphic displays and on a digital plotter. The sampling rate for the data acquisition in each of the 60 channels connected to the system is 720/24 h. Provisions have been made to guarantee uninterrupted data uptake for these long-term measurements by including an auto-restart module and by providing extremely reliable software for the experimenter using menu techniques.     

Angiovision: Aortic stent-graft placement by augmented angionavigation

The endovascular treatment of abdominal aortic aneurysm (EVAR - EndoVascular Aneurism Repair) has become an alternative therapy to conventional open surgery. The objective of Angiovision project was to contribute to the improvement of EVAR procedures in terms of accuracy and customization of the interventional strategy. Our approach was mainly based on the use of patient-specific data, computer-aided endovascular navigation and numerical simulation. We proposed a new FEM-based patient-specific simulation solution to estimate the deformations caused by the introduction of stiff endovascular devices. We developed and implemented an original endovascular navigation system to augment the intraoperative fluoroscopy with the visualization of deformed preoperative aorto-iliac structure, and related information concerning vessel wall (calcifications), as well as stent-graft virtual deployment. The proposed solution, that requires only lightweight computer equipment, can be used in a standard operating room in order to optimize device placement (from a single angle of incidence). Evaluation is currently under way.     

On-line data acquisition and evaluation of long-term measurements of circadian rhythms in individual cells ofAcetabularia

A multitasking time-sharing computer system was implemented for studies of different circadian rhythms in individual cells of the unicellular green alga,Acetabularia. This fully automatized system allows simultaneous data acquisition and analysis. Graphical presentation of untreated and mathematically treated data is permanently available on three graphic displays and on a digital plotter. The sampling rate for the data acquisition in each of the 60 channels connected to the system is 720/24 h. Provisions have been made to guarantee uninterrupted data uptake for these long-term measurements by including an auto-restart module and by providing extremely reliable software for the experimenter using menu techniques.     

Evaluation of a cosmid contig physical map of human chromosome 16.

A cosmid contig physical map of human chromosome 16 has been developed by repetitive sequence finger-printing of approximately 4000 cosmid clones obtained from a chromosome 16-specific cosmid library. The arrangement of clones in contigs is determined by (1) estimating cosmid length and determining the likelihoods for all possible pairwise clone overlaps, using the fingerprint data, and (2) using an optimization technique to fit contig maps to these estimates. Two important questions concerning this contig map are how much of chromosome 16 is covered and how accurate are the assembled contigs. Both questions can be addressed by hybridization of single-copy sequence probes to gridded arrays of the cosmids. All of the fingerprinted clones have been arrayed on nylon membranes so that any region of interest can be identified by hybridization. The hybridization experiments indicate that approximately 84% of the euchromatic arms of chromosome 16 are covered by contigs and singleton cosmids. Both grid hybridization (26 contigs) and pulsed-field gel electrophoresis experiments (11 contigs) confirmed the assembled contigs, indicating that false positive overlaps occur infrequently in the present map. Furthermore, regional localization of 93 contigs and singleton cosmids to a somatic cell hybrid mapping panel indicates that there is no bias in the coverage of the euchromatic arms.     

Microbial sensor cell arrays

Motivated by the advantages endowed by high-throughput analysis, researchers have succeeded in incorporating multiple reporter cells into a single platform; the technology now allows the simultaneous scrutiny of a large collection of sensor strains. We review current aspects in cell array technology with emphasis on microbial sensor arrays. We consider various techniques for patterning live cells on solid surfaces, describe different array-based applications and devices, and highlight recent efforts for live cell storage. We review mathematical approaches for deciphering the data emanating from bioreporter collections, and discuss the future of single cell arrays. Innovative technologies for cell patterning, preservation and interpretation are continuously being developed; when they all mature, cell arrays may become an efficient analytical tool, in a scope resembling that of DNA microarray biochips.     

Head Pilot: A new webcam-based Head Tracking System tested in permanently disabled patients

Persons with cerebral palsy (CP) need to modify their lifestyle in order to carry out daily activities. Assistive technology facilitates communication and improves the domestic environment and mobility. The STARNAV Company has developed a Head Tracking System, Head Pilot, which uses a robust algorithm that measures, in real-time, head motion from a webcam. Head Pilot aims to control any informatic and domotic interface controlling the pointer of a PC. This work aims to create an assistive technology that is easy to use once it is set up and used. The system offers an interface control, which allows individual users to adjust the system for their comfort. The system displays a toolbar allowing the patient to choose the velocity of the pointer and to choose from several different ways to validate a task. The objective of this study was to evaluate the performance of Head Pilot by using five computerized tests of validation. Seven participants with disabilities were compared to seven participants with no relevant medical history (control group). Two versions of the software were developed and displayed on a computer screen. The time to complete the tests were measured and compared to a control group. Before testing, the disabled persons had received an orthoptic assessment, a cognitive evaluation, and a cervical motor check. Head Pilot was validated for use by the majority of users with CP who were able to control a computer except for the subject with incomplete locked-in syndrome, who required an Eye Tracker System.     

Computerized Meiotic Mapping in ASPERGILLUS NIDULANS

A computer system for the storage and processing of microbial meiotic data has been developed. Based on the language Fortran 4, the program retrieves relevant data and determines the order, map distances, and coefficient of coincidence for any three-gene group. Meiotic data from Aspergillus nidulans were used to test the program. A total of 61 three-gene sequences were processed, and the results were found to be compatible with the published values. The advantages and disadvantages of computer analysis for genetic analysis are discussed.     

A minicomputer system for analyzing and reporting pilot plant fermentor data

In 1979, a minicomputer system was developed for Hoffmann-La Roche by ABEC, Inc. for the purpose of achieving on-line analysis and reporting of data from 16 70-L pilot-plant fermentors (New Brunswick Scientific Co.). The system consists of a PDP 11/60 computer with 96K core capacity, two RL01 disk drives, two RX01 floppy-disk drives, LA-36 DECwriter terminal, Tektronix CRT, and Versatec printer plotter. DEC, PDP, RSX, RL01, RX01, LA-36, and DECwriter are trademarks of Digital Equipment Corporation. The computer software comprises three distinct groups of programs. RSX-11M is a disk-based operating system that allows quick response to realtime events, such as process monitoring and data acquisition, while carrying out less time-dependent activities, such as program development and graphical output. The AIM (Biles, Inc.) system is used to acquire and convert the voltage signals produced by pilot-plant instrumentation into engineering units. Analysis and graphical output are executed by ABEC and Versatec supplied programs. The most beneficial task performed by the computer is the production of graphical output of a variety of measured and analyzed data. This has led to an increase in personnel productivity and design of more meaningful experiments. An ancillary function of the system is to pick up data logged by a PDP 11/03 computer from a remote fermentation production plant by means of a MODEM interfaced communication link. Production data are analyzed and presented in a form identical with pilot-plant data. The experience with the system is discussed in this article.     

The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction

The TMEM16 family of membrane proteins displays a remarkable functional dichotomy – while some family members function as Ca²⁺-activated anion channels, the majority of characterized TMEM16 homologs are Ca²⁺-activated lipid scramblases, which catalyze the exchange of phospholipids between the two membrane leaflets. Furthermore, some TMEM16 scramblases can also function as channels. Due to their involvement in important physiological processes, the family has been actively studied ever since their molecular identity was unraveled. In this review, we will summarize the recent advances in the field and how they influenced our view of TMEM16 family function and evolution. Structural, functional and computational studies reveal how relatively small rearrangements in the permeation pathway are responsible for the observed functional duality: while TMEM16 scramblases can adopt both ion- and lipid conductive conformations, TMEM16 channels can only populate the former. Recent data further provides the molecular details of a stepwise activation mechanism, which is initiated by Ca²⁺ binding and modulated by various cellular factors, including lipids. TMEM16 function and the surrounding membrane properties are inextricably intertwined, with the protein inducing bilayer deformations associated with scrambling, while the surrounding lipids modulate TMEM16 conformation and activity.     

黑龙江省野生东北虎调查管理信息系统的构建

文章以黑龙江省野生东北虎（Panthera tigris altaica）野外调查数据为基础,利用地理信息系统技术、计算机技术与野生动物资源调查管理技术,构建了黑龙江省野生东北虎调查管理信息系统。主要运用面向对象程序设计语言C#和ArcGIS Engine嵌入式组件技术以及SQL Server数据库技术,设计并构建东北虎调查管理系统,实现了对野生东北虎调查数据的图形可视化操作管理。同时,结合研究区域内的自然因素和人文因素对调查资源进行动态的空间分析,及时准确地反映出东北虎的种群数量和空间变化规律,并制作出相应的分类专题图及野外分布信息统计图表等。该管理信息系统将有助于野生东北虎种群及栖息地调查数据与资料的科学管理,对于推动我国野生东北虎就地保护和科学管理具有重要意义。     

Immediate free TRAM reconstruction in lumpectomy and radiation failure patients

Local recurrence after lumpectomy and radiation therapy indicates failed breast conservation surgery. These patients often proceed to mastectomy and are candidates for autogenous breast reconstruction. Free transverse rectus abdominus muscle (TRAM) reconstruction in these patients is complicated by repeated axillary dissection and the use of irradiated tissue. Complication rates for pedicled TRAMs have been reported at 33 percent when used in irradiated tissue beds. We report our results using the free TRAM for breast reconstruction after lumpectomy and radiation failure. All patients within this study developed a local recurrence after lumpectomy and radiation therapy. All patients had undergone axillary dissection for staging at the time of their lumpectomy. Patient records were reviewed for patient age, total radiation dose, associated risk factors for TRAM failure, operative time, donor vessels used for anastomosis, status of the native thoracodorsal vessels at the time of surgery, and postoperative complications. Over a 7-year period, 16 TRAM patients had undergone previous breast conservation surgery. Of these 16 patients, 14 underwent reconstruction with a planned free TRAM after simple mastectomy. Average operating room time was 7 hours. There were no partial or total flap losses. Complications were seen in 14 percent of the overall group. Overall, we found that the free TRAM provided an excellent aesthetic result with a lower complication rate than previously reported for pedicled TRAM flaps in irradiated beds. The thoracodorsal vessels provided an adequate donor vessel in 93 percent of the cases. The free TRAM provides a superior alternative in immediate reconstruction in patients who have failed breast conservative surgery.     

Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping

Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat-H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2H(ch), 3H(ch) and 5H(ch) in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.     

An integrated haptic-enabled virtual reality system for orthognathic surgery planning

Conventional Orthognathic surgery (OGS) planning involves cephalometric analyses and dental casts to be mounted on an articulator. Dental segments are subsequently identified, cut and repositioned to allow the fabrication of intraoral wafers that guide the positioning of the osteotomy bone segments. This conventional planning introduces many inaccuracies that affect the post-surgery outcomes. Although computer technologies have advanced computational tools for OGS planning, they have failed in providing a practical solution. Many focuses only on some specific stages of the planning process, and their ability to transfer preoperative planning data to the operating room is limited. This paper proposes a new integrated haptic-enabled virtual reality (VR) system for OGS planning. The system incorporates CAD tools and haptics to facilitate a complete planning process and is able to automatically generate preoperative plans. A clinical pre-diagnosis is also provided automatically by the system based on the patient’s digital data. A functional evaluation based on a real patient case study demonstrates that the proposed virtual OGS planning method is feasible and more effective than the traditional approach at increasing the intuitiveness and reducing errors and planning times.