Computerisation of diabetic clinic records.

A simple system for putting diabetic records on a computer file is achieved by using stationery that combines the usual handwritten records (not computerised) with the minimum of essential data suitable for punching on to computer tape. The record may be brought up to date at a selected time time interval. This simple, cheap system has been in use in a busy clinic for six years. The information on about 8000 diabetics now held in the computer file is used chiefly to help research by creating registers of patients with specified characteristics, such as treatment, heredity complications, and pregnancy. A complete up-to-date index of the entire clinic population is always available, and routine clinic statistics are returned every six months.     

PISCES: a protein sequence culling server

PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.     

Retention in care and connection to care among HIV-infected patients on antiretroviral therapy in Africa: estimation via a sampling-based approach

Introduction

Current estimates of retention among HIV-infected patients on antiretroviral therapy (ART) in Africa consider patients who are lost to follow-up (LTF) as well as those who die shortly after their last clinic visit to be no longer in care and to represent limitations in access to care. Yet many lost patients may have “silently” transferred and deaths shortly after the last clinic visit more likely represent limitations in clinical care rather than access to care after initial linkage.

Methods

We evaluated HIV-infected adults initiating ART from 1/1/2004 to 9/30/2007 at a clinic in rural Uganda. A representative sample of lost patients was tracked in the community to obtain updated information about care at other ART sites. Updated outcomes were incorporated with probability weights to obtain “corrected” estimates of retention for the entire clinic population. We used the competing risks approach to estimate “connection to care”—the percentage of patients accessing care over time (including those who died while in care).

Results

Among 3,628 patients, 829 became lost, 128 were tracked and in 111, updated information was obtained. Of 111, 79 (71%) were alive and 35/48 (73%) of patients interviewed in person were in care and on ART. Patient retention for the clinic population assuming lost patients were not in care was 82.3%, 68.9%, and 60.1% at 1, 2 and 3 years. Incorporating updated care information from the sample of lost patients increased estimates of patient retention to 85.8% to 90.9%, 78.9% to 86.2% and 75.8% to 84.7% at the same time points.

Conclusions

Accounting for “silent transfers” and early deaths increased estimates of patient retention and connection to care substantially. Deaths soon after the last clinic visit (potentially reflecting limitations in clinical effectiveness) and disconnection from care among patient who were alive each accounted for approximately half of failures of retention.     

Development and Evaluation of Patient‐Centered Software for a Weight‐Management Clinic

Objective: To describe a weight‐management clinic software system and to report on its preliminary evaluation. Research Methods and Procedures: The software system standardizes the collection of relevant patient information from an initial medical assessment, weekly clinic visits, and laboratory testing protocol of a medically supervised proprietary meal‐replacement program in a university‐based referral clinic. It then generates monthly patient feedback reports with graphs of clinical and laboratory parameters to support a patient‐centered approach to weight management. After patients and clinic physicians review the data to ensure accuracy, the database is used for subsequent patient feedback reports, reports to referring physicians, quality assurance, and research. Clinic physicians and referring physicians were asked to rate their acceptance of the system. In addition, in a retrospective analysis of data generated by the system, outcomes for patients who received system‐generated feedback (n = 620) were compared with those who participated in the program before the introduction of feedback (n = 130). Results: Clinic and referring physicians reported that they had high overall satisfaction with the software and that the system saved them time, and the latter group reported that it decreased laboratory use. Regarding patients, the feedback group had lower dropout rates in the latter half of the program, better rates of attendance, completion of laboratory tests, and weight loss after 8 weeks. Discussion: The software seems to facilitate the effectiveness of the treatment protocol for obesity and generates a high‐quality database for patient care, clinic administration, quality assurance, and research purposes.     

A database on alternative splice forms on the integrated genetic map service (IGMS)

The IGMS is a comprehensive information system that combines the knowledge from genomic sequence, genetic map and genetic disorders databases. This system is updated weekly and focuses on the analysis of EST data. The IGMS identifies UniGene clusters that are differentially expressed in different types of cancer with respect to different reference tissues. The results can be combined with clinical data to asses the potential relevance of specific genes for patient survival or metastatic spread. The second application maps EST with a specific expression profile. Our third application generates a database of alternative splice forms for nine organisms from EST and mRNA sequence data. The results can be used to find splicing patterns specific for certain tissues or tumour types. Availability: http://www.bioinf.mdc-berlin.de/igms/.     

Sensitivity to Rifampicin: Incidence,Mechanism, and Prevention

Five out of 200 patients taking rifampicin 900 mg twice weekly and three out of 91 patients taking rifampicin who attended an immunology clinic developed intolerance to the drug. Antibodies to rifampicin, which were found in most cases, decreased steadily after the end of treatment but were detectable for up to 16 months. The dose of rifampicin and the blood levels are predominating factors in the occurrence of reactions. Thus the dose should be reduced in patients in whom rifampicin blood levels rise abnormally. When it is important to continue rifampicin treatment despite intolerance antibody titres within 24 hours after administration of the drug must be measured to find when they are lowest, which determines the “unreactive period,” and when a further dose may be safely given.     

Child Injury Intensive Monitoring System

A system for the acquisition and recording of child injuries is described. This computer-based system is designed for implementation in three stages. Each successive stage covers wider geographical areas and provides more comprehensive facilities.Stage 1 collects basic identification information on injured children. It provides an intensive monitoring service which alerts the agencies properly concerned with child abuse to repeated or suspicious injury cases. Misleading or suppressed information increases rather than limits the precision of diagnosis. More comprehensive details of those children thought to be at risk are collected when stage 2 is introduced. The printed results of the processing of these details are circulated to certain authorized users, and they are organized for rapid information retrieval. A central office which receives a weekly copy of this cross-referenced file provides a 24-hour information service.In stage 3 a register containing fully structured, standardized case reports will be established. We believe that this system ensures medical confidentiality and respects the rights of parents and children.     

PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.     

X-MATE: a flexible system for mapping short read data

SUMMARY: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software. AVAILABILITY: Executables, source code, junction libraries, test data and results and the user manual are available from http://grimmond.imb.uq.edu.au/X-MATE/.     

Behavioral treatment of isolated systolic hypertension in the elderly

Fifteen hypertensive patients were recruited from a geriatric medicine clinic for a "research project designed to evaluate a Behavioral Stepped-Care treatment program of high blood pressure (HBP)." All patients met the selection criteria of the Isolated Systolic Hypertension (ISH) in the Elderly (SHEP) clinical trial. During baseline, subjects recorded BP at home 9 times/day (3 times each, shortly after awakening, during the middle of the day, and within an hour of retiring) for 1 month and mailed that data to us daily. In addition, they came to the clinic weekly and had their BP recorded by a nurse. During treatment 1, systolic (SBP) feedback, they were trained to lower SBP at home using their sphygmomanometers. They also continued to monitor BP and to obtain weekly professional BP readings. During treatment 2 (relaxation), they were trained to relax; they followed the self-administration and data-collection protocol as in treatment 1. Each treatment phase lasted 3 months. Average monthly self-determined BP fell significantly from 166.4/85.8 (SBP/DBP) mm Hg during baseline to 153.3/81.2 by the end of the relaxation phase; average monthly professionally measured BP fell significantly, from 164.7/87.1 to 156.9/81.5. These findings show that a nurse-supervised, patient-administered behavioral treatment program of ISH can yield sustained, significant falls in BP.     

Bartonella and bartonellosis--emerging and re-emerging infections: epidemiology, clinical course, diagnosis

Information on the epidemiology, clinic and diagnostics of bartonellosis is updated. The importance of bartonellosis lies in the fact that its main risk group embraces patients with immunodeficiencies of different origin, the number of such patients constantly growing. The diagnostics of bartonellosis is insufficiently developed and the research on Bartonella organisms, except for the trunch (Volynia) fever causative agent, is insufficient in our country.     

Adaptive hybrid storage systems leveraging SSDs and HDDs in HPC cloud environments

Cloud computing should inherently support various types of data-intensive workloads with different storage access patterns. This makes a high-performance storage system in the Cloud an important component. Emerging flash device technologies such as solid state drives (SSDs) are a viable choice for building high performance computing (HPC) cloud storage systems to address more fine-grained data access patterns. However, the bit-per-dollar SSD price is still higher than the prices of HDDs. This study proposes an optimized progressive file layout (PFL) method to leverage the advantages of SSDs in a parallel file system such as Lustre so that small file I/O performance can be significantly improved. A PFL can dynamically adjust chunk sizes and stripe patterns according to various I/O traffics. Extensive experimental results show that this approach (i.e. building a hybrid storage system based on a combination of SSDs and HDDs) can actually achieve balanced throughput over mixed I/O workloads consisting of large and small file access patterns.     

Recurrent malignant melanoma: effect of adjuvant immunotherapy on survival.

Twenty-nine patients referred consecutively to a cancer clinic because of recurrent metastatic malignant melanoma were given 5 mg of Connaught Laboratories bacillus Calmette-Guérin (BCG) by multiple cutaneous puncture at weekly and later at monthly intervals. Eight were also treated with autologous tumour vaccine and three with intralesional BCG. This group was compared with a retrospective control group of 54 patients treated with surgery and radiotherapy alone after recurrence. Prognostic features such as site of primary and of first metastasis, disease-free interval, age and sex were similar in the two groups. However, the median survival from the time of first recurrence was 12 months in the control group but 21 months in the BCG-treated group. The major improvement was in patients with disease limited to the regional lymph nodes: the median survival was 16 months in the control group but over 32 months in the BCG-treated group. Autologous tumour vaccine appeared to have no effect on survival. Serial testing of immunocompetence did not offer any prognostic advantage, although the results of some tests correleated well with extent of disease.     

Transmission dynamics of cholera in Yemen, 2017: a real time forecasting

Background

A large epidemic of cholera, caused by Vibrio cholerae, serotype Ogawa, has been ongoing in Yemen, 2017. To improve the situation awareness, the present study aimed to forecast the cholera epidemic, explicitly addressing the reporting delay and ascertainment bias.

Methods

Using weekly incidence of suspected cases, updated as a revised epidemic curve every week, the reporting delay was explicitly incorporated into the estimation model. Using the weekly case fatality risk as calculated by the World Health Organization, ascertainment bias was adjusted, enabling us to parameterize the family of logistic curves (i.e., logistic and generalized logistic models) for describing the unbiased incidence in 2017.

Results

The cumulative incidence at the end of the epidemic, was estimated at 790,778 (95% CI: 700,495, 914,442) cases and 767,029 (95% CI: 690,877, 871,671) cases, respectively, by using logistic and generalized logistic models. It was also estimated that we have just passed through the epidemic peak by week 26, 2017. From week 27 onwards, the weekly incidence was predicted to decrease.

Conclusions

Cholera epidemic in Yemen, 2017 was predicted to soon start to decrease. If the weekly incidence is reported in the up-to-the-minute manner and updated in later weeks, not a single data point but the entire epidemic curve must be precisely updated.

     

NPIDB: a database of nucleic acids-protein interactions

The database NPIDB (Nucleic Acids-Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from PDB (1834 complexes in July 2007). It is organized as a collection of files in PDB format and is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. The content of the database is weekly updated. AVAILABILITY: http://monkey.belozersky.msu.ru/NPIDB/     

Microcomputer programs for DNA sequence analysis.

Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system.     

Failure-Atomic File Access in the Slice Interposed Network Storage System

This paper presents a recovery protocol for block I/O operations in Slice, a storage system architecture for high-speed LANs incorporating network-attached block storage. The goal of the Slice architecture is to provide a network file service with scalable bandwidth and capacity while preserving compatibility with off-the-shelf clients and file server appliances. The Slice prototype virtualizes the Network File System (NFS) protocol by interposing a request switching filter at the client's interface to the network storage system. The distributed Slice architecture separates functions typically combined in central file servers, introducing new challenges for failure atomicity. This paper presents a protocol for atomic file operations and recovery in the Slice architecture, and related support for reliable file storage using mirrored striping. Experimental results from the Slice prototype show that the protocol has low cost in the common case, allowing the system to deliver client file access bandwidths approaching gigabit-per-second network speeds.     

UNDERGRADUATE PSYCHIATRIC EDUCATION—Senior Medical Students Study Patients with the Clinical Team

A course in psychiatry for senior medical students, designed to give all members of the class some direct experience, particularly in therapeutic interviewing as well as in total psychiatric study of patients by the clinically integrated work of medical specialists, psychiatric social workers, and clinical psychologists in collaboration with psychotherapeutically trained and experienced psychiatrists is conducted in the following manner: A third of the class, about 25 students, is divided into four sections of six or seven members, and each section attends five hours one forenoon a week for approximately three months. Each student, after an initial demonstration interview by the instructor, sees weekly the same two clinic patients alone, for 45-minute individual interviews, followed by a one and a half hour supervisory session. After this a 50-minute seminar or treatment review conference is followed by a similar period for writing records of interviews and summaries of the therapeutic work. Of four seminars, two are conducted by the psychiatric faculty, and one each by the social worker and the psychologist. Each student reads a written summary of all his interviews with one patient for discussion by his colleagues in the section and by the faculty from all three disciplines.     

DOCKGROUND resource for studying protein-protein interfaces

MOTIVATION: Public resources for studying protein interfaces are necessary for better understanding of molecular recognition and developing intermolecular potentials, search procedures and scoring functions for the prediction of protein complexes. RESULTS: The first release of the DOCKGROUND resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes, providing foundation for the upcoming expansion to unbound (experimental and simulated) protein-protein complexes, modeled protein-protein complexes and systematic sets of docking decoys. The bound-bound part of DOCKGROUND is a relational database of annotated structures based on the Biological Unit file (Biounit) provided by the RCSB as a separated file containing probable biological molecule. DOCKGROUND is automatically updated to reflect the growth of PDB. It contains 67,220 pairwise complexes that rely on 14,913 Biounit entries from 34,778 PDB entries (January 30, 2006). The database includes a dynamic generation of non-redundant datasets of pairwise complexes based either on the structural similarity (SCOP classification) or on user-defined sequence identity. The growing DOCKGROUND resource is designed to become a comprehensive public environment for developing and validating new methodologies for modeling of protein interactions. AVAILABILITY: DOCKGROUND is available at http://dockground.bioinformatics.ku.edu. The current first release implements the bound-bound part.     

NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single‐sample estimators (updated versions of the linkage disequilibrium and heterozygote‐excess methods, and a new method based on molecular coancestry), as well as the two‐sample (moment‐based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross‐method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.