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PubMed1991

A sequence assembly and editing program for efficient management of large projects.

We describe a sequence assembly and editing program for managing large and small projects. It is being used to sequence complete cosmids and has substantially reduced the time taken to process the data. In addition to handling conventionally derived sequences it can use data obtained from Applied Biosystems,Inc. 373A and Pharmacia A.L.F. fluorescent sequencing machines. Readings are assembled automatically. All editing is performed using a mouse operated contig editor that displays aligned sequences and their traces together on the screen. The editor, which can be used on single contigs or for joining contigs, permits rapid movement along the aligned sequences. Insertions, deletions and replacements can be made in individual aligned readings and global changes can be made by editing the consensus. All changes are recorded. A click on a mouse button will display the traces covering the current cursor position, hence allowing quick resolution of problems. Another function automatically moves the cursor to the next unresolved character. The editor also provides facilities for annotating the sequences. Typical annotations include flagging the positions of primers used for walking, or for marking sites, such as compressions, that have caused problems during sequencing. Graphical displays aid the assessment of progress.

Base Sequence↗
PubMed2002

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.

BACKGROUND: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs. RESULTS: I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N) memory complexity, at the expense of a small constant factor in time. CONCLUSIONS: Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.

Algorithms↗
PubMed2003

Characteristics of effective and efficient rehabilitation programs.

OBJECTIVE: To investigate the characteristics of rehabilitation hospitals and units correlated with gains in motor and cognitive function, after adjusting for case severity of the patients admitted and for length of stay (LOS). DESIGN: The Uniform Data System for Medical Rehabilitation (UDSMR) database was first analyzed to develop a method of adjusting for patient case severity on admission. Rehabilitation programs were surveyed to assess characteristics commonly thought to be associated with efficiency and effectiveness. Data on these characteristics were linked to UDSMR data on patient characteristics and functional gain. SETTING: Seventy-seven rehabilitation hospitals across the United States. PARTICIPANTS: A total of 37,692 inpatients from the participating rehabilitation hospitals. INTERVENTION: Comprehensive rehabilitation programs not altered by researcher. MAIN OUTCOME MEASURES: Program effectiveness was estimated by gains in motor and cognitive subscale scores of the FIM trade mark instrument between admission and discharge, adjusted for indicators of caseload severity at admission. Efficiency was estimated by adjusting gains for LOS as well. RESULTS: Primary factors affecting both motor and cognitive gains included admission function (treated curvilinearly), age, certain diagnostic distinctions, onset-admission interval, admission class, and LOS. Correlations between staffing intensity and numerous other program characteristics with functional gain were meager, each accounting for less than 2% of variance. LOS was predicted by a number of factors, notably by the percentage of managed care cases (r=-.20), but not by staffing intensity. CONCLUSIONS: Relationships between rehabilitation practices and functional gains by patients do not appear to be simple or overt. Continued research is needed to identify reliable connections between rehabilitative processes and patient outcomes in practice.

Aged↗
PubMed2000

The virtual NMR spectrometer: a computer program for efficient simulation of NMR experiments involving pulsed field gradients.

This paper presents a software program, the Virtual NMR Spectrometer, for computer simulation of multichannel, multidimensional NMR experiments on user-defined spin systems. The program is capable of reproducing most features of the modern NMR experiment, including homo- and heteronuclear pulse sequences, phase cycling, pulsed field gradients, and shaped pulses. Two different approaches are implemented to simulate the effect of pulsed field gradients on coherence selection, an explicit calculation of all coherence transfer pathways, and an effective approximate method using integration over multiple positions in the sample. The applications of the Virtual NMR Spectrometer are illustrated using homonuclear COSY and DQF COSY experiments with gradient selection, heteronuclear HSQC, and TROSY. The program uses an intuitive graphical user interface, which resembles the appearance and operation of a real spectrometer. A translator is used to allow the user to design pulse sequences with the same programming language used in the actual experiment on a real spectrometer. The Virtual NMR Spectrometer is designed as a useful tool for developing new NMR experiments and for tuning and adjusting the experimental setup for existing ones prior to running costly NMR experiments, in order to reduce the setup time on a real spectrometer. It will also be a useful aid for learning the general principles of magnetic resonance and contemporary innovations in NMR pulse sequence design.

Algorithms↗
PubMed1974

Rural health care in Mexico?

A very large percentage of Mexico's population living in rural areas lacks resources for health care. Any new effort to provide such care must emphasize the health of the infant population because of the high percentage of infants in the country. Plans made at the national level have not been correlated with the conditions that exist in rural areas. For example, the majority of university programs are oriented toward urban medical practice, and the construction of more schools of medicine to solve the problem of doctors in rural areas is based on a mistaken premise. This problem has not been solved even in developed countries such as the United States where, as in Mexico, graduates in medicine migrate to the cities where optimal conditions are met for practicing the type of medicine for which they have been trained. Furthermore, it is both expensive and illogical to maintain urban doctors in rural areas where they cannot practice their profession for lack of resources; to do so is to deny the purpose of their education (27). Conventional schools of medicine, for reasons of investment and of structure, should teach only very selected groups of students who, on finishing their training, are fully capacitated to practice specialized medicine. A different system is required if we are to provide adequate health care in the rural communities. A system such as that described herein, adapted to the real need of rural communities, would avoid the necessity to create dysfunctional bureaucracies and would not destroy those institutions which have proved useful in the past. This study should be considered as one of the many pilot programs that should be initiated in order to determine the type of program that would best solve the problem of health care in rural Mexico. Other programs already being considered at the National Autonomous University of Mexico include the A36 plan of the Faculty of Medicine, now in operation; the work of C. Biro carried out in Netzahualcoyotl City (both focused on providing medical care to the urban poor); and the Open University program. Unless an efficient program designed to meet the needs of rural communities is quickly put into operation, Mexico will, in the near future, be facing the same problems now confronting Southeast Asia.

Community Medicine↗
PubMedDate not supplied

The use of efficiency linear programs for sensitivity analysis in medical decision making.

Sensitivity analysis in most medical problems is a complex process involving repeated calculations that can be computationally cumbersome, and its results are only approximate. The authors present a linear program-based approach that reveals the optimum strategies in a decision problem when event probabilities are not known exactly but their value ranges are available. Its application in a clinical decision-making situation is demonstrated. The approach promises to provide a flexible, precise, and computationally efficient technique for sensitivity analysis in medical decision making.

Aged↗
PubMedDate not supplied

Management of neonatal hip instability: an analysis of the efficiency in a consistent treatment program.

The efficiency of a consistent treatment program for children with neonatal hip instability (NHI) was analyzed. Of 165 children who were referred to the orthopedic department with suspected NHI, 91 children had unstable hips and were treated with a von Rosen splint for 8 weeks; 74 children were found to have stable hips and were not treated, but were followed up in the same way as the treated children. All treated and untreated children developed clinically and radiologically normal hips. Treatment with a von Rosen splint is reliable, and with few exceptions 8 weeks is sufficient time for treatment of NHI.

Child, Preschool↗
PubMed2003

The public health benefits of insulation retrofits in existing housing in the United States.

BACKGROUND: Methodological limitations make it difficult to quantify the public health benefits of energy efficiency programs. To address this issue, we developed a risk-based model to estimate the health benefits associated with marginal energy usage reductions and applied the model to a hypothetical case study of insulation retrofits in single-family homes in the United States. METHODS: We modeled energy savings with a regression model that extrapolated findings from an energy simulation program. Reductions of fine particulate matter (PM2.5) emissions and particle precursors (SO2 and NOx) were quantified using fuel-specific emission factors and marginal electricity analyses. Estimates of population exposure per unit emissions, varying by location and source type, were extrapolated from past dispersion model runs. Concentration-response functions for morbidity and mortality from PM2.5 were derived from the epidemiological literature, and economic values were assigned to health outcomes based on willingness to pay studies. RESULTS: In total, the insulation retrofits would save 800 TBTU (8 x 10(14) British Thermal Units) per year across 46 million homes, resulting in 3,100 fewer tons of PM2.5, 100,000 fewer tons of NOx, and 190,000 fewer tons of SO2 per year. These emission reductions are associated with outcomes including 240 fewer deaths, 6,500 fewer asthma attacks, and 110,000 fewer restricted activity days per year. At a state level, the health benefits per unit energy savings vary by an order of magnitude, illustrating that multiple factors (including population patterns and energy sources) influence health benefit estimates. The health benefits correspond to 1.3 billion dollars per year in externalities averted, compared with 5.9 billion dollars per year in economic savings. CONCLUSION: In spite of significant uncertainties related to the interpretation of PM2.5 health effects and other dimensions of the model, our analysis demonstrates that a risk-based methodology is viable for national-level energy efficiency programs.

Air Pollution, Indoor↗
PubMedDate not supplied

Programming for efficiency: the effects of motion economy on vocational tasks for adults with severe and profound mental retardation.

Principles of motion economy were assessed with two vocational tasks for two adults with severe to profound mental retardation. Study 1 assessed task acquisition by comparing two tasks (collating three pages, bagging three ribbons), one task trained using the standard job site task analysis, the other trained using a motion economy-based task analysis (requiring less total distance movement to task completion) in two alternating treatments designs. Study 2 assessed task fluency by examining the effects of the motion economy-based task analysis on collating and bagging separately across the same two adults in four reversal designs. Neither task analysis was superior overall in acquisition (Study 1), but once each task was mastered, the motion economy-based task analysis enhanced fluency across both tasks for both participants (Study 2). The use of distance movement as a parameter of response efficiency is discussed when targeting job performance, productivity, and preference.

Adult↗
PubMed2002

Fully human, HLA-DR-specific monoclonal antibodies efficiently induce programmed death of malignant lymphoid cells.

The Human Combinatorial Antibody Library (HuCAL) was screened for antibodies specific to human leukocyte antigen-DR (HLA-DR) that induce programmed death of lymphoma/leukemia cells expressing the target antigen. The active Fab fragments were affinity-matured, and engineered to IgG(4) antibodies of sub-nanomolar affinity. The antibodies exhibited potent in vitro tumoricidal activity on several lymphoma and leukemia cell lines and on chronic lymphocytic leukemia patient samples. They were also active in vivo in xenograft models of non-Hodgkin lymphoma. Cell death occurred rapidly, without the need for exogenous immunological effector mechanisms, and was selective to activated/tumor-transformed cells. Although the expression of HLA-DR on normal hematopoietic cells is a potential safety concern, the antibodies caused no long-lasting hematological toxicity in primates, in vivo. Such monoclonal antibodies offer the potential for a novel therapeutic approach to lymphoid malignancies.

Animals↗