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PubMed1997

Transcriptional strategy of closteroviruses: mapping the 5' termini of the citrus tristeza virus subgenomic RNAs.

Citrus tristeza virus (CTV) induces formation of a nested set of at least nine 3' coterminal subgenomic RNAs (sgRNAs) in infected tissue. The organization and expression of the 19,296-nucleotide (nt) CTV genome resembles that of coronaviruses, with polyprotein processing, translational frameshifting, and multiple sgRNA formation, but phylogenetically the CTV polymerase, like polymerases of other closteroviruses, belongs to the Sindbis virus-like lineage of RNA virus polymerases. Both positive-strand RNA virus supergroups, coronaviruses and Sindbis-like viruses, utilize different mechanisms of transcription. To address the mechanism of CTV transcription, 5' termini for the two most abundant sgRNAs, 1.5 and 0.9 kb, respectively, were mapped by runoff reverse transcription. The two sgRNAs were demonstrated to have 48- and 38-nt 5' untranslated regions (5'-UTRs), respectively. The 5'-UTR for the 1.5-kb RNA was cloned, sequenced, and demonstrated to be colinear with the 48-nt genomic sequence upstream of the initiator codon of the respective open reading frame 10, i.e., to be of continuous template origin. The data obtained suggest that the sgRNA transcription of CTV is dissimilar from the coronavirus transcription and consistent with the transcriptional mechanism of other Sindbis-like viruses. Thus, the Sindbis virus-like mechanism of transcription of the positive-strand RNA genomes might be successfully utilized by the closterovirus genome of up to 19.3 kb with multiple sgRNAs.

Base Sequence↗

PubMed1986

Eosinophilic myositis and muscular sarcocystosis in the carcasses of slaughtered cattle and lambs.

Fifty-three bovine and 7 ovine carcasses condemned for having eosinophilic myositis were evaluated. Four (7.3%) of the bovine carcasses had a few, large local lesions in skeletal muscles (category A), and 49 (92.7%) of the bovine carcasses and 7 (100%) of the ovine carcasses had multiple, small, disseminated lesions in tongue, esophagus, heart, diaphragm, or skeletal muscles (category B). Tissue from carcasses of category B were evaluated for bacteria, viruses, selenium, and pathologic changes. Pathogenic bacteria and viruses were not isolated and selenium concentrations were normal. In category B, all carcasses had granulomas; of the 49 bovine carcasses and 7 ovine carcasses, 38 (77.6%) and 7 (100%), respectively, had one or more granulomas with opened dead sarcocysts. The data indicated that opened sarcocysts killed the host myocyte and adjacent myocytes and stroma, thereby initiating granuloma formation.

Animals↗

PubMed2006

Case-control comparison of laparoscopic versus open distal pancreatectomy.

Laparoscopic distal pancreatectomy is becoming an increasingly used modality in the surgical treatment of pancreatic disease. The assumption is that this will lead to shorter hospitalization and faster recovery. However, actual comparative data between open and laparoscopic distal pancreatectomy is lacking. The purpose of this study is to compare these surgical procedures. All patients who underwent either laparoscopic or open distal pancreatectomy/splenectomy were reviewed. Fifteen patients underwent laparoscopic resection, whereas 41 underwent an open resection. The 15 laparoscopic patients were matched to 15 open patients for age, gender, and pancreatic pathology. Data gathered included length of stay, pancreatic leak, postoperative complications, and return to normal activity. Of the 15 laparoscopic patients, three were converted to open operations. Laparoscopic patients had a median length of stay of 5 days (range, 3-9) compared with 8 days (range, 6-23) for the open patients (P = 0.02). The pancreatic leak rate was 13% in each group. Overall postoperative complication rate was 20% in the laparoscopic group compared with 27% in the open group. Laparoscopic patients reported a return to normal activity in 3 weeks (range, 2-7) compared with 6 weeks (range, 4-10) for open patients (P = 0.03). Laparoscopic distal pancreatectomy/splenectomy does lead to shorter hospital stay and faster return to normal activity. Pancreatic leak rate and overall complication rate appear similar.

Aged↗

PubMed2004

MedlineR: an open source library in R for Medline literature data mining.

SUMMARY: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed database; to construct the co-occurrence matrix; and to visualize the network topology of query terms. The open source nature of this library allows users to extend it freely in the statistical programming language of R. To demonstrate its utility, we have built an application to analyze term-association by using only 10 lines of code. We provide MedlineR as a library foundation for bioinformaticians and statisticians to build more sophisticated literature data mining applications. AVAILABILITY: The library is available from http://dbsr.duke.edu/pub/MedlineR.

Abstracting and Indexing↗

PubMed1996

Infection after open reduction and internal fixation with dynamic compression plates--clinical and experimental data.

Infection rates for open reduction and internal fixation (ORIF) with the DCP in clinical studies are based on heterogeneous data on general risk factors and do not take into account the direct effect of the implant (material, design, surface, technique). The initial degree of bacterial contamination is generally unknown and the applied definition of the term infection is not mentioned. In our own prospective randomized clinical study including 281 cases of ORIF with the DCP (154 steel vs 127 titanium), the influence of the implant material on susceptibility to local infection was examined in relation to initial bacteria contamination (109 non-contaminated / 172 contaminated). Although in the group of contaminated DCPs the difference in the infection rates for stainless steel (sSt) and commercially pure titanium (cpTi) showed no statistical significance, a tendency was apparent. In an animal experiment, the lower rates of infection for c.p.Ti-DCP compared to sSt-DCP in the presence of a local bacterial challenge could be demonstrated with statistical significance. The need for further experimental research in the field of implant related local infection after ORIF will be discussed and strategies for further investigations proposed.

Animals↗

PubMed2006

Surgical Infection Society guideline: prophylactic antibiotic use in open fractures: an evidence-based guideline.

BACKGROUND: Prolonged courses of broad-spectrum antibiotics are often cited as the standard of care for prevention of infective complications of open fractures. The origins of these recommendations are obscure, however, and multi-drug-resistant systemic infections attributable to antibiotic overuse are common life-threatening problems in current intensive care unit practice. OBJECTIVE: To review systematically the effects of prophylactic antibiotic administration on the incidence of infections complicating open fractures. DATA SOURCES: Computerized bibliographic search of published research and citation review of relevant articles. STUDY SELECTION: All published clinical trials claiming to evaluate, or cited elsewhere as being authoritative regarding, the role of antibiotics in open fracture management were identified and then evaluated according to published guidelines for evidence-based medicine. Only small studies (<20 patients), practice surveys, pharmacokinetic studies, and reviews or duplicative publications presenting primary data already considered were excluded from analysis. DATA EXTRACTION: Information on demographics, study dates, fracture grade, antibiotic type, duration and route of administration, surgical interventions, infection-related outcomes, and the methodologic quality of the studies was extracted by the authors. The primary results were submitted to the Therapeutic Agents Committee of the Surgical Infection Society for review prior to creation of the final consensus document. DATA SYNTHESIS: Current antibiotic management of open fractures is based on a small number of studies that generally are more than 30 years old and do not reflect current management priorities in trauma and critical care. With a few noteworthy exceptions, these primary studies suffer from a variety of methodologic problems, including co-mingling of prospective and retrospective data sets, absence of or inappropriate statistical analysis, lack of blinding, or failure of randomization. CONCLUSIONS: The data support the conclusion that a short course of first-generation cephalosporins, begun as soon as possible after injury, significantly lowers the risk of infection when used in combination with prompt, modern orthopedic fracture wound management. There is insufficient evidence to support other common management practices, such as prolonged courses or repeated short courses of antibiotics, the use of antibiotic coverage extending to gram-negative bacilli or clostridial species, or the use of local antibiotic therapies such as beads. Large, randomized, blinded trials are needed to prove or disprove the value of these traditional approaches. Such trials should be performed in patients with high-grade fractures who (1) are well-stratified according to the degree of local injury and (2) undergo standardized fracture and wound management. Trials also must be powered to study the effects of extended antibiotic coverage on nosocomial infections. Antibiotic regimens confirmed to improve local fracture outcomes in such studies could then be used rationally, balancing the risks of local fracture-related infections and of multi-drug-resistant systemic infections to achieve optimal global outcomes.

Antibiotic Prophylaxis↗

PubMed1997

An open distributed medical image and signal data server network with World Wide Web front-end.

In modern patient care and medical research diagnostic imaging from multiple modalities plays an essential role. In general these digital image data are acquired at different locations. An efficient access to the data via network is often not provided due to technical, organisational and political reasons. This article presents an approach to solve the problem by means of an open distributed data server network with Web-based front-ends and describes the prototype DACHS that has been developed at the University Hospital of the Technical University of Munich.

Computer Communication Networks↗

PubMed2002

Cueing unavoidable physical but not emotional stress increases long-term behavioural effects in rats.

Cueing a stressor can influence the perception of and the direct reaction to a stressor. Until now, only the direct reaction of an animal to the cue or to the subsequent stressor has been examined. This experiment assesses the long-term behavioural effects of cueing two different stressors. Rats were exposed to physical stress (PS) or emotional stress (ES) in a two-compartment box for 5 consecutive days. PS rats daily received mild foot shocks during 10 min. ES rats were forced to witness the PS rats being foot shocked. A control group was placed in the same box without receiving shocks. Every foot shock was either cued or not cued with a 3-s light signal. In an additional experiment the effect of longer and stronger foot shocks was also investigated. Effects of stress treatments were measured 5 days after the last stress session in a small open field. Data showed that PS and ES had opposite long-term effects on open field activity (activity PS decreased and ES increased). Cueing stress resulted in a more pronounced effect in the PS, but not in the ES group. Presenting the light signal during emotional stress and control treatment resulted in an overall behavioural activation in the open field. All animals were exposed to the light stimulus in an open field after habituation. Both PS groups showed less active exploration during the test, while all cue-naïve animals showed more ambulations. No emotional stress effect was present. The direct reaction of the animals to the cue also differed with treatment: cued PS animals became inactive, while animals of all other groups primarily reacted with active exploration. Increasing the intensity of the foot shocks resulted in an increased physical stress effect, similar to cued physical stress; no effect was found on emotional stress effects. The results indicated that stress associated cues can increase the long-term behavioural effects of physical but not of emotional stress. Exposure to the cue induces a conditioned response in the cued PS group. Witnessing cued or more severe stressors did not influence the emotional stress effect. The findings again demonstrate that emotional and physical stressors are fundamentally different.

Acoustic Stimulation↗

PubMed2002

Generation of multiple isoforms of eukaryotic translation initiation factor 4GI by use of alternate translation initiation codons.

Eukaryotic translation initiation factor 4GI (eIF4GI) is an essential protein that is the target for translational regulation in many cellular processes and viral systems. It has been shown to function in both cap-dependent and cap-independent translation initiation by recruiting the 40S ribosomal subunit to the mRNA cap structure or internal ribosome entry site (IRES) element, respectively. Interestingly eIF4GI mRNA itself has been reported to contain an IRES element in its 5' end that facilitates eIF4GI protein synthesis via a cap-independent mechanism. In HeLa cells, eIF4GI exists as several isoforms that differ in their migration in sodium dodecyl sulfate (SDS) gels; however, the nature of these isoforms was unclear. Here, we report a new cDNA clone for eIF4GI that extends the 5' sequence 340 nucleotides beyond the previously published sequence. The new extended sequence of eIF4GI is located on chromosome 3, within two additional exons immediately upstream of the previously published eIF4GI sequence. When mRNA transcribed from this cDNA clone was translated in vitro, five eIF4GI polypeptides were generated that comigrated in SDS-polyacrylamide gels with the five isoforms of native eIF4GI. Furthermore, translation of eIF4GI-enhanced green fluorescent protein fusion constructs in vitro or in vivo generated five isoforms of fusion polypeptides, suggesting that multiple isoforms of eIF4GI are generated by alternative translation initiation in vitro and in vivo. Mutation of two of the five in-frame AUG residues in the eIF4GI cDNA sequence resulted in loss of corresponding polypeptides after translation in vitro, confirming alternate use of AUGs as the source of the multiple polypeptides. The 5' untranslated region of eIF4GI mRNA also contains an out-of-frame open reading frame (ORF) that may down-regulate expression of eIF4GI. Further, data are presented to suggest that a proposed IRES embedded in the eIF4GI ORF is able to catalyze synthesis of multiple eIF4GI isoforms as well. Our data suggest that expression of the eIF4GI isoforms is partly controlled by a complex translation strategy involving both cap-dependent and cap-independent mechanisms.

5' Untranslated Regions↗

PubMedDate not supplied

Characterization of a fragment containing a putative TLP cDNA sequence.

With the aim of isolating the Tumor Liberated Protein (TLP) gene, reverse transcription-polymerase chain reaction (RT-PCR) was used to isolate a approximately equal to 500 bp fragment containing a putative TLP cDNA sequence. Total RNAs were extracted from several cell lines with RNAzol B reagent (Tel-Test, Inc) and reverse transcribed using the Reverse Transcription System (Promega). PCR was carried out for 35 cycles (1 minute at 95 degrees C, 2 minutes at 40 degrees C and 1 minute at 72 degrees C) using an upstream degenerate oligonucleotide, ACN AAY AAR GAR GCN TCN ATG TG, which corresponds to the amino acid sequence T N K E A S I, and random hexamers as the downstream primer. PCR products were electrophoresed on a 1% agarose gel containing ethidium bromide. The PCR products were cloned in the pGEM-T easy vector (PROMEGA) and the resulting plasmid clones were sequenced with the chain termination method using the Applied Biosystems model 373A DNA sequencer. A putative open reading frame was deducted. The results obtained can be considered as preliminary data that will require more investigation in order to confirm them. We propose to continue the studies to verify that TLP could be a diagnostic marker in human cancer.

Amino Acid Sequence↗

PubMed1989

Open reduction of mandibular condyle fractures. Indications and technique.

The traditional approach of closed reduction for condylar fractures has proved to be effective in an overwhelming majority of patients, but not in all. Some authors have proposed open reduction in selected cases. At present, there are no long-term data supporting open reduction to prevent future joint problems. In view of this, I believe that the best overall indication for open reduction is the surgical need to place the face or jaws in the proper functional position.

Fracture Fixation, Internal↗

PubMed2005

Final Aperture Superposition Technique applied to fast calculation of electron output factors and depth dose curves.

The Final Aperture Superposition Technique (FAST) is described and applied to accurate, near instantaneous calculation of the relative output factor (ROF) and central axis percentage depth dose curve (PDD) for clinical electron beams used in radiotherapy. FAST is based on precalculation of dose at select points for the two extreme situations of a fully open final aperture and a final aperture with no opening (fully shielded). This technique is different than conventional superposition of dose deposition kernels: The precalculated dose is differential in position of the electron or photon at the downstream surface of the insert. The calculation for a particular aperture (x-ray jaws or MLC, insert in electron applicator) is done with superposition of the precalculated dose data, using the open field data over the open part of the aperture and the fully shielded data over the remainder. The calculation takes explicit account of all interactions in the shielded region of the aperture except the collimator effect: Particles that pass from the open part into the shielded part, or visa versa. For the clinical demonstration, FAST was compared to full Monte Carlo simulation of 10 x 10, 2.5 x 2.5, and 2 x 8 cm2 inserts. Dose was calculated to 0.5% precision in 0.4 x 0.4 x 0.2 cm3 voxels, spaced at 0.2 cm depth intervals along the central axis, using detailed Monte Carlo simulation of the treatment head of a commercial linear accelerator for six different electron beams with energies of 6-21 MeV. Each simulation took several hours on a personal computer with a 1.7 Mhz processor. The calculation for the individual inserts, done with superposition, was completed in under a second on the same PC. Since simulations for the pre calculation are only performed once, higher precision and resolution can be obtained without increasing the calculation time for individual inserts. Fully shielded contributions were largest for small fields and high beam energy, at the surface, reaching a maximum of 5.6% at 21 MeV. Contributions from the collimator effect were largest for the large field size, high beam energy, and shallow depths, reaching a maximum of 4.7% at 21 MeV. Both shielding contributions and the collimator effect need to be taken into account to achieve an accuracy of 2%. FAST takes explicit account of the shielding contributions. With the collimator effect set to that of the largest field in the FAST calculation, the difference in dose on the central axis (product of ROF and PDD) between FAST and full simulation was generally under 2%. The maximum difference of 2.5% exceeded the statistical precision of the calculation by four standard deviations. This occurred at 18 MeV for the 2.5 x 2.5 cm2 field. The differences are due to the method used to account for the collimator effect.

Algorithms↗

PubMed2001

The evolving role of topiramate among other mood stabilizers in the management of bipolar disorder.

OBJECTIVES: Topiramate, a structurally novel anticonvulsant, is being evaluated for other neurological conditions such as migraine, neuropathic pain, and essential tremor, and also for psychiatric conditions such as bipolar disorder, bulimia, post-traumatic stress disorder, and schizoaffective disorder, in addition to obesity. This article will focus on the use of topiramate for bipolar disorder. METHODS: The pharmacological profile of topiramate is compared to other established and putative mood stabilizers, and a rationale for its use in bipolar disorder is presented. Data from open clinical trials of topiramate for depression, mania, and rapid-cycling bipolar disorder are summarized. Preliminary data from one pilot dose-finding, double-blind, random-assignment, placebo-controlled, 3-week parallel group study of two doses of topiramate for acute bipolar I mania is reported. Safety data regarding topiramate was reviewed. Finally, the potential place of this agent in bipolar illness is considered. RESULTS: The pharmacological advantages for topiramate are low protein binding, minimal hepatic metabolism and mainly unchanged renal excretion, a 24-h half-life, and minimal drug interactions. Open clinical studies suggest a 50-65% response for refractory bipolar mania, and a 40-56% response for refractory bipolar depression in mainly add-on treatment. Open clinical studies of topiramate for rapid-cycling subjects and those for comorbid bulimia, substance abuse, post-traumatic stress, migraine, and obesity report effectiveness. The primary efficacy endpoint data (change from baseline Y-MRS total scores) of the placebo-controlled, random assignment parallel group phase II dose-finding study were not statistically significant. However, once the antidepressant-associated manias (28 of the sample, of 97 subjects) were excluded from the controlled study, the post-hoc analyses indicated the higher dose (512 mg/day) topiramate treatment group showed a statistically significant reduction in endpoint Y-MRS change scores as compared to placebo (p < 0.03). Adverse effects of topiramate in bipolar subjects include attention, concentration and memory problems, fatigue, sedation, transient paraesthesias, nausea, and anorexia. Some subjects experience word-finding difficulty. Weight loss may be seen in several topiramate-treated subjects with bipolar disorder. CONCLUSIONS: Topiramate appears to show promise as an addition to the agents available to treat bipolar disorder. More definitive controlled data on the efficacy of topiramate in the acute and continuation phases as well as for the prophylaxis either as monotherapy or as combination treatment of bipolar disorder are ongoing, and the results are awaited.

Acetates↗

PubMed1999

[Epidemiology of open globe injuries].

BACKGROUND: Severe open globe injuries are frequent emergencies in an ophthalmologic clinic and required immediate operation. The extent of these injuries is various depending on the mechanism of the injury and involvement of ocular tissue. In many cases a full visual rehabilitation can be achieved but in a lot of cases blindness results. To prevent such severe eye injuries it is important to judge the leading injury mechanisms. For this we collected our data about open globe injuries. PATIENTS AND METHODS: Retrospectively we collected the data from 103 consecutive patients in the year 1996 and 1997, presenting with an open globe eye injury followed by operation. The data contained personal patients data, information about mechanism of injury, visual acuity, operation and rehabilitation. Statistical analysis was performed using binomimal-test and t-test for paired and unpaired samples (p < 0.05). RESULTS: 85.4% were male. Most of the injuries happened at home (38%) and at the working place (31%). Assaultive injuries happened in 6.8%. 35% of all patients were craftmen (mechanics, electricians, or the locksmith were preferred). Pensioners were affected in 14.6% of all cases followed by small children (7.8%) and school children (7.8%). In 50% of all cases metal and glass were responsible for the trauma, explosions were noticed in 8.7%. An intraocular foreign body was found in 37.9%. In 62% of all cases no second operation was necessary. An enucleation during the follow-up was performed in 2 cases. CONCLUSION: At least a third of all severe eye injuries would have been preventable. Concerning the non-preventable injuries accidents at home and in children were predominating. The rate of the open globe injuries was 2.32 in 100.000 people, which is about the same like in US-American studies. Most of the injuries happened at home because of carelessness and would have been avoidable. The rate of injuries at the working place is significantly higher than in the USA but there were significantly more gun-shot-injuries or offensive accidents abroad. The rate of accidents at home and in traffic were the same. We think that public campaigns and prevention strategies can help to reduce the potential risk of severe eye injuries.

Accidents, Home↗

PubMed2000

Detection, cloning, and sequence analysis of an indigenous plasmid from cellulolytic clostridial strain MCF1.

Nucleotide sequence analysis of a 2451-bp plasmid (pMCF1) from a cellulolytic Clostridium revealed that the protein specified by the largest open reading frame (ORF1) was homologous to RepB of Clostridium butyricum plasmid pCB101. The data suggest that pMCF1 belongs to the pC194 family of rolling-circle replicating plasmids and the ORF1 protein functions as its replication protein.

Amino Acid Motifs↗

PubMedDate not supplied

A wavelet, fourier, and PCA data analysis pipeline: application to distinguishing mixtures of liquids.

Using a new optical engineering technique for the "fingerprinting" of beverages and other liquids, we study and evaluate a range of features. The features are based on resolution scale, invariant frequency information, entropy, and energy. They allow mixtures of beverages to be very precisely placed in principal component plots used for the data analysis. To show this we make use of data sets resulting from optical/near-infrared and ultrasound sensors. Our liquid "fingerprinting" is a relatively open analysis framework in order to cater for different practical applications, in particular, on one hand, discrimination and best fit between fingerprints, and, on the other hand, more exploratory and open-ended data mining.

Journal Article↗

PubMed2006

Midterm follow-up of a single-center experience of endovascular repair of abdominal aortic aneurysms with use of the Talent stent-graft.

PURPOSE: To review the midterm results of endovascular aneurysm repair (EVAR) of abdominal aortic aneurysms (AAAs) with the Talent stent-graft. MATERIALS AND METHODS: All patients who underwent EVAR of AAAs with Talent stent-grafts from February 1998 to April 2002 at a single institution were monitored for a minimum of 2 years or until an endpoint of death or rupture was reached. RESULTS: There were 68 eligible patients, who were monitored for a mean period of 39 months (range, 24-72 months). Forty-nine (72.9%) were alive at 2 years; among the 19 deaths, two resulted from aneurysm rupture and the other 17 were unrelated to EVAR. There was one immediate conversion to open repair and five primary proximal endoleaks; the remaining 62 patients (91.2%) all had a technically successful procedure. There were 33 endoleaks during follow-up: 23 (69.7%) were treated conservatively and 10 (30.3%) underwent secondary intervention in the form of embolization (n=2), attempted embolization (n=2), endovascular stent-graft placement (n=3), combined stent-graft placement and embolization (n=1), or surgical conversion (n=2). Overall, there were five persistent endoleaks, and the remaining patients were free of endoleak at their last review or endpoint. Three stent-grafts migrated and required further endovascular intervention. Wire fracture was seen in two stents but presented no clinical sequelae. There was one case of graft limb thrombosis that required surgical thrombectomy. CONCLUSIONS: EVAR of AAAs with use of the Talent stent-graft is a promising and acceptable alternative to open surgery. Our 30-day mortality rate of zero compares extremely well with historical data from open surgery and the findings of more recently published trials. The risk of endoleak and uncertainty over durability require long-term surveillance.

Aged↗

PubMed1998

The YGR194c (XKS1) gene encodes the xylulokinase from the budding yeast Saccharomyces cerevisiae.

We report the finding of a Saccharomyces cerevisiae gene necessary for growth in culture media with D-xylulose as the sole carbon source. This gene corresponds to the YGR194c open reading frame that we have previously described, and it is renamed now XKS1. Data bank comparisons of the protein encoded by the XKS1 gene showed significant homology with different xylulokinases, indicating a possible role in xylulose phosphorylation. The wild-type gene in a centromeric plasmid complemented defective growth of xks1 S. cerevisiae mutant strains in xylulose. By contrast, overexpression negatively influenced cell growth in this carbon source.

Amino Acid Sequence↗