bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
Authors: Meinicke Peter , Tech Maike , Morgenstern Burkhard , Merkl Rainer 
Published: November 2004

Abstract
Background
Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations in terms of positional and compositional variability of the underlying biological signals.

Results
We propose a kernel-based approach to datamining on biological sequences. With our method it is possible to model and analyze positional variability of oligomers of any length in a natural way. On one hand this is achieved by mapping the sequences to an intuitive but high-dimensional feature space, well-suited for interpretation of the learnt models. On the other hand, by means of the kernel trick we can provide a general learning algorithm for that high-dimensional representation because all required statistics can be computed without performing an explicit feature space mapping of the sequences. By introducing a kernel parameter that controls the degree of position-dependency, our feature space representation can be tailored to the characteristics of the biological problem at hand. A regularized learning scheme enables application even to biological problems for which only small sets of example sequences are available. Our approach includes a visualization method for transparent representation of characteristic sequence features. Thereby importance of features can be measured in terms of discriminative strength with respect to classification of the underlying sequences. To demonstrate and validate our concept on a biochemically well-defined case, we analyze E. coli translation initiation sites in order to show that we can find biologically relevant signals. For that case, our results clearly show that the Shine-Dalgarno sequence is the most important signal upstream a start codon. The variability in position and composition we found for that signal is in accordance with previous biological knowledge. We also find evidence for signals downstream of the start codon, previously introduced as transcriptional enhancers. These signals are mainly characterized by occurrences of adenine in a region of about 4 nucleotides next to the start codon.

Conclusions
We showed that the oligo kernel can provide a valuable tool for the analysis of relevant signals in biological sequences. In the case of translation initiation sites we could clearly deduce the most discriminative motifs and their positional variation from example sequences. Attractive features of our approach are its flexibility with respect to oligomer length and position conservation. By means of these two parameters oligo kernels can easily be adapted to different biological problems.
Discovery of mammalian genes that participate in virus infection
Authors: Organ Edward L , Sheng Jinsong , Ruley H Earl , Rubin Donald H 
Published: November 2004

Abstract
Background
Viruses are obligate intracellular parasites that rely upon the host cell for different steps in their life cycles. The characterization of cellular genes required for virus infection and/or cell killing will be essential for understanding viral life cycles, and may provide cellular targets for new antiviral therapies.

Results
Candidate genes required for lytic reovirus infection were identified by tagged sequence mutagenesis, a process that permits rapid identification of genes disrupted by gene entrapment. One hundred fifty-one reovirus resistant clones were selected from cell libraries containing 2 × 105 independently disrupted genes, of which 111 contained mutations in previously characterized genes and functionally anonymous transcription units. Collectively, the genes associated with reovirus resistance differed from genes targeted by random gene entrapment in that known mutational hot spots were under represented, and a number of mutations appeared to cluster around specific cellular processes, including: IGF-II expression/signalling, vesicular transport/cytoskeletal trafficking and apoptosis. Notably, several of the genes have been directly implicated in the replication of reovirus and other viruses at different steps in the viral lifecycle.

Conclusions
Tagged sequence mutagenesis provides a rapid, genome-wide strategy to identify candidate cellular genes required for virus infection. The candidate genes provide a starting point for mechanistic studies of cellular processes that participate in the virus lifecycle and may provide targets for novel anti-viral therapies.
A systematic review of the effectiveness of antimicrobial rinse-free hand sanitizers for prevention of illness-related absenteeism in elementary school children
Authors: Meadows Emily , Le Saux Nicole 
Published: November 2004

Abstract
Background
Absenteeism due to communicable illness is a major problem encountered by North American elementary school children. Although handwashing is a proven infection control measure, barriers exist in the school environment, which hinder compliance to this routine. Currently, alternative hand hygiene techniques are being considered, and one such technique is the use of antimicrobial rinse-free hand sanitizers.

Methods
A systematic review was conducted to examine the effectiveness of antimicrobial rinse-free hand sanitizer interventions in the elementary school setting. MEDLINE, EMBASE, Biological Abstract, CINAHL, HealthSTAR and Cochrane Controlled Trials Register were searched for both randomized and non-randomized controlled trials. Absenteeism due to communicable illness was the primary outcome variable.

Results
Six eligible studies, two of which were randomized, were identified (5 published studies, 1 published abstract). The quality of reporting was low. Due to a large amount of heterogeneity and low quality of reporting, no pooled estimates were calculated. There was a significant difference reported in favor of the intervention in all 5 published studies.

Conclusions
The available evidence for the effectiveness of antimicrobial rinse-free hand sanitizer in the school environment is of low quality. The results suggest that the strength of the benefit should be interpreted with caution. Given the potential to reduce student absenteeism, teacher absenteeism, school operating costs, healthcare costs and parental absenteeism, a well-designed and analyzed trial is needed to optimize this hand hygiene technique.
Validating the Time and Change test to screen for dementia in elderly Koreans
Authors: Rhee Jung-Ae , Chung Eun-Kyung , Shin Min-Ho 
Published: November 2004

Abstract
Background
We assessed the applicability of the T&C test as an accurate and convenient means to screen for dementia in primary care and community settings.

Methods
The study group comprised 59 patients and 405 community participants, all of who were aged 65 years and over. The time component of the T&C test evaluated the ability of a subject to comprehend clock hands that indicated a time of 11:10, while the change component of the T&C test evaluated the ability of a subject to make 1,000 Won from a group of coins with smaller denominations (one 500, seven 100, and seven 50 Won coins).

Results
The T&C test had a sensitivity and specificity of 73.0 and 90.9%, respectively, and positive and negative predictive values of 93.1, and 66.7%, respectively. The test-retest and interobserver agreement rates were both 95% (κ = 0.91) (time interval, 24 hours). The association between the T&C test and K-MMSE test was modest, while significant (r = 0.422, p < 0.001). The T&C test scores were not influenced by educational status.

Conclusions
We conclude that the T&C test is useful as supplemental testing of important domains (e.g., calculation, conceptualization, visuospatial) to traditional measures such as the MMSE. However, because T&C test is simple, rapid, and easy to use, it can be applied conveniently to elderly subjects by non-specialist personnel who receive training.
Recruiting pregnant smokers for a placebo-randomised controlled trial of nicotine replacement therapy
Authors: Coleman Tim , Antoniak Marilyn , Britton John , Thornton Jim , Lewis Sarah , Watts Kim 
Published: November 2004

Abstract
Background
Smoking in pregnancy is a public health problem and effective methods for reducing this are required. Although nicotine replacement therapy (NRT) is effective for smoking cessation in non-pregnant people, there is no direct evidence concerning its effectiveness in pregnancy. Despite this, clinical guidelines recommend the cautious use of NRT during pregnancy. Randomised controlled trials are needed to determine the safety and efficacy of NRT when used by pregnant women for smoking cessation, but the feasibility of recruiting women to such trials is unknown. Consequently, in this study we aimed to determine i) the feasibility of recruiting women to a RCT of NRT in pregnancy as they attend hospital antenatal ultrasound examinations, ii) the proportion of such women who are eligible for and interested in trial enrolment and iii) research staff perceptions of how one method of trial recruitment could be improved.

Methods
During a one month period, all women attending for antenatal ultrasound examination in an English teaching hospital were asked to complete a questionnaire which determined their eligibility to enrol in a proposed placebo controlled randomised trial investigating the effectiveness of NRT in pregnancy. Women who were eligible to participate were asked whether they would do so and those who accepted enrolment were offered an appointment with a smoking cessation advisor.

Results
Over 99% (851/858) of women agreed to complete a questionnaire about smoking habits whilst waiting for ultrasound examinations. 10.3% (88/851) of women attending for antenatal ultrasound fitted eligibility criteria for a proposed RCT of NRT in pregnancy, but only 3.6% [(31/851), 95% CI, 2.4 to 4.9%] indicated on the questionnaire that they would like to take part in a study involving randomisation to placebo or active patches. Researchers offered trial enrolment to 26 of these 31 women and 96% (25) accepted. Staff recruiting women believed that trial recruitment would be maximised if women attending the ultrasound department knew about trial recruitment before attending and greater staff resources were made available for this. It was also perceived that women generally under-reported the amount they smoked on questionnaires completed whilst waiting in ultrasound department areas.

Conclusions
It is feasible to recruit women for a trial of NRT in pregnancy as they wait for antenatal ultrasound examinations. Using similar recruitment methods, researchers can expect to recruit between 24 and 49 women per 1000 approached.
A two-layered mechanical model of the rat esophagus. Experiment and theory
Authors: Fan Yanhua , Gregersen Hans , Kassab Ghassan S 
Published: November 2004

Abstract
Background
The function of esophagus is to move food by peristaltic motion which is the result of the interaction of the tissue forces in the esophageal wall and the hydrodynamic forces in the food bolus. The structure of the esophagus is layered. In this paper, the esophagus is treated as a two-layered structure consisting of an inner collagen-rich submucosa layer and an outer muscle layer. We developed a model and experimental setup for determination of elastic moduli in the two layers in circumferential direction and related the measured elastic modulus of the intact esophagus to the elastic modulus computed from the elastic moduli of the two layers.

Methods
Inflation experiments were done at in vivo length and pressure-diameters relations were recorded for the rat esophagus. Furthermore, the zero-stress state was taken into consideration.

Results
The radius and the strain increased as function of pressure in the intact as well as in the individual layers of the esophagus. At pressures higher than 1.5 cmH2O the muscle layer had a larger radius and strain than the mucosa-submucosa layer. The strain for the intact esophagus and for the muscle layer was negative at low pressures indicating the presence of residual strains in the tissue. The stress-strain curve for the submucosa-mucosa layer was shifted to the left of the curves for the muscle layer and for the intact esophagus at strains higher than 0.3. The tangent modulus was highest in the submucosa-mucosa layer, indicating that the submucosa-mucosa has the highest stiffness. A good agreement was found between the measured elastic modulus of the intact esophagus and the elastic modulus computed from the elastic moduli of the two separated layers.
Mercury exposure, malaria, and serum antinuclear/antinucleolar antibodies in amazon populations in Brazil: a cross-sectional study
Authors: Silva Ines A , Nyland Jennifer F , Gorman Andrew , Perisse Andre , Ventura Ana Maria , Santos Elizabeth CO , de Souza Jose M , Burek CL , Rose Noel R , Silbergeld Ellen K 
Published: November 2004

Abstract
Background
Mercury is an immunotoxic metal that induces autoimmune disease in rodents. Highly susceptible mouse strains such as SJL/N, A.SW, B10.S (H-2s) develop multiple autoimmune manifestations after exposure to inorganic mercury, including lymphoproliferation, elevated levels of autoantibodies, overproduction of IgG and IgE, and circulating immune complexes in kidney and vasculature. A few studies have examined relationships between mercury exposures and adverse immunological reactions in humans, but there is little evidence of mercury-associated autoimmunity in humans.

Methods
To test the immunotoxic effects of mercury in humans, we studied communities in Amazonian Brazil with well-characterized exposures to mercury. Information was collected on diet, mercury exposures, demographic data, and medical history. Antinuclear and antinucleolar autoantibodies (ANA and ANoA) were measured by indirect immunofluorescence. Anti-fibrillarin autoantibodies (AFA) were measured by immunoblotting.

Results
In a gold mining site, there was a high prevalence of ANA and ANoA: 40.8% with detectable ANoA at ≥1:10 serum dilution, and 54.1% with detectable ANA (of which 15% had also detectable ANoA). In a riverine town, where the population is exposed to methylmercury by fish consumption, both prevalence and levels of autoantibodies were lower: 18% with detectable ANoA and 10.7% with detectable ANA. In a reference site with lower mercury exposures, both prevalence and levels of autoantibodies were much lower: only 2.0% detectable ANoA, and only 7.1% with detectable ANA. In the gold mining population, we also examined serum for AFA in those subjects with detectable ANoA (≥1:10). There was no evidence for mercury induction of this autoantibody.

Conclusions
This is the first study to report immunologic changes, indicative of autoimmune dysfunction in persons exposed to mercury, which may also reflect interactions with infectious disease and other factors.
Influence of oxygen tension on myocardial performance. Evaluation by tissue Doppler imaging
Authors: Frøbert Ole , Moesgaard Jacob , Toft Egon , Poulsen Steen Hvitfeldt , Søgaard Peter 
Published: November 2004

Abstract
Background
Low O2 tension dilates coronary arteries and high O2 tension is a coronary vasoconstrictor but reports on O2-dependent effects on ventricular performance diverge. Yet oxygen supplementation remains first line treatment in cardiovascular disease. We hypothesized that hypoxia improves and hyperoxia worsens myocardial performance.

Methods
Seven male volunteers (mean age 38 ± 3 years) were examined with echocardiography at respiratory equilibrium during: 1) normoxia (≈21% O2, 79% N2), 2) while inhaling a hypoxic gas mixture (≈11% O2, 89% N2), and 3) while inhaling 100% O2. Tissue Doppler recordings were acquired in the apical 4-chamber, 2-chamber, and long-axis views. Strain rate and tissue tracking displacement analyses were carried out in each segment of the 16-segment left ventricular model and in the basal, middle and apical portions of the right ventricle.

Results
Heart rate increased with hypoxia (68 ± 4 bpm at normoxia vs. 79 ± 5 bpm, P < 0.001) and decreased with hyperoxia (59 ± 5 bpm, P < 0.001 vs. normoxia). Hypoxia increased strain rate in four left ventricular segments and global systolic contraction amplitude was increased (normoxia: 9.76 ± 0.41 vs hypoxia: 10.87 ± 0.42, P < 0.001). Tissue tracking displacement was reduced in the right ventricular segments and tricuspid regurgitation increased with hypoxia (7.5 ± 1.9 mmHg vs. 33.5 ± 1.8 mmHg, P < 0.001). The TEI index and E/E' did not change with hypoxia. Hyperoxia reduced strain rate in 10 left ventricular segments, global systolic contraction amplitude was decreased (8.83 ± 0.38, P < 0.001 vs. normoxia) while right ventricular function was unchanged. The spectral and tissue Doppler TEI indexes were significantly increased but E/E' did not change with hyperoxia.

Conclusion
Hypoxia improves and hyperoxia worsens systolic myocardial performance in healthy male volunteers. Tissue Doppler measures of diastolic function are unaffected by hypoxia/hyperoxia which support that the changes in myocardial performance are secondary to changes in vascular tone. It remains to be settled whether oxygen therapy to patients with heart disease is a consistent rational treatment.
Treatment outcomes in locally advanced colorectal carcinoma
Authors: Harish K , Narayanaswamy YV , Nirmala S 
Published: November 2004

Abstract
Background
Locally advanced colorectal cancers form a distinct subgroup where contiguous organs could be involved without distant metastases and so may be amenable to curative surgical resection. It was our objective to report our experience in treating six such patients with operable locally advanced colorectal carcinomas.

Methods
We retrospectively reviewed the case notes of 47 patients who were diagnosed with colorectal cancers at M S Ramaiah Medical Teaching Hospital between the years 1996 – 2001. Six patients were identified with T4 lesions, adjacent organ involvement and with no nodal involvement. The treatments and outcomes for these patients were then reviewed.

Results
Two of three patients with rectal malignancies who underwent pelvic exenteration succumbed to disease recurrence within the first 18 months. One of the three patients with colonic cancers died of non malignant causes. The other two are disease free till date.

Conclusions
Aggressive multivisceral resections for locally advanced colonic cancers might be appropriate. Rectal cancers when locally advanced may be considered for pelvic exenteration, but a more guarded prognosis may apply.
SIVdrl detection in captive mandrills: are mandrills infected with a third strain of simian immunodeficiency virus?
Authors: van der Kuyl Antoinette C , van den Burg Remco , Hoyer Mark J , Gruters Rob A , Osterhaus Albert DME , Berkhout Ben 
Published: November 2004

AbstractA pol-fragment of simian immunodeficiency virus (SIV) that is highly related to SIVdrl-pol from drill monkeys (Mandrillus leucophaeus) was detected in two mandrills (Mandrillus sphinx) from Amsterdam Zoo. These captivity-born mandrills had never been in contact with drill monkeys, and were unlikely to be hybrids. Their mitochondrial haplotype suggested that they descended from founder animals in Cameroon or northern Gabon, close to the habitat of the drill. SIVdrl has once before been found in a wild-caught mandrill from the same region, indicating that mandrills are naturally infected with a SIVdrl-like virus. This suggests that mandrills are the first primate species to be infected with three strains of SIV: SIVmnd1, SIVmnd2, and SIVdrl.
Laboratory measurements of water vapour continuum absorption in spectral region 5000–5600 cm−1: Evidence for water dimers
Authors: Ptashnik Igor V. , Smith Kevin M. , Shine Keith P. , Newnham David A. 
Published: November 2004

AbstractIn spite of decades of extensive studies, the role of water dimers (WD) in the atmospheric radiation budget is still controversial. In order to search for evidence of the dimer in the solar near infrared, high spectral resolution pure water vapour absorption spectra were obtained in laboratory conditions for two different pressures and temperatures in the spectral region 5000–5600 cm−1 (1.785 to 2 µm). The residual was derived as a difference between the measured optical depth and the calculated one for water monomer, using the modified HITRAN database and two different representations of the water vapour continuum: CKD‐2.4 (Clough–Kneizys–Davies) and the Ma and Tipping continuum. In both cases the residuals obtained are very similar to those expected from a recent theoretical calculation of the WD absorption. However, the WD band half‐width at half maximum (HWHM) and dimerization equilibrium constant, Keq, required to provide a best fit to the residual, differ for each case. To be in best agreement with the residual calculated by using the Ma and Tipping continuum, the WD bands HWHM should be ∼28 cm−1, and Keq=0.02±0.0035 atm−1 and 0.043±0.0055 atm−1 for temperatures 342 and 299 K respectively. For the residual calculated using the CKD‐2.4 continuum the fitted value of the HWHM is ∼18cm−1, and Keq=0.011±0.0025 atm−1 (342 K) and 0.018±0.003 atm−1 (299 K). It is concluded that a substantial part of the WD absorption is already implicitly included within the CKD‐2.4 continuum model. The increase in estimated clear‐sky global mean absorption of solar radiation due to WD varies from 0.5% to 2.0%, depending on the set of WD parameters used. On the basis of a comparison of the derived Keq values with others in the literature, the higher estimate is favoured. Copyright © 2004 Royal Meteorological Society
SLICE‐S: A Semi‐Lagrangian Inherently Conserving and Efficient scheme for transport problems on the Sphere
Authors: Zerroukat Mohamed , Wood Nigel , Staniforth Andrew 
Published: November 2004

AbstractThe Semi‐Lagrangian Inherently Conserving and Efficient (SLICE) scheme developed for Cartesian geometry is generalized to spherical geometry. The spherical version, SLICE‐S, is similarly based on a Control Volume approach and multiple sweeps of a one‐dimensional O(Δs4) (where s is the spherical distance) conservative remapping algorithm along Eulerian latitudes, then along Lagrangian longitudes. The resulting conservative scheme requires no restriction on either the polar meridional or zonal Courant numbers. SLICE‐S is applied to the standard problems of solid‐body rotation and deformational flow, and results are compared with those of a standard non‐conservative and other published conservative semi‐Lagrangian schemes. In addition to mass conservation, and consistent with the performance of SLICE, the present scheme is competitive in terms of accuracy and efficiency. © Crown copyright, 2004. Royal Meteorological Society