bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement in the prediction of the translation initiation site through balancing methods, inclusion of acquired knowledge and addition of features to sequences of mRNA
Authors: Silva Lívia Márcia , de Souza Teixeira Felipe Carvalho , Ortega José Miguel , Zárate Luis Enrique , Nobre Cristiane Neri 
Published: December 2011

Abstract

Background
The accurate prediction of the initiation of translation in sequences of mRNA is an important activity for genome annotation. However, obtaining an accurate prediction is not always a simple task and can be modeled as a problem of classification between positive sequences (protein codifiers) and negative sequences (non-codifiers). The problem is highly imbalanced because each molecule of mRNA has a unique translation initiation site and various others that are not initiators. Therefore, this study focuses on the problem from the perspective of balancing classes and we present an undersampling balancing method, M-clus, which is based on clustering. The method also adds features to sequences and improves the performance of the classifier through the inclusion of knowledge obtained by the model, called InAKnow.

Results
Through this methodology, the measures of performance used (accuracy, sensitivity, specificity and adjusted accuracy) are greater than 93% for the Mus musculus and Rattus norvegicus organisms, and varied between 72.97% and 97.43% for the other organisms evaluated: Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Nasonia vitripennis. The precision increases significantly by 39% and 22.9% for Mus musculus and Rattus norvegicus, respectively, when the knowledge obtained by the model is included. For the other organisms, the precision increases by between 37.10% and 59.49%. The inclusion of certain features during training, for example, the presence of ATG in the upstream region of the Translation Initiation Site, improves the rate of sensitivity by approximately 7%. Using the M-Clus balancing method generates a significant increase in the rate of sensitivity from 51.39% to 91.55% (Mus musculus) and from 47.45% to 88.09% (Rattus norvegicus).

Conclusions
In order to solve the problem of TIS prediction, the results indicate that the methodology proposed in this work is adequate, particularly when using the concept of acquired knowledge which increased the accuracy in all databases evaluated.
Obesity management and continuing medical education in primary care: results of a Swiss survey
Authors: Huber Carola A , Mohler-Kuo Meichun , Zellweger Ueli , Zoller Marco , Rosemann Thomas , Senn Oliver 
Published: December 2011

Abstract

Background
The worldwide increase in obesity is becoming a major health concern. General practitioners (GPs) play a central role in managing obesity. We aimed to examine Swiss GPs self-reported practice in diagnosis and treatment of obesity with a special focus on the performance of waist measurement.

Methods
A structured self-reported questionnaire was mailed to 323 GPs recruited from four urban physician networks in Switzerland. Measures included professional experience, type of practice, obesity-related continuing medical education (CME) and practice in dealing with obesity such as waist measurement. We assessed the association between the performance of waist measurement and obesity-related CME by multivariate ordered logistic regression controlling for GP characteristics as potential confounders.

Results
A total of 187 GPs responded to the questionnaire. More than half of the GPs felt confident in managing obesity. The majority of the GPs (73%) spent less than 4 days in the last 5 years on obesity-related CME. More than half of GPs gave advice to reduce energy intakes (64%), intakes of high caloric and alcoholic drinks (56%) and to increase the physical activity (78%). Half of the GPs seldom performed waist measurement and documentation. The frequency of obesity-related CME was independently associated with the performance of waist measurement when controlled for GPs' characteristics by multivariate ordered logistic regression.

Conclusions
The majority of GPs followed guideline recommendations promoting physical activity and dietary counselling. We observed a gap between the increasing evidence for waist circumference assessment as an important measure in obesity management and actual clinical practice. Our data indicated that specific obesity-related CME might help to reduce this gap.
Comparison of resource use by COPD patients on inhaled therapies with long-acting bronchodilators: a database study
Authors: Kozma Chris M , Paris Andrew L , Plauschinat Craig A , Slaton Terra , Mackowiak John I 
Published: December 2011

Abstract

Background
The purpose of this analysis was to compare health care costs and utilization among COPD patients who had long-acting beta-2 agonist (LABA) OR long-acting muscarinic antagonist (LAMA); LABA AND LAMA; or LABA, LAMA, AND inhaled corticosteroid (ICS) prescription claims.

Methods
This was a 12 month pre-post, retrospective analysis using COPD patients in a national administrative insurance database. Propensity score and exact matching were used to match patients 1:1:1 between the LABA or LAMA (formoterol, salmeterol, or tiotropium), LABA and LAMA (tiotropium/formoterol or tiotropium/salmeterol), and LABA, LAMA and ICS (bronchodilators plus steroid) groups. Post-period comparisons were evaluated with analysis of covariance. Costs were evaluated from a commercial payer perspective.

Results
A total of 523 patients were matched using 29 pre-period variables (e.g., demographics, medication exposure). Post-match assessments indicated balance among the cohorts. COPD-related costs differed among groups (LABA or LAMA $2,051 SE = 91; LABA and LAMA $2,823 SE = 62; LABA, LAMA and ICS $3,546 SE = 89; all p < .0001) with the differences driven by study medication costs. However, non-study COPD medication costs were higher for the LABA or LAMA therapy group ($911 SE = 91) compared to the LABA and LAMA therapy group ($668 SE = 58; p = 0.0238) and non-study respiratory medications were approximately $100 greater for the LABA or LAMA therapy group relative to both LABA and LAMA (p = .0018) and LABA, LAMA, and ICS (p = .0071) therapy groups. While there was no observed difference in outpatient costs, there was a slightly higher number of outpatient visits per patient in the LABA and LAMA (25.5 SE = 0.9, p = 0.0070) relative to the LABA or LAMA therapy group (22.3 SE = 0.8) and higher utilization (89.7% of patients) with COPD visits in the LABA and LAMA therapy group relative to both the LABA or LAMA (73.8%; p < .0001) and LABA, LAMA and ICS therapy groups (85.3; p = 0.0305).

Conclusions
Significant cost differences driven mainly by pharmaceuticals were observed among LABA or LAMA, LABA and LAMA and LABA, LAMA and ICS therapies. A COPD-related cost offset was observed from single bronchodilator to two bronchodilators. Addition of an ICS with two bronchodilators resulted in higher treatment costs without reduction in other COPD-related costs compared with two bronchodilators.
Bovine pericardium retail preserved in glutaraldehyde and used as a vascular patch
Authors: Saporito Wladimir F , Pires Adílson C , Cardoso Sérgio H , Correa João A , de Abreu Luiz Carlos , Valenti Vitor E , Miller Luciano MR , Colombari Eduardo 
Published: December 2011

Abstract

Background
In this study we evaluated the performance of bovine pericardium preserved in glutaraldehyde used as a vascular patch.

Methods
Fourteen young pigs, six females and eight males, weighting 10.3 - 18.4 kg were used in our study. We implanted three remnants in each pig, two in the abdominal aorta and one was juxtaposed to the peritoneum. The smooth face (SF) and rough face (RF) of each remnant were implanted turned to the vessel inner portion and one remnant was juxtaposed to the peritoneum. The animals were sacrificed in 4.5 - 8 months after surgery (75 - 109 kg). The remnants were assessed for aorta wall, fibroses formation in inner apposition and calcification related to the face turned to the vessel inner portion.

Results
The rough face showed a lower dilatation level compared to the face implanted in adjacent aorta. There was no difference between intensity and/or incidence of graft calcification when the superficies were compared. The bovine pericardium preserved in glutaraldehyde did not show alterations in its structure when implanted with different faces turned to the inner portion of vessel.

Conclusion
When turned to the inner portion of the vessel, the rough face of the remnant presented a lower dilatation in relation to the adjacent aorta and a better quality of endothelium layer and did not show a difference between intensity and/or incidence of graft calcification.
Molecular preservation by extraction and fixation, mPREF: a method for small molecule biomarker analysis and histology on exactly the same tissue
Authors: Shuster Jeffrey R , Lance Raymond S , Troyer Dean A 
Published: December 2011

Abstract

Background
Histopathology is the standard method for cancer diagnosis and grading to assess aggressiveness in clinical biopsies. Molecular biomarkers have also been described that are associated with cancer aggressiveness, however, the portion of tissue analyzed is often processed in a manner that is destructive to the tissue. We present here a new method for performing analysis of small molecule biomarkers and histology in exactly the same biopsy tissue.

Methods
Prostate needle biopsies were taken from surgical prostatectomy specimens and first fixed, each in a separate vial, in 2.5 ml of 80% methanol:water. The biopsies were fixed for 24 hrs at room temperature and then removed and post-processed using a non-formalin-based fixative (UMFIX), embedded, and analyzed by hematoxylin and eosin (H&E) and by immunohistochemical (IHC) staining. The retained alcohol pre-fixative was analyzed for small molecule biomarkers by mass spectrometry.

Results
H&E analysis was successful following the pre-fixation in 80% methanol. The presence or absence of tumor could be readily determined for all 96 biopsies analyzed. A subset of biopsy sections was analyzed by IHC, and cancerous and non-cancerous regions could be readily visualized by PIN4 staining. To demonstrate the suitability for analysis of small molecule biomarkers, 28 of the alcohol extracts were analyzed using a mass spectrometry-based metabolomics platform. All extracts tested yielded successful metabolite profiles. 260 named biochemical compounds were detected in the alcohol extracts. A comparison of the relative levels of compounds in cancer containing vs. non-cancer containing biopsies showed differences for 83 of the compounds. A comparison of the results with prior published reports showed good agreement between the current method and prior reported biomarker discovery methods that involve tissue destructive methods.

Conclusions
The Molecular Preservation by Extraction and Fixation (mPREF) method allows for the analysis of small molecule biomarkers from exactly the same tissue that is processed for histopathology.
Impact of tubewell access and tubewell depth on childhood diarrhea in Matlab, Bangladesh
Authors: Wu Jianyong , Yunus Mohammad , Streatfield Peter Kim , van Geen Alexander , Escamilla Veronica , Akita Yasuyuki , Serre Marc , Emch Michael 
Published: December 2011

Abstract

Background
During the past three decades in Bangladesh, millions of tubewells have been installed to reduce the prevalence of diarrheal disease. This study evaluates the impacts of tubewell access and tubewell depth on childhood diarrhea in rural Bangladesh.

Methods
A total of 59,796 cases of diarrhea in children under 5 were recorded in 142 villages of Matlab, Bangladesh during monthly community health surveys between 2000 and 2006. The location and depth of 12,018 tubewells were surveyed in 2002-04 and integrated with diarrhea and other data in a geographic information system. A proxy for tubewell access was developed by calculating the local density of tubewells around households. Logistic regression models were built to examine the relationship between childhood diarrhea, tubewell density and tubewell depth. Wealth, adult female education, flood control, population density and the child's age were considered as potential confounders.

Results

Baris (patrilineally-related clusters of households) with greater tubewell density were associated with significantly less diarrhea (OR (odds ratio) = 0.87, 95% confidence interval (CI): 0.85-0.89). Tubewell density had a greater influence on childhood diarrhea in areas that were not protected from flooding. Baris using intermediate depth tubewells (140-300 feet) were associated with more childhood diarrhea (OR = 1.24, 95% CI: 1.19-1.29) than those using shallow wells (10-140 feet). Baris using deep wells (300-990 feet) had less diarrheal disease than those using shallow wells, however, the difference was significant only when population density was low (< 1000 person/km2) or children were at the age of 13-24 months.

Conclusions
Increased access to tubewells is associated with a lower risk of childhood diarrhea. Intermediate- depth wells are associated with more childhood diarrhea compared to shallower or deeper wells. These findings may have implications for on-going efforts to reduce exposure to elevated levels of arsenic contained in groundwater that is pumped in this study area primarily from shallow tubewells.
Variations in maternal care alter corticosterone and 17beta-estradiol levels, estrous cycle and folliculogenesis and stimulate the expression of estrogen receptors alpha and beta in the ovaries of UCh rats
Authors: Amorim João PA , Chuffa Luiz GA , Teixeira Giovana R , Mendes Leonardo O , Fioruci Beatriz A , Martins Otávio A , Júnior Wílson Mello , Anselmo-Franci Janete A , Pinheiro Patricia FF , Martinez Marcelo , Martinez Francisco E 
Published: December 2011

Abstract

Background
Variations in maternal care are associated with neonatal stress, hormonal disturbances and reproductive injuries during adulthood. However, the effects of these variations on sex hormones and steroid receptors during ovary development remain undetermined. This study aimed to investigate whether variations in maternal care are able to influence the hormonal profile, follicular dynamics and expression of AR, ER-alpha and ER-beta in the ovaries of UCh rat offspring.

Methods
Twenty-four adult UCh rats, aged 120 days, were randomly divided into two groups (UChA and UChB) and mated. Maternal care was assessed from birth (day 0) to the 10th postnatal day (PND). In adulthood, twenty adult female rats (UChA and UChB offspring; n = 10/group), aged 120 days, were euthanized by decapitation during the morning estrus.

Results
UChA females (providing high maternal care) more frequently displayed the behaviors of carrying pups, as well as licking/grooming and arched back nursing cares. Also, mothers providing high care had elevated corticosterone levels. Additionally, offspring receiving low maternal care showed the highest estrous cycle duration, increased corticosterone and 17beta-estradiol levels, overexpression of receptors ER-alpha and ER-beta, increased numbers of primordial, antral and mature follicles and accentuated granulosa cell proliferation.

Conclusions
Our study suggests that low maternal care alters corticosterone and 17beta-estradiol levels, disrupting the estrous cycle and folliculogenesis and differentially regulating the expression of ER-alpha and ER-beta in the ovaries of adult rats.
Flexible intramedullary nailing in paediatric femoral fractures. A report of 73 cases
Authors: Lohiya Ramprakash , Bachhal Vikas , Khan Usman , Kumar Deepak , Vijayvargiya Vishwapriya , Sankhala Sohan S , Bhargava Rakesh , Jindal Nipun 
Published: December 2011

Abstract

Background
Flexible intramedullary nailing has emerged as an accepted procedure for paediatric femoral fractures. Present indications include all patients with femoral shaft fractures and open physis. Despite its excellent reported results, orthopaedic surgeons remain divided in opinion regarding its usefulness and the best material used for nails. We thus undertook a retrospective study of paediatric femoral fractures treated with titanium or stainless steel flexible nails at our institute with a minimum of 5 years follow up.

Material and methods
We included 73 femoral shaft fractures in 69 patients treated with retrograde flexible intramedullary nailing with a minimum follow up of 5 years. Final limb length discrepancy and any angular or rotational deformities were determined.

Results
Mean age at final follow up was 15.5 years (10-21 years). Mean follow up was 7.16 years (5.0-8.6 years). Titanium and stainless steel nails were used in 43 and 30 cases respectively. There were 51 midshaft, 17 proximal, and 5 distal fractures.
All fractures united at an average of 11 weeks but asymptomatic malalignment and LLD were seen in 19% and 58% fractures respectively. LLD ranged from -3 cm to 1.5 cm. Other complications included superficial infection(2), proximal migration of nail(3), irritation at nail insertion site(5) and penetration of femoral neck with nail tip(1). There were 59 excellent, 10 satisfactory and 4 poor results.

Conclusion
Flexible intramedullary nailing is reliable and safe for treating paediatric femoral shaft fractures. It is relatively free of serious complications despite asymptomatic malalignment and LLD in significant percentage of fractures.
Association between magnetic susceptibilities and hydrocarbon deposits in the Barinas-Apure Basin, Venezuela
Authors: Perez-Perez A. , D’Onofrio L. , Bosch M. , Zapata E. 
Published: December 2011

We have measured the magnetic susceptibility of 5425 drill cuttings, coming from 20 oil wells distributed in eight fields of the Petroliferous Barinas-Apure Basin (Barinas, Venezuela), seeking evidence of magnetic anomalies associated with the presence of hydrocarbon deposits. The rock samples are located between the near earth’s surface and the basement’s top (approximately 4000 m). In the magnetic susceptibility profiles, we observed high magnetic susceptibilities at the top of the sedimentary units corresponding to reservoir and source rocks of oil-producing wells, whereas in the case of nonproducing wells we observed low magnetic susceptibilities. A basic statistical analysis of the magnetic susceptibility measurements shows a significant difference between the mean values across producing and nonproducing wells at the correspondent oil-related formations, with a ratio of [Formula: see text] of producing to nonproducing wells. In the producing wells, we have found a relation between the magnitudes of the magnetic susceptibility and the age of the formation; the larger the magnetic susceptibility, the younger the geological stratum. The age and depth of the formations where the cuts were obtained exclude the presence of cultural (human origin) contamination of the samples, suggesting the evidence of authigenic origin of the magnetic minerals due to the reductive effect of hydrocarbons in rocks.
Monitoring a shallow subsurface gas flow by time-lapse refraction analysis
Authors: Mehdi Zadeh Hossein , Landrø Martin 
Published: December 2011

Studying time-lapse time shifts for refracted events is a complementary method to conventional 4D analysis. Especially for detecting changes in relatively shallow subsurface layers, we find that this method has potential. By studying data associated with an old underground blowout, we find consistent time shifts of up to 4 ms when comparing a base survey that was acquired before the underground blowout with a monitor survey acquired 20 months after the blowout. These time shifts are interpreted as caused by shallow gas migration. The 4D refraction time shifts are estimated by a standard windowed crosscorrelation technique. Observed time shifts are compared with a simple synthetic modeling to find the possible property and location of the anomaly. The synthetic result was qualitatively matched with real data. We believe that more quantitative matches can obtained when the method is combined with full waveform inversions. Time-lapse refraction analysis has some clear limitations, for instance, the presence of refracted events, which requires a positive velocity contrast for the interface to be studied. Another limitation is that for deeper events, the signal from shallower refractions and noise associated with the water layer will distort the 4D time shifts. However, we found that these results demonstrate the potential of refraction time shifts as a complementary 4D analysis technique. We believe that the method has a significant potential for quantitative 4D interpretation.
Vertebrectomy Model for the Mechanical Assessment of Fusionless Scoliosis Growth Rods
Authors: Shorez J. P. 
Published: December 2011

Abstract
Fusionless scoliosis growth rod systems pose many challenges to benchtop biomechanical testing. This study was conducted in order to develop a vertebrectomy model capable of evaluating shear/corrective reduction forces, anterior/posterior load sharing, and long term fatigue properties of these systems. Portions of ASTM F1717 and ISO 12189 were used to develop a custom dynamic construct. Results from the corrective/shear reduction force test demonstrate an expected reduced shear/corrective force at the completion of fatigue testing. Additionally, a bimodal force–displacement curve was demonstrated during confined static compression testing, indicating an anterior/posterior load sharing function of the system. Fatigue testing of the dynamic construct demonstrated the potential to develop a fatigue curve and endurance limit of a growth rod system. Moreover, fatigue testing replicated common in vivo failures. The complexities of scoliosis treatment make the definition of a standardized construct difficult. However, application of the current model can serve as a tool to understand the basic mechanical interactions in these complex systems.
5083 Aluminum Alloy Welded Joints: Measurements of Mechanical Properties by DIC
Authors: Rivolta B. , Silvestri A. , Zappa E. , Garghentini A. 
Published: December 2011

Abstract
The mechanical behaviour of heterogeneous regions like weldings is strongly affected by the local response, depending on the microstructural characteristics and the presence of defects. In this experimental work, 5083 H111 plates are welded by MIG method and DIC measurements were performed during uniaxial tensile tests to investigate the local mechanical behaviour in the area of interest. Digital Image Correlation (DIC) is a measuring technique capable of estimating the full displacement and strain field of an object through image acquisition and processing. The DIC techniques relates the intensity distribution of a small sub-set of pixel from a reference image and the image of the deformed specimen in order to estimate the full displacement field. The strain field is obtained relying on the displacement data. Specific tests are performed on specimens characterized by the presence of defects and porosity in the welding, to investigate the potentiality of the method and the obtained results show that the method is able to predict the position from which the final crack starts its propagation, giving rise to the final rupture of the specimen. Moreover, the work shows the possibility of determining the deformation field of the welded zone and of the heat affected zone by the DIC analysis, thanks to the capability of this measuring technique to estimate the mechanical behaviour of the specific regions of a welded joint (base material, HAZ and weld).