LLukas22/scidocs huggingface dataset:
Microbial aetiology, outcomes, and costs of hospitalisation for community-acquired pneumonia; an observational analysis

BACKGROUND
The aim of this study was to investigate the clinical outcome and especially costs of hospitalisation for community-acquired pneumonia (CAP) in relation to microbial aetiology. This knowledge is indispensable to estimate cost-effectiveness of new strategies aiming to prevent and/or improve clinical outcome of CAP.


METHODS
We performed our observational analysis in a cohort of 505 patients hospitalised with confirmed CAP between 2004 and 2010. Hospital administrative databases were extracted for all resource utilisation on a patient level. Resource items were grouped in seven categories: general ward nursing, nursing on ICU, clinical chemistry laboratory tests, microbiology exams, radiology exams, medication drugs, and other.linear regression analyses were conducted to identify variables predicting costs of hospitalisation for CAP.


RESULTS
Streptococcus pneumoniae was the most identified causative pathogen (25%), followed by Coxiella burnetii (6%) and Haemophilus influenzae (5%). Overall median length of hospital stay was 8.5 days, in-hospital mortality rate was 4.8%.Total median hospital costs per patient were €3,899 (IQR 2,911-5,684). General ward nursing costs represented the largest share (57%), followed by nursing on the intensive care unit (16%) and diagnostic microbiological tests (9%). In multivariate regression analysis, class IV-V Pneumonia Severity Index (indicative for severe disease), Staphylococcus aureus, or Streptococcus pneumonia as causative pathogen, were independent cost driving factors. Coxiella burnetii was a cost-limiting factor.


CONCLUSIONS
Median costs of hospitalisation for CAP are almost €4,000 per patient. Nursing costs are the main cause of these costs.. Apart from prevention, low-cost interventions aimed at reducing length of hospital stay therefore will most likely be cost-effective.
Ratio of oleic to palmitic acid is a dietary determinant of thrombogenic and fibrinolytic factors during the postprandial state in men.

BACKGROUND
The nature of dietary fats affects the postprandial activation of the hemostatic system.


OBJECTIVE
We investigated whether the ratio of oleic to palmitic acid [and that of monounsaturated to saturated fatty acids (MUFA:SFA)] in the diet affects postprandial concentrations of triacylglycerols, tissue factor (TF), fibrinogen, tissue-type plasminogen activator (t-PA), and plasminogen activator inhibitor 1 (PAI-1).


DESIGN
We studied the effects of diets enriched in olive oil (ROO), high-palmitic sunflower oil (HPSO), butter, or a mixture of vegetable and fish oils (VEFO) on circulating concentrations of the aforementioned factors in 14 healthy men. The fats had ratios of oleic to palmitic acid (MUFA:SFA) of 6.83 (5.43), 2.36 (2.42), 0.82 (0.48), and 13.81 (7.08).


RESULTS
The largest and longest-lasting postprandial changes in plasma triacylglycerol concentrations were found with the butter-based diet (all P < 0.05). No correlation was observed between the net incremental area under the curve (netAUC) for triacylglycerol and the ratio of oleic to palmitic acid (or MUFA:SFA) in the dietary fats. The netAUCs for TF and PAI-1, however, were inversely related to the ratio of oleic to palmitic acid (and MUFA:SFA) in ROO, HPSO, butter, and VEFO. Similar results were found for the fibrinogen netAUC when VEFO was omitted from the analysis. The netAUC for t-PA was inversely correlated with postprandial concentrations of triacylglycerol.


CONCLUSIONS
Postprandial concentrations of TF, fibrinogen, and PAI-1 are associated with the ratio of oleic to palmitic acid (MUFA:SFA) in dietary fats. The postprandial t-PA response is related to postprandial concentrations of triacylglycerol.
Urine biomarkers of kidney injury among adolescents in Nicaragua, a region affected by an epidemic of chronic kidney disease of unknown aetiology.

BACKGROUND
An epidemic of chronic kidney disease (CKD) of non-traditional aetiology has been recently recognized by health authorities as a public health priority in Central America. Previous studies have identified strenuous manual work, agricultural activities and residence at low altitude as potential risk factors; however, the aetiology remains unknown. Because individuals are frequently diagnosed with CKD in early adulthood, we measured biomarkers of kidney injury among adolescents in different regions of Nicaragua to assess whether kidney damage might be initiated during childhood.


METHODS
Participants include 200 adolescents aged 12-18 years with no prior work history from four different schools in Nicaragua. The location of the school served as a proxy for environmental exposures and geographic locations were selected to represent a range of factors that have been associated with CKD in adults (e.g. altitude, primary industry and CKD mortality rates). Questionnaires, urine dipsticks and kidney injury biomarkers [interleukin-18, N-acetyl-d-glucosaminidase (NAG), neutrophil gelatinase-associated lipocalin (NGAL) and albumin-creatinine ratio] were assessed. Biomarker concentrations were compared by school using linear regression models.


RESULTS
Protein (3.5%) and glucose (1%) in urine measured by dipstick were rare and did not differ by school. Urine biomarkers of tubular kidney damage, particularly NGAL and NAG, showed higher concentrations in those schools and regions within Nicaragua that were defined a priori as having increased CKD risk. Painful urination was a frequent self-reported symptom.


CONCLUSIONS
Although interpretation of these urine biomarkers is limited because of the lack of population reference values, results suggest the possibility of early kidney damage prior to occupational exposures in these adolescents.
Aesthetic package design : A behavioral , neural , and psychological investigation

In four experiments, this research sheds light on aesthetic experiences by rigorously investigating behavioral, neural, and psychological properties of package design. We find that aesthetic packages significantly increase the reaction time of consumers' choice responses; that they are chosen over products with well-known brands in standardized packages, despite higher prices; and that they result in increased activation in the nucleus accumbens and the ventromedial prefrontal cortex, according to functional magnetic resonance imaging (fMRI). The results suggest that reward value plays an important role in aesthetic product experiences. Further, a closer look at psychometric and neuroimaging data finds that a paper-and-pencil measure of affective product involvement correlates with aesthetic product experiences in the brain. Implications for future aesthetics research, package designers, and product managers are discussed. © 2010 Society for Consumer Psychology. Published by Elsevier Inc. All rights reserved.
The effect of cognitive strategies of association and dissociation on central nervous activation : A controlled trial with long distance runners

The purpose of the present study was to experimentally assess the effect of cognitive strategies of association and dissociation while running on central nervous activation. A total of 30 long distance runners volunteered for the study. The study protocol consisted on three sessions (scheduled in three different days): (1) maximal incremental treadmill test, (2) associative task session, and (3) dissociative task session. The order of sessions 2 and 3 was counterbalanced. During sessions 2 and 3, participants performed a 55 min treadmill run at moderate intensity. Both, associative and dissociative tasks responses were monitoring and recording in real time through dynamic measure tools. Consequently, was possible to have an objective control of the attentional. Results showed a positive session (exercise+attentional task) effect for central nervous activation. The benefi ts of aerobic exercise at moderate intensity for the performance of self-regulation cognitive tasks are highlighted. The used methodology is proposed as a valid and dynamic option to study cognitions while running in order to overcome the retrospective approach. Research Article
A network approach to response inhibition: dissociating functional connectivity of neural components involved in action restraint and action cancellation.

The ability to inhibit action tendencies is vital for adaptive human behaviour. Various paradigms are supposed to assess action inhibition and are often used interchangeably. However, these paradigms are based on different conceptualizations (action restraint vs. action cancellation) and the question arises as to what extent different conceptualizations of inhibitory processing are mirrored in a distinct neural activation pattern. We used functional magnetic resonance imaging to investigate the neural correlates of action restraint vs. action cancellation. Analyses of local activity changes as well as network connectivity measures revealed a strong overlap of activation within a common action inhibition network including inferior frontal, pre-supplementary motor and thalamic brain areas as well as the anterior cingulate cortex. Furthermore, our findings pointed to additional neural networks that are distinct for action restraint (i.e. right superior frontal gyrus, left middle frontal gyrus, and bilateral anterior cingulate cortex) and action cancellation (i.e. right middle frontal gyrus, posterior cingulate cortex, and parietal regions). Our connectivity analyses showed that different inhibitory modalities largely relied on a task-independent global inhibition network within the brain. Furthermore, they suggested that the conceptually distinct inhibitory aspects of action restraint vs. action cancellation also activated additional specific brain regions in a task-dependent manner. This has implications for the choice of tasks in an empirical setting, but is also relevant for various clinical contexts in which inhibition deficits are considered a diagnostic feature.
Yield of colonoscopy in patients with nonacute rectal bleeding: a multicenter database study of 1766 patients

OBJECTIVE:There are few data to guide the choice between colonoscopy and flexible sigmoidoscopy in patients with nonacute rectal bleeding, especially in younger age groups. Our aim was to determine the yield of colonoscopy for significant proximal large bowel disease in the absence of significant distal disease, with special reference to young patients.METHODS:This was a retrospective study of data collected prospectively in 1766 patients (median age 57 yr, 711 women). The endoscopic database (GI-Trac) contained 152 discrete fields for data input. Multiple logistic regression analysis was performed to identify variables independently associated with the presence of isolated significant proximal disease.RESULTS:Young patients had a higher percentage of normal examinations than did older patients. The incidence of diverticular disease, small polyps, large polyps, and cancer rose with increasing age. No patient aged <40 yr had an isolated proximal cancer, but 7% had other significant isolated proximal disease. There was no overall association between age and significant proximal disease in the absence of significant distal disease (p = 0.66). The only variable associated with isolated proximal disease was anemia (odds ratio = 1.81; 95% CI = 1.11–2.93; p = 0.02).CONCLUSION:The yield of colonoscopy (beyond the range of sigmoidoscopy) for neoplasia is low in patients aged <40 yr, but other significant disease may be missed if age is the only criterion determining colonoscopy use.
Thrombus Aspiration in Patients With ST-Segment Elevation Myocardial Infarction Presenting Late After Symptom Onset.

OBJECTIVES
The aim of this study was to examine whether manual thrombus aspiration reduces microvascular obstruction assessed by cardiac magnetic resonance imaging in patients with ST-segment elevation myocardial infarction (STEMI) presenting late after symptom onset.


BACKGROUND
Thrombus aspiration is an established treatment option in patients with STEMI undergoing primary percutaneous coronary intervention (PCI). However, there are only limited data on the efficacy of thrombus aspiration in patients with STEMI presenting ≥12 h after symptom onset.


METHODS
Patients with subacute STEMI presenting ≥12 and ≤48 h after symptom onset were randomized to primary PCI with or without manual thrombus aspiration in a 1:1 ratio. Patients underwent cardiac magnetic resonance imaging 1 to 4 days after randomization. The primary endpoint was the extent of microvascular obstruction.


RESULTS
A total of 152 patients underwent randomization. The mean time between symptom onset and PCI was 28 ± 12 h. Baseline characteristics were comparable between groups. The majority of patients (60%) showed at least a moderate amount of viable myocardium in the affected region. Extent of microvascular obstruction was not significantly different between patients assigned to thrombus aspiration and the control group (2.5 ± 4.0% vs. 3.1 ± 4.4% of left ventricular mass, p = 0.47). There were also no significant differences in infarct size, myocardial salvage, left ventricular ejection fraction, and angiographic and clinical endpoints between groups.


CONCLUSIONS
In this first randomized trial of thrombectomy in patients with STEMI presenting late after symptom onset, routine thrombus aspiration before PCI failed to show a benefit for markers of reperfusion success. (Effect of Thrombus Aspiration in Patients With Myocardial Infarction Presenting Late After Symptom Onset; NCT01379248).
Questions in quantum physics: a personal view

An assessment of the present status of the theory, some immediate tasks which are suggested thereby and some questions whose answers may require a longer breath since they relate to significant changes in the conceptual and mathematical structure of the theory.
THE TIME DEPENDENT VEHICLE ROUTING PROBLEM WITH TIME WINDOWS: BENCHMARK PROBLEMS, AN EFFICIENT SOLUTION ALGORITHM, AND SOLUTION CHARACTERISTICS

An algorithm that can tackle time dependent vehicle routing problems with hard or soft time windows without any alteration in its structure is presented. Analytical and experimental results indicate that average computational time increases proportionally to the number of customers squared. New replicable test problems that capture the typical speed variations of congested urban settings are proposed. Solution quality, time window perturbations, and computational time results are discussed as well as a method to study the impact of perturbations by problem type. The algorithm efficiency and simplicity is well suited for urban areas where fast running times may be required. 2011 Elsevier Ltd. All rights reserved.
Children of a parent with a mental illness: perspectives on need

Being a child of a parent who has a mental illness involves considerable risk to the child’s secure attachment and long-term mental health. Parental mental health concerns place children at a significantly greater risk of lower social, psychological and physical health than children in families not affected by mental illness. In this paper, previous research is extended by examining the needs of these children from the perspectives of children, parents and mental health and welfare professionals. The study involved qualitative and quantitative data collection from focus groups with children and parents, and a comparison of quantitative findings with mental health professionals. Similar responses from the children and parents included problems with major episodes (e.g. parent hospitalisation), issues regarding coping and the importance of sibling support. Parents also identified a number of different issues (e.g. external support) compared with children (e.g. the importance of friendships). A final component of the research undertook a quantitative comparison of seven core ‘things that might help’ children in the circumstance of their parent being hospitalised. The findings showed differences between parents and mental professionals but most significantly with children. The findings overall are discussed in relation to the needs of children whose parent has a mental illness and recommendations are made regarding policy and service provision.
Transmembrane protein topology prediction using support vector machines

Alpha-helical transmembrane (TM) proteins are involved in a wide range of important biological processes such as cell signaling, transport of membrane-impermeable molecules, cell-cell communication, cell recognition and cell adhesion. Many are also prime drug targets, and it has been estimated that more than half of all drugs currently on the market target membrane proteins. However, due to the experimental difficulties involved in obtaining high quality crystals, this class of protein is severely under-represented in structural databases. In the absence of structural data, sequence-based prediction methods allow TM protein topology to be investigated. We present a support vector machine-based (SVM) TM protein topology predictor that integrates both signal peptide and re-entrant helix prediction, benchmarked with full cross-validation on a novel data set of 131 sequences with known crystal structures. The method achieves topology prediction accuracy of 89%, while signal peptides and re-entrant helices are predicted with 93% and 44% accuracy respectively. An additional SVM trained to discriminate between globular and TM proteins detected zero false positives, with a low false negative rate of 0.4%. We present the results of applying these tools to a number of complete genomes. Source code, data sets and a web server are freely available from http://bioinf.cs.ucl.ac.uk/psipred/ . The high accuracy of TM topology prediction which includes detection of both signal peptides and re-entrant helices, combined with the ability to effectively discriminate between TM and globular proteins, make this method ideally suited to whole genome annotation of alpha-helical transmembrane proteins.
Automatic code generation by model transformation from sequence diagram of system ’ s internal behavior

Software engineering process aims to help leading an IT project from requirements specification to code implementation in a specific platform. Such process can be improved by the model driven architecture (MDA) proposed by the OMG. Indeed, during the whole development process a set of models are used to represent different views of system and which can be enriched by additional information and transformed from more abstract into more concrete ones by applying a set of model-to-model transformation. Moreover, the MDA allows also the code generation from platform specific models (PSM) by the means of generators that automatically transform models into source code for the chosen platform. Within this context, this presents code generator that allows generating source code from the sequence diagram of system’s internal behavior platform independent model by the mean of a set of model transformations. An intermediate structural model representing the Java PSM is generated instead of the source code directly to allow the extension of target platform by enabling the transformation of this model after. To illustrate this feature, we have extended the JAVA platform with the enterprise java beans capabilities by applying an Ecore Meta Facility profile for EJB to produce persistent entities and session beans that provide an interface for different data access operations. Also, the persistent entities can be used to create the different tables of the schema corresponding to those entities, thereby another contribution of this work. Also since the sequence diagram implements the MVC design pattern, we will generate controllers with the detail implementation of their methods that allows to coordinate system’s objects to execute the use case. The main objective of the approach is to concentrate the entire efforts on the system’s abstraction and business logic by building different views of systems through PIMs or PSMs and feed the generator with this knowledge to be able to transform those abstract models automatically to implementation code. Keywords-component; Model Transformation; Code generation; software process; EMF profile; sequence diagram.
Annual movements of Mongolian gazelles: Nomads in the Eastern Steppe

Determining the scale and pattern of, and the influences on, the movements of Mongolian gazelles is important because their numbers and range have been reduced significantly, and their remaining grassland habitat faces further fragmentation and degradation. Therefore, during 2000e2005 we monitored movements of individually marked Mongolian gazelle calves and adult females in the Eastern Steppe of Mongolia to identify variation in seasonal range sizes and locations, group sizes, and range characteristics. Annual range size for calves varied over an order of magnitude (800e18 700 km2), and none of 9 calves tracked for a full year returned to their birth site. Adult gazelles ranged widely (14 000e32 000 km2 annually) and individuals captured together showed little range overlap. Seasonal shifts in range use suggested gazelles are readily able to take advantage of changing conditions, but the lack of consistent use of seasonal ranges is characteristic of a nomadic movement strategy. Developing strategies that protect ungulate populations that demonstrate nomadic movements is an important consideration in future conservation decisions. Understanding the ecology driving these movements will be an important next step. ! 2010 Elsevier Ltd. All rights reserved.
Two decades of statistical language modeling: where do we go from here?

Statistical language models estimate the distribution of various natural language phenomena for the purpose of speech recognition and other language technologies. Since the first significant model was proposed in 1980, many attempts have been made to improve the state of the art. We review them, point to a few promising directions, and argue for a Bayesian approach to integration of linguistic theories with data.
Appreciation of Food Safety Practices Based on Level of Experience

This study sought to determine if no experience, basic experience, or well-informed experience (defined as basic experience and formal food safety training) in a foodservice operation would influence attitudes, subjective norms, and perceived behavioral control toward three important behaviors that can help prevent foodborne illness (handwashing, using thermometers, and sanitizing work surfaces). Results suggest that formal training increases respondents’ appreciation of the importance of these food safety practices. Those with formal food safety training identified more attitude, subjective norm, and perceived behavioral control constructs than participants with basic experience or no experience in foodservice. Factors that help and impede employees in following proper food safety practices were identified. Foodservice operators and sanitarians can utilize these results to employ strategies to address the barriers preventing employees from applying food safety practices and to increase compliance with food safety regulations during individual inspections within operations, respectively.