Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the prevalence of genes coding for enterotoxins, exfoliatins, panton-valentine leukocidin and tsst-1 between methicillin-resistant and methicillin-susceptible isolates of Staphylococcus aureus at the university hospital in olomouc.

AIMS Staphylococcus aureus is an important pathogen characterised by its potential to express many virulence factors. Currently, special attention is being paid to methicillin-resistant strains of S. aureus (MRSA). The aim of this study was to compare the prevalence of 13 selected virulence factor genes in methicillin-resistant versus methicillin-susceptible S. aureus (MSSA) isolates and to investigate their accumulation in the same isolate. METHODS Real-time PCR was used to detect the presence of genes in 200 isolates of S. aureus (100 MRSA and 100 MSSA) from the University Hospital Olomouc collected in 2005-2006. RESULTS Six out of the 13 monitored genes were detected more frequently in MRSA isolates: sea, seb, seg, sei, sej and eta, coding for the production of the enterotoxins A, B, G, I, J and the exfoliative toxin A. On the other hand, the pvl and tst genes coding for Panton-Valentine leukocidin and TSST-1 were more frequent in MSSA. Statistical analysis (chi-squared test) of the prevalence of virulence factors in the two groups showed a significant difference (P<0.05) in two cases (seg, sei). CONCLUSIONS A higher prevalence of selected virulence genes was not confirmed in the methicillin-resistant S. aureus group. This indicates no further increase in their threat.
On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data

MOTIVATION Genome-wide association (GWA) studies have proven to be a successful approach for helping unravel the genetic basis of complex genetic diseases. However, the identified associations are not well suited for disease prediction, and only a modest portion of the heritability can be explained for most diseases, such as Type 2 diabetes or Crohn's disease. This may partly be due to the low power of standard statistical approaches to detect gene-gene and gene-environment interactions when small marginal effects are present. A promising alternative is Random Forests, which have already been successfully applied in candidate gene analyses. Important single nucleotide polymorphisms are detected by permutation importance measures. To this day, the application to GWA data was highly cumbersome with existing implementations because of the high computational burden. RESULTS Here, we present the new freely available software package Random Jungle (RJ), which facilitates the rapid analysis of GWA data. The program yields valid results and computes up to 159 times faster than the fastest alternative implementation, while still maintaining all options of other programs. Specifically, it offers the different permutation importance measures available. It includes new options such as the backward elimination method. We illustrate the application of RJ to a GWA of Crohn's disease. The most important single nucleotide polymorphisms (SNPs) validate recent findings in the literature and reveal potential interactions. AVAILABILITY The RJ software package is freely available at http://www.randomjungle. org
Information Asymmetry in Information Systems Consulting: Toward a Theory of Relationship Constraints

Opportunism, or self-interest seeking with guile, is often witnessed in human behavior, and it bedevils human interactions and relationships. Organizations expend considerable effort to reduce opportunism. Agency theory espouses formal contracts as effective constraints on opportunism; however, a consultant's use of tacit knowledge subjects clients to information asymmetry that is not amenable to formal contracts. The principal-professional lens was developed to accommodate the presence of tacit knowledge, but it ignores formal contracts and, like agency theory, ignores the existence of principal opportunism. This examination of information systems (IS) consulting notes that when information asymmetry is present, both clients and consultants sometimes behave opportunistically. The level of information asymmetry, the type of knowledge, and the level of contract specificity in an IS consulting engagement determine the mixture of legal and social constraints that are efficacious. Based on these revelations and the inadequacy of other theories, a theoretical model of relationship constraints is developed to explain the interplay between signaling and screening, knowledge type, contract specificity, and the levels of information asymmetry in predicting adopted constraint mechanisms. For researchers, this new model offers a lens to study opportunism from a knowledge-based perspective, whereas for practitioners it offers the possibility of forestalling a decline in markets due to rampant opportunism.
A reassessment of carotid endarterectomy in the face of contralateral carotid occlusion: surgical results in symptomatic and asymptomatic patients.

OBJECTIVE Total occlusion of the contralateral internal carotid artery has often been considered to be a predictor of poor outcome after carotid endarterectomy (CEA) of ipsilateral carotid stenosis. Data from both the North American Symptomatic Carotid Endarterectomy Trial and the Asymptomatic Carotid Atherosclerosis Study have suggested this to be true. However, each of these trials had relatively few patients with contralateral occlusion in the surgical arms of the studies. Recently, advocates of carotid angioplasty and stenting have suggested that this technique may be preferable in patients with a contralateral occlusion because of the perceived poor outcome with surgery. The purpose of this study was to review a large series of CEAs performed in patients with contralateral occlusion to see whether results differed from patients with patent contralateral arteries and to determine whether the presence of preoperative symptoms was an important factor in outcome in these cases. PATIENTS AND METHODS A review was conducted of a prospectively compiled database of all primary CEAs performed at our institution from 1985 to 1999. Surgery was performed on 2420 patients, of whom 338 (14.0%) had contralateral total occlusion. RESULTS Patients with contralateral total occlusion were more likely to be symptomatic (65.7% versus 60.1%; P =.1), male (70.9% versus 58%; P <.001), and hypertensive (63.9% versus 58.4%; P =.07) with a positive smoking history (42.6% versus 31.4%; P <.001) than patients with patent contralateral carotid artery. No significant difference was seen in the rates of perioperative neurologic events between patients with contralateral occlusion (3.0%) and those without (2.1%; P =.34). Among the total of 913 asymptomatic patients, of whom 115 had contralateral occlusion, no difference was seen in the rate of perioperative neurologic events (1.8% for contralateral occlusion cases; 1.9% for cases without contralateral occlusion). Among the total of 1507 symptomatic patients, of whom 223 had contralateral occlusion, no significant difference was seen in the rate of perioperative neurologic events (3.7% for contralateral occlusion cases; 2.2% for cases without contralateral occlusion; P =.2). CONCLUSION The presence of contralateral occlusion does not appear to increase the perioperative risk of CEA. Although the risk of CEA in symptomatic patients with contralateral occlusion may be slightly increased, this must be weighed against the risk with medical treatment alone. CEA can be performed safely in patients with contralateral occlusion, which should not necessarily be considered a high-risk condition for surgery in favor of angioplasty and stenting.
Expression of ACE and ACE2 in Patients with Hypertensive Nephrosclerosis

Background: The interplay between intrarenal angiotensin-converting enzyme (ACE) and type 2 ACE (ACE2) might play important roles in the pathogenesis of hypertensive nephrosclerosis (HTN), but human data are limited. Methods: Renal biopsy specimens of 41 patients with HTN and 10 transplant donors as controls (CTL) were studied. The glomerular and tubulointerstitial mRNA expression of ACE and ACE2 was measured by laser microdissection and real-time quantitative polymerase chain reaction. The corresponding protein level was determined by immunohistochemistry. Results: Neither the glomerular nor tubulointerstitial mRNA expression of ACE or ACE2 correlated with the corresponding protein level by immunohistochemistry. The tubulointerstitial levels of ACE and ACE2 were significantly lower in HTN than CTL, while the glomerular ACE and ACE2 levels were similar between the groups. The tubulointersitial ACE and ACE2 levels significantly correlated with the estimated glomerular filtration rate (GFR) and inversely with the degree of histological damage. The glomerular ACE and ACE2 levels significantly correlated with the rate of GFR decline. The ratio of glomerular ACE and ACE2 level correlated with the estimated GFR and the degree of glomerulosclerosis. Conclusion: Our results suggest that intrarenal ACE and ACE2 may play an important role in the pathogenesis and progression of HTN. Studies based on the mRNA expression of ACE and ACE2 should be cautiously interpreted.
Use of Shape-Memory Alloy Devices in Earthquake Engineering: Mechanical Properties, Advanced Constitutive Modelling and Structural Applications

Shape-memory alloys (SMAs) are a class of solids showing mechanical properties not present in materials usually utilized in engineering. SMAs have the ability to undergo reversible micromechanical phase transition processess by changing their cristallographic structure. This capacity results in two major features at the macroscopic level which are the superelasticity and the shape-memory effect. Due to these unique characteristics, SMA materials lend themselves to innovative applications in many scientific fields, ranging from biomedical devices, such as stents or orthodontic archwires, to apparatus for the deployment and control of space structures, such as antennas and satellites. Recent experimental and numerical investigations have also shown that the use of SMAs as vibration control devices seems to be an effective mean of improving the dynamic response of buildings and bridges subjected to earthquake-induced excitations. In this respect, the present work focuses on the seismic performance of steel frames equipped with either steel or superelastic SMA braces, in order to evaluate the possibility of adopting an innovative bracing system in place of a traditional one. Also, a contribution on the modelling of superelastic SMA materials for seismic applications is given and two uniaxial rate-dependent constitutive equations are developed, implemented and compared with experimental data. Finally, preliminary results concerning shake table tests of a reduce-scale frame equipped with superelastic SMA braces are provided and numerical results from the corresponding finite element study are reported and discussed.
Hard Core Drinking Drivers

The term “hard core” has been used extensively over the past 15 years to identify persons who drink and drive regularly, typically at high blood alcohol levels. This article discusses how the term arose and clarifies what it means, both as a concept and in practice. It describes the characteristics of hard core drinking drivers and estimates their contribution to drinking driver trips, arrests, and crashes. It summarizes current knowledge and recommendations on the most effective means to affect their behavior and reduce their drinking and driving.
Firmato: a novel firewall management toolkit

In recent years, packet filtering firewalls have seen some impressive technological advances (e.g., stateful inspection, transparency, performance, etc.) and widespread deployment. In contrast, firewall and security management technology is lacking. We present Firmato, a firewall management toolkit, with the following distinguishing properties and components: (1) an entity relationship model containing, in a unified form, global knowledge of the security policy and of the network topology; (2) a model definition language, which we use as an interface to define an instance of the entity relationship model; (3) a model compiler translating the global knowledge of the model into firewall-specific configuration files; and (4) a graphical firewall rule illustrator. We demonstrate Firmato's capabilities on a realistic example, thus showing that firewall management can be done successfully at an appropriate level of abstraction. We implemented our toolkit to work with a commercially available firewall product. We believe that our approach is an important step towards streamlining the process of configuring and managing firewalls, especially in complex, multi firewall installations.
Molecular and genetic evidence for a virus-encoded glycosyltransferase involved in protein glycosylation.

The major capsid protein, Vp54, of chlorella virus PBCV-1 is a glycoprotein that contains either one glycan of approximately 30 sugar residues or two similar glycans of approximately 15 residues. Previous analysis of PBCV-1 antigenic mutants that contained altered Vp54 glycans led to the conclusion that unlike other glycoprotein-containing viruses, most, if not all, of the enzymes involved in the synthesis of the Vp54 glycan are probably encoded by PBCV-1 (I.-N. Wang et al., 1993, Proc. Natl. Acad. Sci. USA 90, 3840-3844). In this report we used molecular and genetic approaches to begin to identify these virus genes. Comparing the deduced amino acid sequences of the putative 375 PBCV-1 protein-encoding genes to databases identified seven potential glycosyltransferases. One gene, designated a64r, encodes a 638-amino-acid protein that has four motifs conserved in "Fringe type" glycosyltransferases. Analysis of 13 PBCV-1 antigenic mutants revealed mutations in a64r that correlated with a specific antigenic variation. Dual-infection experiments with different antigenic mutants indicated that viruses that contained wild-type a64r could complement and recombine with viruses that contained mutant a64r to form wild-type virus. Therefore, we conclude that a64r encodes a glycosyltransferase involved in synthesizing the Vp54 glycan. This is the first report of a virus-encoded glycosyltransferase involved in protein glycosylation.
Comparative study of adhesive systems applied to different regions of dental substrate

OBJECTIVE: The aim of this study was to evaluate the bond strength (BS) of different self-etching adhesive systems to bovine dentin. METHODS: For this purpose, 50 teeth were flattened with silicon carbide abrasive papers and randomly divided into 5 groups: SB – Single Bond Plus; Group AEO – Adper Easy One; Group ADH – AdheSE; Group ASE – Adper SE Plus and Group Clear – Clear Fill. After adhesive system application, 5 Tygon cylinders (1.8 mm×2 mm) were placed on the vestibular surface of each tooth, filled with resin composite (Filtek Z350) and light activated. Three composite resin cylinders were fabricated for each bovine crown, one being located in the incisal region, one in the middle third and one in the cervical region, totaling 30 composite resin test specimens (TS) for each group. The TS were submitted to the microshear bond strength test in a Universal Test Machine Kratos), at a cross-head speed of 0.5 mm/min. RESULTS: The BS was calculated and analyzed by ANOVA (one-way) and Tukey’s test (p<0.05). The highest BS values were obtained in Group SB and there were no significant differences between the adhesive systems tested in the middle and cervical thirds. In the fracture type analysis it was found that adhesive failure was dominant for all groups. CONCLUSION: The conventional two-step adhesive system SB presented the highest bond strength mean to bovine dentin for all the regions.
Loss of chromatic sensitivity in AMD and diabetes: a comparative study

Background: Abnormalities in rod and cone photoreceptor morphology have been reported in normal aging retinas in the absence of known pathology and have been taken as an indicator of susceptibility to retinal disease. Some loss of visual performance may therefore precede retinal structural changes that can be detected reliably using conventional fundus imaging techniques. Red/green (RG) and yellow/blue (YB) colour discrimination thresholds are sensitive measures of normal retinal function and poor YB discrimination is often taken as an indicator of retinal disease, though it is generally acknowledged that RG loss is also present in most cases of acquired deficiency. Although structural changes in age‐related macular degeneration (AMD) and diabetes share some similarities, significant differences remain and this may result in different patterns of RG and YB loss.
Current insights in the development of children’s motor imagery ability

Over the last two decades, the number of studies on motor imagery in children has witnessed a large expansion. Most studies used the hand laterality judgment paradigm or the mental chronometry paradigm to examine motor imagery ability. The main objective of the current review is to collate these studies to provide a more comprehensive insight in children’s motor imagery development and its age of onset. Motor imagery is a form of motor cognition and aligns with forward (or predictive) models of motor control. Studying age-related differences in motor imagery ability in children therefore provides insight in underlying processes of motor development during childhood. Another motivation for studying age-related differences in motor imagery is that in order to effectively apply motor imagery training in children (with motor impairments), it is pertinent to first establish the age at which children are actually able to perform motor imagery. Overall, performance in the imagery tasks develops between 5 and 12 years of age. The age of motor imagery onset, however, remains equivocal, as some studies indicate that children of 5 to 7 years old can already enlist motor imagery in an implicit motor imagery task, whereas other studies using explicit instructions revealed that children do not use motor imagery before the age of 10. From the findings of the current study, we can conclude that motor imagery training is potentially a feasible method for pediatric rehabilitation in children from 5 years on. We suggest that younger children are most likely to benefit from motor imagery training that is presented in an implicit way. Action observation training might be a beneficial adjunct to implicit motor imagery training. From 10 years of age, more explicit forms of motor imagery training can be effectively used.
Automatical vessel wall detection in intravascular coronary OCT

The aim of this study is to automatically detect the boundary of vessel walls in optical coherence tomography (OCT) sequences. We developed a new method to eliminate guide-wire shadow artifacts and accurately estimate the vessel wall. The estimation of the position of the guide-wire is the key concept for the elimination of guide-wire shadow artifacts. After identification of the artifacts we propose a geometrically-based method which can be applied to OCT cross-section images to remove the artifacts. The segmentation approach is based on a novel combination of expectation maximization (EM) based segmentation and graph cut (GC) based segmentation. Validation is performed using simulated data and 4 typical in vivo OCT sequences. The comparison against manual expert segmentation demonstrates that the proposed vessel wall identification is robust and accurate.
The relationship between insomnia and depressive symptoms: genuine or artifact?

Background: Somatic symptom overlap between depression and insomnia has emerged as a major concern. Self-report measures such as the Beck Depression Inventory Second Edition (BDI-II) include somatic symptoms related to depression that are also present in the research diagnostic criteria for insomnia. This study aimed firstly to examine the relationship between the cognitive and somatic factors of the BDI-II and global scores on the Pittsburgh Sleep Quality Index (PSQI) in individuals presenting for insomnia treatment and secondly to examine whether treating insomnia in depressed individuals with insomnia will lead to a reduction in their depressive symptoms and whether this reduction is related to a decrease in the somatic or cognitive factors of depressive symptoms. Methods: A total of 379 individuals (133 males and 246 females), with a mean (M) age of 49.95 (standard deviation [SD] = 14.15) years, were used to address the first aim. To address the second aim, a total of 64 participants (27 males and 37 females) with both insomnia and depressive symptoms were treated for their insomnia. Their ages ranged between 22 and 87 (M = 50.97, SD = 15.13) years. Results: A significant relationship was found between both the cognitive and somatic factors of the BDI-II and global scores on the PSQI. Furthermore, although results in this study are only suggestive, they lend support to the idea that the relationship between insomnia and depression is not due to somatic symptom overlap. Results may also support the hypothesis that insomnia is primary to the presentation of depressive symptoms. Conclusion: Clinicians and health care providers could initially treat insomnia in individuals suffering from insomnia who also experience depressive symptoms, as this will not only remit insomnia but also abate the accompanying depressive symptoms.
Inhalation of Sidestream Cigarette Smoke Accelerates Development of Arteriosclerotic Plaques

BackgroundEnvironmental tobacco smoke has been blamed for $-40 000 excess deaths from heart disease annually in the United States. As yet, no pathophysiological process that could be responsible for these deaths has been identified. Environmental tobacco smoke is composed mainly of aged and diluted sidestream smoke but also contains 15% to 20% exhaled mainstream smoke. Carcinogens, including nitrosamines and polynuclear aromatic hydrocarbons, are present in mainstream smoke and sidestream smoke. Carcinogen levels in sidestream smoke, unlike those in mainstream smoke, are not reduced in filtered cigarettes. The US Environmental Protection Agency has designated environmental tobacco smoke as a human (class A) carcinogen. In cockerels, subtumorigenic doses of polynuclear aromatic hydrocarbons carcinogens accelerate aortic arteriosclerotic plaque development. Methods and ResultsTo determine whether sidestream smoke inhalation affects arteriosclerotic plaque development, we exposed cockerels to sidestream smoke (n=30) or to filtered air (n=12) in inhalation chambers for 6 hours per day, 5 days a week from 6 to 22 weeks of age (0.4% of projected lifespan). Chamber levels of carbon monoxide, total suspended particulates, and nicotine were measured regularly during the exposures. The abdominal aorta from each cockerel was cut into 10 segments, and the plaque index (mean plaque cross-sectional area [mm2]/mean luminal circumference [mm]× 100) was calculated for each segment. There were no differences in plaque incidence or distribution between sidestream smoke-exposed and control cockerels; however, plaque indexes were significantly greater for sidestream smoke-exposed than control cockerels in all segments ConclusionsThus, relatively brief exposures to sidestream smoke early in life are sufficient to enhance arteriosclerotic plaque development.