Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of bone marrow on superficial digital flexor tendon healing in sheep

Summary The present study was to compare the effectiveness of bone marrow transplantation on the healing of experimentally transected superficial digital flexor tendon in sheep. Eight adult sheep, aged between 9 months to one year were used. The animals were divided into two equal groups (control and allograft). An transverse cutting has been made in the superficial digital flexor tendon of the m iddle third of the m etatarsal bone under the effect of sedation and local anesthesia. The tendons were sutured with Bunnell suture by using polypropylene thread (2.0 usp) in the control group. While in allograft groups 2-3ml allograft bone marrow was injected at the site of suture tendon which was induced by similar procedure as in control group. The incision was closed as a routine manner. Gross examination showed adhesions between the tendon and adjacent structures which were severe in the control group , less than that in allograft. Histopathological observations of biopsies harvested after (15,30 and 60 days) showed dense immature collagen fibers which was characterized by regular direction, uniform of their cellular elements filled the gap space of tendon injury with more adhesion in l ate stages of the control group. In allograft t reated group inflammatory cells and arrangement fibrous connective tissue with collagen fibers appear more than in the control group in the same period with less adhesion.
Web Links as User Artefacts

The Distributed Link Service, a distributed system of link services for the World Wide Web [Carr et al 95, Carr et al 96], has been used to impose configurable navigation structures upon suites of static document resources in the World-Wide Web. This paper describes the integration of the link service functionality into a Web proxy server, and examines the implications for the service's user interface in terms of including, representing, discriminating, prioritising and traversing links.
Expression of WNT-5a and ROR2 correlates with disease severity in osteosarcoma

Osteosarcoma, a common malignancy primarily affecting children, generally has a poor prognosis. Novel diagnostic, prognostic and therapeutic markers are required to ameliorate the negative outcomes of this disease. We investigated two potential markers, WNT-5a and ROR2, which are hypothesized to dysregulate WNT signaling pathways to promote tumorigenesis in other types of cancer. We investigated WNT-5a and ROR2 expression using immunohistochemistry in 42 osteosarcoma and 12 osteochondroma specimens, and compared the expression of these proteins with one another as well as with clinicopathological parameters. WNT-5a was detected in 34/42 (81.0%) cases and ROR2 was detected in 31/42 (73.8%) cases, significantly higher than in osteochondroma (16.7 and 25.0%, respectively; both P<0.05). Expression of these proteins was positively correlated (r=0.552, P<0.05). Furthermore, expression of WNT-5a and ROR2 was both correlated with Enneking surgical stage and tumor metastasis (P<0.05), but not with patient gender, age or pathological type. Thus, WNT-5a and ROR2 were more highly expressed in more severe disease states, and therefore may play a coordinated role in the occurrence and progression of osteosarcoma.
Investigation of Copy Number Variation in Children with Conotruncal Heart Defects

Background Congenital heart defects (CHD) are the most prevalent group of structural abnormalities at birth and one of the main causes of infant morbidity and mortality. Studies have shown a contribution of the copy number variation in the genesis of cardiac malformations. Objectives Investigate gene copy number variation (CNV) in children with conotruncal heart defect. Methods Multiplex ligation-dependent probe amplification (MLPA) was performed in 39 patients with conotruncal heart defect. Clinical and laboratory assessments were conducted in all patients. The parents of the probands who presented abnormal findings were also investigated. Results Gene copy number variation was detected in 7/39 patients: 22q11.2 deletion, 22q11.2 duplication, 15q11.2 duplication, 20p12.2 duplication, 19p deletion, 15q and 8p23.2 duplication with 10p12.31 duplication. The clinical characteristics were consistent with those reported in the literature associated with the encountered microdeletion/microduplication. None of these changes was inherited from the parents. Conclusions Our results demonstrate that the technique of MLPA is useful in the investigation of microdeletions and microduplications in conotruncal congenital heart defects. Early diagnosis of the copy number variation in patients with congenital heart defect assists in the prevention of morbidity and decreased mortality in these patients.
FOXN1: A Master Regulator Gene of Thymic Epithelial Development Program

T cell ontogeny is a sophisticated process, which takes place within the thymus through a series of well-defined discrete stages. The process requires a proper lympho-stromal interaction. In particular, cortical and medullary thymic epithelial cells (cTECs, mTECs) drive T cell differentiation, education, and selection processes, while the thymocyte-dependent signals allow thymic epithelial cells (TECs) to maturate and provide an appropriate thymic microenvironment. Alterations in genes implicated in thymus organogenesis, including Tbx1, Pax1, Pax3, Pax9, Hoxa3, Eya1, and Six1, affect this well-orchestrated process, leading to disruption of thymic architecture. Of note, in both human and mice, the primordial TECs are yet unable to fully support T cell development and only after the transcriptional activation of the Forkhead-box n1 (FOXN1) gene in the thymic epithelium this essential function is acquired. FOXN1 is a master regulator in the TEC lineage specification in that it down-stream promotes transcription of genes, which, in turn, regulate TECs differentiation. In particular, FOXN1 mainly regulates TEC patterning in the fetal stage and TEC homeostasis in the post-natal thymus. An inborn null mutation in FOXN1 leads to Nude/severe combined immunodeficiency (SCID) phenotype in mouse, rat, and humans. In Foxn1−/− nude animals, initial formation of the primordial organ is arrested and the primordium is not colonized by hematopoietic precursors, causing a severe primary T cell immunodeficiency. In humans, the Nude/SCID phenotype is characterized by congenital alopecia of the scalp, eyebrows, and eyelashes, nail dystrophy, and a severe T cell immunodeficiency, inherited as an autosomal recessive disorder. Aim of this review is to summarize all the scientific information so far available to better characterize the pivotal role of the master regulator FOXN1 transcription factor in the TEC lineage specifications and functionality.
Optical coherence tomographic characteristics in morning glory disc anomaly.

CASE REPORT Optical coherence tomography (OCT) confirms increased optic nerve head dimensions in morning glory anomaly, and provides evidence of increased retinal nerve fibre layer thickness and reduced macular thickness. COMMENTS This first report of quantitative data from OCT may provide more useful information to corroborate clinical diagnosis of this rare congenital disorder.
The role of haemoglobin A2 testing in the diagnosis of thalassaemias and related haemoglobinopathies

The increase in haemoglobin (Hb)A2 level is the most significant parameter in the identification of β thalassaemia carriers. However, in some cases the level of HbA2 is not typically elevated and some difficulties may arise in making the diagnosis. For these reasons the quantification of HbA2 has to be performed with great accuracy and the results must be interpreted together with other haematological and biochemical evidence. The present document includes comments on the need for accuracy and standardisation, and on the interpretation of the HbA2 value, reviewing the most crucial aspects related to this test. A practical flow-chart is presented to summarise the significance of HbA2 estimation in different thalassaemia syndromes and related haemoglobinopathies.
The effects of isosorbide dinitrate on methemoglobin reductase enzyme activity and antioxidant states

Isosorbide dinitrate (ISDN) has been used in the treatment of ischaemic cardiovascular diseases for many years. ISDN is the most popular nitric oxide donor and causes methemoglobinemia as an important side‐effect. The purpose of this study was to examine antioxidant states and methemoglobin reductase activity after giving ISDN and ISDN plus vitamin E. Rats were divided into three groups according to the treatment: control group, ISDN group and ISDN plus vit. E group. We measured reduced glutathione in blood (GSH), plasma malondialdehyde (MDA), erythrocyte superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and NADH‐dependent methemoglobin reductase activities. In the ISDN group, plasma MDA levels were significantly high compared to the control and ISDN+vit. E groups (p < 0.001). In the ISDN and ISDN+vit. E groups, blood GSH levels were higher than those of the control group (p < 0.05). Changes of SOD and GPx activities were not significant. In the ISDN and ISDN+vit. E groups the erythrocyte catalase and NADH‐dependent methemoglobin reductase activities were significantly higher than that in the control group (p < 0.001). We conclude that oxidant drugs such as ISDN need to be carefully used because of lipid peroxidation and methemoglobinemia. These findings support the notion that vitamine E protects tissues against oxidative stress. Copyright © 2004 John Wiley & Sons, Ltd.
Case–Control Analysis with Partial Knowledge of Exposure Misclassification Probabilities

Summary. Consider case‐control analysis with a dichotomous exposure variable that is subject to misclassification. If the classification probabilities are known, then methods are available to adjust odds‐ratio estimates in light of the misclassification. We study the realistic scenario where reasonable guesses, but not exact values, are available for the classification probabilities. If the analysis proceeds by simply treating the guesses as exact, then even small discrepancies between the guesses and the actual probabilities can seriously degrade odds‐ratio estimates. We show that this problem is mitigated by a Bayes analysis that incorporates uncertainty about the classification probabilities as prior information.
Pain sensitivity in patients with temporomandibular disorders: relationship to clinical and psychosocial factors.

OBJECTIVE We have previously reported that patients with temporomandibular disorders (TMD) exhibit enhanced sensitivity to experimentally evoked pain (1); however, the clinical relevance of this increased pain sensitivity remains unclear. The purpose of this study was to investigate the relationship of experimental pain sensitivity to clinical and psychosocial variables among patients with TMD. DESIGN Thirty-six TMD patients were studied, half of whom were pain sensitive (PS) and the other half pain tolerant (PT), based on their ability to tolerate an ischemic pain task. Responses to painful thermal and nonpainful visual stimuli as well as clinical/diagnostic symptoms and psychosocial variables were compared for the two groups (i.e., PS vs. PT). RESULTS Results indicated that, compared with PT patients, the PS group exhibited greater sensitivity to thermal pain and rated innocuous visual stimuli as more intense. PS patients also reported greater clinical pain, but in general the groups did not differ on diagnostic and psychosocial measures. CONCLUSIONS The results suggest that ischemic pain tolerance is a clinically relevant marker of pain sensitivity in TMD patients. These findings are consistent with the hypothesis that impairments in CNS inhibitory pathways may contribute to the pain associated with TMD.
Deep Boltzmann Machines as Feed-Forward Hierarchies

The deep Boltzmann machine is a powerful model that extracts the hierarchical structure of observed data. While inference is typically slow due to its undirected nature, we argue that the emerging feature hierarchy is still explicit enough to be traversed in a feedforward fashion. The claim is corroborated by training a set of deep neural networks on real data and measuring the evolution of the representation layer after layer. The analysis reveals that the deep Boltzmann machine produces a feed-forward hierarchy of increasingly invariant representations that clearly surpasses the layer-wise approach.
The effects of gender and age on occurrence of clinically suspected myocarditis in adulthood

Objective To study the effects of gender and age on occurrence of myocarditis. Design Nationwide, multicentre registry study in Finland. Setting All medical hospital admissions (n=1 698 397) of patients aged ≥16 years during 9.5 years in 29 hospitals. Patients 3198 myocarditis patients. Results Myocarditis was more common in men (76.61%; 95% CI 75.11% to 78.05%) than in women (23.39%; 95% CI 21.95% to 24.89%, p<0.0001). Median age of patients was 33 years (IQR 23–50 years). Male patients were significantly younger than females (mean age 34.1±SD 15.1 vs 49.0±18.7 years, p<0.0001). In men, occurrence was highest at 16–20 yrs of age, with a linear decline to elderliness (r=−0.95, p<0.0001). By contrast, myocarditis affected women more evenly at all ages with highest occurrence at the age of 56–60 years. Myocarditis caused 0.19% (95% CI 0.18% to 0.19%) of all medical admissions, and 0.48% (95% CI 0.46% to 0.49%) of admissions due to cardiovascular reasons with an inverse logarithmic association with age (r=−0.97, p<0.0001). Admissions were more commonly caused by myocarditis in men (risk ratio 3.11; 95% CI 2.87 to 3.38, p<0.0001). Conclusions Men are significantly more susceptible to myocarditis than women. Young men are especially at risk for acquiring myocarditis, while women are affected most commonly at the postmenopausal age. The proportion of hospital admissions caused by myocarditis has an inverse, logarithmic association with age.
Permanent Magnet Eddy-Current Losses in 2-D FEM Simulations of Electrical Machines

The prediction and calculation of eddy current losses occurring in permanent magnets (PMs) of electrical machines is of great interest. Most accurate results are achieved using 3-D finite-element (FE) simulations, which require long computation times and elaborate models. Due to this, 3-D methods are only applied in the final stage of the machine design process. This paper presents different methods to calculate eddy-current losses in PMs by 2-D FE simulations. A radial 2-D FE solver in combination with an axial 2-D FE solver is developed enabling the prediction of the eddy current paths in three dimensions with the associated losses. This approach is applicable to both surface mounted and interior PMs.
The Magic Number 4: Evolutionary Pressures on Semantic Frame Structure

We propose that the “magic number 4” puzzle of argument structure in semantic frames across most human languages is explained by selection pressures given inherent computational efficiency properties naturally arising from fundamental combinatorial mathematics of compositionality. Irrespective of language, school, or theoretical bias, linguists have long observed that what are now generally called “semantic frames” empirically bear a maximum limit of four core arguments per frame, for unknown reasons. We explain how this limit would automatically emerge as a consequence of evolutionary preference for the formal equivalence class of inversion transductions as an optimal balance between expressivity and fast tractable polynomial-time language learning and interpretation/transduction between different representation languages.
OnTheFly: a tool for automated document-based text annotation, data linking and network generation

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database. Availability: http://onthefly.embl.de, http://onthefly.embl.de/FAQ.html Contact: pavlopou@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
Transistor Sizing Using Particle Swarm Optimisation

We describe an application of particle swarm optimisation to the problem of determining the optimal sizing of transistors in an integrated circuit. The algorithm minimises the total area of silicon utilised by a given circuit, whilst maintaining the propagation delay of the circuit within a hard limit. It assesses designs using the well-known circuit simulation engine SPICE, making allowance for the inability of SPICE to assess poorly-designed circuits within a reasonable timeframe. Experiments on three different types of circuits demonstrate that the algorithm is able to derive excellent designs for a range of problem instances, including several problems where the Monte Carlo method is unable to find any feasible solutions at all.
Interactions between Core and Matrix Thalamocortical Projections in Human Sleep Spindle Synchronization

Sleep spindles are bursts of 11–15 Hz that occur during non-rapid eye movement sleep. Spindles are highly synchronous across the scalp in the electroencephalogram (EEG) but have low spatial coherence and exhibit low correlation with the EEG when simultaneously measured in the magnetoencephalogram (MEG). We developed a computational model to explore the hypothesis that the spatial coherence spindles in the EEG is a consequence of diffuse matrix projections of the thalamus to layer 1 compared with the focal projections of the core pathway to layer 4 recorded in the MEG. Increasing the fanout of thalamocortical connectivity in the matrix pathway while keeping the core pathway fixed led to increased synchrony of the spindle activity in the superficial cortical layers in the model. In agreement with cortical recordings, the latency for spindles to spread from the core to the matrix was independent of the thalamocortical fanout but highly dependent on the probability of connections between cortical areas.
Human autonomy and the frontal lobes. Part I: Imitation and utilization behavior: A neuropsychological study of 75 patients

A type of pathological behavior, imitation behavior (IB), is newly described. In this behavior patients imitate the examiner's gestures, although not instructed to do so. Patients explain that they thought they had to imitate the examiner. IB is the first stage of utilization behavior (UB). Neuropsychological examination of 40 patients with IB, of 35 with UB, and of 50 disease controls demonstrates the existence of a frontal syndrome and two determining features of such behavior: dependence on (1) the social and (2) the physical environments. Loss of intellectual control was also required for the occurrence of such behavior. UB and/or IB were present in 96% of the 29 patients with focal lesions of the frontal lobes. Computed tomographic scans in 26 of these patients showed involvement of the inferior half of the anterior part of one or both frontal lobes. IB and UB are interpreted as release of parietal lobe activities, resulting from impairment of frontal lobe inhibition.
Leptin resistance protects mice from hyperoxia-induced acute lung injury.

RATIONALE Human data suggest that the incidence of acute lung injury is reduced in patients with type II diabetes mellitus. However, the mechanisms by which diabetes confers protection from lung injury are unknown. OBJECTIVES To determine whether leptin resistance, which is seen in humans with diabetes, protects mice from hyperoxic lung injury. METHODS Wild-type (leptin responsive) and db/db (leptin resistant) mice were used in these studies. Mice were exposed to hyperoxia (100% O(2)) for 84 hours to induce lung injury and up to 168 hours for survival studies. Alveolar fluid clearance was measured in vivo. MEASUREMENTS AND MAIN RESULTS Lung leptin levels were increased both in wild-type and leptin receptor-defective db/db mice after hyperoxia. Hyperoxia-induced lung injury was decreased in db/db compared with wild-type mice. Hyperoxia increased lung permeability in wild-type mice but not in db/db mice. Compared with wild-type control animals, db/db mice were resistant to hyperoxia-induced mortality (lethal dose for 50% of mice, 152 vs. 108 h). Intratracheal instillation of leptin at a dose that was observed in the bronchoalveolar lavage fluid during hyperoxia caused lung injury in wild-type but not in db/db mice. Intratracheal pretreatment with a leptin receptor inhibitor attenuated leptin-induced lung edema. The hyperoxia-induced release of proinflammatory cytokines was attenuated in db/db mice. Despite resistance to lung injury, db/db mice had diminished alveolar fluid clearance and reduced Na,K-ATPase function compared with wild-type mice. CONCLUSIONS These results indicate that leptin can induce and that resistance to leptin attenuates hyperoxia-induced lung injury and hyperoxia-induced inflammatory cytokines in the lung.
Frailty, Disability and Physical Exercise in the Aging Process and in Chronic Kidney Disease

Frailty in the elderly is a state of vulnerability to poor resolution of homoeostasis after a stressor event and is a consequence of cumulative decline in many physiological systems during a lifetime. This cumulative decline depletes homoeostatic reserves until minor stressor events trigger disproportionate changes in health status. It is usually associated to adverse health outcomes and to one-year mortality risk. Physical exercise has found to be effective in preventing frailty and disability in this population. Chronic kidney disease (CKD) is also a clinical condition where protein energy-wasting, sarcopenia and dynapenia ,very common symptoms in the frail elderly, may occur. Moreover elderly and CKD patients are both affected by an impaired physical performance that may be reversed by physical exercise with an improvement of the survival rate. These similarities suggest that frailty may be a common pathway of aging and CKD that may induce disability and that can be prevented by a multidimensional approach in which physical exercise plays an important role.
The Yeast Golgi Apparatus

The Golgi apparatus is an organelle that has been extensively studied in the model eukaryote, yeast. Its morphology varies among yeast species; the Golgi exists as a system of dispersed cisternae in the case of the budding yeast Saccharomyces cerevisiae, whereas the Golgi cisternae in Pichia pastoris and Schizosaccharomyces pombe are organized into stacks. In spite of the different organization, the mechanism of trafficking through the Golgi apparatus is believed to be similar, involving cisternal maturation, in which the resident Golgi proteins are transported backwards while secretory cargo proteins can stay in the cisternae. Questions remain regarding the organization of the yeast Golgi, the regulatory mechanisms that underlie cisternal maturation of the Golgi and transport machinery of cargo proteins through this organelle. Studies using different yeast species have provided hints to these mechanisms.