Miracle-dz/UniFAR-FTUs huggingface dataset:
Static Model Analysis with Lattice-based Ontologies

This thesis demonstrates a correct, scalable and automated method to infer semantic concepts using lattice-based ontologies, given relatively few manual annotations. Semantic concepts and their relationships are formalized as a lattice, and relationships within and between program elements are expressed as a set of constraints. Our inference engine automatically infers concepts wherever they are not explicitly specified. Our approach is general, in that our framework is agnostic to the semantic meaning of the ontologies that it uses. Where practical use-cases and principled theory exist, we provide for the expression of infinite ontologies and ontology compositions. We also show how these features can be used to express of value-parametrized concepts and structured data types. In order to help find the source of errors, we also present a novel approach to debugging by showing simplified errors paths. These are minimal subsets of the constraints that fail to type-check, and are much more useful than previous approaches in finding the cause of program bugs. We also present examples of how this analysis tool can be used to express analyses of abstract interpretation; physical dimensions and units; constant propagation; and checks of the monotonicity of expressions.
Predictors of type of vascular access in hemodialysis patients.

OBJECTIVE Complications from vascular access account for 15% of hospital admissions among US hemodialysis patients. Complications are less frequent with arteriovenous fistulas than with synthetic grafts. We assessed clinical and nonclinical predictors of whether patients with end-stage renal disease (ESRD) starting hemodialysis receive a fistula or graft. We also investigated changes in practice between 1986-1987 and 1990. DESIGN Cross-sectional study. SETTING United States hemodialysis population. PATIENTS Random, national samples of ESRD patients who started hemodialysis in 1986-1987 (n=2741) or 1990 (n=1409) from United States Renal Data System Special Studies. MAIN OUTCOME MEASURE Type of permanent vascular access (arteriovenous fistula vs synthetic graft), analyzed using multivariate logistic regression. RESULTS Clinical and demographic factors as well as socioeconomic status, region of residence, and year starting hemodialysis predicted the type of vascular access. Overall, 56% of patients had grafts 30 days after starting dialysis, but graft use increased from 51% in 1986-1987 to 65% in 1990 (adjusted odds ratio [AOR], 1.67 for 1990 vs 1986-1987; 95% confidence interval [CI], 1.43-1.95; P<.001). Graft use (relative to fistula) varied by region of residence (ranging from AOR, 0.20; 95% CI, 0.14-0.28; P<.001 [New England], to AOR, 2.69; 95% CI, 2.03-3.58; P<.001 [East South Central]; both relative to the national average). CONCLUSIONS This national study documents large variations in the relative use of fistulas and grafts and a trend away from fistulas. The prevalence of comorbid conditions fails to explain these findings. Presentation and referral of patients early in the process of their ESRD, teaching surgeons to place fistulas, and training dialysis nurses to access fistulas may increase their use.
Necking in 2 D incompressible polyconvex materials : theoretical framework and numerical simulations

We show examples of 2D incompressible isotropic homogeneous hyperelastic materials with a polyconvex stored-energy function that present necking. The construction of the stored-energy function of a material satisfying all those properties requires a fine search. We used the software Algencan to perform numerical experiments and visualize necking for the examples constructed. The algorithm is based on minimization of the elastic energy under the nonconvex constraint of incompressibility.
Expression of class II major histocompatibility complex antigens (HLA-DR) and lymphocyte subset immunotyping in chronic pulmonary transplant rejection.

OBJECTIVE Currently, the bronchiolitis obliterans syndrome (BOS) of chronic airway rejection represents the most significant obstacle to the long-term function of isolated pulmonary allografts in humans. Between 20% and 30% of recipients are affected by this condition. To define the possible pathogenetic role of altered expression of class II major histocompatibility complex antigens (ie, HLA-DR) in BOS, the authors studied well-characterized examples of this process immunohistologically. DESIGN Eleven BOS specimens were compared with seven controls, represented by allografts with no pathologic abnormalities taken from patients with normal posttransplant respiratory function, as well as 14 biopsies showing acute rejection. In addition, immunophenotypic subtyping of lymphocytes in all specimens was undertaken. RESULTS Control tissues exhibited variable but weak expression of HLA-DR in bronchiolar epithelium and alveolar pneumocytes. In comparison, immunostaining for class II major histocompatibility complex antigens in BOS showed no statistically significant differences, whereas the 14 examples of acute rejection manifested intense HLA-DR expression in epithelia and endothelial cells. The numbers of intrabronchiolar and peribronchiolar lymphocytes were clearly higher in both acute rejection and BOS than in controls, but these cells differed in lineage in the two rejection states. Acute rejection showed an obvious preponderance of CD43-positive T lymphocytes, whereas lymphoid cells in BOS were a relatively equal mixture of CD20-positive B cells and CD43-positive T cells. Moreover, incipient peribronchiolar B-cell follicles were observed in BOS. Natural killer (CD57-positive) lymphocytes were rare in all specimens. CONCLUSIONS These data suggest that alterations in HLA-DR expression probably do not play a central role in the genesis of BOS, as they do in acute rejection. In contrast, the results of lymphocyte immunophenotyping and correlative histologic findings in BOS suggest that both T cells and B lymphocytes may be involved in the mechanism of chronic airway rejection.
The effect of histamine on kidney by fasting in rats.

BACKGROUND The aim of this study was to investigate ultrastructural and apoptotic changes occurring in the kidneys in fasting individuals and to examine the effects of histamine treatment at the electron-microscopic and immunohistochemical levels. METHODS Eighteen adult Wistar male rats were randomly divided into three groups (n=6 for each). Control group (1), fasting group (12 h) (2), and fasting+histamine injection (0.5 mg/kg) (3) group. Expression of caspase-3 and caspase-9 was determined in the tissue sections using immunohistochemical techniques. Quantitative data were obtained using H-SCORE, and statistical evaluations were then performed. The ultrastructure of the kidney tissues was examined using transmission electron microscopy. RESULTS Weak caspase-3 and caspase-9 expression was observed in the renal tubules and glomeruli in the control group, while immunoreactivity was more intense in the fasting group (p<0.05). In the fasting+histamine group, caspase-3 and caspase-9 immunostaining was significantly positive in both renal tubules and glomeruli (p<0.05). At electron microscopic evaluation, degenerative changes were seen in the glomeruli of the fasting group, as well as partial vacuolization and disruption at the basal foldings in the tubular epithelial cells. In the fasting+histamine group, in addition to significant dilatation of all glomerular capillaries, there were degenerative changes in all tubular and canalicular epithelial cells in the proximal tubules. CONCLUSIONS Fasting, an important metabolic stress factor, accompanied by histamine treatment may cause significant disruptions in the kidneys, particularly in the glomerular capillaries and proximal and distal tubules (Tab. 1, Fig. 2, Ref. 34).
Analysis of Coupled Tilted Slot Antennas in FDTD Using a Novel Time Domain Huygens Method With Application to Body Area Networks

Despite the undoubted versatility and effectiveness of the finite-difference time-domain (FDTD) method and its enhancements, there remain some problems which require more computer power than is practical. An example of such a problem is the coupling between two or more tilted antennas in the presence of a scattering environment such as is encountered in a body area network (BAN). The dual challenge of a wide range of scales and complicated structures which are not aligned with a Cartesian mesh are addressed using a novel Time Domain Huygens (TDH) approach. Results and comparisons with measurements are presented showing the effectiveness of the method. In addition, the measured and predicted variations of BAN propagation characteristics with body size are investigated.
Brain volume abnormalities in major depressive disorder: a Meta-analysis of magnetic resonance imaging studies

Objective. So far, there have been no attempts to integrate the growing number of all brain volumetric magnetic resonance imaging studies in depression. In this comprehensive meta‐analysis the magnitude and extent of brain volume differences between 2,418 patients with major depressive disorder and 1,974 healthy individuals from 64 studies was determined. Methods. A systematic research was conducted for volumetric magnetic resonance imaging studies of patients with major depressive disorder in relation to healthy control subjects. Studies had to report sufficient data for computation of effect sizes. For each study, the Cohen's d was calculated. All analyses were performed using the random effects model. Additionally, meta‐regression analyses were done to explore the effects of potential sources of heterogeneity. Results. Patients showed large volume reductions in frontal regions, especially in the anterior cingulate and orbitofrontal cortex with smaller reductions in the prefrontal cortex. The hippocampus, the putamen and caudate nucleus showed moderate volume reductions. Conclusions. This is the first comprehensive meta‐analysis in major depressive disorder demonstrating structural brain abnormalities, particularly in those brain areas that are involved in emotion processing and stress‐regulation. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
Tailoring Dispersion and Confinement Losses of Photonic Crystal Fibers Using Hybrid Cladding

We present a hybrid cladding photonic crystal fiber (PCF) for shaping nearly zero ultraflattened dispersion and low confinement losses in a wide range of wavelengths. The finite difference method with anisotropic perfectly matched boundary layer is used to investigate the guiding properties. It has been shown theoretically that it is possible to obtain nearly zero ultraflattened dispersion of 0 plusmn0.25 mups/nm/km in a wavelength range of 1.44 to 2.0 mum with low confinement losses less than 0.005 dB/km within the entire band of interest from a five-ring hybrid cladding PCF.
Genetic Clues to Alzheimer's Disease

All cases of familial Alzheimer's disease are caused by mutations in either the gene for beta-amyloid precursor protein or the protein S182/STM. The normal functions of these transmembrane proteins are unknown, and it is unclear how they relate to one another. N. N. Dewji and S. J. Singer propose that these two proteins interact in a way analogous to the Sevenless and Bride of Sevenless proteins in the developing Drosophila eye and the lin-12 and sel-12 proteins in the developing vulva of Caenorhabditis elegans. He suggests that excess deposition of amyloid, a hallmark and likely cause of Alzheimer's disease, would be a result of the abnormal processing of the protein-protein complex. This proposal is likely to provoke responses from the community. If you have a question or would like to comment on the ideas presented by Drs. Dewji and Singer in this Perspective or if you would like to read the comments posted by others, please go to our interactive Forum (click on the Forum button below). You can also read the full text of this Perspective by clicking on the Full Text button below.
Discovering Potential and Realizing Value from Information Technology Investments

Abstract: Information technology (IT) value has been measured at various levels of analysis, yet few authors would contend that the search for value has reached a point where practitioners and theoreticians are satisfied with its outcomes. We present a new perspective that emphasizes the importance of understanding where potential value lies and how best to relate it contextually to the measurement of the firm’s realized value across multiple levels of analysis. We develop the idea that complementary assets (especially business process design and human capital) influence the firm’s realization of value, using concepts such as locus of value and value conversion contingencies. Expanding beyond earlier process models of IT value, which begin with IT expenditure, our analysis of IT value emphasizes the consideration of potential value for an IT investment both in ex ante project selection, and ex post investment evaluation. We illustrate and validate the application of our framework using IT investments in a variety of business domains.
Lymphoproliferative Disorders with Early Lethality in Mice Deficient in Ctla-4

The role of the cell-surface molecule CTLA-4 in the regulation of T cell activation has been controversial. Here, lymph nodes and spleens of CTLA-4-deficient mice accumulated T cell blasts with up-regulated activation markers. These blast cells also infiltrated liver, heart, lung, and pancreas tissue, and amounts of serum immunoglobulin were elevated. The mice invariably became moribund by 3 to 4 weeks of age. Although CTLA-4-deficient T cells proliferated spontaneously and strongly when stimulated through the T cell receptor, they were sensitive to cell death induced by cross-linking of the Fas receptor and by gamma irradiation. Thus, CTLA-4 acts as a negative regulator of T cell activation and is vital for the control of lymphocyte homeostasis.
Clades of Adeno-Associated Viruses Are Widely Disseminated in Human Tissues

ABSTRACT The potential for using Adeno-associated virus (AAV) as a vector for human gene therapy has stimulated interest in the Dependovirus genus. Serologic data suggest that AAV infections are prevalent in humans, although analyses of viruses and viral sequences from clinical samples are extremely limited. Molecular techniques were used in this study to successfully detect endogenous AAV sequences in 18% of all human tissues screened, with the liver and bone marrow being the most predominant sites. Sequence characterization of rescued AAV DNAs indicated a diverse array of molecular forms which segregate into clades whose members share functional and serologic similarities. One of the most predominant human clades is a hybrid of two previously described AAV serotypes, while another clade was found in humans and several species of nonhuman primates, suggesting a cross-species transmission of this virus. These data provide important information regarding the biology of parvoviruses in humans and their use as gene therapy vectors.
[Overweight among eight and twelve-year-old children in Oslo in 2004].

BACKGROUND Overweight among children is an increasing problem internationally. The body mass index of the parents and their children influences body mass index during adulthood and the probability of overweight and obesity. The aim of this survey was to obtain reliable data on weight and height for eight and twelve-year-olds in Oslo. MATERIAL AND METHODS School health nurses in Oslo took measurements of the children's weight and height. The survey includes 3453 eight-year-olds and 3597 twelve-year-olds. RESULTS The prevalence of overweight among eight-to-twelve-year-olds is 21%. There is a significant difference in the prevalence of overweight children between the local districts of Oslo. One in four of eight-year-old and one in five of twelve-year old girls are overweight. There is no significant difference between boys in different age groups. INTERPRETATION The prevalence of overweight among eight to twelve-year-old children in Oslo is alarming. There are big differences between districts.
Malignant epithelial tumors of the anal canal

A simplified staging for malignant epithelial tumors of the anal canal is presented. The pattern of recurrence in males is pelvic and perineum, in females pelvis and posterior vaginal wall. Concomitant posterior vaginectomy is advocated. The disease is more common in females than males (4:1). There is little difference between histologic types, i.e. cloacagenic or squamous cell type. Recurrence and survival depend upon depth of invasion and extent of spread rather than histologic cell type. The tumors respond to well‐designed surgery, radiotherapy and probably chemotherapy.
Raloxifene, tamoxifen, nafoxidine, or estrogen effects on reproductive and nonreproductive tissues in ovariectomized rats

For the first time, four well‐charac‐ terized compounds from four distinct chemical classes were directly compared for efficacy and potency in bone, uteri, lipids, and adipose tissues in an ovariectomized model with 6 month old rats. Five weeks of oral dosing confirmed that ethynyl estradiol, tamoxifen, and raloxifene are potent inhibitors of the loss in volumetric bone mineral density (BMD, mg/cc) induced by ovariectomy, as measured by computed tomography. In the metaphysis of distal femora from ovariectomized rats, analysis showed a significant 12‐20% decrease (P< 0.01) in the BMD. Linear regression analysis was used to calculate half‐ maximal efficacious doses for ethynyl estradiol ED50 = 0.04 mg/kg, which was threefold more potent than tamoxifen, which in turn was threefold more potent than raloxifene, which was knore efficacious than nafoxidine. In the uterus, raloxifene had minimal effects on the endometrium and smaller effects on uterine eosinophil peroxidase activity than nafoxidine, tamoxifen, or estrogen, respectively. Estrogen was the most potent in reducing cholesterol levels in ovariectomized rats, whereas tamoxifen and nafoxidine were more effective than raloxifene in blocking gain in body weight. Distinct Compounds had advantages in the management of bone, uterine, serum cholesterol, and adipose tissues after ovariectomy. The distinct pattern of pharnjiacological effects may be best understood in terms of their respective chemical structure, specifically estrogens, ben‐ zothiophenes (raloxifene), dihydronapthylenes (nafoxidine), and triphenylethylenes (tamoxifen). These data point to advantages of Separate compounds in the management of bone, uterine, serum cholesterol, and adipose tissues after estrogen deficiency, and show that the benzothiophene raloxifene has potentially important advantages over estrogen, tamoxifen, or nafoxidine in the uterus. —Sato, M. , Rippy, M. K. , Bryant, H. U. Raloxifene, tamoxifen, nafoxidine, or estrogen effects on reproductive and nonreproductive tissues in ovariectomized rats. FASEB J. 10, 905‐912 (1996)
Sociodemographic and clinical features of patients with depressive disorder in Khartoum, Sudan.

BACKGROUND It's known worldwide that depression is becoming a major health problem and its prevalence is increasing. The main objective of this study is to find out the prevalence of depression among patients attending a general psychiatric clinic, and study their sociodemographic and clinical features. METHODS Files of patients attending a private psychiatric clinic in Khartoum in the period June 2005-June 2010 were reviewed. Only those with a diagnosis of depression were chosen, sociodemographic date and clinical features were documented and results were shown below. RESULTS AND DISCUSSION Total numbers of patients with depression were 137 (11.4%). Females were more than males (56.2%), the majority are between ages 41-60 (40.9%), married (65%), (14.9%) had family history of psychiatric disorders and (52%) had a previous history of psychiatric treatment. Depressed mood is the commonest symptom (98.5%), loss of interest (91.9%), reduced energy (57%), guilt feelings (17.9%) and (35.8%) of our samples expressed suicidal ideations. The commonest type of somatic symptom is generalized aches and pain (30.7%), (18%) were psychotic. CONCLUSION The present study is a retrospective descriptive study, based on a private psychiatric clinic sample. It provided a useful baseline for more comprehensive field based studies, to try to aid planning and development of services to meet the needs of the population.
Transformation des concepts du diagramme de classe UML en OWL full

Résumé. Le web peut être considéré comme une grande base de connaissances. La recherche des informations pertinentes sur la toile est rendue de plus en plus difficile, voire impossible avec l’accroissement de la volumétrie des pages disponibles. Le problème réside dans le fait que les outils existants ne peuvent pas s’appuyer actuellement sur une description du contenu des documents. Le web sémantique utilise différents langages pour mieux exploiter et traiter les contenus des ressources web. Dans le but de passer de UML vers OWL, il est intéressant d’étudier la possibilité de transformer chacun des concepts du diagramme de classe UML en OWL.
Wilms’ Tumor: A 24-year Retrospective Study from a Single Center

Medical records of 71 children with Wilms’ tumor at Sisli Etfal Education and Research Hospital between 1990 and 2014 were reviewed. Mean age at diagnosis was 3.11 years (2 days–7 years). Male to female ratio was M/F = 6/10. The incidence of associated anomaly was 16.9%. Clinical manifestations included abdominal mass (89%), hematuria (30%), hypertansion (25%), abdominal pain (15%), fever (5%), restlessness (2%), weight loss (2%), varicocele (1%). Ultrasound (USG) was the most often initial study in a child presenting with abdominal mass. Doppler USG was also made to evaluate the inferior vena cava (IVC) for the presence of tumor extension in children with renal mass. The left kidney was affected in 33 patients (46.5%), the right was affected in 31 patients (43.7%). Two patients was extrarenal (2.8%). And 5 patients (7.04%) were bilateral on the presentation. Preoperative chemotheraphy was done in 14 cases. In 63 patients with unilateral Wilm tm, unilateral radical nefrectomy is performed. In one patient with solitary kidney, nephron sparing surgery (NSS) is performed. In 3 patients with bilateral tm NSS is performed and in 2 patients with bilateral Wilms’ tm NSS is performed in one side and nefrectomy on the other side. Out of 71 Wilms tumor (WT) patients, 17 of them has been out of our follow. And 4 of them are died. Ten of them has metastases. Forty children are under follow with no metastases. Patients with WT needs a multimodal, multidisiplinary treatment with the cooperation of pediatric oncologist and pediatric surgeon and needs close follow-up.
Monetite formed in mixed solvents of water and ethylene glycol and its transformation to hydroxyapatite.

Agglomerated nanorods of hydroxyapatite have been synthesized using monetite as a precursor in a NaOH solution. Monetite consisting of nanosheets has been successfully synthesized by a one-step microwave-assisted method using CaCl(2). 2.5H(2)O, NaH(2)PO(4), and sodium dodecyl sulfate (SDS) in water/ethylene glycol (EG) mixed solvents. The effects of the molar ratio of water to EG and the reaction time on the products were investigated. The products were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier transform infrared spectrometry (FTIR).