Miracle-dz/UniFAR-FTUs huggingface dataset:
Pt-CdTe Detectors Spectroscopic Performances and RBS and XRF Interface Composition Analysis

X- and Gamma-Ray spectroscopy measurements have been performed on differently prepared CdTe samples (as-grown or annealed, different surface treatments, etc.) with Pt electrodes deposited by electroless technique in order to extract the typical figures of merit of the material and the detectors. Moreover, Rutherford Backscattering Spectrometry (RBS) using 8 MeV $^{7}{\hbox {Li}}^{+++}$ ions and X-Ray Fluorescence (XRF) using a Pd-anode X-Ray generator were performed to characterize the crystal surface as well as the semiconductor-electrode interface. The thickness, the stoichiometry and the concentration profiles of platinum, cadmium and tellurium present at the surface layers were determined. The distribution of Cd deficiency at the interface layers was profiled using simulations and showed complex profiles in the samples, that can greatly affect the electrical quality of the detectors. In addition, resistivity and mu-tau product mapping and electrical measurements have been performed for material characterization. The aim of this work is to understand and improve the structure of the material-electrode interface; in particular, to understand the effect of the annealing process on the fabrication of the contacts and, at the end, on the performances of the detectors. For this reason a large number of detectors have been produced applying various chemical surface treatments on as-grown and annealed material, in order to determine the best routine way to fabricate high-quality X- and Gamma-ray detectors to be used both as large size planar detectors and as elements of imaging systems in medical or industrial applications.
Independent regulation of short and long forms of latent TGF‐β binding protein (LTBP)‐4 in cultured fibroblasts and human tissues

Transforming growth factor (TGF)‐β is secreted and targeted into the extracellular matrix (ECM) in association with one of the latent TGF‐β binding proteins (LTBPs). Activation of these latent complexes is an important regulatory step in TGF‐β signaling. LTBPs target the growth factor into the ECM and expose it to activating mechanisms. Disruption of LTBP‐4 gene causes severe developmental abnormalities in both humans and mice. Transcripts for two N‐terminally distinct LTBP‐4 variants, LTBP‐4S (short) and ‐4L (long), have been identified. In the current work, we have characterized differences in the expression, processing, and ECM targeting of these LTBP‐4 variants. Heart and skeletal muscle displayed expression of both variants, while liver expressed mainly LTBP‐4L and lung as well as small intestine LTBP‐4S. This tissue‐specific expression pattern was found to originate from control of transcription by two independent promoters. Furthermore, LTBP‐4S and ‐4L proteins were secreted and processed differently. During secretion, LTBP‐4L was complexed with TGF‐β1, whereas the majority of LTBP‐4S was secreted in a free form. In addition, LTBP‐4S was incorporated into the ECM, while full‐length LTBP‐4L was not readily detectable in the ECM. These data suggest that LTBP‐4 functions are modified by tissue‐specific expression of the two N‐terminally distinct variants, which in addition exhibit significant differences in cellular processing and targeting, that is, this provides a basis for understanding molecular diversity in LTBP‐4 structure and function. J. Cell. Physiol. 223:727–736, 2010. © 2010 Wiley‐Liss, Inc.
Decision tree SAR models for developmental toxicity based on an FDA/TERIS database

Humans are exposed to thousands of environmental chemicals for which no developmental toxicity information is available. Structure-activity relationships (SARs) are models that could be used to efficiently predict the biological activity of potential developmental toxicants. However, at this time, no adequate SAR models of developmental toxicity are available for risk assessment. In the present study, a new developmental database was compiled by combining toxicity information from the Teratogen Information System (TERIS) and the Food and Drug Administration (FDA) guidelines. We implemented a decision tree modeling procedure, using Classification and Regression Tree software and a model ensemble approach termed bagging. We then assessed the empirical distributions of the prediction accuracy measures of the single and ensemble-based models, achieved by repeating our modeling experiment many times by repeated random partitioning of the working database. The decision tree developmental SAR models exhibited modest prediction accuracy. Bagging tended to enhance the accuracy of prediction. Also, the model ensemble approach reduced the variability of prediction measures compared to the single model approach. Further research with data derived from animal species- and endpoint-specific components of an extended and refined FDA/TERIS database has the potential to derive SAR models that would be useful in the developmental risk assessment of the thousands of untested chemicals.
Measuring Early Cortical Visual Processing in the Clinic

We describe a mobile app that measures early cortical visual processing suitable for use in clinics. The app is called Component Extraction and Motion Integration Test (CEMIT). Observers are asked to respond to the direction of translating plaids that move in one of two very different directions. The plaids have been selected so that the plaid components move in one of the directions and the plaid pattern moves in the other direction. In addition to correctly responding to the pattern motion, observers demonstrate their ability to correctly extract the movement (and therefore the orientation) of the underlying components at specific spatial frequencies. We wanted to test CEMIT by seeing if we could replicate the broader tuning observed at low spatial frequencies for this type of plaid. Results from CEMIT were robust and successfully replicated this result for 50 typical observers. We envisage that it will be of use to researchers and clinicians by allowing them to investigate specific deficits at this fundamental level of cortical visual processing. CEMIT may also be used for screening purposes where visual information plays an important role, for example, air traffic controllers.
Morbidity and mortality data of cystic fibrosis patients.

OBJECTIVE To identify factors that contributed to morbidity and mortality of cystic fibrosis (CF) population in the Kingdom of Saudi Arabia (KSA). METHODS This retrospective chart review was carried out in King Faisal Specialist Hospital and Research Centre, Riyadh, KSA, during a 9 year period, November 1993 to November 2002, on confirmed CF patients, for demographic, clinical and mortality data. RESULTS A total of 190 CF patients were diagnosed during the 9 years. One hundred and sixty-four (86%) patients are alive, 26 (14%) died. Ninety-nine (52%) were males and 91 (48%) were females. Age at diagnosis 2.8 3.5 years, and period of follow up 3 3 years. In 80% of patients, symptoms started <1 year of age. Sixty-five percent of patients were in the mild to moderate malnutrition stage (<90th percentile), and 63% are in the mild to moderate stunted growth (<90th percentile). Factors that contributed to early mortality are: calculated weight/height (p-value 0.01), low albumin level at follow up (0.001), high hematocrit (HCT) (p-values=0.0002), low mean corpuscular volume (MCV) (p-0.0002), low mean corpuscular hemoglobin concentration (MCHC) (p-value 0.001), early development of antibiotic resistance (p-value=< 0.01). CONCLUSION High HCT, low MCV, low MCHC and low albumin are factors related to poor prognosis and early death in CF patients. Iron supplement should be given to these patients even in the presence of normal hemoglobin. Early nutritional rehabilitation is needed to improve survival of our CF patients. Cohort isolation should be encouraged in CF centres. Early treatment of chronic pseudo colonization should be adopted to improve survival.
Clustering of genes involved in replication, copy number control, incompatibility, and stable maintenance of the resistance plasmid R1drd-19

Plasmid R1drd-19 is present in a small number of copies per cell of Escherichia coli. The plasmid was reduced in size by in vivo as well as in vitro (cloning) techniques, resulting in a series of plasmid derivatives of different molecular weight. All plasmids isolated contain a small region (about 2 x 10(6) daltons of deoxyribonucleic acid) of the resistance transfer factor part of the plasmid located close to one of the IS1 sequences that separates the resistance transfer factor part from the resistance determinant. All these derivatives were present at the same copy number, retained the incompatibility properties of plasmid R1drd-19, and were stably maintained during cell division. Genes mutated to yield copy mutations also were found to be located in the same region.
The effect of ventricular assist devices on cerebral blood flow and blood pressure fractality

Biological signals often exhibit self-similar or fractal scaling characteristics which may reflect intrinsic adaptability to their underlying physiological system. This study analysed fractal dynamics of cerebral blood flow in patients supported with ventricular assist devices (VAD) to ascertain if sustained modifications of blood pressure waveform affect cerebral blood flow fractality. Simultaneous recordings of arterial blood pressure and cerebral blood flow velocity using transcranial Doppler were obtained from five cardiogenic shock patients supported by VAD, five matched control patients and five healthy subjects. Computation of a fractal scaling exponent (α) at the low-frequency time scale by detrended fluctuation analysis showed that cerebral blood flow velocity exhibited 1/f fractal scaling in both patient groups (α = 0.95 ± 0.09 and 0.97 ± 0.12, respectively) as well as in the healthy subjects (α = 0.86 ± 0.07). In contrast, fluctuation in blood pressure was similar to non-fractal white noise in both patient groups (α = 0.53 ± 0.11 and 0.52 ± 0.09, respectively) but exhibited 1/f scaling in the healthy subjects (α = 0.87 ± 0.04, P < 0.05 compared with the patient groups). The preservation of fractality in cerebral blood flow of VAD patients suggests that normal cardiac pulsation and central perfusion pressure changes are not the integral sources of cerebral blood flow fractality and that intrinsic vascular properties such as cerebral autoregulation may be involved. However, there is a clear difference in the fractal scaling properties of arterial blood pressure between the cardiogenic shock patients and the healthy subjects.
Two New Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction Assays with Unique Target Sites for the Specific and Sensitive Detection of Lineages 1 and 2 West Nile Virus Strains

Two novel 1-step real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays for the simultaneous detection of West Nile virus (WNV) lineage 1 and 2 strains were developed. Primers and the probe of assay 1 target the 5′-untranslated region (UTR), whereas the amplicon of assay 2 is located in the nonstructural region NS2A, which enables an unambiguous and independent WNV diagnosis based on 2 different amplicons. Both assays allow the detection of as few as 2–4 genome copies of WNV strains NY99, Uganda B956, Kunjin, and Sarafend (all cultured on Vero cells). A new synthetic RNA mutant of the 5′-UTR amplicon, which contains 6 twist inverted base-pair changes at the probe attachment site, was used as external calibrator control.
Rejection evaluation after renal transplantation using MR diffusion tensor imaging

Background Renal allograft dysfunction monitoring is mainly performed using the serum creatinine (SC) level, Doppler ultrasound (US), or renal biopsy. Recently proposed diffusion-based magnetic resonance imaging (MRI) methods have been explored as new, non-invasive tools for assessing renal function after transplantation. Purpose To investigate the value of fractional anisotropy (FA) measurements in the evaluation of acute rejection cases after renal transplant. Material and Methods Doppler US and MRI diffusion tensor imaging (DTI) were performed in 21 patients with graft dysfunction requiring graft biopsy after renal transplantation and in 21 patients with normal graft function. The MR examinations were performed on a 1.5-T MRI using two b-values (0 and 800 s/mm2). FA values were measured from the cortex and medulla of the transplanted kidney at the upper, middle, and lower poles. Results Twenty-one transplant patients diagnosed with acute rejection (Group 1) were compared to the control group of 21 transplant patients with normal graft function (Group 2). The measured FA values of the medulla were 0.19 ± 0.02 and 0.22 ± 0.05 (P = 0.017) for Groups 1 and 2, respectively. On the other hand, the measured FA values of the renal cortex were 0.18 ± 0.04 and 0.18 ± 0.04 (P = 0.97) for Groups 1 and 2, respectively. Conclusion The good correlation between the renal medulla FA values and allograft function shows that MR DTI has potential for non-invasive functional assessment of transplanted kidneys. On the other hand, the renal cortex FA values had no correlation with the allograft function.
Analysis of automobile scattering center locations by SAR measurements

Synthetic aperture radar (SAR) is known to have the capability for a range independent high-resolution cross range processing. In this paper the SAR processing is used to localize the scattering centers of an automotive target at 24 GHz and 77 GHz at different bandwidths. Furthermore, the combination of digital beam forming (DBF) with SAR initiates the opportunity to determine the exact location of the scattering center in azimuth, height, and range.
Ethnicity and infant health in Southern Brazil. A birth cohort study.

BACKGROUND Black children present more health problems than white children, but little information is available from less developed countries. Ethnic inequalities may vary according to country, and studies from developing countries are needed to evaluate possible differentials and their magnitude, and identify social and health interventions. METHODS Birth cohort study in Pelotas, Southern Brazil. Information collected during the perinatal period in hospitals, and at home at 1, 3, 6 and 12 months of age. In all, 5305 children were studied at birth, 96.8% of the sample of 1461 at 6 months, and 93.4% of this sample at 12 months of age. RESULTS Of the children, 28% were African Brazilian. Socioeconomic position was lower among families of black children, and mothers presented a number of unfavourable characteristics. Black children presented higher prevalences of low birthweight (LBW), preterm and small-for-gestational age (SGA), were less often immunized, had more deficits of weight-for-age and height-for-age, and higher early neonatal and infant mortality. When a number of covariates, including antenatal care, were added to a multiple regression analysis the odds ratios were markedly reduced, but there was still a clear trend towards worse results for black children. Black mothers had some aspects of antenatal care of lower quality and were submitted less frequently to caesarean sections and episiotomies. CONCLUSIONS Black infants experienced a much worse health status than white infants. Socioeconomic and other variables played a major role in determining inequalities between these ethnic groups. Antenatal care was especially important in explaining differentials in risk between black and white children.
The Voronoi Implicit Interface Method for computing multiphase physics

We introduce a numerical framework, the Voronoi Implicit Interface Method for tracking multiple interacting and evolving regions (phases) whose motion is determined by complex physics (fluids, mechanics, elasticity, etc.), intricate jump conditions, internal constraints, and boundary conditions. The method works in two and three dimensions, handles tens of thousands of interfaces and separate phases, and easily and automatically handles multiple junctions, triple points, and quadruple points in two dimensions, as well as triple lines, etc., in higher dimensions. Topological changes occur naturally, with no surgery required. The method is first-order accurate at junction points/lines, and of arbitrarily high-order accuracy away from such degeneracies. The method uses a single function to describe all phases simultaneously, represented on a fixed Eulerian mesh. We test the method’s accuracy through convergence tests, and demonstrate its applications to geometric flows, accurate prediction of von Neumann’s law for multiphase curvature flow, and robustness under complex fluid flow with surface tension and large shearing forces.
Imatinib mesylate (Gleevec) in advanced breast cancer-expressing C-Kit or PDGFR-beta: clinical activity and biological correlations.

BACKGROUND Novel molecular therapies for metastatic breast cancer (MBC) are necessary to improve the dismal prognosis of this condition. Imatinib mesylate (Gleevec) inhibits several protein tyrosine kinases, including platelet-derived growth factor receptor (PDGFR) and c-kit, which are preferentially expressed in tumor cells. We tested the activity of imatinib mesylate in MBC with overexpression of PDGFR or c-kit. Additionally, we sought to determine the biological correlates and immunomodulatory effects. PATIENTS AND METHODS Thirteen patients were treated with Imatinib administered orally at 400 mg p.o. b.i. d. (800 mg/day), until disease progression. All patients demonstrated PDGFR-beta overexpression and none showed c-kit expression. RESULTS No objective responses were observed among the 13 patients treated in an intention-to-treat analysis. All patients experienced disease progression, with a median time to progression of 1.2 months. Twelve patients have died, and the median overall survival was 7.7 months. No patient had a serious adverse event. Imatinib therapy had no effect on the plasma levels of the angiogenesis-related cytokines, vascular endothelial growth factor, PDGF, b-fibroblast growth factor, and E-selectin. Immune studies showed imatinib inhibits interferon-gamma production by TCR-activated CD4(+) T cells. CONCLUSION Imatinib as a single agent has no clinical activity in PDGFR-overexpressing MBC and has potential immunosuppressive effects.
Insight and Psychosis

The concept of insight into psychosis has received scant attention in the psychiatric literature. Drawing on sources such as phenomenology, clinical research and experimental psychology, it is proposed that insight is not an ‘all-or-none’ phenomenon but is composed of three distinct, overlapping dimensions, namely, the recognition that one has a mental illness, compliance with treatment, and the ability to relabel unusual mental events (delusions and hallucinations) as pathological. A scheme is proposed to standardise the assessment of insight to assist further research.
Reduced Incidence and Severity of Collagen-Induced Arthritis in Mice Lacking IL-181

We have recently reported the presence and a potential proinflammatory role of IL-18 in the synovium of patients with rheumatoid arthritis. To obtain direct evidence that IL-18 plays an influential role in articular inflammation, we investigated the development of collagen-induced arthritis in a strain of mice lacking IL-18 (IL-18−/−) of DBA/1 background. IL-18−/− mice developed markedly reduced incidence of arthritis compared with heterozygous or wild-type mice. Of the IL-18−/− mice that developed arthritis, the severity of the disease was significantly reduced compared with the intact mice. This was accompanied by reduced articular inflammation and destruction evident on histology. IL-18−/− mice also had significantly reduced Ag-specific proliferation and proinflammatory cytokine (IFN-γ, TNF-α, IL-6, and IL-12) production by spleen and lymph node cells in response to bovine type II collagen (CII) in vitro compared with wild-type mice, paralleled in vivo by a significant reduction in serum anti-CII IgG2a Ab level. Treatment with rIL-18 completely reversed the disease of the IL-18−/− mice to that of the wild-type mice. These data directly demonstrate a pivotal role of IL-18 in the development of inflammatory arthritis and suggest that antagonists to IL-18 may have therapeutic potential in rheumatic diseases.
Experimental Design for Learning Causal Graphs with Latent Variables

We consider the problem of learning causal structures with latent variables using interventions. Our objective is not only to learn the causal graph between the observed variables, but to locate unobserved variables that could confound the relationship between observables. Our approach is stage-wise: We first learn the observable graph, i.e., the induced graph between observable variables. Next we learn the existence and location of the latent variables given the observable graph. We propose an efficient randomized algorithm that can learn the observable graph using O(d\log^2 n) interventions where d is the degree of the graph. We further propose an efficient deterministic variant which uses O(log n + l) interventions, where l is the longest directed path in the graph. Next, we propose an algorithm that uses only O(d^2 log n) interventions that can learn the latents between both non-adjacent and adjacent variables. While a naive baseline approach would require O(n^2) interventions, our combined algorithm can learn the causal graph with latents using O(d log^2 n + d^2 log (n)) interventions.
Neural connectivity in children with bipolar disorder: impairment in the face emotion processing circuit.

BACKGROUND Pediatric bipolar disorder (BD), a highly debilitating illness, is characterized by amygdala abnormalities, i.e., volume reduction and hyperactivation during face processing. Evidence of perturbed amygdala functional connectivity with other brain regions would implicate a distributed neural circuit in the pathophysiology of BD, and would further elucidate the neural mechanisms associated with BD face emotion misinterpretation. METHODS Thirty-three BD and 24 healthy age, gender, and IQ-matched subjects completed a functional magnetic resonance imaging (fMRI) task of face emotion identification in which attention was directed to emotional (hostility, fearfulness) and nonemotional (nose width) aspects of faces. Voxel-wise analyses examined whole brain functional connectivity with the left amygdala. RESULTS Compared to healthy subjects, BD subjects had significantly reduced connectivity between the left amygdala and two regions: right posterior cingulate/precuneus and right fusiform gyrus/parahippocampal gyrus. Deficits were evident regardless of mood state and comorbid diagnoses. CONCLUSIONS BD youth exhibit deficient connectivity between the amygdala and temporal association cortical regions previously implicated in processing facial expressions and social stimuli. In conjunction with previously documented volumetric and functional perturbations in these brain regions, dysfunction in this distributed neural circuit may begin to clarify the pathophysiology of the face emotion misperceptions and social deficits seen in BD youth.