Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic characterization of HHV‐8/KSHV–positive primary effusion lymphoma reveals frequent mutations of BCL6: Implications for disease pathogenesis and histogenesis

Human herpesvirus‐8/Kaposi sarcoma‐associated herpesvirus–positive primary effusion lymphoma (PEL) is a recently identified B‐cell non‐Hodgkin lymphoma category characterized by liquid growth in the serous body cavities. Apart from viral infection, no genetic alteration is known to be associated with PEL and no recurrent cytogenetic abnormality has been identified in these lymphomas. Yet the consistent monoclonality of PEL indicates that the disease is not solely a virus‐driven proliferation. Here we report that PEL is associated with a high frequency of mutations of BCL6 5' noncoding regions, and we identify karyotypic abnormalities that may be recurrently involved in these lymphomas. Mutations of BCL‐6 5' noncoding regions occurred in 8/13 PEL. Mutations occurred in the absence of BCL6 gross rearrangements were often multiple in the same patient (7/8 mutated cases), and occurred in both HIV‐positive and HIV‐negative individuals. Since BCL6 mutations are regarded as a genetic marker of B‐cell transition through the germinal center (GC), these data are consistent with histogenetic derivation of PEL from GC or post‐GC B‐cells. Cytogenetic and FISH analysis of seven PEL cell lines showed frequent occurrence of complete or partial trisomy 12 (7/7 cases), trisomy 7 (4/7 cases), and abnormalities of bands 1q21–25 (5/7 cases). Genes Chromosomes Cancer 24:16–23, 1999. © 1999 Wiley‐Liss, Inc.
Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of ≈8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 μM is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a “charged brush” to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl− PMF. The difference in affinity and hence selectivity is due to the “Lys-cluster” motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl− by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.
Fuzzy type-2 sliding mode control of matrix converter using indirect space vector modulation

Employing sliding mode controller in matrix converters presents advantages such as easy on-line implementation, quick and reliable choice of the correct switching combinations and ensuring that the system tracks their references. The main drawback of the sliding mode controller is chattering phenomenon which affects the performance of the controller by injecting high frequency variation in controller object variables. To solve chattering problem, this paper proposes a new input current control method for matrix converter using interval fuzzy type-2 integrated with sliding mode control. Theoretical analysis and simulation results demonstrate the authenticity of the proposed input current control method of matrix converter in various conditions.
Ureaplasma urealyticum urease genes; use of a UGA tryptophan codon

Nucleotide sequence analysis of a Ureaplasma urealyticum DNA fragment, homologous to cloned urease genes of other prokaryotes, revealed three consecutive open reading frames. The molecular weights of the three deduced polypeptides are 11.2kD, 13.6kD and 66.6 kD. These values are consistent with the size of the three subunits previously reported for purified native urease. A significant sequence homology was found between the three polypeptides of the ureaplasmal urease and the single polypeptide of jack bean (Canavalia ensiformis) urease. Codon usage indicates that UGA is a tryptophan codon in this mollicute. Use of polymerase chain reactions has disclosed the existence of genetic polymorphism among the urease genes of different serotypes of U. urealyticum.
Crustal magnetization and accretion at the Southwest Indian Ridge near the Atlantis II fracture zone, 0–25 Ma

[1] We analyze geophysical data that extend from 0 to 25-Myr-old seafloor on both flanks of the Southwest Indian Ridge (SWIR). Lineated marine magnetic anomalies are consistent and identifiable within the study area, even over seafloor lacking a basaltic upper crust. The full spreading rate of 14 km/Myr has remained nearly constant since at least 20 Ma, but crustal accretion has been highly asymmetric, with half rates of 8.5 and 5.5 km/Myr on the Antarctic and African flanks, respectively. This asymmetry may be unique to a ∼400 km wide corridor between large-offset fracture zones of the SWIR. In contrast to the Mid-Atlantic Ridge, crustal magnetization amplitudes correlate directly with seafloor topography along the present-day rift valleys. This pattern appears to be primarily a function of along-axis variations in crustal thickness, rather than magnetic mineralogy. Off-axis, magnetization amplitudes at paleo-segment ends are more positive than at paleo-segment midpoints, suggesting the presence of an induced component of magnetization within the lower crust or serpentinized upper mantle. Alteration of the magnetic source layer at paleo-segment midpoints reduces magnetization amplitudes by 70–80% within 20 Myr of accretion. Magnetic and Ocean Drilling Program (ODP) Hole 735B data suggest that the lower crust cooled quickly enough to lock in a primary thermoremanent magnetization that is in phase with that of the overlying upper crust. Thus magnetic polarity boundaries within the intrusive lower crust may be steeper than envisioned in prior models of ocean crustal magnetization. As the crust ages, the lower crust becomes increasingly important in preserving marine magnetic stripes.
An accurate conjugate gradient fast Fourier transform method for electromagnetic scattering

An accurate conjugate gradient fast Fourier transform (CG-FFT) for solving electromagnetic scattering problems is developed by improving the accuracy of estimating the spectrum of the Green's function. Compared to the traditional CG-FFT algorithm, this new approach reduces the relative error by a factor of 5 to 20 for one-dimensional electromagnetic scattering models while maintaining the computational cost in terms of CPU time and memory requirement.
The metabolism of midazolam and comparison with other CYP enzyme substrates during intestinal absorption: in vitro studies with rat everted gut sacs.

PURPOSE The purpose of this study was to quantify the intestinal metabolism of midazolam, a CYP P450 substrate, usually used as a probe for the activity of the isoform CYP3A4/1 and to compare it with previous results obtained for other P450 substrates such as testosterone, dextromethorphan and bupropion, which show some specificities for different CYP isoforms. The aim was to shed light on the role of metabolism in the intestinal tissues and the relationship with efflux mechanisms, such as by P-glycoprotein (P-gp) and the influence of metabolism on bioavailability. METHODS We used the improved everted rat gut sac model to study in vitro the absorption and metabolism of the different CYP isoenzyme probes: midazolam, testosterone, bupropion and dextromethorphan. This method enables drug metabolism to be studied during absorption, conditions which mimic the in vivo situation. The drugs and their metabolites were measured by LC-MS in the mucosal and serosal media and in the mucosal tissue, to give a complete picture of the transport and metabolism. RESULTS Midazolam, as with the other CYP probes, was metabolized in everted gut sacs. The metabolites were detected in the same proportions in both the serosal and mucosal compartments for midazolam, testosterone and bupropion. In the case of dextromethorphan, the metabolite methoxymorphinan was found at a higher concentration in the mucosal compartment, indicating efflux from the cells. The transport of dextromethorphan and its metabolite was not modified in the presence of verapamil, a P-gp inhibitor, thus demonstrating that dextromethorphan and methoxymorphinan were not P-gp substrates. CONCLUSION Given that the rat is a widely used species for pre-clinical studies, the everted gut sac model provides a useful tool to assess the role of metabolism during drug absorption by the intestine and is also capable of demonstrating P-glycoprotein mediated transport.
Caractérisation et classification moléculaire des pathologies thyroïdiennes par approche transcriptomique

L'accident de Tchernobyl, en 1986, a mis en lumiere le cancer de la thyroide. Ce cancer, assez rare, est pourtant en forte augmentation, et cela avant meme 1986. Le diagnostic des tumeurs folliculaires thyroidiennes par analyses anatomopathologiques est parfois difficile. Ce travail s'interesse a la classification moleculaire de ces tumeurs ainsi qu'a la recherche de marqueurs specifiques a chaque pathologie. En regroupant et en analysant le transcriptome de plus de 90% des types de lesions folliculaires de la thyroide, nous avons etabli une classification moleculaire globale de ces lesions, nous avons defini des marqueurs specifiques faisant l'objet d'un brevet, et nous avons permis de preciser le diagnostic de la majorite des tumeurs de malignite incertaine. L'etude bioinformatique des donnees issues de biopuces apporte des precisions a la classification internationale des tumeurs, particulierement pour les tumeurs oncocytaires, microfolliculaires et de malignite incertaine.
Development of an Assay for Human Growth Hormone in Urine Using Commercially Available Reagents

An assay for the measurement of human growth hormone in urine (u-HGH) has been developed using commercially available reagents and its analytical variables have been investigated. The procedure is sensitive to 0·50 μU/L urine, has an interassay precision of 6·2–7·5 (CV%) over the standard curve, and shows good parallelism and recovery. Urine samples for the assay can be collected in plain plastic bottles, stored at room temperature for up to 24 h and, after adding preservative, at −20°C before assay for three months. There was a good correlation between the responses of HGH in serum and in urine during clonidine and insulin stimulation tests.
Symmetric Operation in an Extended Back Gate JLFET for Scaling to the 5-nm Regime Considering Quantum Confinement Effects

In this paper, we propose a double gate junctionless FET (DGJLFET) with an extended back gate (EBG) architecture for significantly improved performance in the sub-10-nm regime. Even for a channel length of 5 nm, we show using calibrated 2-D simulations that the EBG DGJLFET, when compared with the DGJLFET, exhibits: 1) an improved subthreshold swing; 2) a significantly low off-state leakage current; and 3) a considerably high ION/IOFF ratio of ~108. Furthermore, we demonstrate, for the first time, that the quantum confinement-induced bandgap widening diminishes the parasitic bipolar junction transistor (BJT) action and, therefore, facilitates the scaling of the conventional DGJLFETs to the sub-5-nm channel regime where the quantization effects are significant. Moreover, we also show, for the first time, that the DG junctionless accumulation mode FET suffers from an enhanced parasitic BJT action and, therefore, a significantly high off-state leakage current compared with the DGJLFET. In addition, we demonstrate that the loss of gate control for negative gate voltages in the DGJLFETs with larger silicon film doping (ND ≥ 2 × 1019 cm-3) is due to a shielding effect initiated by the band-to-band tunneling.
Reliability of a Magnetic Resonance Imaging-based Grading System for Cervical Intervertebral Disc Degeneration

Study Design This was a radiographic reliability study of a novel grading system for cervical intervertebral disc degeneration. Objectives This study aimed to develop and test the reliability of a reproducible grading system for cervical intervertebral disc degeneration on the basis of the routine magnetic resonance imaging (MRI). Summary of Background Data Cervical disc degeneration is common after middle age, and the morphology of cervical disc degenerative disease has often been studied using MRI. There are few specific MRI-based grading systems for cervical intervertebral disc degeneration despite the clinical importance of this problem. This study proposes a novel reproducible grading system for cervical disc degeneration and demonstrates the reliability of this classification scheme. Methods A grading system for cervical intervertebral disc degeneration was developed based on relevant previous literature. MRI grading of 300 cervical intervertebral discs using T2-weighted sagittal images was performed by 4 spinal surgeons (observers) in a blinded fashion. Intraobserver and interobserver reliabilities were assessed by calculating κ statistics. Results Grade I degeneration was observed in 27 discs (9.0%); grade II, in 56 (18.7%); grade III, in 124 (41.3%); grade IV, in 67 (22.3%); and grade V, in 26 (8.7%) discs. Kappa coefficients for intraobserver and interobserver agreements ranged from substantial to excellent (intraobserver, 0.907 to 0.950 and interobserver, 0.730 to 0.826). Complete agreement was obtained, on an average, in 72.1% of the discs. A difference of 1, 2, and 3 grades was observed in 22.4%, 3.3%, and 0.2% discs, respectively. Conclusions This grading system is comprehensive and easily applicable with sufficient reproducibility. It can be used as a common nomenclature for research and discussions.
3D statistical shape models for medical image segmentation

A novel method that allows the development of surface point-based three-dimensional statistical shape models is presented. The method can be applied to shapes of arbitrary topology. Given a set of medical objects, a statistical shape model can be obtained by principal component analysis. This technique requires that a set of complex shaped objects is represented as a set of vectors that on the one hand uniquely determine the shapes of the objects and on the other hand are suitable for a statistical analysis. The correspondence between the vector components and the respective shape features has to be the same in order for all shape parameter vectors to be considered. We present a novel approach to the correspondence problem for complex three-dimensional objects. The underlying idea is to develop a template shape and to fit this template to all objects to be analyzed. The method is successfully applied to obtain a statistical shape model for the lumbar vertebrae. The obtained shape model is well suited to support image segmentation tasks.
PDF and Breakdown Time Prediction for Unobservable Wear Using Enhanced Particle Filters in Precognitive Maintenance

Machine health prognosis is crucial to reduce unexpected downtime, maintenance costs, and safety hazards in industrial systems. In this paper, a novel methodology to predict probability density function (pdf) and breakdown time of unobservable degradation processes is proposed. A transition-based autoregressive moving average model and an enhanced particle filter (EPF) are developed at the prognosis stage for the pdf prediction of industrial wear. The strictly monotonic increasing behavior of degradation is ensured by executing a monotonic resampling scheme in EPF, and the number of particles is chosen to be time-varying to reduce computation costs. The effectiveness of our proposed framework is tested on the tool wear in an industrial milling machine, and achieves the predicted bounds with accuracies of at least 90.3% as well as saves more than 50% calculation time without loss of accuracy.
Characterization of Imidazo[4,5-d]Pyridazine Nucleosides as Modulators of Unwinding Reaction Mediated by West Nile Virus Nucleoside Triphosphatase/Helicase: Evidence for Activity on the Level of Substrate and/or Enzyme

ABSTRACT Compounds that interact with DNA or RNA generally act as inhibitors of enzymes that unwind DNA or RNA. In the present study we describe the synthesis and properties of some nucleoside analogues that interact with double-stranded DNA but that, in contrast, facilitate the unwinding reaction mediated by West Nile (WN) virus nucleoside triphosphatase (NTPase)/helicase. The nucleoside analogues described, 1-(2′-O-methyl-β-d-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)-dione (HMC-HO4), 1-(β-d-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)-dione, and 1-(2′-deoxy-α-d-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)dione, all contain the imidazo[4,5-d]pyridazine ring system. The extent of the enhancing effect on helicase activity was found to be dependent on the time of exposure of the DNA substrate to the compounds and their concentrations. The nucleoside analogues were nevertheless found to be capable of uncoupling the ATPase and helicase activities of the enzyme by a mechanism operating on the level of the enzyme. Thus, in the case of HMC-HO4, the direct interaction with the enzyme caused inhibition of its helicase activity, with a half-maximal inhibitory concentration of 30 μM. The similar potency of the compound against replication of WN virus in cell culture suggests that inhibition of the helicase activity of the viral enzyme is responsible for the observed antiviral activity of HMC-HO4 and may indeed represent an important mode of action of antiviral drugs in general. Comparative studies performed with the related NTPase/helicase from hepatitis C virus revealed that the extent of the effects mediated by imidazo[4,5-d]pyridazine nucleosides is enzyme specific. The substances described may represent a starting point for the development of a new class of helicase-specific antivirals.
Somatosensory‐evoked cortical activity in spastic diplegic cerebral palsy

Somatosensory deficits have been identified in cerebral palsy (CP), but associated cortical brain activity in CP remains poorly understood. Functional MRI was used to measure blood oxygenation level‐dependent (BOLD) responses during three tactile tasks in 10 participants with spastic diplegia (mean age: 18.70 years, SD: 7.99 years; 5 females) and 10 age‐matched controls (mean age: 18.60 years, SD: 3.86 years; 5 females). Tactile stimulation involved servo‐controlled translation of smooth or embossed surfaces across the right index finger pad; the discrimination tasks with embossed surfaces involved judging whether (1) paired shapes were similar or different, and (2) a rougher set of horizontal gratings preceded or followed a smoother one. Velocity and duration of surface translation was identical across all trials. In addition, an event‐related design revealed response dynamics per trial in both groups. Compared to controls, individuals with spastic diplegia had significantly reduced spatial extents in activated cortical areas and smaller BOLD response magnitudes in cortical areas for somatosensation, motor, and goal‐directed/attention behaviors. These results provide mechanisms for the widespread somatosensory deficits in CP. The reduced activation noted across multiple cortical areas might contribute to motor deficits in CP. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Multimedia system for e-learning about modulation techniques in three phase voltage inverters

The multimedia system for e-learning about modulation techniques in three phase voltage controlled inverters is introduced. The multimedia system features for Block commutation, Sine Pulse Width Modulation (SPWM) and Space Vector Pulse Width Modulation (SVPWM) are illustrated. Advantages of proposed multimedia system for e-learning about modulation techniques in three phase voltage inverters are indicated as well as improvements. The approach for obtaining SPWM parameter is proposed.
Evaluation of Formalin — Acetone Sedimentation in the Concentration of Stool for Intestinal Parasites

Formalin-acetone sedimentation was compared with the formalin-ether method for the concentration of stool for intestinal parasites. Of 80 stool specimens, 45 (56.25%) were positive for parasites by the formalin-acetone method. The figures for the two methods were formalin-ether 35 (43.75%) and for the direct lacto-phenol cotton blue wet mount method 17 (21.25%). There was no statistically significant difference in the parasite recovery rate between the two methods. Acetone is more stable, safer, and a cheaper fat solvent and promises to be a useful alternative to ether.
A concurrent dual-band CMOS low-noise amplifier for ISM-band application

A dual-band CMOS low-noise amplifier (LNA) for ISM-band application is reported. For low power and dual band operation, the designed LNA adopts a positive-feedback LC-ladder network. Moreover, for cost effective approach, the LNA has been fabricated using a 0.18-mum mixed-signal CMOS process. The implemented LNA shows gain of 8.3 dB and 11.2 dB, and noise figure (NF) of 6.1 dB and 6.6 dB at 19 GHz and 25 GHz, respectively. The proposed LNA exhibits 8.1 mW power consumption from 0.8 V supply and the active chip area including pad is about 720 times 460 mum2.
Data science on the ground: Hype, criticism, and everyday work

Modern organizations often employ data scientists to improve business processes using diverse sets of data. Researchers and practitioners have both touted the benefits and warned of the drawbacks associated with data science and big data approaches, but few studies investigate how data science is carried out “on the ground. ” In this paper, we first review the hype and criticisms surrounding data science and big data approaches. We then present the findings of semistructured interviews with 18 data analysts from various industries and organizational roles. Using qualitative coding techniques, we evaluated these interviews in light of the hype and criticisms surrounding data science in the popular discourse. We found that although the data analysts we interviewed were sensitive to both the allure and the potential pitfalls of data science, their motivations and evaluations of their work were more nuanced. We conclude by reflecting on the relationship between data analysts' work and the discourses around data science and big data, suggesting how future research can better account for the everyday practices of this profession.