gebhart/patrepeval huggingface dataset:
Molecular cytogenetics of cutaneous melanocytic lesions – diagnostic, prognostic and therapeutic aspects (2009)

This review intends to update current knowledge regarding molecular cytogenetics in melanocytic tumours with a focus on cutaneous melanocytic lesions. Advantages and limitations of diverse, already established methods, such as (fluorescence) in situ hybridization and mutation analysis, to detect these cytogenetic alterations in melanocytic tumours are described. In addition, the potential value of more novel techniques such as multiplex ligation-dependent probe amplification is pointed out. This review demonstrates that at present cytogenetics has mainly increased our understanding of the pathogenesis of melanocytic tumours, with an important role for activation of the mitogen-activated protein kinase (MAPK) signalling pathway in the initiation of melanocytic tumours. Mutations in BRAF (in common naevocellular naevi), NRAS (congenital naevi), HRAS (Spitz naevi) and GNAQ (blue naevi) can all cause MAPK activation. All these mutations seem early events in the development of melanocytic tumours, but by themselves are insufficient to cause progression towards melanoma. Additional molecular alterations are implicated in progression towards melanoma, with different genetic alterations in melanomas at different sites and with varying levels of sun exposure. This genetic heterogeneity in distinct types of naevi and melanomas can be used for the development of molecular tests for diagnostic purposes. However, at the moment only few molecular tests have become of diagnostic value and are performed in daily routine practice. This is caused by lack of large prospective studies on the diagnostic value of molecular tests including follow-up, and by the low prevalence of certain molecular alterations. For the future we foresee an increasing role for cytogenetics in the treatment of melanoma patients with the increasing availability of targeted therapy. Potential targets for metastatic melanoma include genes involved in the MAPK pathway, such as BRAF and RAS. More recently, KIT has emerged as a potential target in melanoma patients. These targeted treatments all need careful evaluation, but might be a promising adjunct for treatment of metastatic melanoma patients, in which other therapies have not brought important survival advantages yet.
<i>lpt6</i> , a Gene Required for Addition of Phosphoethanolamine to Inner-Core Lipopolysaccharide of <i>Neisseria meningitidis</i> and <i>Haemophilus influenzae</i> (2004)

We previously described a gene, lpt3, required for the addition of phosphoethanolamine (PEtn) at the 3 position on the beta-chain heptose (HepII) of the inner-core Neisseria meningitidis lipopolysaccharide (LPS), but it has long been recognized that the inner-core LPS of some strains possesses PEtn at the 6 position (PEtn-6) on HepII. We have now identified a gene, lpt6 (NMA0408), that is required for the addition of PEtn-6 on HepII. The lpt6 gene is located in a region previously identified as Lgt-3 and is associated with other LPS biosynthetic genes. We screened 113 strains, representing all serogroups and including disease and carriage strains, for the lpt3 and lpt6 genes and showed that 36% contained both genes, while 50% possessed lpt3 only and 12% possessed lpt6 only. The translated amino acid sequence of lpt6 has a homologue (72.5% similarity) in a product of the Haemophilus influenzae Rd genome sequence. Previous structural studies have shown that all H. influenzae strains investigated have PEtn-6 on HepII. Consistent with this, we found that, among 70 strains representing all capsular serotypes and nonencapsulated H. influenzae strains, the lpt6 homologue was invariably present. Structural analysis of LPS from H. influenzae and N. meningitidis strains where lpt6 had been insertionally inactivated revealed that PEtn-6 on HepII could not be detected. The translated amino acid sequences from the N. meningitidis and H. influenzae lpt6 genes have conserved residues across their lengths and are part of a family of proven or putative PEtn transferases present in a wide range of gram-negative bacteria.
Automated contour detection in X-ray left ventricular angiograms using multiview active appearance models and dynamic programming (2006)

This paper describes a new approach to the automated segmentation of X-ray left ventricular (LV) angiograms, based on active appearance models (AAMs) and dynamic programming. A coupling of shape and texture information between the end-diastolic (ED) and end-systolic (ES) frame was achieved by constructing a multiview AAM. Over-constraining of the model was compensated for by employing dynamic programming, integrating both intensity and motion features in the cost function. Two applications are compared: a semi-automatic method with manual model initialization, and a fully automatic algorithm. The first proved to be highly robust and accurate, demonstrating high clinical relevance. Based on experiments involving 70 patient data sets, the algorithm's success rate was 100% for ED and 99% for ES, with average unsigned border positioning errors of 0.68 mm for ED and 1.45 mm for ES. Calculated volumes were accurate and unbiased. The fully automatic algorithm, with intrinsically less user interaction was less robust, but showed a high potential, mostly due to a controlled gradient descent in updating the model parameters. The success rate of the fully automatic method was 91% for ED and 83% for ES, with average unsigned border positioning errors of 0.79 mm for ED and 1.55 mm for ES.
MIMO MAP equalization and turbo decoding in interleaved space-time coded systems (2003)

Decoding of space-time codes in frequency-selective fading channels is considered. The approach is based on iterative soft-in soft-out equalization and decoding. It is applicable to space-time coded systems that deploy symbol/bit interleavers. We focus on the equalization stage by extending the Ungerboeck equalizer formulation to a multiple-input multiple-output time-variant channel. The resulting structure comprises a bank of matched filters, followed by an a posteriori probabilities calculator that runs the Bahl-Cocke-Jelinek-Raviv/maximum a posteriori algorithm with an appropriate metric. Simulation results are reported for space-time bit-interleaved codes designed over the enhanced data rates for GSM evolution (EDGE) air interface.
Thioltransferase (Glutaredoxin) Is Detected Within HIV-1 and Can Regulate the Activity of Glutathionylated HIV-1 Protease in Vitro (1997)

Previous studies have suggested that the two conserved cysteines of the HIV-1 protease may be involved in regulating protease activity. Here, we examined diglutathionylated wild type protease (Cys-67-SSG, Cys-95-SSG) and the monoglutathionylated protease mutants (C67A, Cys-95-SSG and C95A, Cys-67-SSG) as potential substrates for thioltransferase (glutaredoxin). Time-dependent changes in the extent of deglutathionylation of each protein were assayed by reverse phase-high performance liquid chromatography. Glutathione alone was not an effective reductant, whereas thioltransferase displayed differential catalysis toward the Cys-95-SSG and Cys-67-SSG sites. At low thioltransferase concentrations (5 nM), deglutathionylation occurred almost exclusively at Cys-95-SSG. With substantially more thioltransferase (100 nM) Cys-67-SSG was partially deglutathionylated but only at 20% of the rate of Cys-95-SSG reduction. Treatment of the diglutathionylated protease with thioltransferase not only restored protease activity but generated an enzyme preparation that had a 3- to 5-fold greater specific activity relative to the fully reduced form. Immunoblot analysis of HIV-1MN virus with an antibody to thioltransferase detected a band co-migrating with recombinant thioltransferase that persisted following subtilisin treatment, indicating the presence of thioltransferase within HIV-1. Our results implicate thioltransferase in the regulation and/or maintenance of protease activity in HIV-1 infected cells.
Endogenous expression of transforming growth factor beta1 inhibits growth and tumorigenicity and enhances Fas-mediated apoptosis in a murine high-grade glioma model. (1998)

It has been hypothesized that transforming growth factor beta (TGF-beta) may prevent immune-mediated glioma cell elimination; however, previous work has also indicated that increased TGF-beta may lead to reduced proliferation, induction of apoptosis, and enhancement of Fas-induced apoptosis. We have investigated the role of TGF-beta in the progression of malignant glioma using an immunocompetent murine model. SMA 560 malignant glioma cells were stably transfected with constructs that resulted in over- or underproduction of active TGF-beta1. Using these cell lines, we have shown that (a) TGF-beta1 inhibits induction of antitumor cytotoxicity when the tumor cells are given s.c. but not when they are given intracranially; (b) Fas/APO-1 is expressed on SMA 560 cells in vitro and in vivo, SMA 560 cells are susceptible to TGF-beta1- and Fas-induced apoptosis in vitro, and TGF-beta1 and Fas act synergistically to induce glioma cell death; (c) increased levels of endogenous TGF-beta1 production by SMA 560 cells lead to increased sensitivity to Fas-mediated apoptosis; (d) overproduction of endogenous TGF-beta1 reduces the rate of s.c. SMA 560 tumor growth and also reduces the tumorigenicity of tumors located in the central nervous system, with opposite effects observed with underproduction of TGF-beta1 using antisense cell lines; and (e) the observed changes in growth parameters in vivo were associated with increased rates of apoptosis in TGF-beta1-overproducing cells. Taken together, these results indicate that, despite decreased induction of CTL responses, the dominant net effect of TGF-beta1 on the growth of the SMA 560 murine high-grade glioma in vivo is growth inhibition. This contrasts with results seen with non-central nervous system malignant tumors in immunocompetent animals, in which TGF-beta1 production provides a major growth advantage.
Experimental Characterization, Modeling, and Analysis of Crosstalk in a Quantum Computer (2020)

In this article, we present the experimental characterization of crosstalk in quantum information processor using idle tomography and simultaneous randomized benchmarking. We quantify both “quantum” and “classical” crosstalk in the device and analyze quantum circuits considering crosstalk. We show that simulation considering only gate-error deviates from experimental results up to 27%, whereas simulation considering both gate error and crosstalk match the experiments more accurately with an average mismatch as low as 4.52%. This article enables simulation of quantum circuits with experimental crosstalk error rates.
Eroded human telomeres are more prone to remain uncapped and to trigger a G2 checkpoint response (2012)

Telomeres cap the ends of chromosomes and regulate the replicative life span of human somatic cells. Telomere function is lost upon critical shortening and a p53-dependent checkpoint that detects altered telomere states at the G1/S transition was proposed to act as a regulator of the telomere damage response. We show that telomerase-negative human fibroblasts spend more time in G2 phase as they approach senescence and this delay is associated with manifestations of telomere dysfunction and the triggering of an ATM/ATR-dependent DNA damage signal. This correlates with a partial release of telomeric proteins TRF1 and TRF2. Analysis of the consequences of TRF1 and TRF2 depletion or over-expression of mutated versions revealed that telomere uncapping or telomere replication stress also led to DNA damage signalling in G2. Progression through mitosis of these cells was associated with signs of incomplete telomere terminal processing. We also observed an increase in sister chromatid-type telomere aberrations in senescing fibroblasts indicating that defects of telomere post-replicative events increased as cells age. Our results link a post-replicative damage response at eroded telomeres to G2 arrest signalling and challenge the current paradigm that the checkpoint response to short telomeres occurs primarily at the G1/S transition in human cells.
Extension of the Schottky barrier detector to 70 μm (4.3 THz) using submicron-dimensional contacts (1977)

Schottky barrier diode detection in both video and mixing modes of operation has been extended to 4.252 THz (70.5 μm) using 0.5-μm-diam diodes fabricated from heavily doped nonepitaxial n-type GaAs. These ultrasmall, and consequently ultralow capacitance, junctions were prepared using electron-beam lithography and have yielded the smallest reported series-resistance junction-capacitance product for a Schottky barrier diode. The potential for extending diode operation to still higher frequencies is discussed.
Ultra-compact close-up microoptical imaging system (2010)

Although several applications of machine vision and biomedical imaging ask for the close-up imaging of extended object fields, only few, mostly bulky solutions exist. We demonstrate the optical design and realization of an ultra-compact close-up imaging system with unity magnification. It uses a multi-aperture approach in order to shorten its total track length to less than 4 mm while achieving a large field of view. The system is made of a stack of several two-dimensional arrays of refractive microlenses. The potential of this setup lies in the combination of digital imaging with microoptical fabrication techniques leading to thin optical components which can be directly attached to an image sensor. Hence, these systems fit into tight spaces and they achieve a high resolution without scanning.
One-Step Instant Synthesis of Protein-Conjugated Quantum Dots at Room Temperature (2013)

We present a new general facile strategy for the preparation of protein-functionalized QDs in a single step at ambient conditions. We demonstrated that highly luminescent red to near-infrared (NIR) protein-functionalized QDs could be synthesized at room temperature in one second through a one-pot reaction that proceeds in aqueous solution. Herein protein-functionalized QDs were successfully constructed for a variety of proteins with a wide range of molecular weights and isoelectric points. The as-prepared protein-conjugated QDs exhibited high quantum yield, high photostabiliy and colloidal stability, and high functionalization efficiency. Importantly, the proteins attached to the QDs maintain their biological activities and are capable of catalyzing reactions and biotargeting. In particular, the as-prepared transferrin-QDs could be used to label cancer cells with high specificity. Moreover, we demonstrated that this synthetic strategy could be extended to prepare QDs functionalized with folic acids and peptides, which were also successfully applied to cancer cell imaging.
Semantic sky (2012)

These days, the number of data sources an ordinary computer user works with every day is very large and continues to grow. With the increasing number of cloud services with specialized functionalities, the users are faced with the necessity to routinely perform manual actions to interchange data among different cloud and web services, in order to perform more complex and composite actions. These actions always require a certain amount of dedicated time from the user, who has to change the context in which he work, in order to take the actions and transfer data from one system to another. In this paper, we present a software platform, based on the concepts and technologies of the Semantic Web, which provides the users with a unified and simple composite approach to the different services they use, and crates a simple flow of information from one infrastructure to another. The system is able to automatically discover the context in which the user is working, and offer him the actions which can be used over the data within the context. In this way, the user can completely focus on his tasks in his work environment, and get relevant information and possible actions in that context. This system automates the execution of the users' tasks, which leads to improvements in their productivity, information exchange and efficiency. The system is called "Semantic Sky" and represents a platform where many cloud services are interconnected by the use of semantic web technologies.
Fat redistribution syndromes associated with HIV-1 infection and combination antiretroviral therapy. (2012)

More than 15 years after the introduction of highly active antiretroviral therapy, HIV/HAART-associated lipodystrophy syndrome still shadows the indisputable efficacy of antiretroviral therapy. Several issues related to this complication (prevalence, diagnosis, pathogenesis, prevention, or clinical management) have not been completely clarified. However, in the last years, substantial progress has been made in elucidating some of these basic aspects. This includes a better knowledge of the pathogenic mechanisms underlying HIV/HAART-associated lipodystrophy syndrome such as genetic host determinants, the impact of HIV infection per se, as well as the contribution of antiretroviral therapy. In regard to treatment, we have learned that certain drugs are especially prone to cause HIV/HAART-associated lipodystrophy syndrome (i.e. thymidine analogues). Pharmacological interventions to treat this condition have yielded mostly disappointing results, and the only intervention which offers an immediate aesthetical improvement for patients with HIV/HAART-associated lipodystrophy syndrome is plastic surgery. Even under the most favorable conditions (ideal host genetic make-up, and the timely initiation of HIV therapy with less toxic drugs), current data show that HIV/HAART-associated lipodystrophy syndrome is a complication of HIV infection and/or antiretroviral treatment that we are unable to avoid. In the context of HIV-1-infected patients under long-term antiretroviral therapy, fat toxicity is still the dark side of the rainbow.
High-resolution grayscale image hidden in a laser beam (2017)

Images perceived by human eyes or recorded by cameras are usually optical patterns with spatially varying intensity or color profiles. In addition to the intensity and color, the information of an image can be encoded in a spatially varying distribution of phase or polarization state. Interestingly, such images might not be able to be directly viewed by human eyes or cameras because they may exhibit highly uniform intensity profiles. Here, we propose and experimentally demonstrate an approach to hide a high-resolution grayscale image in a square laser beam with a size of less than half a millimeter. An image with a pixel size of 300 × 300 nm is encoded into the spatially variant polarization states of the laser beam, which can be revealed after passing through a linear polarizer. This unique technology for hiding grayscale images and polarization manipulation provides new opportunities for various applications, including encryption, imaging, optical communications, quantum science and fundamental physics.
Comparison of the Inhibitory Effects of the TXA2 Receptor Antagonist, Vapiprost, and Other Antiplatelet Drugs on Arterial Thrombosis in Rats: Possible Role of TXA2 (1992)

The antithrombotic effect of the thromboxane A2 receptor antagonist, vapiprost, was compared with those of other antiplatelet drugs using an arterial thrombosis model which utilized photochemical reaction in the rat femoral artery. Vapiprost prolonged the time required to occlude the artery with thrombus and inhibited collagen-induced rat platelet aggregation in whole blood ex vivo, in a dose-dependent manner. The potency ranking of antithrombotic effect was vapiprost > ketanserin (serotonin 5-HT2 receptor antagonist) >> ticlopidine (inhibitor of ADP-induced platelet aggregation) = dipyridamole (adenosine uptake inhibitor) > aspirin (cyclooxygenase inhibitor). On the other hand, the ranking of antiplatelet effect was ticlopidine > or = vapiprost > or = aspirin. Ketanserin and dipyridamole were ineffective. Relative to their antiplatelet effect, vapiprost and ketanserin had powerful antithrombotic effects. It is possible that the potent antithrombotic effects of vapiprost and ketanserin in vivo reflect the ability of these drugs to inhibit mediator-induced vascular contractions in addition to platelet aggregation. The results of the present study also suggest that TXA2 may play an important role in thrombogenesis in rats.
DESIGN AND OPERATING EXPERIENCE OF TRIODE ELECTRON GUNS (2007)

arvjain @ barc.gov.in The Accelerator and Pulse Power Division of BARC is presently constructing three industrial electron accelerators for radiation applications. a) a 500keV, 10 KW Cockcroft-Walton accelerator b) a 10MeV, 10kW electron linac and c) a 3MeV, 30kW DC machine. While the DC machines require an almost parallel beam with less than 1.0 degree divergence, the RF linac gun requires a 50keV, 2 ampere pulsed beam of low emittance. Using relativistic electron optics, including space charge effects, very simple triode gun designs with flat cathode, grid and anode apertures which fulfil these requirements and are easy to fabricate experimentally are described. Our operating experience with these guns are also described.
Chemical Engineering Division Research Highlights: January - December 1970 (1970)

During 1970, the Chemical Engineering Division has continued its investigations in the areas of fuel-cycle technology, sodium technology, materials properties, analytical and reactor chemistry, liquid-metal and molten- salt studies, energy conversion, and fluidized-bed combustion of fossil fuels. For reprocessing LMFBR irradiated fuel, a head-end process for decladding the fuel in liquid metal, a process for converting recovered plutonium and uranium nitrate solutions to oxides, and a centrifugal contactor suitable for high plutonium content are being developed. Analytical procedures adaptable to in-line use in the fabrication of LMFBR fuel are also being studied. In the sodium technology program, major emphasis is being placed on the measurement of sodium quality by chemical analyse s and on-line monitors. An effort is also being made to develop failed-fuel-element detectors. Materials and chemistry studies are concerned with various aspects of the behavior of materials in fast reactors. Fuelcladding interactions and material-transport phenomena in mixed-oxide fuel are being studied. Thermodynamic studies of the U-C-O and U-Pu-O systems are being carried out, and a considerable effort is being made to obtain information on the sodium-fuel reaction. High-temperature physical- property data needed for fast-reactor safety analysis are being obtained. Calorimetric procedures are being used to obtain thermochemical data on materials of interest in reactor technology . Determinations of fast-reactor cross sections and fission yields are continuing. Development efforts also continue on secondary electrical batteries for vehicle propulsion and for powering an artificial heart as well as on fluidized combustion of fossil fuels as a means of reducing pollutants. A new program on nuclear safeguards has been started.