gebhart/patrepeval huggingface dataset:
Dislocations in hexagonal and cubic GaN (2000)

The structure and electronic activity of several types of dislocations in both hexagonal and cubic GaN are calculated using first-principles methods. Most of the stoichiometric dislocations investigated in hexagonal GaN do not induce deep acceptor states and thus cannot be responsible for the yellow luminescence. However, it is shown that electrically active point defects, in particular gallium vacancies and oxygen-related defect complexes, can be trapped at the stress field of the dislocations and may be responsible for this luminescence. For cubic GaN, we find the ideal stoichiometric 60° dislocation to be electrically active and the glide set to be more stable than the shuffle. The dissociation of the latter is considered.
A 0.5&#x2013;20GHz quadrature downconverter (2008)

A quadrature downconverter with 4 GHz IF bandwidth and working over the 0.5-20 GHz RF frequency range has been designed, fabricated, and tested. The downconverter uses a frequency doubling and dividing scheme to generate quadrature local oscillator signals from 0.5-17 GHz and a pair of Gilbert-cell mixers to perform downconversion. When the IF outputs are combined with a commercial quadrature hybrid, the mixer achieves an image rejection ratio greater than 35 dB over the entire band with no on-chip calibration or tuning. The active die area is approximately 0.5times1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Glypican‐3 antibodies: A new therapeutic target for liver cancer (2013)

Glypican-3 (GPC3) is an emerging therapeutic target in hepatocellular carcinoma (HCC), even though the biological function of GPC3 remains elusive. Currently human (MDX-1414 and HN3) and humanized mouse (GC33 and YP7) antibodies that target GPC3 for HCC treatment are under different stages of preclinical or clinical development. Humanized mouse antibody GC33 is being evaluated in a phase II clinical trial. Human antibodies MDX-1414 and HN3 are under different stages of preclinical evaluation. Here, we summarize current evidence for GPC3 as a new target in liver cancer, discuss both its oncogenic function and its mode of actions for current antibodies, and evaluate potential challenges for GPC3-targeted anti-cancer therapies.
Cloning and high level expression of a chimeric antibody with specificity for human carcinoembryonic antigen. (1988)

A mouse/human chimeric antibody has been constructed by using variable light and variable heavy regions from a murine hybridoma specific for human carcinoembryonic antigen (CEA) (CEM231.6.7). These V regions were combined with kappa and gamma-1 constant region genes cloned from human lymphocytes. The chimeric constructs were sequentially electroporated into murine non-Ig-producing myeloma (P3.653) and hybridoma (SP2/0) cell. Significant differences were seen in expression levels between the two cell types. High levels of expression (24 to 32 micrograms/ml/10(6) cells) were seen with several of the anti-CEA SP2/0 transfectomas but not with the P3.653 cells. The SP2/0 transfectoma lines were adapted to serum-free, chemically defined media and grown in large scale fermentation cultures where they continued to secrete high levels of antibody. The chimeric antibodies remain reactive against human CEA with affinity constants comparable to that of the parental hybridoma antibody. High level expression will make practical the production of chimeric antibodies for in vivo therapeutic and diagnostic purposes.
Molecular cloning, characterization, and nucleotide sequence of the tagatose 6-phosphate pathway gene cluster of the lactose operon of Lactococcus lactis. (1991)

The tagatose 6-phosphate pathway gene cluster (lacABCD) encoding galactose-6-phosphate isomerase, tagatose-6-phosphate kinase, and tagatose-1,6-diphosphate aldolase of Lactococcus lactis subsp. lactis MG1820 has been characterized by cloning, nucleotide sequence analysis, and enzyme assays. Transcription studies showed that the four tagatose 6-phosphate pathway genes are the first genes of the lactose-inducible lactose-phosphotransferase operon consisting of the lacABCDFEGX genes. Using a T7 expression system, it could be shown that the lacA, lacB, lacC, and lacD genes code for proteins with apparent molecular masses of 15, 19, 33, and 36 kDa, respectively. Cell-free extracts of induced and noninduced Escherichia coli cells expressing the lacABCD genes were used to determine the functions of the encoded proteins. Expression of both lacA and lacB was required to obtain galactose-6-phosphate isomerase activity. The lacC gene codes for tagatose-6-phosphate kinase, the deduced amino sequence of which is similar to that of E. coli Pfk-2 phosphofructokinase, and Staphylococcus aureus LacC protein. The tagatose-1,6-diphosphate aldolase is encoded by the lacD gene, and its deduced primary sequence, which is homologous to that of the S. aureus LacD protein, predicts an amino acid composition which is virtually identical to that of the previously purified L. lactis E8 tagatose-1,6-diphosphate aldolase.
Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles (2017)

Recombinant vaccine strain-derived measles virus (MV) is clinically tested both as vaccine platform to protect against other pathogens and as oncolytic virus for tumor treatment. To investigate the potential synergism in anti-tumoral efficacy of oncolytic and vaccine properties, we chose Ovalbumin and an ideal tumor antigen, claudin-6, for pre-clinical proof of concept. To enhance immunogenicity, both antigens were presented by retroviral virus-like particle produced in situ during MV-infection. All recombinant MV revealed normal growths, genetic stability, and proper expression and presentation of both antigens. Potent antigen-specific humoral and cellular immunity were found in immunized MV-susceptible IFNAR<sup>-/-</sup>-CD46Ge mice. These immune responses significantly inhibited metastasis formation or increased therapeutic efficacy compared to control MV in respective novel in vivo tumor models using syngeneic B16-hCD46/mCLDN6 murine melanoma cells. These data indicate the potential of MV to trigger selected tumor antigen-specific immune responses on top of direct tumor lysis for enhanced efficacy.
The effect of low dose omega-3 on plasma lipids in hemodialysis patients. (2007)

Hemodialysis (HD) patients have a high incidence of cardiovascular disease and increased premature mortality. N-3 polyunsaturated fatty acids (PUFAs) are known to decrease plasma triglyceride (TG) levels and have a cardio-protective effect in subjects with normal renal function. The aim of this study was to investigate the effect of Omega-3 on plasma lipid levels in patients on HD. We included 33 patients on HD with serum TG higher than 200 mg/dl and total cholesterol higher than 220 mg/dl, in the study and randomly assigned them to treatment with 2 gm pearls of Omega-3 per day, given in two equal doses or a control group who did not receive this drug. The study was conducted for a period of 12 weeks. Patients were evaluated by measurement of fasting plasma lipid levels before and after the use of Omega-3. There was a significant (28%) increase in high-density lipoprotein levels (P %) decrease in serum TG levels (P < 0.02) in the group that received Omega-3 supplement. There were no changes in total cholesterol or low-density lipoprotein levels in either group. Our study suggests that supplementation with low-dose Omega-3 has a favorable effect on plasma lipid levels in patients on HD.
ChemInform Abstract: Metal‐Catalyzed Olefin Cyclopropanation with Ethyl Diazoacetate: Control of the Diastereoselectivity (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Altered mRNA expression of basement membrane components in a murine model of polycystic kidney disease. (1988)

Basement membranes surround the renal tubules and have been shown to limit their distension in vitro. Therefore, it has been postulated that a defect in a basement membrane component(s) underlies the pathogenesis of polycystic kidney disease. Here we have studied a murine model of congenital polycystic kidney disease and found by immunohistology, that the components of the peri-cyst basement membrane appeared to diminish with time. We also measured mRNA levels for collagen IV and laminin, and found a different pattern than in the normal mouse kidney. In normal kidneys, mRNA levels for the B1 and B2 chains of laminin were maximal at birth, and at 1 week for the alpha 1(IV) chain of collagen IV. With all three chains, the levels then rapidly declined. In contrast, mRNA for the alpha 1(IV) chain in congenital polycystic kidneys was half normal 1 week after birth and then increased. Laminin B1 and B2 chain mRNA's were 80% of normal at 1 week but were maintained at that level. As a control, beta-actin mRNA was examined and found to remain constant in both normal and diseased kidneys. In situ hybridization of cRNA probes for the alpha 1(IV) chain confirmed that cells associated with cysts were the principal source of expression of these basement membrane mRNAs. Thus, there exists an abnormal regulation of basement membrane gene expression in congenital polycystic kidney disease. The first stage is characterized by reduced levels of expression. In the second stage, the levels are abnormally high, perhaps representing a compensatory synthesis of basement membrane as cysts enlarge.
Inhibition of the Antibacterial Target UDP-(3-O-acyl)-N-acetylglucosamine Deacetylase (LpxC):  Isoxazoline Zinc Amidase Inhibitors Bearing Diverse Metal Binding Groups (2002)

UDP-3-O-[R-3-hydroxymyristoyl]-GlcNAc deacetylase (LpxC) is a zinc amidase that catalyzes the second step of lipid A biosynthesis in Gram negative bacteria. Known inhibitors of this enzyme are oxazolines incorporating a hydroxamic acid at the 4-position, which is believed to coordinate to the single essential zinc ion. A new structural class of inhibitors was designed to incorporate a more stable and more synthetically versatile isoxazoline core. The synthetic versatility of the isoxazoline allowed for a broad study of metal binding groups. Nine of 17 isoxazolines, each incorporating a different potential metal binding functional group, were found to exhibit enzyme inhibitory activity, including one that is more active than the corresponding hydroxamic acid. Additionally, a designed affinity label inhibits LpxC in a time-dependent manner.
The role of recombinant stem cell factor in early B cell development. Synergistic interaction with IL-7 (1991)

The cDNA for stem cell factor was recently isolated from Buffalo rat liver cells (BRL-3A) and recombinant rat stem cell factor produced from Escherichia coli (rrSCF164). rrSCF164 synergizes with rhIL-7 to stimulate pre-B clonal growth in agar culture of mouse bone marrow cells, and in this study we have characterized the role of rrSCF164 in B cell development. The combination of rrSCF164 plus rhIL-7 stimulated increased colony numbers compared with the sum of colonies stimulated by rrSCF164 and rhIL-7 alone. Also, increased cell proliferation per colony was stimulated by the combination of rrSCF164 plus rhIL-7 compared with rhIL-7 or rrSCF164 alone. The colonies formed with rrSCF164 plus rhIL-7 and rhIL-7 alone contained exclusively pre-B cells, which expressed B220 Ag and cytoplasmic mu-chain, but were negative for surface Ig expression. Morphological examination of the cells in the colonies showed blast-like characteristics. rrSCF164 alone and in combination with rhIL-7 stimulated generation of B220+ cells in liquid culture of B220- cells, whereas rhIL-7 alone had no stimulatory effect on B220- cells. Both stem cell factor mRNA and bioactivity were detected in a mouse bone marrow-derived stromal cell line, termed OZ-11. We propose that stem cell factor is a stromal-derived factor that synergizes with IL-7 to stimulate the proliferation and differentiation of pro-B cells to pre-B cells, which become responsive to IL-7 alone.
Capacitive Epidermal Electronics for Electrically Safe, Long‐Term Electrophysiological Measurements (2013)

Integration of capacitive sensing capabilities to epidermal electronic systems (EES) can enhance the robustness in operation for electrophysiological signal measurement. Capacitive EES designs are reusable, electrically safe, and minimally sensitive to motion artifacts. Experiments on human subjects illustrate levels of fidelity in ECG, EMG, and EOG recordings comparable to those of standard gel electrodes and of direct contact EES electrodes.
Oligodeoxynucleotides inhibit retinal neovascularization in a murine model of proliferative retinopathy. (1996)

Diseases characterized by retinal neovascularization are among the principal causes of visual loss worldwide. The hypoxia-stimulated expression of vascular endothelial growth factor (VEGF) has been implicated in the proliferation of new blood vessels. We have investigated the use of antisense phosphorothioate oligodeoxynucleotides against murine VEGF to inhibit retinal neovascularization and VEGF synthesis in a murine model of proliferative retinopathy. Intravitreal injections of two different antisense phosphorothioate oligodeoxynucleotides prior to the onset of proliferative retinopathy reduced new blood vessel growth a mean of 25 and 31% compared with controls. This inhibition was dependent on the concentration of antisense phosphorothioate oligodeoxynucleotides and resulted in a 40-66% reduction in the level of VEGF protein, as determined by Western blot analysis. Control (sense, nonspecific) phosphorothioate oligodeoxynucleotides did not cause a significant reduction in retinal neovascularization or VEGF protein levels. These data further establish a fundamental role for VEGF expression in ischemia-induced proliferative retinopathies and a potential therapeutic use for antisense phosphorothioate oligodeoxynucleotides.
Pathogenesis of cytomegalovirus pneumonia in immunocompromised hosts. (1995)

Cytomegalovirus (CMV) is capable of establishing persistent or latent infection after primary infections and reactivation in immunocompromised hosts. The understanding of the nature of this latency is incomplete. The acquisition of CMV-specific immune responses appears essential for limiting primary infection and maintenance of a clinical state of latency. Host immunity induced by CMV infection includes both cellular and humoral responses. Cell-mediated responses by both CD4+ (T helper) and CD8+ cytotoxic T lymphocytes (CTLs) are detected in CMV-seropositive individuals. Studies in animal models and in immunocompromised patients have implicated deficiencies in class I MHC-restricted, CD8+CMV-specific CTL responses in the progression of experimental and human CMV infection and pneumonia. Adoptive transfer of CD8+CMV-specific CTLs in immunodeficient marrow transplant recipients provides evidence that adoptive immunotherapy with T-cell clones of defined specificity and function can be used to safely and successfully restore immunity to a human pathogen.
The Methyl-CpG-binding Protein MeCP2 Links DNA Methylation to Histone Methylation (2003)

DNA methylation plays an important role in mammalian development and correlates with chromatin-associated gene silencing. The recruitment of MeCP2 to methylated CpG dinucleotides represents a major mechanism by which DNA methylation can repress transcription. MeCP2 silences gene expression partly by recruiting histone deacetylase (HDAC) activity, resulting in chromatin remodeling. Here, we show that MeCP2 associates with histone methyltransferase activity in vivo and that this activity is directed against Lys(9) of histone H3. Two characterized repression domains of MeCP2 are involved in tethering the histone methyltransferase to MeCP2. We asked if MeCP2 can deliver Lys(9) H3 methylation to the H19 gene, whose activity it represses. We show that the presence of MeCP2 on nucleosomes within the repressor region of the H19 gene (the differentially methylated domain) coincides with an increase in H3 Lys(9) methylation. Our data provide evidence that MeCP2 reinforces a repressive chromatin state by acting as a bridge between two global epigenetic modifications, DNA methylation and histone methylation.
Biochemical Basis of Immunological and Retroviral Responses to DNA-targeted Cytosine Deamination by Activation-induced Cytidine Deaminase and APOBEC3G (2009)

Activation-induced cytidine deaminase (AID) and APOBEC3G catalyze deamination of cytosine to uracil on single-stranded DNA, thereby setting in motion a regulated hypermutagenic process essential for human well-being. However, if regulation fails, havoc ensues. AID plays a central role in the synthesis of high affinity antibodies, and APOBEC3G inactivates human immunodeficiency virus-1. This minireview highlights biochemical and structural properties of AID and APOBEC3G, showing how studies using the purified enzymes provide valuable insight into the considerably more complex biology governing antibody generation and human immunodeficiency virus inactivation.
Condensed Memory Networks for Clinical Diagnostic Inferencing (2017)

Diagnosis of a clinical condition is a challenging task, which often requires significant medical investigation. Previous work related to diagnostic inferencing problems mostly consider multivariate observational data (e.g. physiological signals, lab tests etc.). In contrast, we explore the problem using free-text medical notes recorded in an electronic health record (EHR). Complex tasks like these can benefit from structured knowledge bases, but those are not scalable. We instead exploit raw text from Wikipedia as a knowledge source. Memory networks have been demonstrated to be effective in tasks which require comprehension of free-form text. They use the final iteration of the learned representation to predict probable classes. We introduce condensed memory neural networks (C-MemNNs), a novel model with iterative condensation of memory representations that preserves the hierarchy of features in the memory. Experiments on the MIMIC-III dataset show that the proposed model outperforms other variants of memory networks to predict the most probable diagnoses given a complex clinical scenario.
Mining data streams (2005)

The recent advances in hardware and software have enabled the capture of different measurements of data in a wide range of fields. These measurements are generated continuously and in a very high fluctuating data rates. Examples include sensor networks, web logs, and computer network traffic. The storage, querying and mining of such data sets are highly computationally challenging tasks. Mining data streams is concerned with extracting knowledge structures represented in models and patterns in non stopping streams of information. The research in data stream mining has gained a high attraction due to the importance of its applications and the increasing generation of streaming information. Applications of data stream analysis can vary from critical scientific and astronomical applications to important business and financial ones. Algorithms, systems and frameworks that address streaming challenges have been developed over the past three years. In this review paper, we present the state-of-the-art in this growing vital field.
Nitric Oxide Is a Physiological Substrate for Mammalian Peroxidases (2000)

We now show that NO serves as a substrate for multiple members of the mammalian peroxidase superfamily under physiological conditions. Myeloperoxidase (MPO), eosinophil peroxidase, and lactoperoxidase all catalytically consumed NO in the presence of the co-substrate hydrogen peroxide (H(2)O(2)). Near identical rates of NO consumption by the peroxidases were observed in the presence versus absence of plasma levels of Cl(-). Although rates of NO consumption in buffer were accelerated in the presence of a superoxide-generating system, subsequent addition of catalytic levels of a model peroxidase, MPO, to NO-containing solutions resulted in the rapid acceleration of NO consumption. The interaction between NO and compounds I and II of MPO were further investigated during steady-state catalysis by stopped-flow kinetics. NO dramatically influenced the build-up, duration, and decay of steady-state levels of compound II, the rate-limiting intermediate in the classic peroxidase cycle, in both the presence and absence of Cl(-). Collectively, these results suggest that peroxidases may function as a catalytic sink for NO at sites of inflammation, influencing its bioavailability. They also support the potential existence of a complex and interdependent relationship between NO levels and the modulation of steady-state catalysis by peroxidases in vivo.
Sensory feedback structures for robots with supervised learning (2005)

A concept for sensory feedback and sensor-based teach-in in robotics is presented. Based on previous work of different authors a scheme of hybrid sensory-position control is proposed and has been realized that interpretes every "rudimentary" teach command in terms of sensory interaction with the environment by generating the socalled "artificial constraints" and the refined path automatically. Robots with arbitrarily programmable stiffness are one outcome of our technique. Motion commands and sensor data are stored together. The latter ones are then available as reference values for the repetition mode in a possibly changing environment. It is shown that by introducing pseudo-forces/torques the proposed techniques are equally applicable to different kinds of sensor, as are force-torque-sensors, range finders or inductive sensors. The "sensor-ball"-technique as developed at DFVLR is discussed as one physical realization. Operational systems of this kind, first tested with an ASEA robot in our lab, are going into industrial application now.
Inhibition of small G proteins of the Rho family by statins or Clostridium difficile toxin B enhances cytokine‐mediated induction of NO synthase II (2000)

In order to investigate the involvement of Ras and/or Rho proteins in the induction of the inducible isoform of nitric oxide synthase (NOS II) we used HMG-CoA reductase inhibitors (statins) and Clostridium difficile toxin B (TcdB) as pharmacological tools. Statins indirectly inhibit small G proteins by preventing their essential farnesylation (Ras) and/or geranylgeranylation (Rho). In contrast, TcdB is a glucosyltransferase and inactivates Rho-proteins directly. Human A549/8- and DLD-1 cells as well as murine 3T3 fibroblasts were preincubated for 18 h with statins (1 - 100 microM) or TcdB (0.01-10 ng ml(-1)). Then NOS II expression was induced by cytokines. NOS II mRNA was measured after 4 - 8 h by RNase protection assay, and NO production were measured by the Griess assay after 24 h. Statins and TcdB markedly increased cytokine-induced NOS II mRNA expression and NO production. Statin-mediated enhancement of NOS II mRNA expression was reversed almost completely by cotreatment with mevalonate or geranylgeranylpyrophosphate. It was only slightly reduced by farnesylpyrophosphate. Therefore, small G proteins of the Rho family are likely to be involved in NOS II induction. In A549/8 cells stably transfected with a luciferase reporter gene under the control of a 16 kb fragment of the human NOS II promoter (pNOS2(16)Luc), statins produced only a small increase in cytokine-induced NOS II promoter activity. In contrast, statins had a considerable superinducing effect in DLD-1 cells stably transfected with pNOS2(16)Luc. In conclusion, our studies provide evidence that statins and TcdB potentiate cytokine-induced NOS II expression via inhibition of small G proteins of the Rho family. This in turn results in an enhanced NOS II promoter activity and/or a prolonged NOS II mRNA stability.