gebhart/patrepeval huggingface dataset:
Immune Deficiency Syndrome in Children (1983)

The present epidemic of acquired immune deficiency syndrome (AIDS) was originally described in homosexual men and subsequently in intravenous drug abusers, Haitians, and hemophiliacs. Profound defects in cell-mediated immunity (CMI) are associated with Kaposi's sarcoma and a variety of serious opportunistic infections. Recently, we and others have encountered a group of children with an otherwise unexplained immune deficiency syndrome and infections of the type found in adults with AIDS. In this report, we describe eight children from the Newark, NJ, metropolitan area born into families with recognized risks for AIDS. These patients have had recurrent febrile illnesses, failure to thrive, hypergammaglobulinemia, and depressed CMI. Four of these children have died. Our experience suggests that children living in high-risk households are susceptible to AIDS and that sexual contact, drug abuse, or exposure to blood products is not necessary for disease transmission.
Sandwich‐Like, Stacked Ultrathin Titanate Nanosheets for Ultrafast Lithium Storage (2010)

Sandwich-like stacked titanate nanosheets with the thickness of ≈0.4 nm are successfully synthesized on a large scale using a clean and facile method. The unique material exhibits superior capacity and excellent high rate performance for ultrafast lithium storage.
Identification of grapevine MLO gene candidates involved in susceptibility to powdery mildew (2008)

The European cultivated grapevine, Vitis vinifera L., is a host for the powdery mildew pathogen Erisyphe necator, which is the most economically important fungal disease of viticulture. MLO proteins mediate powdery mildew susceptibility in the model plant species Arabidopsis and the crop plants barley and tomato. Seven VvMLO cDNA sequences were isolated from grapevine and were subsequently identified as part of a 17 member VvMLO gene family within the V. vinifera genome. Phylogenetic analysis of the 17 VvMLO genes in the grape genome indicated that the proteins they encode fall into six distinct clades. The expression of representative VvMLOs from each clade were analysed in a range of grape tissues, as well as in response to a range of biotic and abiotic factors. The VvMLOs investigated have unique, but overlapping tissue expression patterns. Expression analysis of VvMLO genes following E. necator infection identified four upregulated VvMLOs which are orthologous to the Arabidopsis AtMLO2, AtMLO6 and AtMLO12 and tomato SlMLO1 genes required for powdery mildew susceptibility. This suggests a degree of functional redundancy between the proteins encoded by these genes in terms of susceptibility to powdery mildew, and, as such, represent potential targets for modification to generate powdery mildew resistant grapevines.
Slippery Liquid‐Infused Porous Surfaces that Prevent Microbial Surface Fouling and Kill Non‐Adherent Pathogens in Surrounding Media: A Controlled Release Approach (2016)

Many types of slippery liquid-infused porous surfaces (or 'SLIPS') can resist adhesion and colonization by microorganisms. These 'slippery' materials thus offer new approaches to prevent fouling on a range of commercial and industrial surfaces, including biomedical devices. However, while SLIPS can prevent fouling on surfaces to which they are applied, they can currently do little to prevent the proliferation of non-adherent (planktonic) organisms, stop them from colonizing other surfaces, or prevent them from engaging in other behaviors that could lead to infection and associated burdens. Here, we report an approach to the design of multi-functional SLIPS that addresses these issues and expands the potential utility of slippery surfaces in antimicrobial contexts. Our approach is based on the incorporation and controlled release of small-molecule antimicrobial agents from the porous matrices used to host infused slippery oil phases. We demonstrate that SLIPS fabricated using nanoporous polymer multilayers can prevent short- and longer-term colonization and biofilm formation by four common fungal and bacterial pathogens (<i>Candida albicans, Pseudomonas aeruginosa</i>, <i>Escherichia coli</i>, and <i>Staphylococcus aureus</i>), and that the polymer and oil phases comprising these materials can be exploited to load and sustain the release of triclosan, a model hydrophobic and broad-spectrum antimicrobial agent, into surrounding media. This approach both improves the inherent anti-fouling properties of these materials and endows them with the ability to efficiently kill planktonic pathogens. Finally, we show that this approach can be used to fabricate dual-action SLIPS on complex surfaces, including the luminal surfaces of flexible catheter tubes. This strategy has the potential to be general; we anticipate that the materials, strategies, and concepts reported here will enable new approaches to the design of slippery surfaces with improved anti-fouling properties and open the door to new applications of slippery liquid-infused materials that host or promote the release of a variety of other active agents.
Rat Serum Carboxylesterase (1995)

Multiple forms of carboxylesterase have been identified in rat liver, and five carboxylesterases (designated hydrolases A, B, C, S, and egasyn) have been cloned. Hydrolases A, B, C, and egasyn all have a C-terminal consensus sequence (HXEL) for retaining proteins in the endoplasmic reticulum, and these carboxylesterases are found in rat liver microsomes. In contrast, hydrolase S lacks this C-terminal consensus sequence and is presumed to be secreted. In order to test this hypothesis, a polyclonal antibody was raised against recombinant hydrolase S from cDNA-directed expression in Escherichia coli. In addition to hydrolases A, B, and C (57-59 kDa), this antibody recognized a 67-kDa protein in rat liver microsomes and a 71-kDa protein in rat serum. The 71-kDa protein detected in rat serum was also detected in the extracellular medium from primary cultures of rat hepatocytes. Non-denaturing gel electrophoresis with staining for esterase activity showed that a serum carboxylesterase comigrated with the 71-kDa protein. Immunoprecipitation of the 71-kDa enzyme from rat serum decreased esterase activity toward 1-naphthylacetate and para-nitrophenylacetate. The 71-kDa protein immunoprecipitated from rat serum had an N-terminal amino acid sequence identical to that predicted from the cDNA encoding hydrolase S, providing further evidence that hydrolase S is synthesized in and secreted by the liver. The levels of the 67-kDa protein in rat liver microsomes and the levels of the 71-kDa protein in rat serum were co-regulated. Deglycosylation of microsomes and serum converted the 67- and 71-kDa proteins to a 58-kDa peptide, which matches the molecular mass calculated from the cDNA for hydrolase S. These results suggest that the 67-kDa protein in liver microsomes is a precursor form of hydrolase S that undergoes further glycosylation before being secreted into serum. In rats, liver appears to be the only source of hydrolase S because no mRNA encoding hydrolase S could be detected in several extrahepatic tissues. Serum carboxylesterases have been found to play an important role in lipid metabolism and detoxication of organophosphates, therefore, the secretion of hydrolase S and the modulation of its expression by xenobiotics may have physiological as well as toxicological significance.
Protein arrays: The current state‐of‐the‐art (2003)

The completion of projects for sequencing whole genomes such as those of human, Saccaromyces cerevisiae and Caenorhabditis elegans has led to a rapid increase in the availability of genetic information. The technology by which such information is acquired is having a major impact on the way we think about analysing the RNA and protein products of the gene transcription. Transcriptome analysis has, via microarray technology, managed to achieve a near genomic scale quantitative analysis of mRNA levels. Several other technologies such as quantitative reverse transcriptase polymerase chain reaction and representational differential analysis are also available for analysing gene products. Traditionally, protein analysis has been performed by assaying one particular protein at a time, with very little parallel analysis. As protein function is a direct consequence of the protein product of the gene and as mRNA levels do not always correlate well with protein, it is desirable to analyse the entire protein complement of a cell etc. on a similar scale to mRNA. Despite the clear interest in analysing the expression, structure and function of proteins at a genomic scale, they have proven less amenable to such generic, high-throughput approaches. This review highlights the current thinking in the area of proteome analysis and considers the potential for future technology development in the area of protein arrays.
c-Myc is essential for vasculogenesis and angiogenesis during development and tumor progression (2002)

c-Myc promotes cell growth and transformation by ill-defined mechanisms. c-myc(-/-) mice die by embryonic day 10.5 (E10.5) with defects in growth and in cardiac and neural development. Here we report that the lethality of c-myc(-/-) embryos is also associated with profound defects in vasculogenesis and primitive erythropoiesis. Furthermore, c-myc(-/-) embryonic stem (ES) and yolk sac cells are compromised in their differentiative and growth potential. These defects are intrinsic to c-Myc, and are in part associated with a requirement for c-Myc for the expression of vascular endothelial growth factor (VEGF), as VEGF can partially rescue these defects. However, c-Myc is also required for the proper expression of other angiogenic factors in ES and yolk sac cells, including angiopoietin-2, and the angiogenic inhibitors thrombospondin-1 and angiopoietin-1. Finally, c-myc(-/-) ES cells are dramatically impaired in their ability to form tumors in immune-compromised mice, and the small tumors that sometimes develop are poorly vascularized. Therefore, c-Myc function is also necessary for the angiogenic switch that is indispensable for the progression and metastasis of tumors. These findings support the model wherein c-Myc promotes cell growth and transformation, as well as vascular and hematopoietic development, by functioning as a master regulator of angiogenic factors.
Cooperative Molecular Motors (1995)

We present a simple stochastical model for motor molecules that cooperate in large groups. This model could apply for actin-myosin motors in muscles and for motility assays with a high concentration of motor molecules. We calculate the dependence of the velocity on the applied force as a function of ATP concentration and show the existence of a dynamical phase transition allowing for spontaneous directed motion even if the system is spatially symmetric. In the symmetric case, the problem is isomorphous to a paramagnet-ferromagnet transition, in the asymmetric case to a liquid-vapor transition.
Interaction of Felbamate with Several Other Antiepileptic Drugs Against Seizures Induced by Maximal Electroshock in Mice (1993)

The anticonvulsant effects of felbamate (FBM) alone or in combination with phenytoin (PHT), carbamazepine (CBZ), valproate (VPA), or phenobarbital (PB) were investigated against maximal electroshock (MES) seizures in mice. Nonprotective doses of the prototype antiepileptic drugs (AEDs) enhanced the protective effects of FBM against electrically induced seizures, as shown by significant reduction of FBM ED50 values. Toxicity as determined by rotorod test was not significantly potentiated, however, and the protective index (PI = TD50/ED50) of FBM was increased by > 100% for each AED interaction. The increase in anticonvulsant potency of FBM after its combination with nonprotective doses of AEDs could not be accounted for by a pharmacokinetic mechanism.
Regulation of bone matrix protein expression and induction of differentiation of human osteoblasts and human bone marrow stromal cells by bone morphogenetic protein‐2 (1997)

We have examined the effects of BMP-2 on the expression of bone matrix proteins in both human bone marrow stromal cells (HBMSC) and human osteoblasts (HOB) and their proliferation and mineralization. Both HBMSC and HOB express BMP-2/-4 type I and type II receptors. Treatment of these two cell types with BMP-2 for 4 weeks in the presence of β-glycerophosphate and ascorbic acid results in mineralization of their matrix. BMP-2 increases the mRNA level and activities of alkaline phosphatase and elevates the mRNA levels and protein synthesis of osteopontin, bone sialoprotein, osteocalcin, and α1(I) collagen in both cell types. Whereas the mRNA level of decorin is increased, the mRNA concentration of biglycan is not altered by BMP-2. No effect on osteonectin is observed. The effect of BMP-2 on bone matrix protein expression is dose dependent from 25 to 100 ng/ml and is evident after 1–7 days treatment. In the presence of BMP-2, proliferation of HBMSC and HOB is decreased under either serum-free condition or in the presence of serum. Thus, BMP-2 has profound effects on the proliferation, expression of most of the bone matrix proteins and the mineralization of both relatively immature human bone marrow stromal preosteoblasts and mature human osteoblasts. J. Cell. Biochem. 67:386–398, 1997. © 1997 Wiley-Liss, Inc.
State of the Art: Automated Black-Box Web Application Vulnerability Testing (2010)

Black-box web application vulnerability scanners are automated tools that probe web applications for security vulnerabilities. In order to assess the current state of the art, we obtained access to eight leading tools and carried out a study of: (i) the class of vulnerabilities tested by these scanners, (ii) their effectiveness against target vulnerabilities, and (iii) the relevance of the target vulnerabilities to vulnerabilities found in the wild. To conduct our study we used a custom web application vulnerable to known and projected vulnerabilities, and previous versions of widely used web applications containing known vulnerabilities. Our results show the promise and effectiveness of automated tools, as a group, and also some limitations. In particular, "stored" forms of Cross Site Scripting (XSS) and SQL Injection (SQLI) vulnerabilities are not currently found by many tools. Because our goal is to assess the potential of future research, not to evaluate specific vendors, we do not report comparative data or make any recommendations about purchase of specific tools.
Responsive Micromolds for Sequential Patterning of Hydrogel Microstructures (2011)

Microscale hydrogels have been shown to be beneficial for various applications such as tissue engineering and drug delivery. A key aspect in these applications is the spatial organization of biological entities or chemical compounds within hydrogel microstructures. For this purpose, sequentially patterned microgels can be used to spatially organize either living materials to mimic biological complexity or multiple chemicals to design functional microparticles for drug delivery. Photolithographic methods are the most common way to pattern microscale hydrogels but are limited to photocrosslinkable polymers. So far, conventional micromolding approaches use static molds to fabricate structures, limiting the resulting shapes that can be generated. Herein, we describe a dynamic micromolding technique to fabricate sequentially patterned hydrogel microstructures by exploiting the thermoresponsiveness of poly(N-isopropylacrylamide)-based micromolds. These responsive micromolds exhibited shape changes under temperature variations, facilitating the sequential molding of microgels at two different temperatures. We fabricated multicompartmental striped, cylindrical, and cubic microgels that encapsulated fluorescent polymer microspheres or different cell types. These responsive micromolds can be used to immobilize living materials or chemicals into sequentially patterned hydrogel microstructures which may potentially be useful for a range of applications at the interface of chemistry, materials science and engineering, and biology.
Activated Human T Cells Accomplish MHC Class II Expression Through T Cell-Specific Occupation of Class II Transactivator Promoter III (2002)

Activated human T cells express HLA-DR, HLA-DQ, and HLA-DP on their surface, but the regulation and functioning of MHC class II molecules in T lymphocytes are poorly understood. Because the MHC class II transactivator (CIITA) is essential for MHC class II expression, we have investigated transcriptional activation of CIITA in activated T cells. In this study, we show that in human activated CD4(+) T cells, CIITA promoter III (CIITA-PIII) drives the expression of CIITA. The in vivo genomic footprint analysis revealed activated T cell-specific occupation of CIITA-PIII. Subsequent EMSA analysis of several promoter regions showed differences in banding pattern among activated T cells, naive T cells, primary B cells, and Raji B cells. Activating response element (ARE)-1 is shown to interact with the acute myeloid leukemia 2 transcription factor in nuclear extracts derived from both T and B cells. Interestingly, the acute myeloid leukemia 3 transcription factor was bound in nuclear extracts of T cells only. The ARE-2 sequence is able to bind CREB/activating transcription factor family members in both T and B cells. In addition, a yet unidentified Ets family member was found to interact with site C in activated T cells, whereas in B cells site C was bound by PU.1 and Pip/IFN regulatory factor 4/IFN consensus sequence binding protein for activated T cells. In Jurkat T cells, both ARE-1 and ARE-2 are crucial for CIITA-PIII activity, similar to Raji B cells. The differential banding pattern in in vivo genomic footprinting and transcription factor binding at the ARE-1 and site C between T cells and B cells probably reflects differences in CIITA-PIII activation pathways employed by these cell types.
Protein microchips in biomedicine and biomarker discovery (2007)

Protein microarray technology is of high recent interest, especially for generating confirmatory and complementary information for transcriptomic studies. In this paper, the advantages, technical limitations, main application fields, and some early results of protein microarrays are reviewed. Today protein microchip technology is mostly available in the form of printed glass slides, bioaffinity surfaces, and tissue microarray (TMA)-based techniques. The advantages of glass slide-based microchips are the simplicity of their application and their relatively low cost. Affinity surface-based protein chip techniques are applicable to minute amounts of starting material (< 1 microg), but interrogation of these chips requires expensive instrumentation, such as mass spectrometers. TMAs are useful for parallel testing of antibody specificities on a broad range of histological specimens in a single slide. Protein microarrays have been successfully implemented for serum tumor marker profiling, cell physiology studies, and mRNA expression study verification. Some of the bottlenecks of the technology are protein instability, problems with nonspecific interactions, and the lack of amplification techniques to generate sufficient amounts of the lower abundance proteins. In spite of the current difficulties, protein microchips are envisioned to be available for routine biomedical and diagnostic applications provided that the ongoing technological developments are successful in improving sensitivity, specificity, and reducing costs.
PEROXYNITRITE IS INVOLVED IN THE PATHOGENESIS OF THE VASCULAR CONTRACTILE AND ENERGETIC FAILURE IN ENDOTOXIC SHOCK (1996)

Szabó, C.1; Zingarelli, B.1; O'Connor, M.1; Day, B. J.2; Crapo, J. D.2; Salzman, A. L.1 Author Information
Widely-linear beamforming and RF impairment suppression in massive antenna arrays (2013)

In this paper, the sensitivity of massive antenna arrays and digital beamforming to radio frequency (RF) chain in-phase quadrature-phase (I/Q) imbalance is studied and analyzed. The analysis shows that massive antenna arrays are increasingly sensitive to such RF chain imperfections, corrupting heavily the radiation pattern and beamforming capabilities. Motivated by this, novel RF-aware digital beamforming methods are then developed for automatically suppressing the unwanted effects of the RF I/Q imbalance without separate calibration loops in all individual receiver branches. More specifically, the paper covers closed-form analysis for signal processing properties as well as the associated radiation and beamforming properties of massive antenna arrays under both systematic and random RF I/Q imbalances. All analysis and derivations in this paper assume ideal signals to be circular. The well-known minimum variance distortionless response (MVDR) beamformer and a widely-linear (WL) extension of it, called WL-MVDR, are analyzed in detail from the RF imperfection perspective, in terms of interference attenuation and beamsteering. The optimum RF-aware WL-MVDR beamforming solution is formulated and shown to efficiently suppress the RF imperfections. Based on the obtained results, the developed solutions and in particular the RF-aware WL-MVDR method can provide efficient beamsteering and interference suppressing characteristics, despite of the imperfections in the RF circuits. This is seen critical especially in the massive antenna array context where the cost-efficiency of individual RF chains is emphasized.
Resolution of hypervariable regions in T-cell receptor beta chains by a modified Wu-Kabat index of amino acid diversity. (1990)

The Wu-Kabat variability coefficient is a well-established descriptor of the susceptibility of an amino acid position to evolutionary replacements. It conveniently highlights stretches of accentuated amino acid variation that, for example, in an antibody molecule account for most of the antigen contacts (complementarity-determining regions). Diverse opinion are held as to why the index yields unclear results when applied instead to the polypeptide sequences of the T-cell antigen receptor. We show that a simple modification enhances the resolving power of the index by increasing the weight on the frequency distribution of the amino acids in the formula. Application of the improved index to T-cell receptor beta chains highlights four unambiguous hypervariable regions, three of which are positioned similar to immunoglobulin complementarity-determining regions along the chain. In a Fab-like three-dimensional model of the T-cell receptor, the four hypervariable regions coincide with the four loops on the surface of the domain and form a contiguous area available for binding.
Excellent electrical characteristics of lanthanide (Pr, Nd, Sm, Gd, and Dy) oxide and lanthanide-doped oxide for MOS gate dielectric applications (2002)

In this paper, we report on an investigation of the electrical characteristics of various amorphous lanthanide oxides prepared by e-beam evaporation. Excellent electrical characteristics were found for the amorphous lanthanide oxide including a high oxide capacitance, low leakage current, and high thermal stability. We also confirmed the excellent thermal stability and mobility characteristics of lanthanide silicate (PrSi/sub x/O/sub y/). In addition, lanthanide-doped HfO/sub 2/ also exhibited a significant reduction in leakage current at the same equivalent oxide thickness.