gebhart/patrepeval huggingface dataset:
E105 Exploring the role of conformational heterogeneity in the V1/V2 domain of HIV-1 gp120 on the immunological properties of Env immunogens (2013)

The importance of the V1/V2 domain as a target in HIV-1 vaccines has been shown by demonstrations that epitopes to potently neutralizing antibodies are localized to this region, that binding between a site in V1/V2 and 4 7 receptors facilitates infection of primary CD4-positive T cells, and that the presence of antibodies binding to a fusion glycoprotein expressing the isolated V1/V2 domain correlates with protection in the RV144 vaccine trial. The native V1/V2 domain of the CaseA2 clade B Env sequence was expressed by fusion to the C-terminus of a 273 amino acid fragment of the MuLV gp70 domain. This fusion glycoprotein was characterized by SDS-PAGE after radioimmunoprecipitation with a panel of mAbs directed against V1/V2-specific epitopes, and by MALDI-TOF analysis of immunologically fractionated forms. SDS-PAGE analysis of this protein after deglycosylation under non-reducing conditions revealed the presence of a closely migrating doublet, and the two forms reacted differentially with a panel of V1/V2-specific antibodies and various polyclonal sera. Mass-spec analysis of the immunologically fractionated forms suggested that these consisted of different disulfide-linked conformers. These studies demonstrate a conformational heterogeneity in the V1/V2 domain that is due to alternative disulfide bonding patterns. These conformations profoundly affect the immunoreactivity of this region, and will presumably influence their immunogenicity as well. This structural heterogeneity may impact the immunogenicity of standard Env-based immunogens, and methods for resolving this heterogeneity may improve the efficacy of induction of relevant antibodies to this region by HIV Env vaccines.
Mass‐scale high‐throughput multiplex polymerase chain reaction for human platelet antigen single‐nucleotide polymorphisms screening of apheresis platelet donors (2011)

BACKGROUND: Treatment with human platelet antigen (HPA)‐matched platelets (PLTs) is the optimal therapy for bleeding secondary to neonatal alloimmune thrombocytopenia. Recent advances in high‐throughput DNA‐based blood group and PLT antigen genotyping have made it possible to screen plateletpheresis donors for potential HPA‐matched PLT transfusion. STUDY DESIGN AND METHODS: This prospective study evaluated genomic DNA from plateletpheresis donors for single‐nucleotide polymorphisms (SNPs) associated with HPA‐1, ‐2, ‐3, ‐4, ‐5, and ‐15 to determine whether high‐throughput multiplex genomic DNA PCR and oligonucleotide extension technology can be used for mass‐scale PLT antigen genotyping. Genotyping using SNP technology was confirmed using sequence‐specific polymerase chain reaction (SSP‐PCR). RESULTS: Of the 748 donors screened, 277 were found to be negative for antigens implicated in alloimmune thrombocytopenia. In addition, two donors were homozygous for HPA‐1b/b and ‐2b/b, six donors for HPA‐1b/b and ‐3b/b, one for HPA‐2b/b and ‐3b/b, one for HPA‐1b/b and ‐5b/b, 10 for HPA‐1b/b and ‐15 b/b, four for HPA‐5b/b and ‐15b/b, and one for HPA‐2b/b and ‐15b/b. Retesting using SSP‐PCR was conducted for 60 donors. Discrepant results occurred between SNP and SSP‐PCR in less than 20% of samples for HPA‐1b/1b/HPA‐3b/3b, HPA‐5b/5b, and HPA‐15b/b. DISCUSSION: High‐throughput multiplex PCR SNP and confirmatory molecular genotyping are useful for mass‐scale screening of apheresis PLT donors to provide antigen‐negative genotypes. Refinements to mass‐scale multiplex analysis technology would reduce further the confirmatory testing needed.
Metal organic frameworks with exceptional gas storage capacity (2010)

The challenges surrounding the realization of viable hydrogen or methane storage by adsorption means are described. We have employed metal-organic frameworks due to their exceptional surface areas. Advancement of gas storage requires the development of metal-organic frameworks based on light metals so that the weight percentage of gas stored may be increased, and the operating temperature must be increased by control of the potential energy for adsorption well depth. We describe possible solutions to each of these challenges.
A 1.5 μm GaInNAs(Sb) laser grown on GaAs by MBE (2003)

Summary form only given. Ever increasing bandwidth demands have lead to the commercialization of lasers emitting in the range 1.3-1.55 /spl mu/m. It was not until the recent discovery of the large bowing parameter of the GaInNAs quaternary that a suitable active layer was found. Recent work has focused on increasing the indium concentration through the use of antimony, both as a constituent and a surfactant. The results of a photoluminescence (PL) study are summarized. We have found that it is possible to maintain high PL intensity for samples out to 1.6 /spl mu/m.
Purification of Influenza Virus Polypeptide Antigens and Studies of their Immunogenicity and Toxicity (1975)

Abstract : A technique for the isolation and purification of the influenza viral polypeptides with special reference to the neuraminidase and hemagglutinin glycoprotein antigens has been improved. A very important finding has been that biologically active and antigenically functional polypeptides can be isolated from influenza vaccine batches which provide a virtually unlimited source of material. Using authenticated vaccine as a starting material prepared in accord with BOB specifications anticipates the use and acceptance of the purified antigens as vaccines. A modification of the Weber and Kuter technique for the renaturation of enzymes has made it possible to remove residual SDS from the hemagglutinin polypeptides with restoration of both biologic and immunogenic activity. Removal of SDS has permitted the beginning of automated amino acid sequence analysis of the viral hemagglutinin. Purification of specific antibodies to the hemagglutinin and its cleavage products has been achieved by immobilization of the antigens on agarose columns. Using another approach, the hemagglutinin and neuraminidase antigens have been isolated together by extraction following Triton X-100 disruption.
Low-noise multistage avalanche photodetector (1979)

We propose a multistage compound semiconductor avalanche detector for low-noise amplification of photoelectronic signals. In this device, the junctions where amplification takes place are separated by heterojunctions, which act as traps for one species of charge carriers. We demonstrate by a calculation that such a structure will have a substantially improved signal/noise ratio.
Porous functionalised silica particles: a potential platform for biomolecular screening (2005)

Novel, porous, functionalised silica particles have been developed with controlled morphology, which promote covalent attachment of fluorescent dyes which can act as an optical barcode.
Laser-beam annealing of discharge-produced amorphous silicon (1979)

Amorphous silicon films prepared by dc glow discharge of silane on room-temperature substrates darken when exposed to a focused laser beam. The process is primarily thermal, has an activation energy of ∼1 eV, and is accompanied by the desorption of hydrogen. It also affects the etch rate in basic solutions. A bleaching effect, not reported before, is seen at low exposures. All coloration changes are permanent. Possible applications for optical storage of information are discussed.
Performance analysis and validation of the picoJava processor (1999)

In the process of designing high performance microprocessors, architects and designers build processor models at varying levels of abstraction for a range of purposes. Examples of such uses are simulating and verifying the processor, predicting processor performance, and developing operating systems and applications for the processor before silicon is available. Such models can range in complexity from simple analytical performance models in spreadsheet format to the detailed design expressed in a hardware description language (HDL). Other models that fall in between on the range of complexity include instruction-accurate simulators, trace-driven performance simulators, and cycle-accurate simulators. There is usually a trade-off between runtime performance and accuracy while using these models. Developing a large number of models for a processor is an expensive proposition. Beyond the engineering resources to build the initial models, developers must verify each of the models for correctness against the design specification; they must also maintain and update the models as the design evolves. Clearly, a strategy that limits the number of models yet meets the requirements of early software developers, verification engineers, and performance analysts is desirable. During the course of the picoJava processor design, we developed a simple and effective methodology that meets the goals of both accurate performance analysis and design validation. Although we applied this technique to the picoJava processor, the technique can be applied to other processor designs.
The Hexavalent CD40 Agonist HERA-CD40L Induces T-Cell–mediated Antitumor Immune Response Through Activation of Antigen-presenting Cells (2018)

CD40 ligand (TNFSF5/CD154/CD40L), a member of the tumor necrosis factor (TNF) superfamily is a key regulator of the immune system. The cognate receptor CD40 (TNFRSF5) is expressed broadly on antigen-presenting cells and many tumor types, and has emerged as an attractive target for immunologic cancer treatment. Most of the CD40 targeting drugs in clinical development are antibodies which display some disadvantages: their activity typically depends on Fcγ receptor-mediated crosslinking, and depletion of CD40-expressing immune cells by antibody-dependent cellular cytotoxicity compromises an efficient antitumor response. To overcome the inadequacies of antibodies, we have developed the hexavalent receptor agonist (HERA) Technology. HERA compounds are fusion proteins composed of 3 receptor binding domains in a single chain arrangement, linked to an Fc-silenced human IgG1 thereby generating a hexavalent molecule. HERA-CD40L provides efficient receptor agonism on CD40-expressing cells and, importantly, does not require FcγR-mediated crosslinking. Strong activation of NFκB signaling was observed upon treatment of B cells with HERA-CD40L. Monocyte treatment with HERA-CD40L promoted differentiation towards the M1 spectrum and repolarization of M2 spectrum macrophages towards the M1 spectrum phenotype. Treatment of in vitro co-cultures of T and B cells with HERA-CD40L-triggered robust antitumor activation of T cells, which depended upon direct interaction with B cells. In contrast, bivalent anti-CD40 antibodies and trivalent soluble CD40L displayed weak activity which critically depended on crosslinking. In vivo, a murine surrogate of HERA-CD40L-stimulated clonal expansion of OT-I-specific murine CD8 T cells and showed single agent antitumor activity in the CD40 syngeneic MC38-CEA mouse model of colorectal cancer, suggesting an involvement of the immune system in controlling tumor growth. We conclude that HERA-CD40L is able to establish robust antitumor immune responses both in vitro and in vivo.
Gradient Adaptive Image Restoration and Enhancement (2006)

Various methods have been proposed for image enhancement and restoration. The main difficulty is how to enhance the structures uniformly while suppressing the noise without artifacts. In this paper, we tackle this problem in the gradient domain instead of the traditional intensity domain. By enhancing the gradient field, we can enhance the structure uniformly without overshooting at the boundary. Because the gradient field is very sensitive to noise, we apply an orientation-isotropy adaptive filter to the gradient field, suppressing the gradients in the noise regions while enhancing along the object boundaries. Thus we obtain a modulated gradient field, which is usually not integrable. We reconstruct the enhanced image from the modulated gradient field with least square errors by solving a Poisson equation. This method can enhance the object contrast uniformly, suppress the noise with no artifacts, and avoid setting stopping time as in PDE methods. Experiments on noisy images show the efficacy of our method.
Performance optimization of sequential circuits by eliminating retiming bottlenecks (1992)

Retiming is an effective technique to optimize the performance of synchronous sequential circuits. This paper proposes a method to improve the effectiveness of retiming by transforming the sequential circuit. Bottlenecks which prevent retiming to achieve a desired clock period are identified. Conditions to eliminate the retiming bottlenecks are derived. These conditions are satisfied by a process of identifying sub-circuits and satisfying a set of timing constraints on the sub-circuits. The transformed circuit, which satisfies the timing constraints, can be retimed to achieve the desired clock period. If the original circuit has its initial state specified, our method always generates the final circuit with an equivalentinitial state. Experimental results on a variety of sequential benchmark circuits demonstrate significant performance improvement.
Biomolecule separation by steric hindrance using nanofluidic filters (2005)

Micro/nanofluidics technologies can be used to solve toughest challenges in the biomolecule analysis. It is now possible to fabricate nanofluidic channels with the dimension of 30-500 nm, and these nanofluidic structures have been formerly used to separate large DNA molecules where molecular dimension is larger than the nanofluidic filter gap size. In this work, we demonstrate separation of biomolecules (DNA and proteins) that are smaller than the nanofluidic filter gap size. This is possible due to the steric hindrance effect of the biomolecules; the entropy of biomolecules has to be decreased for the molecules to enter the nanofluidic filter, which leads to the free energy barrier for the molecular transport. Double stranded DNA molecules as small as 100 bp approximately 34 nm extended length), as well as SDS-coated proteins have been separated in a nanofluidic channel that has the filter gap thickness between 60-120 nm. This result clearly shows the potential of using nanofluidic filters as a sieving medium for smaller biomolecules such as proteins. Compared with traditional random nanoporous materials such as gel or polymer monolith, nanofluidic channels can be made precisely to have a pre-determined 'pore' size and shape, which allows characterization and optimization of biomolecule separation process.
Long‐term cannabidiol treatment for seizures in patients with tuberous sclerosis complex: An open‐label extension trial (2021)

In patients with TSC, long-term add-on CBD treatment was well tolerated and sustainably reduced seizures through 48 weeks, with most patients/caregivers reporting global improvement.
Interferometric quantum wire switch (1997)

A device topology is proposed and analyzed which is based upon quantum wire components. The device controls the conductance between an input line and a pair of output lines by varying the phase shift around a quantum wire ring connecting the external nodes. The phase shift is controlled using a simple electron stub tuner. Switching characteristics with efficiencies greater than 95% for certain geometries have been calculated.
Process for separating fission product molybdenum from an irradiated target material. [thermal chromatography] (1978)

A process for the separation and collection of molybdenum-99 from an irradiated uranium-containing target material utilizes thermal chromatographic separation. The irradiated target material containing the molybdenum-99 is heated in an oxidizing atmosphere to form an oxidized target material and gaseous molybdenum-99 trioxide. The gaseous molybdenum-99 trioxide is carried by the oxidizing atmosphere along with other vaporized materials to a cooling zone for progressive condensation and collection of the molybdenum-99 trioxide and the other materials in the form of separate deposits.
Automatically Reducing Repetitive Synchronization with a Just-in-Time Compiler for Java (2005)

We describe an automatic technique to remove repetitive synchronization in Java/spl trade/ programs by removing selected MONITORENTER/EXIT operations. Once these operations are removed, parts of a method that were not originally locked become protected by a lock. If it is unsafe to synchronize the code between the original locked regions, however, the code is not transformed. Scalability is also protected by not allowing a lock to be held for a significantly longer time than it would be held in the original program code. Our base algorithm improved the throughput of the industry-standard SPECjbb2000 benchmark by 2% to 5% for three different platforms. We also describe an extension to our algorithm to better handle virtual calls, which are prevalent in Java code, and this extension provides up to a further 5% improvement. Our computationally efficient algorithm was implemented and evaluated in a production Just-In-Time (JIT) compiler.
Wide limited switch dynamic logic circuit implementations (2006)

Wide circuit implementation of limited switch dynamic logic (LSDL), a high performance logic circuit, with a modified pseudo-nMOS style load has been studied in this paper. A conventional two levels of 8-way mux implementation and a wide 64-way mux implementation of the 64-bit rotator circuit were used in the analysis. The resultant wide circuit implementation consumes less power, maintains robustness to noise and power rail bounce and reduces the pipeline depth to a single stage. The effect of process variation on circuit performance is evaluated. Based on the analysis, a new circuit style known as hybrid LSDL has been proposed.
Rapid evaluation of fresh chicken meat quality by electronic nose (2018)

A prototype of electronic nose (e-nose) with the gas sensor system for evaluation of fresh chicken meat freshness was developed. In this paper a rapid, simple and not expensive system for fresh chicken meat spoilage detection was investigated that provides objective and reliable results. Quality changes in fresh chicken meat during storage were monitored by the metal oxide sensor (MOS) system and compared with the results of traditional chemical measurements. Gas sensor selection was tested for evaluation of volatile fatty acids (VFA) mainly representing meat spoilage.The study demonstrated that a correlation coefficient (R2 = 0.89) between e-nose signals and traditional chemical method was high. These results prove that the developed e-nose prototype has a potential for assessing fresh chicken meat freshness and allows discriminating meat into fresh, unsafe and spoiled.
Single‐Crystal Gallium Nitride Nanotubes. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
ChemInform Abstract: SYNTHESIS AND ANTIHYPERTENSIVE PROPERTIES OF NEW 3‐HYDRAZINOPYRIDAZINE DERIVATES (1975)

Abstract 3,6‐Dichlor‐pyridazin (I) reagiert unter Chloraustausch zu den Amino‐chlor‐pyridazinen (II), die zu den Hydrazinen (III) und (IV) umgesetzt werden.
Univalent Binding of the Cry1Ab Toxin of <i>Bacillus thuringiensis</i> to a Conserved Structural Motif in the Cadherin Receptor BT-R<sub>1</sub> (2007)

The Cry1Ab toxin produced by Bacillus thuringiensis (Bt) exerts insecticidal action upon binding to BT-R1, a cadherin receptor localized in the midgut epithelium of the tobacco hornworm Manduca sexta [Dorsch, J. A., Candas, M., Griko, N. B., Maaty, W. S., Midboe, E. G., Vadlamudi, R. K., and Bulla, L. A., Jr. (2002) Cry1A toxins of Bacillus thuringiensis bind specifically to a region adjacent to the membrane-proximal extracellular domain of BT-R1 in Manduca sexta: involvement of a cadherin in the entomopathogenicity of Bacillus thuringiensis, Insect Biochem. Mol. Biol. 32, 1025-1036]. BT-R1 represents a family of invertebrate cadherins whose ectodomains (ECs) are composed of multiple cadherin repeats (EC1 through EC12). In the present work, we determined the Cry1Ab toxin binding site in BT-R1 in the context of cadherin structural determinants. Our studies revealed a conserved structural motif for toxin binding that includes two distinct regions within the N- and C-termini of EC12. These regions are characterized by unique sequence signatures that mark the toxin-binding function in BT-R1 as well as in homologous lepidopteran cadherins. Structure modeling of EC12 discloses the conserved motif as a single broad interface that holds the N- and C-termini in close proximity. Binding of toxin to BT-R1, which is univalent, and the subsequent downstream molecular events responsible for cell death depend on the conserved motif in EC12.
PK20, a New Opioid-Neurotensin Hybrid Peptide That Exhibits Central and Peripheral Antinociceptive Effects (2010)

The opioid-neurotensin hybrid analogue PK20, in which opioid and neurotensin pharmacophores overlap partially, expresses high antinociceptive tail-flick effects after central as well as peripheral applications.
The bryostatins inhibit growth of B16/F10 melanoma cells in vitro through a protein kinase C-independent mechanism: dissociation of activities using 26-epi-bryostatin 1. (1996)

Bryostatin 1 is a potential cancer chemotherapeutic agent in Phase II clinical trials, with positive responses observed for malignant melanoma, among other tumors. The bryostatins are known to be potent ligands for protein kinase C (PKC), functioning as partial antagonists. In the present study, we explore the mechanism by which the bryostatins inhibit growth to B16/F10 mouse melanoma cells in vitro. Three experimental approaches suggest that the growth inhibition is independent of PKC. First, we characterized in detail the translocation and down-regulation of the PKC isozymes alpha, delta, and epsilon in response to phorbol ester and bryostatin 1 in these cells. Although the dose-response curves obtained for the translocation-activation of PKC isozymes showed good correlation with the growth-enhancing activity of phorbol 12-myristate 13-acetate, for no PKC isozyme was there a good correlation with the growth-inhibitory activity of bryostatin 1. Second, inhibition PKC, inhibited the growth of the B16/F10 melanoma cell lines with potency similar to that of bryostatin 1. We confirmed here that 26-epi-bryostatin 1 showed 60-fold reduced affinity for PKC and 30-60-fold reduced potency to translocate and downregulate PKC isozymes compared with bryostatin 1. We presumed that the principal toxicity of bryostatin 1 reflects its interaction with PKC, and we would thus predict that epi-bryostatin 1 would be less toxic. Indeed, we found at least 10-fold reduced toxicity of 26-epi-bryostatin 1 in C57BL/6 mice compared with bryostatin 1. We conclude that the growth inhibition of the bryostatins, at least in this system, does not result from interaction with PKC. As exemplified by 26-epi-bryostatin 1, this insight permits the design of analogues with comparable growth inhibition to bryostatin 1 but with reduced toxicity.