gebhart/patrepeval huggingface dataset:
Protective Immunity to SIV Challenge Elicited by Vaccination of Macaques with Multigenic DNA Vaccines Producing Virus-Like Particles (2004)

We utilized SIV(mne) infection of Macaca fascicularis to assess the efficacy of DNA vaccination alone, and as a priming agent in combination with subunit protein boosts. All SIV(mne) structural and regulatory genes were expressed using the human cytomegalovirus Immediate Early-1 promoter in plasmids that directed the formation of virus-like particles in vitro. Macaques (n = 4) were immunized intradermally and intramuscularly four times over 36 weeks with 3 mg plasmid DNA. A second group (n = 4) received two DNA priming inoculations followed by two intramuscular boosts consisting of 250 microg recombinant Env gp160 and 250 microg recombinant Gag-Pol particles in MF-59 adjuvant. These regimens elicited modest cellular immunity prior to challenge. Humoral immune responses to Env gp160 were elicited and sustained by both vaccine protocols, and as expected antibody titers were higher in the protein subunit-boosted animals. Neutralizing antibodies prior to challenge were measurable in two of four subunit-boosted macaques. The two vaccine regimens elicited comparable helper T cell responses at the time of challenge. Vaccinees and mock-immunized controls (n = 4) were challenged intrarectally at week 38 with uncloned SIV(mne). Following challenge all macaques became infected, but both vaccine regimens resulted in reduced peak virus loads (p = 0.07) and significantly improved maintenance of peripheral CD4(+) T cell counts postchallenge (p = 0.007, DNA alone and p = 0.01, all vaccinees). There was no significant difference between the two vaccine groups in levels of plasma viremia or maintenance of CD4(+) T cell counts postchallenge.
Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae (1998)

We present the complete inventory of currently recognized and putative transporters encoded within the genome of Saccharomyces cerevisiae. These 258 transporters are classified into 42 families according to phylogenetic and substrate specificity criteria. Twelve of these yeast families are found only in eukaryotic organisms, and four are so far unique to yeast. Putative yeast-specific families transport heavy metals, arsenite and calcium. The phylogenetic analyses reported allow classification of 139 functionally uncharacterized yeast transporters into families of known functions. The relative proportions of yeast transporters specific for different classes of substrates differ only slightly from those reported for Escherichia coli. However, the ratio of secondary transporters (uniporters, cation symporters and antiporters) to primary ATP-driven transporters is much higher for yeast than for bacteria.
Sickle cell disease in childhood: Part II. Diagnosis and treatment of major complications and recent advances in treatment. (2000)

Treatment advances over the past 25 years have significantly decreased morbidity and mortality in children with sickle cell disease. Aggressive management of fever, early diagnosis of acute chest syndrome, judicious use of transfusions and proper treatment of pain can improve quality of life and prognosis for these children. Prophylactic hydroxyurea therapy has been shown to reduce the incidence and severity of pain crises in adults with sickle cell disease and has been effective in limited studies conducted in children. Research into stem cell transplantation provides hope that a cure for sickle cell disease may be possible.
ATRP-mediated continuous assembly of polymers for the preparation of nanoscale films (2011)

The continuous assembly of polymers (CAP) via atom transfer radical polymerisation (ATRP) is reported as an efficient approach for the preparation of dense, cross-linked, nanoscale engineered films as surface coatings, hollow capsules and replica particles. These films can be reinitiated to allow the preparation of thicker films without loss of film growth efficiency while maintaining similar film density.
Low-latency communication on the IBM RISC system/6000 SP (1996)

The IBM SP is one of the most powerful commercial MPPs, yet, in spite of its fast processors and high network bandwidth, the SP's communication latency is inferior to older machines such as the TMC CM-5 or Meiko CS-2. This paper investigates the use of Active Messages (AM) communication primitives as an alternative to the standard message passing in order to reduce communication overheads and to offer a good building block for higher layers of software. The first part of this paper describes an implementation of Active Messages (SP AM) which is layered directly on top of the SP's network adapter (TB2). With comparable bandwidth, SP AM's low overhead yields a round-trip latency that is 40% lower than IBM MPL's. The second part of the paper demonstrates the power of AM as a communication substrate by layering Split-C as well as MPI over it. Split-C benchmarks are used to compare the SP to other MPPs and show that low message overhead and high throughput compensate for SP's high network latency. The MPI implementation is based on the freely available MPICH version and achieves performance equivalent to IBM's MPI-F on the NAS benchmarks.
The Autoactivation of Trypsinogen (1971)

The ability of trypsinogen to catalyze its own activation was studied at pH 8.1 in the presence of Ca++ ions. The lag phase portion of the classical S-shaped curve of activation was shortened by increasing the trypsinogen concentration but was extended by pretreatment of the zymogen with diisopropyl fluorophosphate or soybean trypsin inhibitor. Despite these pretreatments, however, full activation was achieved. In confirmation of the proposed catalytic activity of trypsinogen, acetyltrypsinogen, which cannot be activated by trypsin or acetyltrypsin, was able to activate chymotrypsinogen at a rate about 10-5 that of trypsin and to hydrolyze p-toluenesulfonyl arginine methyl ester at a very slow rate. Pretreatment of the acetyltrypsinogen with diisopropyl fluorophosphate and soybean trypsin inhibitor did not affect the rate at which it carried out these two reactions, thus excluding the presence of trypsin or acetyltrypsin. The conclusion is drawn that the activities observed were not due to contamination of the zymogen preparations with active enzyme but were due to an activity inherent in the zymogens. The S-shaped curve of trypsinogen activation is now interpreted as two separate phases: a slow initial formation of trypsin by self-activation of the zymogen, followed by a rapid acceleration of the reaction due to catalysis by the product, trypsin.
Selectivity of Potentiometric Ion Sensors (2000)

Selectivities of solvent polymeric membrane ion-selective electrodes (ISEs) are quantitatively related to equilibria at the interface between the sample and the electrode membrane. However, only correctly determined selectivity coefficients allow accurate predictions of ISE responses to real-world samples. Moreover, they are also required for the optimization of ionophore structures and membrane compositions. Best suited for such purposes are potentiometric selectivity coefficients as defined already in the 1960s. This paper briefly reviews the basic relationships and focuses on possible biases in the determination of selectivity coefficients. The traditional methods to determine selectivity coefficients (separate solution method, fixed interference method) are still the same as those originally proposed by IUPAC in 1976. However, several precautions are needed to obtain meaningful data. For example, errors arise when the response to a weakly interfering ion is also influenced by the primary ion leaching from the membrane. Wrong selectivity coefficients may be also obtained when the interfering agent is highly preferred and the electrode shows counterion interference. Recent advances show how such pitfalls can be avoided. A detailed recipe to determine correct potentiometric selectivity coefficients unaffected by such biases is presented.
[Differentially expressed genes of cell signal transduction associated with benzene poisoning by cDNA microarray]. (2005)

cDNA microarray technology is an effective technique for screening the differentially expressed genes of cell signal transduction. Disorder in cell signal transduction may play certain role in the pathogenic mechanism of benzene poisoning.
Importance of VEGF for breast cancer angiogenesis in vivo: implications from intravital microscopy of combination treatments with an anti-VEGF neutralizing monoclonal antibody and doxorubicin. (2000)

In the present study, we evaluated the effects of a neutralizing anti-Vascular Endothelial Growth Factor (VEGF) mAb, A4.6.1(200 micrograms twice weekly, i.p.), on angiogenesis and growth of tumor spheroids of human breast cancer cell lines (MCF-7, ZR-75 and, SK-BR-3) in nude mice. Furthermore, we investigated if in the presence of effective VEGF blockade, a conventional chemotherapeutic drug (doxorubicin, (5 mg/kg, weekly) could be effective, and if so would there be an additive effect of the combination regimen. Tumor Spheroids were implanted in dorsal skinfold chambers in nude mice. Tumor cells were pre-labeled with a fluorescent vital dye (CMTMR), which allowed the estimation of growth of implanted tumor spheroids. FITC (fluorescein isothiocyanate)-Dextran was used to evaluate formation of neo-vasculature at the tumor site. In control animals all three cell-lines produced extensive neovasculature and there was significant tumor growth throughout the observation period. Treatment with the anti-VEGF mAb caused significant suppression of angiogenic activity for all cell lines, stressing the critical role VEGF plays in breast tumor angiogenesis. Doxorubicin alone reduced the growth rate of MCF-7 cells, but did not significantly affect angiogenesis. Doxorubicin in combination with A4.6.1 resulted in significant tumors regression. Histology indicated that some chambers lacked viable tumor cells at the end of the two week observation period, lending strong support that neutralization of VEGF in combination with conventional cytotoxic agents could be a new innovative treatment regimen for metastatic breast cancer.
Sequence context-specific profiles for homology searching (2009)

Sequence alignment and database searching are essential tools in biology because a protein's function can often be inferred from homologous proteins. Standard sequence comparison methods use substitution matrices to find the alignment with the best sum of similarity scores between aligned residues. These similarity scores do not take the local sequence context into account. Here, we present an approach that derives context-specific amino acid similarities from short windows centered on each query sequence residue. Our results demonstrate that the sequence context contains much more information about the expected mutations than just the residue itself. By employing our context-specific similarities (CS-BLAST) in combination with NCBI BLAST, we increase the sensitivity more than 2-fold on a difficult benchmark set, without loss of speed. Alignment quality is likewise improved significantly. Furthermore, we demonstrate considerable improvements when applying this paradigm to sequence profiles: Two iterations of CSI-BLAST, our context-specific version of PSI-BLAST, are more sensitive than 5 iterations of PSI-BLAST. The paradigm for biological sequence comparison presented here is very general. It can replace substitution matrices in sequence- and profile-based alignment and search methods for both protein and nucleotide sequences.
Status And Progress in DYE and Perovskite Sensitized Solar Cells (2014)

Solar cells using dyes or perovskites as light harvesters supported by mesoscopic oxide films have emerged as credible contenders to conventional p-n junction photovoltaic devices. Separating light absorption from charge carrier transport, dye sensitized mesoscopic solar cells (DSCs) were the first to use a three-dimensional nanocrystalline junction for solar electricity production. The profound knowledge developed during the last 2 decades in DSC technology enabled the stunning rise of perovskite solar cells, and the certified power conversion efficiency (PCE) of perovskite solar cells has reached 17.9% under AM 1.5G 100 mW cm-2 illumination. For the dye sensitized solar cells under ambient and indoor light conditions PCE values up to 26 % have been reached; outperforming silicon based solar cells by a large margin. These features along with excellent long-term stability have fostered first commercial applications, the industrial production of DSC’s attaining presently the MW/year scale.
Social hash partitioner (2017)

We design and implement a distributed algorithm for balanced k -way hypergraph partitioning that minimizes fanout, a fundamental hypergraph quantity also known as the communication volume and ( k - 1)-cut metric, by optimizing a novel objective called probabilistic fanout. This choice allows a simple local search heuristic to achieve comparable solution quality to the best existing hypergraph partitioners. Our algorithm is arbitrarily scalable due to a careful design that controls computational complexity, space complexity, and communication. In practice, we commonly process hypergraphs with billions of vertices and hyperedges in a few hours. We explain how the algorithm's scalability, both in terms of hypergraph size and bucket count, is limited only by the number of machines available. We perform an extensive comparison to existing distributed hypergraph partitioners and find that our approach is able to optimize hypergraphs roughly 100 times bigger on the same set of machines. We call the resulting tool Social Hash Partitioner , and accompanying this paper, we open-source the most scalable version based on recursive bisection.
Preparation of heterodifunctional polyethyleneglycols: Network formation, characterization, and cell culture analysis (2001)

Polyethyleneglycols (PEG) are employed extensively in the development of biomaterials; however, the hydroxyl groups in PEG-diols have very limited chemical activity. We developed a synthesis scheme for a library of heterodifunctional PEG (hPEG) with two distinct terminal moieties to improve the reactivity and physicochemical properties of PEG. hPEG were employed in the formulation of polymer networks with various surface physicochemical properties and utilized to study cell-material interaction. Extensive NMR and HPLC analyses confirmed the chemical structure of hPEG. The hydrophilicity of the polymer network was predominantly dependent on the hPEG concentration with the molecular weight and terminal functional group playing lesser roles. Adherent human fibroblast density on the network remained constant with increasing hPEG concentration in the network formulation but decreased rapidly on networks containing 0.8-1.25 g ml(-1) of hPEG. This trend was independent of the hPEG terminal moiety and molecular weight. No adherent cell was observed on all films containing 2.5 g ml(-1) or more of hPEG.
Self-Ordered, Controlled Structure Nanoporous Membranes Using Constant Current Anodization (2008)

We report a constant current (CC) based anodization technique to fabricate and control structure of mechanically stable anodic aluminum oxide (AAO) membranes with a long-range ordered hexagonal nanopore pattern. For the first time we show that interpore distance (Dint) of a self-ordered nanopore feature can be continuously tuned over a broad range with CC anodization and is uniquely defined by the conductivity of sulfuric acid as electrolyte. We further demonstrate that this technique can offer new degrees of freedom for engineering planar nanopore structures by fine tailoring the CC based anodization process. Our results not only facilitate further understanding of self-ordering mechanism of alumina membranes but also provide a fast, simple (without requirement of prepatterning or preoxide layer), and flexible methodology for controlling complex nanoporous structures, thus offering promising practical applications in nanotechnology.
Partial functional mapping of the human interleukin-8 type A receptor. Identification of a major ligand binding domain. (1993)

We have previously demonstrated that a basic amino acid residue of interleukin (IL)-8, namely Arg-6, is critical for the binding of IL-8 to its receptor. We reasoned that this residue is likely to be poised to directly interact with a counterpart acidic residue on the receptor. To identify this key residue, we systematically mutated to Ala all acidic residues present on the ligand accessible surface of IL-8 receptor type A. Using this strategy, we demonstrate that two residues which are present in extracellular loop 3 of the receptor, namely Glu-275 and Arg-280, are critical for ligand binding. In addition, we show that although Asp-11 is critical for ligand binding, a conservative mutation of Asp-11 to Glu or a substitution of Asp-11 with Lys (the residue found at position 11 in IL-8 receptor type B) does not affect the Kd of the receptor/ligand interaction. These data suggest that Lys-11 recruits a new and favorable interaction with IL-8 (analogous to that of IL-8 receptor type B with IL-8) or that the cavity created by mutating Asp-11 to Ala is particularly deleterious. Finally, we discuss fluorescence-activated cell sorter staining data which support the hypothesis that the N-terminal region and the extracellular loop 3 of the receptor may lie in close proximity of one another and constitute a major binding domain for IL-8.
Characterization of Rat Testicular Peritubular Myoid Cells in Culture: α-Smooth Muscle Isoactin is a Specific Differentiation Marker1 (1989)

In frozen sections of testes from 20-day-old rats, alpha-smooth muscle (SM) isoactin was prominently immunostained in the peritubular tissue and in vascular walls, but not in areas populated by germinal cells, interstitial cells, or Sertoli cells. Peritubular myoid cell (PMC)-enriched preparations were isolated by two different procedures involving our previously published sequential enzymatic treatment ("conventional peritubular cell [PC]-enriched preparation") and by density-gradient purification of PMC from these preparations. The properties of different populations of PMC in culture were compared with respect to plating efficiency, rates of proliferation, and presence of cytoskeletal proteins. PMC, maintained in culture under defined conditions, contained proteins immunoreactive with monoclonal antibodies against alpha-SM isoactin. This was detected by immunostaining and by Western blots of cell extracts subjected to gel electrophoresis. Neither Sertoli cells, skin fibroblasts, bovine endothelial cells, nor glial cells contained alpha-SM isoactin detectable by the above techniques. We report the ontogeny of alpha-SM isoactin in the peritubular tissue of testes at different stages of gonadal development, and show that it is detectable within 8 days after birth. In addition, we describe immunocytochemical changes that occur during culture in various media of PMC prepared from testes of 20-day-old rats. We compare the use of alpha-SM isoactin as a differentiation marker for PMC with the use of desmin in facilitating the identification of PMC, and in following alterations in phenotype during culture in various culture media. Data presented demonstrate that about 81% of cells in the "conventional PC-enriched preparation," and about 94% of cells in the more purified populations of PMC were positive for alpha-SM isoactin in cells maintained in culture for 18 h after plating. These same PMC also were shown to express vimentin and plasminogen activator inhibitor, type 1. We conclude that alpha-SM isoactin is an excellent specific marker for PMC in seminiferous tubules and in culture.
Identification of the Aggregation Pheromone of the Brown-Winged Green Bug, Plautia stali SCOTT (Heteroptera: Pentatomidae) (1996)

Identification of the aggregation pheromone responsible for the aggregation phenomena of the brown-winged green bug, plautia stali SCOTT (Heteroptera: Pentatomidae) was attempted. Volatiles collected from adult males which attracted adults showed attraction activity under field conditions. Volatiles were then collected from a total of 180, 000 adult males and the activity of the fractionated samples was field tested using water pan traps. A mixture of hexane and 5% ether in hexane fractions from Florisil LC showed attraction activity, and this was further purified with HPLC and GC. By GC-MS and NMR analysis (COSY), the chemical structure of the active compound was identified as methyl (E, E, Z)-2, 4, 6-decatrienoate. The attraction activity of the synthesized compound of this structure was confirmed by field tests.
Multidrug Resistance Phosphoglycoprotein (ABCB1) in the Mouse Placenta: Fetal Protection1 (2005)

The multidrug resistance phosphoglycoprotein ATP-binding cassette subfamily B (ABCB1) actively extrudes a range of structurally and functionally diverse xenobiotics as well as glucocorticoids. ABCB1 is present in many cancer cell types as well as in normal tissues. Although it has been localized within the mouse placenta, virtually nothing is known about its regulation. In the mouse, two genes, Abcb1a and Abcb1b, encode ABCB1. We hypothesized that there are changes in placental Abcb1a and Abcb1b gene expression and ABCB1 protein levels during pregnancy. Using in situ hybridization, we demonstrated that Abcb1b mRNA is the predominant placental isoform and that there are profound gestational changes in the expression of both Abcb1a and Abcb1b mRNA. Placentas from pregnant mice were analyzed between Embryonic Days (E) 9.5 and 19 (term approximately 19.5d). Abcb1b mRNA was detected in invading trophoblast cells by E9.5, peaked within the placental labyrinth at E12.5, and then progressively decreased toward term (P < 0.0001). Abcb1a mRNA, although lower than that of Abcb1b at midgestation, paralleled changes in Abcb1b mRNA. Changes in Abcb1 mRNA were reflected by a significant decrease in ABCB1 protein (P < 0.05). A strong correlation existed between placental Abcb1b mRNA and maternal progesterone concentrations, indicating a potential role of progesterone in regulation of placental Abcb1b mRNA. In conclusion, there are dramatic decreases in Abcb1a and Abcb1b mRNA and in ABCB1 at the maternal-fetal interface over the second half of gestation, suggesting that the fetus may become increasingly susceptible to the influences of xenobiotics and natural steroids in the maternal circulation.
THE GENE STRUCTURE AND REPLICATION OF INFLUENZA VIRUS (1983)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Application of knowledge-based network management techniques for packet radio networks (2002)

The authors developed a preliminary version of a knowledge-based model for network management and reconfiguration using blackboard techniques and have applied to it packet radio networks. The analysis is concerned with developing procedures for evaluation of candidate recovery/reconfiguration methodologies and techniques for fault isolation and related monitoring functions. As an initial step, the generic blackboard was chosen as the artificial intelligence environment to develop the management tools and interlink it to a packet radio network simulator that was used as a testbed network to be controlled and monitored. The details of the interaction of the management environment and the packet radio simulator as implemented in the model so far, and present numerical results obtained through the execution of some preliminary rules are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>