gebhart/patrepeval huggingface dataset:
Synthesis and Structure Verification of the Vaccine Adjuvant QS-7-Api. Synthetic Access to Homogeneous<i>Quillaja saponaria</i>Immunostimulants (2008)

QS-7-Api is an exceedingly potent immuno-adjuvant isolated from the bark of Quillaja saponaria. It is significantly less toxic than QS-21, a related saponin that is currently the favored adjuvant in anticancer and antiviral vaccine clinical trials. Tedious isolation/purification protocols and uncertainty in its structural constitution have hindered the clinical development of QS-7. A chemical synthesis of QS-7-Api is described, providing structural verification of the adjuvant. A novel semisynthetic sequence to QS-7-Api has also been established, greatly facilitating access to QS-7 for preclinical and clinical evaluation.
Towards the transformation of onions <i>(Allium cepa)</i> (1995)

Abstract This review outlines the potential for developing a reliable transformation system for onions (Allium cepa). A summary of the onion tissue culture literature is presented along with descriptions of the gene transfer systems available. The most suitable regulatory sequences and selective genes that could be used for onion transformation are described, together with the problems which may be encountered following the integration into the particularly large genome of onion. The review proposes likely routes by which transformation and regeneration may be achieved, and suggests possible characteristics of onions which may be altered using such a technique.
Influence of an anti-tumor necrosis factor monoclonal antibody on cytokine levels in patients with sepsis (1993)

The murine anti-TNF-alpha monoclonal antibody CB0006 has proven to be safe in this clinical trial and may prove to be useful in septic patients with increased circulating TNF concentrations. Further studies are needed to determine efficacy and the ultimate clinical utility of this immunotherapeutic agent in sepsis.
Determination of formation permeability from a long-spaced acoustic log (1984)

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Expression of <i>Babesia equi</i> Merozoite Antigen 1 in Insect Cells by Recombinant Baculovirus and Evaluation of Its Diagnostic Potential in an Enzyme-Linked Immunosorbent Assay (2001)

The gene encoding the entire Babesia equi merozoite antigen 1 (EMA-1) was inserted into a baculovirus transfer vector, and a recombinant virus expressing EMA-1 was isolated. The expressed EMA-1 was transported to the surface of infected insect cells, as judged by an indirect fluorescent-antibody test (IFAT). The expressed EMA-1 was also secreted into the supernatant of a cell culture infected with recombinant baculovirus. Both intracellular and extracellular EMA-1 reacted with a specific antibody in Western blots. The expressed EMA-1 had an apparent molecular mass of 34 kDa that was identical to that of native EMA-1. The secreted EMA-1 was used as an antigen in an enzyme-linked immunosorbent assay (ELISA). The ELISA differentiated B. equi-infected horse sera from Babesia caballi-infected horse sera or normal horse sera. The ELISA was more sensitive than the complement fixation test and IFAT. These results demonstrated that the recombinant EMA-1 expressed in insect cells might be a useful diagnostic reagent for detection of antibodies to B. equi.
pH-sensitive liposomes: acid-induced liposome fusion. (1984)

Sonicated unilamellar liposomes containing phosphatidylethanolamine and palmitoylhomocysteine fuse rapidly when the medium pH is lowered from 7 to 5. Liposome fusion was demonstrated by (i) mixing of the liposomal lipids as shown by resonance energy transfer, (ii) gel filtration, and (iii) electron microscopy. The pH-sensitive fusion of liposomes was observed only when palmitoylhomocysteine (greater than or equal to 20 mol%) was present in the liposomes. The presence of phosphatidyl-ethanolamine in the liposomes greatly enhanced fusion whereas the presence of phosphatidylcholine inhibited fusion. During fusion of liposomes containing phosphatidylethanolamine and palmitoylhomocysteine (8:2, mol/mol), almost all of the encapsulated calcein was released. Inclusion of cholesterol (40 mol%) in the liposomes substantially decreased leakage without impairing fusion.
Spliceosome-Mediated RNA <i>Trans</i> -Splicing Facilitates Targeted Delivery of Suicide Genes to Cancer Cells (2011)

Patients suffering from recessive dystrophic epidermolysis bullosa (RDEB), a hereditary blistering disease of epithelia, show susceptibility to develop highly aggressive squamous cell carcinoma (SCC). Tumors metastasize early and are associated with mortality in the 30th-40th years of life in this patient group. So far, no adequate therapy is available for RDEB SCC. An approach is suicide gene therapy, in which a cell death-inducing agent is introduced to cancer cells. However, lack of specificity has constrained clinical application of this modality. Therefore, we used spliceosome-mediated RNA trans-splicing technology, capable of replacing a tumor-specific transcript with one encoding a cell death-inducing peptide/toxin, to provide tumor-restricted expression. We designed 3' pre-trans-splicing molecules (PTM) and evaluated their efficiency to trans-splice an RDEB SCC-associated target gene, the matrix metalloproteinase-9 (MMP9), in a fluorescence-based test system. A highly efficient PTM was further adapted to insert the toxin streptolysin O (SLO) of Streptococcus pyogenes into the MMP9 gene. Transfection of RDEB SCC cells with the SLO-PTM resulted in cell death and induction of toxin function restricted to RDEB SCC cells. Thus, RNA trans-splicing is a suicide gene therapy approach with increased specificity to treat highly malignant SCC tumors.
Generation and Characterization of Recombinant Antibody-like ADP-Ribose Binding Proteins (2017)

ADP-ribosylation is an enzyme-catalyzed post-translational modification of proteins in which the ADP-ribose (ADPR) moiety of NAD<sup>+</sup> is transferred to a specific amino acid in a substrate protein. The biological functions of ADP-ribosylation are numerous and diverse, ranging from normal physiology to pathological conditions. Biochemical and cellular studies of the diverse forms and functions of ADPR require immunological reagents that can be used for detection and enrichment. The lack of a complete set of tools that recognize all forms of ADPR [i.e., mono-, oligo-, and poly(ADP-ribose)] has hampered progress. Herein, we describe the generation and characterization of a set of recombinant antibody-like ADP-ribose binding proteins, in which naturally occurring ADPR binding domains, including macrodomains and WWE domains, have been functionalized by fusion to the Fc region of rabbit immunoglobulin. These reagents, which collectively recognize all forms of ADPR with different specificities, are useful in a broad array of antibody-based assays, such as immunoblotting, immunofluorescent staining of cells, and immunoprecipitation. Observations from these assays suggest that the biology of ADPR is more diverse, rich, and complex than previously thought. The ARBD-Fc fusion proteins described herein will be useful tools for future exploration of the chemistry, biochemistry, and biology of ADP-ribose.
Hybrid perovskites: Approaches towards light-emitting devices (2016)

The high optical gain and absorption of organic-inorganic hybrid perovskites have attracted extensive research for photonic device applications. Using the bromide halide as an example, we present key approaches of our work towards realizing efficient perovskites based light-emitters. The approaches involved determination of optical constants for the hybrid perovskites thin films, fabrication of photonic nanostructures in the form of subwavelength grating reflector patterned directly on the hybrid perovskites as light manipulation layer, and enhancing the emission property of the hybrid perovskites by using microcavity structure. Our results provide a platform for realization of hybrid perovskites based light-emitting devices for solid-state lighting and display applications.
An Application Development Platform for neuromorphic computing (2016)

Dynamic Adaptive Neural Network Arrays (DANNAs) are neuromorphic computing systems developed as a hardware based approach to the implementation of neural networks. They feature highly adaptive and programmable structural elements, which model artificial neural networks with spiking behavior. We design them to solve problems using evolutionary optimization. In this paper, we highlight the current hardware and software implementations of DANNA, including their features, functionalities and performance. We then describe the development of an Application Development Platform (ADP) to support efficient application implementation and testing of DANNA based solutions. We conclude with future directions.
Effect of multiple light paths on retinal vessel oximetry (2000)

Techniques for noninvasively measuring the oxygen saturation of blood in retinal arteries and veins are reported in the literature, but none have been sufficiently accurate and reliable for clinical use. Addressing the need for increased accuracy, we present a series of oximetric equations that explicitly consider the effects of backscattering by red blood cells and lateral diffusion of light in the ocular fundus. The equations are derived for the specific geometry of a scanning-beam retinal vessel oximeter; however, the results should also be applicable to photographic oximeters. We present in vitro and in vivo data that suggest the validity of these equations.
A Near-Capacity GDFE-Like Precoder with Reduced Feedback Overhead for MIMO Broadcast Channel (2011)

Downlink multi user multiple input multiple output (MU-MIMO) systems are of increasing importance in current and upcoming wireless applications. The improvement in data rates offered by such systems depends on the design of precoding schemes for the broadcast channel (BC) which is their theoretical generalization. A precoding scheme based on generalized decision feedback equalizer (GDFE) is known to achieve MIMO BC capacity. However, GDFE precoder suffers from huge computational complexity and feedback overhead that renders it unsuitable for practical systems. While the computational complexity has been dealt elsewhere, the feedback overhead issue has not yet been resolved. Thus in this paper we propose an algorithm to significantly reduce the feedback requirements of GDFE and show that the performance loss is minimal. We do this by first presenting a variant of the conventional GDFE algorithm, which we prove has the same theoretical performance.
Marker assisted selection for herbicide resistance in sunflower (2013)

IMISUN, SURES, and CLPlus are three herbicide tolerance traits in sunflower\n (Helianthus annuus L.) which are determined by the expression of different\n alleles at the same locus, Ahasl1. Introgression of these genes into high\n yielding sunflower germplasm should be complemented through the use of\n molecular markers in order to unambiguously identify the different alleles\n involved in tolerance. The aim of this work was to present a set of allele\n specific molecular markers for the different herbicide resistant traits of\n sunflower, which can be used with various technological platforms, and\n applied to different objectives in a breeding program. The Ahasl1 gene\n sequences from lines carrying different alleles for susceptibility or\n resistance showed single nucleotide polymorphisms and length variations for a\n simple sequence repeat. These differences were utilized to develop three\n types of PCR markers (SSRs, CAPS and SNPs) which allow the precise\n identification of each allele at the Ahasl1 locus. Usefulness of these\n markers with respect to the application of phenotypic selection for herbicide\n tolerance, and the strategic implementation of these techniques for\n developing inbred lines with herbicide resistance is discussed.
Structure‐activity relationships in a group of azoles, with special reference to 1,3‐dioxolan‐2‐ylmethyl derivatives (1984)

Abstract Substituted imidazoles and substituted 1,2,4‐triazoles are active to varying degrees in the control of fungi pathogenic to plants, animals and man. The relationship between chemical structure and their antifungal activity, both in‐vitro and in‐vivo, is reviewed.
The <i>Candida albicans KRE9</i> gene is required for cell wall β-1,6-glucan synthesis and is essential for growth on glucose (1998)

We have isolated CaKRE9 , a gene from Candida albicans , that is a functional homologue of the Saccharomyces cerevisiae KRE9 gene involved in β-1,6-glucan synthesis. Disruption of the CaKRE9 gene in C. albicans shows that CaKre9p is required for the synthesis or assembly of this fungal polymer. Homozygous null disruptants of CaKRE9 grow poorly on galactose and fail to form hyphae in serum, and, in growth medium containing glucose, the gene is essential. Thus, the CaKRE9 gene product is a potentially useful candidate as a target for fungal-specific drugs.
Deposition of Fluoride on Tooth Surfaces by a Two-Solution Mouthrinse in vitro (1991)

A constant-composition fluoride (F) titration method was used to measure the amount of leachable F deposited on tooth surfaces in vitro by a 1-min rinse with a 228-ppm F solution (12 mmol/l sodium fluoride). The mean F uptake was 0.23 +/- (SE) 0.07 microgram/cm2, corresponding to less than 0.2% of the F contained in the rinse. The present study describes a new F rinse system that consisted of two solutions. Solution A contained a soluble calcium salt and a buffer. Solution B contained sodium fluorosilicate, a complex fluoride salt. When solutions A and B were combined, the free F ions produced by hydrolysis of fluorosilicate caused precipitation of calcium fluoride during the 1-min application time. The F uptake produced by the two-solution rinse was 4.36 +/- 0.16 micrograms/cm2, which was approximately 19 times greater than that produced by the sodium F rinse with the same F content. Since the cariostatic effects from F rinses are believed to derive from their ability to deposit labile F in the oral cavity, the two-solution rinse may be more efficacious than the rinses currently in use.
Novel therapies for prevention of erythrocyte dehydration in sickle cell anemia (2001)

Sickle cell anemia is a genetic disorder characterized by mutant hemoglobin (Hb) polymerization and resultant cell deformation (sickling) under conditions of reduced oxygen tension. The disease is caused by mutation of wild-type Glu to Val in position 6 of the beta-chain of hemoglobin, yielding hemoglobin S (HbS). The sickling process is markedly accelerated when the intracellular concentration of HbS is increased. A variable fraction of dehydrated erythrocytes is seen in the majority of patients, and these cells are believed to play an important role in the pathophysiology of the vasoocclusive events of sickle cell disease. Therapy of sickle cell disease is extremely limited in range and efficacy. Many patients still receive treatment only for symptomatic relief of sickle crises, painful episodes due to vasoocclusion by sickled cells. The last 15 years, however, have seen the identification of the principal transport pathways that mediate sickle erythrocyte dehydration, and the last 6 years have witnessed promising clinical tests of specific inhibitors of these pathways, with the intent of reducing cell sickling via inhibition of red cell dehydration. This review discusses the pathophysiology of sickle cell dehydration and explores current and future treatment options for in vivo prevention of sickle cell dehydration.
Peptidomimetic-Based Inhibitors of Farnesyltransferase (2001)

Human H-, K-, and N-ras genes encode four structurally related proteins with 188 or 189 amino acids and a molecular weight of 21 kDa (1,2). Analysis of oncogenes in human tumors showed that mutated Ras existed in approx 30% of all human tumors, particularly in over 90% of human pancreatic carcinomas and 50% of human colon cancers (1). The frequency of mutation is dependent on tumor type, with breast, ovary, and stomach carcinomas showing the lowest frequency Ras mutations (3). Ras proteins play a crucial role as a molecular switch transducing signals from receptor tyrosine kinases to the cell nucleus (4). Normal Ras exists in an equilibrium between inactive GDP- and active GTP-bound forms, with a strong preference for Ras-GDP (5). When mutated at positions 12, 13, and 61, Ras proteins lose their ability to hydrolyze GTP to GDP and so deactivate the switch (6). Consequently, the mutated Ras is locked in the GTP-bound form, causing uncontrolled proliferation.
Bid Activation Multiple Access in Ad Hoc Networks (2006)

We present a new protocol for collision-free channel access in ad hoc networks called Bid Activation Multiple Access (BAMA). BAMA is based on bids made by nodes for slots within the context of probabilistic channel access. Winners of the bids for a given slot are determined as a result of a fair election of the bids for that slot. Nodes attempt to acquire varying number of slots depending on their traffic requirements. Nodes transmit their schedule information once in each frame prior to the data packet transmission in the slots acquired by them. Mismatched schedule information for a given slot are corrected based on the same fair election by the nodes that hear the schedule information. BAMA does not require explicit control information (HELLO packets) to build up local or global topology of the nodes to compute a transmission schedule for the nodes. The performance of BAMA is studied by simulations and compared against the performance of comparable protocols. It is found that BAMA provides better throughput and much lower end to end delay when compared to other protocols, both at low loads as well as high loads. The traffic adaptive nature of BAMA allows for the performance of BAMA to be largely independent of the network load. This makes it ideal for deployment in high bandwidth scenarios where low end to end delay is desirable.
Four-frequency ring laser gyroscopes (1982)

All optical rotation sensors make use of the Sagnac effect to generate a phase shift between light waves propagating in opposite directions around an area-enclosing path. The phase shift may be detected interferometrically, as in fiberoptic rotation sensors (Ref 1), or converted into a relative shift of the resonant frequencies in the two directions. If the difference between the frequencies is probed via tunable injected signals, the result is an Ezekiel-Balsamo passive-resonator rotation sensor (Ref 2). If the resonant frequencies are generated within the rotating path itself by laser action, we have a ring laser gyroscope (RLG). The passive schemes require sophisticated signal processing to detect the extremely tiny fringe shifts involved. In a laser gyroscope the problem is not to detect the frequency differences caused by the small phase shifts, but rather to prevent the countertraveling waves from phase-locking together at small rotation rates. This problem is usually solved in two-frequency RLGs (Ref 3) by rotationally dithering the actual massive resonator block, avoiding most of the problems of locking by spending very little time each dither cycle in the lock region, thereby reducing the effective phase-sensitive coupling between the countertraveling waves to such a low level that a small amount of random or deliberate noise in the dither amplitude may wash it out altogether.
A Magneto-Hydrodynamic Micro Fluidic Network (2002)

The magneto hydrodynamic fluidic network’s basic building blocks are conduits equipped with two electrodes positioned on opposing walls. The entire device is either subjected to an external uniform magnetic field or fabricated within a magnetic material. When a prescribed potential difference is applied across each electrode pair, it induces current in the liquid (assumed to be a weakly conductive). The current interacts with the magnetic field to produce a Lorentz force that is perpendicular to both the directions of the current and the magnetic field. Analogously with electric circuits, by judicious application of the potential differences at various branches, one can direct liquid flow in any desired way and rate without a need for mechanical pumps or valves. By equipping the network branches with additional, interior electrodes, the branches double as stirrers capable of generating chaotic advection. The paper describes the basic building blocks for such a network, the operation of these branches as stirrers, a general theory for the analysis and control of fluidic magneto-hydrodynamic networks, and an example of a network fabricated with low temperature, co-fired ceramic tapes.
Identifying Protein Kinase Inhibitors Using an Assay Based on Inhibition of Aerial Hyphae Formation in Streptomyces. (2002)

We have identified a strain of Streptomyces in which aerial hyphae formation appears to be especially sensitive to inhibition by protein kinase inhibitors. Using this assay, a number of bacterial cultures have been screened and novel inhibitors of eukaryotic protein kinases have been identified. Since M. tuberculosis possesses multiple eukaryotic-like protein kinase genes, we tested the active kinase inhibitors for the inhibition of mycobacterial growth and obtained several potent compounds. This identifies a new biochemical class of antimycobacterial agents.
ROCK: a robust clustering algorithm for categorical attributes (1999)

We study clustering algorithms for data with Boolean and categorical attributes. We show that traditional clustering algorithms that use distances between points for clustering are not appropriate for Boolean and categorical attributes. Instead, we propose a novel concept of links to measure the similarity/proximity between a pair of data points. We develop a robust hierarchical clustering algorithm, ROCK, that employs links and not distances when merging clusters. Our methods naturally extend to non-metric similarity measures that are relevant in situations where a domain expert/similarity table is the only source of knowledge. In addition to presenting detailed complexity results for ROCK, we also conduct an experimental study with real-life as well as synthetic data sets. Our study shows that ROCK not only generates better quality clusters than traditional algorithms, but also exhibits good scalability properties.
HYDRAstor: a Scalable Secondary Storage (2009)

External signals that are mediated by specific receptors determine stem cell fate. The thrombin receptor PAR1 plays an important role in haemostasis, thrombosis and vascular biology, but also in tumor biology and angiogenesis. Its expression and function in hematopoietic stem cells is largely unknown. Here, we analyzed expression and function of PAR1 in primary hematopoietic cells and their leukemic counterparts. AML patients' blast cells expressed much lower levels of PAR1 mRNA and protein than CD34+ progenitor cells. Constitutive Par1-deficiency in adult mice did not affect engraftment or stem cell potential of hematopoietic cells. To model an AML with Par1-deficiency, we retrovirally introduced the oncogene MLL-AF9 in wild type and Par1-/- hematopoietic progenitor cells. Par1-deficiency did not alter initial leukemia development. However, the loss of Par1 enhanced leukemic stem cell function in vitro and in vivo. Re-expression of PAR1 in Par1-/- leukemic stem cells delayed leukemogenesis in vivo. These data indicate that Par1 contributes to leukemic stem cell maintenance.