gebhart/patrepeval huggingface dataset:
Immunization with <i>Vibrio cholerae</i> Outer Membrane Vesicles Induces Protective Immunity in Mice (2008)

The gram-negative bacterium Vibrio cholerae releases outer membrane vesicles (OMVs) during growth. In this study, we immunized female mice by the intranasal, intragastric, or intraperitoneal route with purified OMVs derived from V. cholerae. Independent of the route of immunization, mice induced specific, high-titer immune responses of similar levels against a variety of antigens present in the OMVs. After the last immunization, the half-maximum total immunoglobulin titer was stable over a 3-month period, indicating that the immune response was long lasting. The induction of specific isotypes, however, was dependent on the immunization route. Immunoglobulin A, for example, was induced to a significant level only by mucosal immunization, with the intranasal route generating the highest titers. We challenged the offspring of immunized female mice with V. cholerae via the oral route in two consecutive periods, approximately 30 and 95 days after the last immunization. Regardless of the route of immunization, the offspring was protected against colonization with V. cholerae in both challenge periods. Our results show that mucosal immunizations via both routes with OMVs derived from V. cholerae induce long-term protective immune responses against this gastrointestinal pathogen. These findings may contribute to the development of "nonliving," OMV-based vaccines against V. cholerae and other enteric pathogens, using the oral or intranasal route of immunization.
DVB‐S2 low density parity check codes with near Shannon limit performance (2004)

Abstract Low density parity check (LDPC) codes are chosen for the second generation digital video broadcasting (DVB) standard. In this paper, we review LDPC codes in general, present belief propagation decoding algorithm in simple terms, describe the standardized LDPC codes and show their performance. Copyright © 2004 John Wiley & Sons, Ltd.
Cross-Neutralizing Human Monoclonal Anti-HIV-1 Antibody 2F5: Preparation and Crystallographic Analysis of the Free and Epitope-Complexed Forms of its F ab Fragment (2001)

The human monoclonal antibody 2F5 is a potent neutralizer of most clades of HIV-1 and possesses protective effects against viral transmission. It recognizes the linear epitope ELDKWAS of the viral envelope protein gp41. As structural information about epitope recognition may help to develop an HIV-1 vaccine we initiated crystallographic analyses of mAb 2F5 and its epitope complex. We now report the preparation of the corresponding Fab fragments, complexation with the epitope peptide, and crystallization of free mAb 2F5 Fab as well as the peptide complex. Both crystal forms are well suited for high-resolution structural analysis. Keywords: CROSS-NEUTRALIZING, CRYSTALLOGRAPHIC ANALYSIS, peptide complex
Introgression of leaf rust and stripe rust resistance from Sharon goatgrass (<i>Aegilops sharonensis</i> Eig) into bread wheat (<i>Triticum aestivum</i> L.) (2014)

Leaf rust and stripe rust are devastating wheat diseases, causing significant yield losses in many regions of the world. The use of resistant varieties is the most efficient way to protect wheat crops from these diseases. Sharon goatgrass (Aegilops sharonensis or AES), which is a diploid wild relative of wheat, exhibits a high frequency of leaf and stripe rust resistance. We used the resistant AES accession TH548 and induced homoeologous recombination by the ph1b allele to obtain resistant wheat recombinant lines carrying AES chromosome segments in the genetic background of the spring wheat cultivar Galil. The gametocidal effect from AES was overcome by using an "anti-gametocidal" wheat mutant. These recombinant lines were found resistant to highly virulent races of the leaf and stripe rust pathogens in Israel and the United States. Molecular DArT analysis of the different recombinant lines revealed different lengths of AES segments on wheat chromosome 6B, which indicates the location of both resistance genes.
Atlas of Ultrastructure Interaction Proteome Between Barley Yellow Dwarf Virus and Gold Nanoparticles (2021)

Atlas of Ultrastructure Interaction Proteome Between Barley Yellow Dwarf Virus and Gold Nanoparticles includes ultrastructure electron micrographs of the interaction of proteomes between barley yellow dwarf virus (bionanoparticles) and gold nanoparticles (metal nanoparticles) obtained by transmission electron microscopy (TEM). Over six chapters, the book expresses and illustrates the behavior and effects of these two kinds of nanoparticles inside the most important organelles of plant cells. The advantages of using gold nanoparticles as an inert metal therapy against plant virus particles include high efficacy with good tolerability and improvement of plant performance that leads to the disappearance of virus particles inside the plant cells.
Wireless Network-on-Chip analysis of propagation technique for on-chip communication (2016)

Network-on-Chip (NoC) is a communication paradigm capable of facilitating a scalable interconnection infrastructure for multi core processors. Wireless NoCs have been introduced to improve the communication performance over long-distance processing nodes. Current on-chip antennas used in wireless NoCs communicate predominantly through surface waves, where the efficacy of the wireless nodes is partially determined by the radiation efficiency and transmission gain limited due to the conductivity loss of the silicon substrate. Recently, an on-chip propagation technique of radio waves was introduced, through the un-doped silicon layer as opposed to surface-waves prevalent in literature. The through-substrate propagation waves provide a unique solution to overcome the challenge of long-distance communication between processing nodes. In this work, overall improvements are shown compared to traditional wireless NoCs with the placement of antennas on undoped silicon (i.e. communicating through surface waves), simulated in NoC architectures across performance metrics of area, power consumption and latency.
A hybrid Nano/CMOS dynamically reconfigurable system—Part II (2009)

In Part I of this work, a hybrid nano/CMOS reconfigurable architecture, called NATURE, was described. It is composed of CMOS reconfigurable logic and interconnect fabric, and nonvolatile nano on-chip memory. Through its support for cycle-by-cycle runtime reconfiguration and a highly-efficient computation model, temporal logic folding, NATURE improves logic density and area-delay product by more than an order of magnitude compared to existing CMOS-based field-programmable gate arrays (FPGAs). NATURE can be fabricated using mainstream photo-lithography fabrication techniques. Thus, it offers a currently commercially feasible architecture with high performance, superior logic density, and excellent runtime design flexibility. In Part II of this work, we present an integrated design and optimization flow for NATURE, called NanoMap. Given an input design specified in register-transfer level (RTL) and/or gate-level VHDL, NanoMap optimizes and implements the design on NATURE through logic mapping, temporal clustering, temporal placement, and routing. As opposed to other design tools for traditional FPGAs, NanoMap supports and leverages temporal logic folding by integrating novel mapping techniques. It can automatically explore and identify the best temporal logic folding configuration, targeting area, delay or area-delay product optimization. A force-directed scheduling technique is used to optimize and balance resource usage across different folding cycles. By supporting logic folding, NanoMap can provide significant design flexibility in performing area-delay trade-offs under various user-specified constraints. We present details of the mapping procedure and results for different architectural instances. Experimental results demonstrate that NanoMap can judiciously trade off area and delay targeting different optimization goals, and effectively exploit the advantages of NATURE. Part I of this work will appear in JETC Vol. 5, No. 4.
MULTIPLE GLASS TRANSITION TERPOLYMERS OF ISOPRENE, BUTADIENE, AND STYRENE (2010)

Abstract Novel polymers that will contribute to a better combination of traction and tread wear in tire applications, which is historically difficult to achieve, have been developed. In this work, multiple viscoelastic polymers possessing multiple glass transition temperatures terpolymers of isoprene/butadiene/styrene were synthesized containing 45/45/10, 40/40/20, and 35/35/30 polymer ratios in 5-gallon laboratory reactors using tetramethylethylenediamine or bis(dipiperdino) ethane as a modifier. These polymers show two glass transition temperatures ( T g 's); the one that occurs at higher temperatures (–25 to –10 °C) is known to contribute to good wet traction properties, while the lower T g is known to contribute to better tread wear properties. These terpolymers were characterized by the fact that their multiviscoelastic loss modulus has narrow molecular distribution for better rolling resistance. In a standard ASTM D31912 carbon-black-filled tread compound recipe, the polymers having all three terpolymers of isoprene/butadiene/styrene polymerized showed excellent values of loss tangent at 0 and 60 ºC, which is a laboratory predictor for both wet traction and rolling resistance. These terpolymers when evaluated in the same ASTM D3191 delivered better properties in a tread compound recipe than either solution or emulsion styrene-butadiene rubber in a formulation that has natural rubber or polybutadiene.
Orthogonal switched beams for downlink diversity transmission (2005)

A downlink transmission scheme in a switched-beam antenna system for providing diversity and beamforming simultaneously based on the space-time block coding technique is proposed. The scheme involves selecting multiple beams based on the uplink reception of the switched-beam antenna system, and determining multiple orthogonal beams from the selected beams. With the orthogonal transmit beams, the proposed switched-beam antenna system outperforms conventional switched-beam systems and approaches the optimal performance achievable by a much complex adaptive antenna system.
Intent Based Relevance Estimation from Click Logs (2017)

Estimating the relevance of documents based on the user feedback is an essential component of search, retrieval and ranking problems. User click modeling in search has focused primarily on factoring out the position bias. It is easy to see that the query type (generic queries vs specific queries) and user intent (purchase vs exploration) also introduce a bias in the click signal. In other words, the results not matching with the user intent will not be clicked. In this paper, we outline a technique to model the interplay of query, user intent and position bias with respect to the relevance of the retrieved search results. In particular, we define two intents namely purchase and explore, and estimate the relevance of the documents with respect to these two intents. We also relate them to the relevance estimates from considering only the position bias. We empirically demonstrate the effectiveness of the proposed approach by comparing its performance against the well-known CoEC measure and the recently proposed factor model approach for relevance estimation.
Potent, structurally constrained agonists and competitive antagonists of corticotropin-releasing factor. (1995)

Predictive methods, physicochemical measurements, and structure activity relationship studies suggest that corticotropin-releasing factor (CRF; corticoliberin), its family members, and competitive antagonists (resulting from N-terminal deletions) usually assume an alpha-helical conformation when interacting with the CRF receptor(s). To test this hypothesis further, we have scanned the whole sequence of the CRF antagonist [D-Phe12,Nle21,38]r/hCRF-(12-41) (r/hCRF, rat/human CRF; Nle, norleucine) with an i-(i + 3) bridge consisting of the Glu-Xaa-Xaa-Lys scaffold. We have found astressin [cyclo(30-33)[D-Phe12,Nle21,38,Glu30,Lys33]r/ hCRF(12-41)] to be approximately 30 times more potent than [D-Phe12,Nle21,38]r/hCRF-(12-41), our present standard, and 300 times more potent than the corresponding linear analog in an in vitro pituitary cell culture assay. Astressin has low affinity for the CRF binding protein and high affinity (Ki = 2 nM) for the cloned pituitary receptor. Radioiodinated [D-125I-Tyr12]astressin was found to be a reliable ligand for binding assays. In vivo, astressin is significantly more potent than any previously tested antagonist in reducing hypophyseal corticotropin (ACTH) secretion in stressed or adrenalectomized rats. The cyclo(30-33)[Ac-Pro4,D-Phe12,Nle21,38,Glu30,Lys33++ +]r/hCRF-(4-41) agonist and its linear analog are nearly equipotent, while the antagonist astressin and its linear form vary greatly in their potencies. This suggests that the lactam cyclization reinstates a structural constraint in the antagonists that is normally induced by the N terminus of the agonist.
Ambience extraction and synthesis from stereo signals for multi-channel audio up-mix (2002)

In this paper we propose a frequency-domain technique to identify and extract the ambience information in stereo audio signals. The method is based on the computation of an inter-channel coherence index and a non-linear mapping function that allow us to determine time-frequency regions that consist mostly of ambience components in the two-channel signal. Ambience signals are then synthesized and used to feed the surround channels of a multichannel playback system. Simulation results demonstrate the effectiveness of the technique in extracting ambience information and up-mix tests on real audio reveal the various advantages and disadvantages of the system compared to previous up-mix strategies.
Contact with glass interferes with the Erythrocyte Sedimentation Rate (ESR) (2003)

The sedimentation rate (sed rate), also called, the Erythrocyte Sedimentation Rate (ESR) is a blood test for inflammation in the body. If it is elevated, then there is an inflammatory process in the body which can be monitored. The test is broad and non-specific; however, it may determine the effectiveness of therapy for the inflammatory condition. We performed studies on human citrated whole blood by adding 100 microlitres of 1% of MethylCellulose to each of glass and plastic tubes with the blood. The samples (n=12) were incubated at 37/spl deg/ for 10 minutes. Later, the blood from each of the tubes were placed in pipettes, sealed and left undisturbed for an hour. The ESR was measured, and it was found that the sedimentation rate of the blood in plastic settled at a higher rate than the one in glass.
Label-free target identification using in-gel fluorescence difference<i>via</i>thermal stability shift (2016)

Target engagement is a prerequisite for the therapeutic effects of bioactive small molecules, and unbiased identification of their target proteins can facilitate drug discovery and chemical biology research. Structural modifications of bioactive natural products for target identification exhibit potential limitations such as synthetic difficulties, limited supplies from natural sources, and loss of original efficacy. Herein, we developed a label-free method for proteome-wide target identification using in-gel fluorescence difference caused by thermal stability shift, namely TS-FITGE. Quantitative intra-gel image analysis of each protein spot revealed target proteins with shifted thermal stability upon drug engagement, and plotting of melting curves by inter-gel analysis confirmed the positive targets. We demonstrated the robustness and applicability of the TS-FITGE method by identifying target proteins, including membrane-anchored proteins, of complex bioactive compounds. Furthermore, we identified and functionally validated nucleophosmin as a novel target protein of hordenine, a natural product upregulator of <i>in vitro</i> translation.
Recent Advances in the Synthesis of Nicotine and Its Derivatives (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Preintegration HIV-1 Inhibition by a Combination Lentiviral Vector Containing a Chimeric TRIM5α Protein, a CCR5 shRNA, and a TAR Decoy (2009)

Human immunodeficiency virus (HIV) gene therapy offers a promising alternative approach to current antiretroviral treatments to inhibit HIV-1 infection. Various stages of the HIV life cycle including pre-entry, preintegration, and postintegration can be targeted by gene therapy to block viral infection and replication. By combining multiple highly potent anti-HIV transgenes in a single gene therapy vector, HIV-1 resistance can be achieved in transduced cells while prohibiting the generation of escape mutants. Here, we describe a combination lentiviral vector that encodes three highly effective anti-HIV genes functioning at separate stages of the viral life cycle including a CCR5 short hairpin RNA (shRNA) (pre-entry), a human/rhesus macaque chimeric TRIM5 alpha (postentry/preintegration), and a transactivation response element (TAR) decoy (postintegration). The major focus on designing this anti-HIV vector was to block productive infection of HIV-1 and to inhibit any formation of provirus that would maintain the viral reservoir. Upon viral challenge, potent preintegration inhibition of HIV-1 infection was achieved in combination vector-transduced cells in both cultured and primary CD34(+) hematopoietic progenitor cell (HPC)-derived macrophages. The generation of escape mutants was also blocked as evaluated by long-term culture of challenged cells. The ability of this combination anti-HIV lentiviral vector to prevent HIV-1 infection, in vitro, warrants further evaluation of its in vivo efficacy.
Angiotensin-Converting Enzyme 2 Metabolizes and Partially Inactivates Pyr-Apelin-13 and Apelin-17 (2016)

Apelin peptides mediate beneficial effects on the cardiovascular system and are being targeted as potential new drugs. However, apelin peptides have extremely short biological half-lives, and improved understanding of apelin peptide metabolism may lead to the discovery of biologically stable analogues with therapeutic potential. We examined the ability of angiotensin-converting enzyme 2 (ACE2) to cleave and inactivate pyr-apelin 13 and apelin 17, the dominant apelin peptides. Computer-assisted modeling shows a conserved binding of pyr-apelin 13 and apelin 17 to the ACE2 catalytic site. In ACE2 knockout mice, hypotensive action of pyr-apelin 13 and apelin 17 was potentiated, with a corresponding greater elevation in plasma apelin levels. Similarly, pharmacological inhibition of ACE2 potentiated the vasodepressor action of apelin peptides. Biochemical analysis confirmed that recombinant human ACE2 can cleave pyr-apelin 13 and apelin 17 efficiently, and apelin peptides are degraded slower in ACE2-deficient plasma. The biological relevance of ACE2-mediated proteolytic processing of apelin peptides was further supported by the reduced potency of pyr-apelin 12 and apelin 16 on the activation of signaling pathways and nitric oxide production from endothelial cells. Importantly, although pyr-apelin 13 and apelin 17 rescued contractile function in a myocardial ischemia-reperfusion model, ACE2 cleavage products, pyr-apelin 12 and 16, were devoid of these cardioprotective effects. We designed and synthesized active apelin analogues that were resistant to ACE2-mediated degradation, thereby confirming that stable apelin analogues can be designed as potential drugs. We conclude that ACE2 represents a major negative regulator of apelin action in the vasculature and heart.
Design of multioctave spiral-mode microstrip antennas (1991)

The design of spiral-mode microstrip antennas with a bandwidth of 6:1 is demonstrated. The antenna has a small dissipative loss due to a resistive loading outside its active region. As a specific measure of bandwidth at microwave frequencies, the spiral-mode microstrip antenna gain is higher than that of the conventional loaded-cavity spiral over a 5:1 and if the spacing d between the microstrip and the ground plane is 0.25 in. or larger over the 2-12 GHz range. Cursory efficiency calculations show consistent improvement over a loaded-cavity spiral. A study of ground plane spacing showed that the antenna gain remains above the conventional spiral gain as d is reduced until it is as small as 0.1 in.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
O-071 Salt-sparing Diuretic Action Of A Urea Analogue Inhibitor Of Urea Transporters Ut-a And Ut-b In Rats (2014)

<h3>Background and aims</h3> Urea is end metabolite of protein metabolism and is crucial for generation of hypertonic renal medulla. Urea transport to medullary interstitium is facilitated by urea transporters (UT-A and UT-B). UT inhibitors have potential use as a novel class of salt-sparing diuretics. <h3>Methods</h3> UT inhibitor effect of urea analogue dimethylthiourea (DMTU) was investigated and characterised in cell-based assays. Kidney function tests were investigated in both 1-day and 7-days DMTU-treated (500 mg/kg ip initially, then 125 mg/kg ip every 12h) rats. The effect of DMTU on maximum urine concentrating function was investigated in low (6%) and normal (20%) protein-fed rats. <h3>Results</h3> DMTU non-competitively inhibited UT-A and UT-B with IC<sub>50</sub> of ~3 mM. Following 500 mg/kg ip injection, plasma DMTU concentration was initially 10 mM (plasma elimination t<sub>1/2 </sub>~10 h) and urine DMTU concentration was >20 mM for 12 h. DMTU-treated rats showed reversible, sustained reduction in urine osmolality (>60%) and 3-fold increased daily urine output. DMTU increased renal electrolyte-free water excretion without altering solute excretion. DMTU impaired maximum urinary concentrating function only in normal protein-fed rats. Methylurea, a non-UT inhibitor urea analogue, had no effect on either urine volume or osmolality. DMTU-treated rats had greater diuresis and much reduced urinary salt loss compared to that of furosemide-treated rats. <h3>Conclusions</h3> These results establish a rat model of sustained UT inhibition and demonstrate remarkable diuretic efficacy of UT inhibition. Prominent effect of UT inhibitors on net renal water excretion implies a novel therapeutic strategy for treatment of oedema in hypervolemic diseases.