gebhart/patrepeval huggingface dataset:
Antibodies to macrophage stimulating protein (MSP): specificity, epitope interactions, and immunoassay of MSP in human serum (1993)

Macrophage stimulating protein (MSP) is a member of a family of proteins characterized by a triple disulfide loop structure (kringle). We developed antibodies to human MSP for detection in Western blots, quantification in biological fluids, and neutralization of activity. Immunogens included native MSP, reduced and alkylated alpha and beta chains, and peptides of MSP regions with minimal sequence similarity to other kringle proteins. We found three antibody categories based on interaction with the following types of epitope: primary sequence, discontinuous (dependent on disulfide bonds), and cryptic (not exposed in native MSP). None of the antibodies reacted with related kringle proteins. A specific sandwich ELISA was developed for measuring human MSP. The mean serum concentration was 4 nM. Serum MSP did not increase over a 24-h period in response to intravenous lipopolysaccharide, indicating that MSP is not an acute phase protein. These findings are consistent with the hypothesis that regulation of MSP activity is by conversion of pro-MSP to MSP rather than by rapid changes in rates of synthesis.
Quality of service provisioning in 802.11e networks: challenges, approaches, and future directions (2005)

In order to support diverse application requirements, a new standard called IEEE 802.11e is being proposed to improve quality of service in wireless LAN networks. There are, however, a few remaining challenges that need to be addressed in order to enable comprehensive QoS support using 802.11e. In this article we provide an overview of a few of these challenges, describe their possible impact on QoS, and provide a survey of techniques that potentially could be used to address the identified challenges. Specifically, we focus on three challenges: handling time-varying network conditions, adapting to varying application profiles, and managing link layer resources. Additionally, we present several potential future directions toward improved QoS in wireless networks.
Creating Space for Large Acceptors: Rational Biocatalyst Design for Resveratrol Glycosylation in an Aqueous System (2015)

Polyphenols display a number of interesting properties but their low solubility limits practical applications. In that respect, glycosylation offers a solution for which sucrose phosphorylase has been proposed as a cost-effective biocatalyst. However, its activity on alternative acceptor substrates is too low for synthetic purposes and typically requires the addition of organic (co-)solvents. Here, we describe the engineering of the enzyme from Thermoanaerobacterium thermosaccharolyticum to enable glycosylation of resveratrol as test case. Based on docking and modeling studies, an active-site loop was predicted to hinder binding. Indeed, the unbolted loop variant R134A showed useful affinity for resveratrol (K(m)=185 mM) and could be used for the quantitative production of resveratrol 3-α-glucoside in an aqueous system. Improved activity was also shown for other acceptors, introducing variant R134A as promising new biocatalyst for glycosylation reactions on bulky phenolic acceptors.
Design and Synthesis of Aminopropyl Tetrahydroindole‐Based Indolin‐2‐ones as Selective and Potent Inhibitors of Src and Yes Tyrosine Kinase. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Energy-Efficient Heuristics for Insensitive Job Assignment in Processor-Sharing Server Farms (2015)

Energy efficiency of server farms is an important design consideration of the green datacenter initiative. One effective approach is to optimize power consumption of server farms by controlling the carried load on the networked servers. In this paper, we propose a robust heuristic policy called E* for stochastic job assignment in a server farm, aiming to improve the energy efficiency by maximizing the ratio of job throughput to power consumption. Our model of the server farm considers a parallel system of finite-buffer processor-sharing queues with heterogeneous server speeds and energy consumption rates. We devise E* as an insensitive policy so that the stationary distribution of the number of jobs in the system depends on the job size distribution only through its mean. We provide a rigorous analysis of E* and compare it with a baseline approach, known as most energy-efficient server first (MEESF), that greedily chooses the most energy-efficient servers for job assignment. We show that E* has always a higher job throughput than that of MEESF, and derive realistic conditions under which E* is guaranteed to outperform MEESF in energy efficiency. Extensive numerical results are presented and demonstrate that E* can improve the energy efficiency by up to 100%.
Four-color DNA sequencing with 3′- <i>O</i> -modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides (2008)

DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction can decipher many sequences in parallel. We report here a DNA sequencing method that is a hybrid between the Sanger dideoxynucleotide terminating reaction and SBS. In this approach, four nucleotides, modified as reversible terminators by capping the 3'-OH with a small reversible moiety so that they are still recognized by DNA polymerase as substrates, are combined with four cleavable fluorescent dideoxynucleotides to perform SBS. The ratio of the two sets of nucleotides is adjusted as the extension cycles proceed. Sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by ddNTPs. On removing the 3'-OH capping group from the DNA products generated by incorporating the 3'-O-modified dNTPs and the fluorophore from the DNA products terminated with the ddNTPs, the polymerase reaction reinitiates to continue the sequence determination. By using an azidomethyl group as a chemically reversible capping moiety in the 3'-O-modified dNTPs, and an azido-based cleavable linker to attach the fluorophores to the ddNTPs, we synthesized four 3'-O-azidomethyl-dNTPs and four ddNTP-azidolinker-fluorophores for the hybrid SBS. After sequence determination by fluorescence imaging, the 3'-O-azidomethyl group and the fluorophore attached to the DNA extension product via the azidolinker are efficiently removed by using Tris(2-carboxyethyl)phosphine in aqueous solution that is compatible with DNA. Various DNA templates, including those with homopolymer regions, were accurately sequenced with a read length of >30 bases by using this hybrid SBS method on a chip and a four-color fluorescence scanner.
An improved route to 4-demethoxydaunomycinone. A-Ring functionalization and resolution studies of tetracyclic precursors (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn improved route to 4-demethoxydaunomycinone. A-Ring functionalization and resolution studies of tetracyclic precursorsDomingo Dominguez, Robert J. Ardecky, and Michael P. CavaCite this: J. Am. Chem. Soc. 1983, 105, 6, 1608–1613Publication Date (Print):March 1, 1983Publication History Published online1 May 2002Published inissue 1 March 1983https://pubs.acs.org/doi/10.1021/ja00344a031https://doi.org/10.1021/ja00344a031research-articleACS PublicationsRequest reuse permissionsArticle Views166Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Session Based Click Features for Recency Ranking (2010)

Recency ranking refers to the ranking of web results by accounting for both relevance and freshness. This is particularly important for "recency sensitive" queries such as breaking news queries. In this study, we propose a set of novel click features to improve machine learned recency ranking. Rather than computing simple aggregate click through rates, we derive these features using the temporal click through data and query reformulation chains. One of the features that we use is click buzz that captures the spiking interest of a url for a query. We also propose time weighted click through rates which treat recent observations as being exponentially more important. The promotion of fresh content is typically determined by the query intent which can change dynamically over time. Quite often users query reformulations convey clues about the query's intent. Hence we enrich our click features by following query reformulations which typically benefit the first query in the chain of reformulations. Our experiments show these novel features can improve the NDCG5 of a major online search engine's ranking for "recency sensitive" queries by up to 1.57%. This is one of the very few studies that exploits temporal click through data and query reformulations for recency ranking.
Methane hydrate dissociation in the presence of novel benign additives (2019)

The apparent drawbacks of the classical approaches towards dissociation of natural gas hydrates have resulted in a paradigm shift into the development of new hybrid hydrate dissociation practices combining the various basic hydrate dissociation techniques. Another approach that can be followed to maximize the efficiency of gas production from natural gas hydrate reserves is the identification of benign additives which when used even in sparingly small concentrations may enhance the kinetics of hydrate dissociation. In the present work, a class of such additives, never reported before, have been unveiled and christened as Low Dosage Hydrate Dissociation Promoters (LHDPs). The additives were first short listed from a wide potential pool using a lab scale (~250 ml) stirred tank reactor setup and then further studied using a bench scale (~2.35 l) reactor setup where they were injected in the form of a water-additive stream to dissociate hydrates. The dissociation approach followed in the case of the bench scale reactor experiments was a combination of the thermal stimulation and depressurization processes along with the element of injection of additives. For both sets of experiments (lab and bench scale), the newly identified LHDPs were found to enhance the kinetics of methane hydrate dissociation as compared to pure water. It was observed that concentration of additive and its flow rate also affect the kinetics of methane hydrate dissociation. An energy and efficiency analysis for the hydrate dissociation method in the case of bench scale rector revealed that additive presence enhanced the energy ratio and thermal efficiency four fold as compared to pure water.
Improved simultaneous multislice cardiac MRI using readout concatenated k‐space SPIRiT (ROCK‐SPIRiT) (2021)

The proposed ROCK-SPIRiT technique reduces noise and interslice leakage in accelerated SMS cardiac cine MRI, improving on existing methods both quantitatively and qualitatively.
The Structural Genes for a1 and a2 Chains of Human Type IV Collagen Are Divergently Encoded on Opposite DNA Strands and Have an Overlapping (1988)

(1987) 329,721-724). In contrast, most of the genes of complex organisms are dispersed in the ge- nome in widely separated locations. Here, we report that the genes for the a1 and a2 chains of human type IV collagen are encoded on opposite DNA strands from loci that are so closely located that they may be sepa- rated by as little as 42 base pairs. The results provide the first description of two structural genes from a complex organism that code for two polypeptide chains of the same protein molecule but have overlapping 5’- flanking regions.
New liquid crystalline thiadiazole derivatives (1991)

Abstract New ferroelectric smectic thiadiazole derivatives are presented. The dependence of the spontaneous polarization on the chemical structure of the chiral centre and of the mole fraction of achiral-chiral mixtures is discussed.
Occlusion-Aware Method for Temporally Consistent Superpixels (2018)

A wide variety of computer vision applications rely on superpixel or supervoxel algorithms as a preprocessing step. This underlines the overall importance that these approaches have gained in recent years. However, most methods show a lack of temporal consistency or fail in producing temporally stable superpixels. In this paper, we present an approach to generate temporally consistent superpixels for video content. Our method is formulated as a contour-evolving expectation-maximization framework, which utilizes an efficient label propagation scheme to encourage the preservation of superpixel shapes and their relative positioning over time. By explicitly detecting the occlusion of superpixels and the disocclusion of new image regions, our framework is able to terminate and create superpixels whose corresponding image region becomes hidden or newly appears. Additionally, the occluded parts of superpixels are incorporated in the further optimization. This increases the compliance of the superpixel flow with the optical flow present in the scene. Using established benchmark suites, we show the performance of our approach in comparison to state-of-the-art supervoxel and superpixel algorithms for video content.
Tumor Vaccines — Perspectives and Practice (1993)

The immunological approach to cancer treatment and prevention is based on the notion that tumor cells bear antigens that can evoke the production of specific antibodies or more likely cytotoxic T-cells. Numerous studies have indeed implicated such immune reactions, though the number of cases where specific tumor antigens were explicitly demonstrated are much fewer and still controversial. There is, however, an agreement that most of these tumor-associated antigens (TAA) reside in normal cells as well, though, at a concentration and distribution which are below die threshold for immune recognition. Operationally, the long and frustrating debate on whether at all immune approaches for therapy and prevention of cancer can be constituted, is actually behind us.
ONO-4059, A Novel Bruton’s Tyrosine Kinase (Btk) Inhibitor: Synergistic Activity In Combination With Chemotherapy In a ABC-DLBCL Cell Line (2013)

Abstract Purpose Bruton’s tyrosine kinase (Btk) is a key regulator of the B-cell receptor (BCR) signaling pathway and abberant BCR signaling has been implicated in the survival of malignant B-cells. Recent studies indicate that targeting Btk is effective in the treatment of B-cell malignancies. ONO-4059 is a highly potent and selective oral Btk inhibitor with an IC50 in the sub-nmol/L range. The activated B-cell-like (ABC) sub-type of diffuse large B-cell lymphoma (DLBCL) correlates with poor prognosis and a substantial unmet need still exists. The standard treatment with Rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP) for ABC-DLBCL in particular being associated with a poorer outcome. The combination of ONO-4059 with the Bcl-2 inhibitor, ABT-263 has demonstrated greater apoptosis in ABC-DLBCL cell lines than that seen with single agent treatment (Ryohei K. et al., EHA 2013 meeting). To explore rational combinations, ONO-4059 combined with chemotherapy drugs was evaluated in a ABC-DLBCL cell line. Methods ABC-DLBCL cell line (TMD-8) was incubated with ONO-4059 monotherapy (1-1000 nmol/L) and in combination with various agents that target various pathways thought to be involved in DLBCL. Cell viability was determined by the CellTiter-Glo Luminescent Cell Viability Assay. Apoptosis was determined by AnnexinV-FITC/7AAD (AnnV+/7AAD-) staining. Results ONO-4059 inhibited the TMD-8 cell growth and Btk phosphorylation in a concentration-dependent manner, with an IC50 of 3.59 for 72 hr and 23.9 nmol/L for 4 hr respectively. Furthermore, the decrease in Btk phosphorylation subsequently down-regulated Erk phosphorylation. At the 48 hr time-point, 7% of apoptosis occurred in TMD-8 cells at 10 nmol/L, an earlier time-point than that observed for dead cell. After the combination of 10 nmol/L of ONO-4059 with 25 nmol/L of doxorubicin, 500 nmol/L of etoposide, 1.5 nmol/L of vincristine and 1000 nmol/L of dexamethasone, the increased apoptosis ratio was observed, 25, 20, 17 and 29%, respectively. Synergy was observed when ONO-4059 was combined with the CHOP regimen. Conclusion Recent studies indicate that targeting Btk induces BIM expression, the pro-apoptotic protein, following inhibition of Erk phoshphorylation. Our results demonstrate that treatment with ONO-4059 in combination with chemotherapy results in a synergistic effect, inducing apoptosis and is more effective compared with respective monotherapies. ONO-4059 is currently being developed in a Phase I clinical trial for the treatment of B-cell malignancies. Additional combination studies are underway using the TMD-8 xenograft model, testing ONO-4059 in combination with various agents. Disclosures: Yasuhiro: Ono Pharmaceutical Co., Ltd.: Employment. Yoshizawa:Ono Pharmaceutical CO., Ltd: Employment. Birkett:Ono Pharma UK: Employment. Kawabata:Ono Pharmaceutical Co., Ltd.: Employment.
Transparent conductive oxide layer with monolayer closed-pack Al-doped ZnO spheres and their application to a-Si thin-film solar cells (2011)

We report a new (to the best of our knowledge) transparent conductive oxide (TCO) layer with a monolayer of closed-pack Al-doped ZnO (AZO) spheres partly embedded in an AZO thin film. The average transmittance and haze ratio in the wavelength range of 380-800 nm achieves 65% and 55%, respectively, when AZO spheres with a diameter of 500 nm are embedded in a thickness of 240 nm AZO thin films. The a-Si thin-film solar cell with a regular p-i-n TCO structure is demonstrated. Under air mass 1.5 global illumination, conversion efficiencies of 5.6%, a fill factor of 0.55, V(oc) of 0.81 V, and a J(sc) of 2.44 mA/cm² are obtained. The Letter helps us to open up potential applications of a new TCO in advanced solar cells and light-emitting diodes.
ChemInform Abstract: Methods for Drug Discovery: Development of Potent, Selective, Orally Effective Cholecystokinin Antagonists. (1989)

Abstract Various carboxamides such as (III) and (V) are prepared from aminodihydrobenzodiazepinones such as (I).
Newly Identified Pancreatic Protein Islet Amyloid Polypeptide: What Is Its Relationship to Diabetes? (1991)

Islet amyloid polypeptide (IAPP) or amylin is a newly identified 37-amino acid COOH-terminal-amidated polypeptide that is the major protein constituent of amyloid deposits in insulinomas and amyloid deposits in pancreatic islets of non-insulin-dependent (type II) diabetic humans and adult diabetic cats. IAPP is stored with insulin in beta-cell secretory vesicles and is cosecreted with insulin in response to glucose and several secretagogues. IAPP has been demonstrated in normal pancreatic islets of many species, but IAPP-derived amyloid develops commonly in the islets of only a few species (e.g., humans and cats), especially in association with age-related diabetes. IAPP from the human and cat inherently contains a short amyloidogenic sequence that is not present in species that do not form islet amyloid. Studies in animals indicate that an aberration in the synthesis or processing of IAPP, leading to a local increase in concentration of IAPP in the islet, is also required to facilitate the conversion of IAPP to amyloid. The formation of islet amyloid may contribute to the development of type II diabetes by causing disruption of islet cells and by replacement of islets. It has also been proposed that an abnormality of IAPP homeostasis underlies the pathogenesis of type II diabetes. A significant causal relationship between IAPP and type II diabetes is based on reports that IAPP inhibits glucose-stimulated insulin release by beta-cells and that IAPP inhibits insulin-stimulated rates of glycogen synthesis and glucose uptake by skeletal muscle cells.(ABSTRACT TRUNCATED AT 250 WORDS)
DONOR POLYMORPHISM OF TUMOR NECROSIS FACTOR GENE (1999)

The donor TNF-alpha promoter genotype may influence the inflammatory response to HCV reinfection of the graft and contribute to accelerated graft injury. If the association between this genetic marker (TNF308.2) and disease progression is confirmed, it could improve our understanding of HCV pathogenesis and influence donor selection and patient management.
Novel 4'-Substituted and 4',4''-Disubstituted 3.alpha.-(Diphenylmethoxy)tropane Analogs as Potent and Selective Dopamine Uptake Inhibitors (1995)

A series of 4'-substituted and 4',4"-disubstituted 3 alpha-(diphenylmethoxy)tropane analogs were prepared as novel probes for the dopamine transporter. These compounds were evaluated in radiolabeled binding assays for the dopamine, norepinephrine, and serotonin transporters. All of these compounds monophasically displaced [3H]WIN 35,428 binding in rat caudate putamen with Ki values ranging from 11.8 to 2000 nM. The most potent compound in this series was 4',4"-difluoro 3 alpha-(diphenylmethoxy)tropane 7c with a Ki = 11.8 nM. All of the compounds inhibited dopamine uptake in rat caudate putamen (IC50 = 24-4456 nM) which correlated significantly (r = 0.907; p > 0.0001) with binding affinities at the dopamine transporter. None of the compounds demonstrated high-affinity binding at the norepinephrine (Ki > 4800 nM) or serotonin (Ki > 690 nM) transporters. Therefore, the most potent dopamine uptake inhibitors in this series were highly selective for the dopamine transporter. Preliminary behavioral studies of several of these analogs (7a-e) suggested that the compounds did not display a cocaine-like behavioral profile, despite their ability to inhibit dopamine uptake. The present data coupled with the observed differences from cocaine in structure-activity relationships suggested that the 3 alpha-(diphenylmethoxy)tropane analogs may be interacting at a different active site than cocaine on the dopamine transporter and that an additional binding domain might be exploited for the identification of potential therapeutics for the treatment of cocaine abuse.
Identification of New Antigens in Visceral Leishmaniasis by Expression Cloning and Immunoblotting with Sera of Kala-Azar Patients from Bihar, India (2005)

Sera of kala-azar patients from Bihar, India, were used to identify Leishmania donovani antigens encoded by a phage expression library. Ten antigens were identified, five of which have not been described as leishmania antigens before. The antigens specifically react with sera of leishmania-infected patients but not of toxoplasma- or plasmodium-infected patients.