gebhart/patrepeval huggingface dataset:
A Parallel Decomposition Solver for SVM: Distributed dual ascend using Fenchel Duality (2008)

We introduce a distributed algorithm for solving large scale support vector machines (SVM) problems. The algorithm divides the training set into a number of processing nodes each running independently an SVM sub-problem associated with its subset of training data. The algorithm is a parallel (Jacobi) block-update scheme derived from the convex conjugate (Fenchel duality) form of the original SVM problem. Each update step consists of a modified SVM solver running in parallel over the sub-problems followed by a simple global update. We derive bounds on the number of updates showing that the number of iterations (independent SVM applications on sub-problems) required to obtain a solution of accuracy isin is O(log(1/isin)). We demonstrate the efficiency and applicability of our algorithms by running on large scale experiments on standardized datasets while comparing the results to the state-of-the-art SVM solvers.
Constitutive CD40 signaling in B cells selectively activates the noncanonical NF-κB pathway and promotes lymphomagenesis (2008)

CD40, a member of the tumor necrosis factor (TNF) receptor family, plays an essential role in T cell-dependent immune responses. Because CD40 is widely expressed on the surface of tumor cells in various B cell malignancies, deregulated CD40 signaling has been suggested to contribute to lymphomagenesis. In this study, we show that B cell-specific expression of a constitutively active CD40 receptor, in the form of a latent membrane protein 1 (LMP1)/CD40 chimeric protein, promoted an increase in the number of follicular and marginal zone B cells in secondary lymphoid organs in transgenic mice. The B cells displayed an activated phenotype, prolonged survival and increased proliferation, but were significantly impaired in T cell-dependent immune responses. Constitutive CD40 signaling in B cells induced selective and constitutive activation of the noncanonical NF-kappaB pathway and the mitogen-activated protein kinases Jnk and extracellular signal-regulated kinase. LMP1/CD40-expressing mice older than 12 mo developed B cell lymphomas of mono- or oligoclonal origin at high incidence, thus showing that the interplay of the signaling pathways induced by constitutive CD40 signaling is sufficient to initiate a tumorigenic process, ultimately leading to the development of B cell lymphomas.
Verifying and testing expert system conceptual models (2003)

The authors recommend a two-phase approach to validating expert systems: (1) to use verification tools and techniques to establish formally specifiable properties of the expert system, such as freedom from logical redundancy, inconsistency, and deficiency; and (2) to use evaluation techniques to identify critical areas of expert system functionality and to identify sets of test cases for those areas. A verification tool can then be used to establish whether the expert system functions correctly, according to these test cases. This approach is elucidated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Kahalalides:  Bioactive Peptides from a Marine Mollusk Elysia rufescens and Its Algal Diet Bryopsis sp.1 (1996)

In addition to the previously reported bioactive kahalalide F six new peptides are described. Six of these, including kahalalide F, are cyclic depsipeptides, ranging from a C(31) tripeptide to a C(75) tridecapeptide isolated from a sacoglossan mollusk, Elysiarufescens. The mollusk feeds on a green alga, Bryopsis sp., which has also been shown to elaborate some of these peptides in smaller yields, in addition to an acyclic analog of F, kahalalide G. The bioassay results of antitumor, antiviral, antimalarial, and OI (activity against AIDS opportunistic infections) tests are reported.
Identification of a secreted Mr 95,000 glycoprotein in human melanocytes and melanomas by a melanocyte specific monoclonal antibody. (1988)

We have isolated a monoclonal antibody, designated HMB-50, that is highly specific for melanomas and melanocyte derived lesions. The antibody recognizes melanomas, neonatal melanocytes, and junctional nevi but does not react with adult melanocytes, dermal nevi, or a variety of non-melanocyte derived neoplasms. In tissue culture, the antibody reacts with five of seven human melanoma lines and neonatal foreskin melanocytes but fails to recognize fibroblasts and a number of different carcinomas. HMB-50 identifies a Mr 95,000 glycoprotein that is released into the growth medium by melanoma cells and neonatal melanocytes in vitro. This molecule is unrelated to antigens recognized by a variety of antimelanoma monoclonal antibodies isolated in other laboratories. The Mr 95,000 glycoprotein has been purified by antibody affinity chromatography and a polyclonal rabbit antiserum raised that exhibits identical specificity to the monoclonal antibody. The Mr 95,000 glycoprotein is rapidly released by melanoma cells (within 60 min) and one line produces relatively large quantities of the molecule (1 microgram/10(6) cells/24 h). The molecule in normal melanocytes differs slightly in electrophoretic mobility compared to its counterpart in melanomas and this difference appears to result from posttranslational modification.
Stable Expression of the Golgi Form and Secretory Variants of Human Fucosyltransferase III from BHK-21 Cells (1997)

Stable BHK-21 cell lines were constructed expressing the Golgi membrane-bound form and two secretory forms of the human alpha1, 3/4-fucosyltransferase (amino acids 35-361 and 46-361). It was found that 40% of the enzyme activity synthesized by cells transfected with the Golgi form of the fucosyltransferase was constitutively secreted into the medium. The corresponding enzyme detected by Western blot had an apparent molecular mass similar to those of the truncated secretory forms. The secretory variant (amino acids 46-361) was purified by a single affinity-chromatography step on GDP-Fractogel resin with a 20% final recovery. The purified enzyme had a unique NH2 terminus and contained N-linked endo H sensitive carbohydrate chains at its two glycosylation sites. The fucosyltransferase transferred fucose to the O-4 position of GlcNAc in small oligosaccharides, glycolipids, glycopeptides, and glycoproteins containing the type I Galbeta1-3GlcNAc motif. The acceptor oligosaccharide in bovine asialofetuin was identified as the Man-3 branched triantennary isomer with one Galbeta1-3GlcNAc. The type II motif Galbeta1-4GlcNAc in bi-, tri-, or tetraantennary neutral or alpha2-3/alpha2-6 sialylated oligosaccharides with or without N-acetyllactosamine repeats and in native glycoproteins were not modified. The soluble forms of fucosyltransferase III secreted by stably transfected cells may be used for in vitro synthesis of the Lewisa determinant on carbohydrates and glycoproteins, whereas Lewisx and sialyl-Lewisx structures cannot be synthesized.
DCT-based motion estimation (1998)

We propose novel discrete cosine transform (DCT) pseudophase techniques to estimate shift/delay between two one-dimensional(1-D) signals directly from their DCT coefficients by computing the pseudophase shift hidden in DCT and then employing the sinusoidal orthogonal principles, applicable to signal delay estimation remote sensing. Under the two-dimensional (2-D) translational motion model, we further extend the pseudophase techniques to the DCT-based motion estimation (DXT-ME) algorithm for 2-D signals/images. The DXT-ME algorithm has certain advantages over the commonly used full search block-matching approach (BKM-ME) for application to video coding despite certain limitations. In addition to its robustness in a noisy environment and low computational complexity, O(M(2)) for an MxM search range in comparison to the O(N(2) . M(2)) complexity of BKM-ME for an NxN block, its ability to estimate motion completely in DCT domain makes possible the fully DCT-based motion-compensated video coder structure, which has only one major component in the feedback loop instead of three as in the conventional hybrid video coder design, and thus results in a higher system throughput. Furthermore, combination of the DCT and motion estimation units can provide space for further optimization of the overall coder. In addition, the DXT-ME algorithm has solely highly parallel local operations and this property makes feasible parallel implementation suitable for very large scale integration (VLSI) design. Simulation on a number of video sequences is presented with comparison to BKM-ME and other fast block search algorithms for video coding applications even though DXT-ME is completely different from any block search algorithms.
Antiemetic Efficacy of Dexamethasone Therapy in Patients Receiving Cancer Chemotherapy (1983)

To assess the value of high-dose dexamethasone therapy in preventing the gastrointestinal (GI) side effects of chemotherapy, a randomized double-blind study was conducted in women receiving outpatient therapy for breast cancer. Single-dose dexamethasone sodium phosphate (10 mg) or placebo was administered intravenously in 57 trials in 22 women immediately before chemotherapy. Questionnaires (administered before therapy and 24 hours later) were compared for evidence of nausea, vomiting, and anorexia produced by chemotherapy. No GI intolerance to chemotherapy was noted in 24 (83%) of the 29 dexamethasone trials v 16 (57%) of the 28 placebo trials. Dexamethasone trials produced the following results: no side effects in 50% (14/29), insomnia the night after chemotherapy in 21% (6/29), an increase in energy levels in 24% (7/29), and an improvement in mood in 14% (4/29). High-dose dexamethasone therapy has useful application in alleviating the emetic effects of cancer chemotherapy.
MicroRNA in Cutaneous Wound Healing: A New Paradigm (2007)

Repair of a defect in the human skin is a highly orchestrated physiological process involving numerous factors that act in a temporally resolved synergistic manner to re-establish barrier function by regenerating new skin. The inducible expression and repression of genes represents a key component of this regenerative process. MicroRNAs (miRNAs) are approximately 22-nucleotide-long endogenously expressed non-coding RNAs that regulate the expression of gene products by inhibition of translation and/or transcription in animals. miRNAs play a key role in skin morphogenesis and in regulating angiogenesis. The vascular endothelial growth factor signaling path seems to be under repressor control by miRNAs. Mature miRNA-dependent mechanisms impair angiogenesis in vivo. It is critically important to recognize that the understanding of cutaneous wound healing is incomplete without appreciating the functional significance of wound-induced miRNA. Ongoing work in our laboratory has led to the observation that the cutaneous wound healing process involves changes in the expression of specific miRNA at specific phases of wound healing. We hypothesize that dysregulation of specific miRNA is critical in derailing the healing sequence in chronic problem wounds. If tested positive, this hypothesis is likely to lead to completely novel diagnostic and therapeutic strategies for the treatment of problem wounds.
Cytotoxicity and antibacterial activity of Methanolic extract of Hibiscus sabdariffa (2007)

The use of medicinal plants as raw materials in the production of drugs is again gaining popularity. Hibiscus sabdariffa is widely taken in the South-western part of Nigeria for the treatment of various diseases. Aqueous-methanolic extract of H. sabdariffa was investigated for its phytochemical con-stituents, antimicrobial activity and cytotoxicity using brine shrimps lethality assay. The extract was found to contain cardiac glycosides, flavonoids, saponins andalkaloids. It exhibited antibacterial activities (MIC 0.30 ± 0.2- 1.30 ± 0.2 mg/ml) againstStaphylococcus aureus, Bacillus stearothermo-philus, Micrococcus luteus, Serratia mascences, Clostridium sporogenes, Escherichia coli, Klebsiella pneumoniae, Bacillus cereus, Pseudomonas fluorescence. It was also found to be potent against brine shrimps with LC50   value of 55.1 ppm. The present results support the use of this plant in the treatment of diseases like abscesses, bilious conditions, cancer and coughs in traditional medicine and also suggest the possibility of isolating antibacterial and anticancer agents from Hibiscus sabdariffa.

	 

	Key words: Hibiscus sabdariffa; antimicrobial activity; brine shrimps lethality assay
The ParaView Coprocessing Library: A scalable, general purpose in situ visualization library (2011)

As high performance computing approaches exascale, CPU capability far outpaces disk write speed, and in situ visualization becomes an essential part of an analyst's workflow. In this paper, we describe the ParaView Coprocessing Library, a framework for in situ visualization and analysis coprocessing. We describe how coprocessing algorithms (building on many from VTK) can be linked and executed directly from within a scientific simulation or other applications that need visualization and analysis. We also describe how the ParaView Coprocessing Library can write out partially processed, compressed, or extracted data readable by a traditional visualization application for interactive post-processing. Finally, we will demonstrate the library's scalability in a number of real-world scenarios.
High-Density Microwell Chip for Culture and Analysis of Stem Cells (2009)

With recent findings on the role of reprogramming factors on stem cells, in vitro screening assays for studying (de)-differentiation is of great interest. We developed a miniaturized stem cell screening chip that is easily accessible and provides means of rapidly studying thousands of individual stem/progenitor cell samples, using low reagent volumes. For example, screening of 700,000 substances would take less than two days, using this platform combined with a conventional bio-imaging system. The microwell chip has standard slide format and consists of 672 wells in total. Each well holds 500 nl, a volume small enough to drastically decrease reagent costs but large enough to allow utilization of standard laboratory equipment. Results presented here include weeklong culturing and differentiation assays of mouse embryonic stem cells, mouse adult neural stem cells, and human embryonic stem cells. The possibility to either maintain the cells as stem/progenitor cells or to study cell differentiation of stem/progenitor cells over time is demonstrated. Clonality is critical for stem cell research, and was accomplished in the microwell chips by isolation and clonal analysis of single mouse embryonic stem cells using flow cytometric cell-sorting. Protocols for practical handling of the microwell chips are presented, describing a rapid and user-friendly method for the simultaneous study of thousands of stem cell cultures in small microwells. This microwell chip has high potential for a wide range of applications, for example directed differentiation assays and screening of reprogramming factors, opening up considerable opportunities in the stem cell field.
A BLUE FLUORESCENT PROTEIN FROM A YELLOW‐EMITTING LUMINOUS BACTERIUM (1992)

Vibrio fischeri strain Y1 emits yellow light in vivo due to the participation of a yellow fluorescent protein (YFP) in the luciferase reaction. In this study it was found that the organism also produces a protein (referred to as Y1-BFP) emitting strong blue fluorescence. Its molecular weight, about 25 kDa, is the same as or very close to that of YFP. The fluorescence excitation and emission maxima of the purified Y1-BFP are at 416 and 461 nm, respectively, and the fluorescence lifetime is 12.5 ns at 2 degrees C. The molar extinction coefficient of Y1-BFP at 416 nm was estimated to be approx. 9500. With the homologous luciferase, Y1-BFP decreases the intensity and rate of decay in the in vitro reaction but has no effect on its emission spectrum (in contrast to YFP, which has a striking effect on the spectrum). With luciferase isolated from Vibrio harveyi, however, Y1-BFP causes a small blue-shift (approximately 10 nm) in the emission of the enzyme catalyzed reaction, whereas YFP has no effect on the emission spectrum.
Body fat from body density: underwater weighing vs. dual-photon absorptiometry (1989)

We measured fat in 286 healthy volunteers by underwater weighing (FUWW) and dual-photon absorptiometry (FDPA) to develop a translation table for the differing results from these entirely different techniques and to study the sources of these differences. In 99 males and 187 females aged 19-94 yr, fatness was 7-47%. Prediction equations are presented for FUWW-FDPA (delta F), density of lean body mass (DLBM), and FDPA. FUWW and FDPA were significantly different from each other (P less than 0.01). Calculated DLBM is less than the assumed constant of 1.10 (P less than 0.01), ranging widely from 1.05 to 1.13 and being highly correlated with the ratio of total body bone mineral to lean body mass (TBBM/LBM). delta F, the differences between FUWW and FDPA measurements in individual subjects, varied widely (-7 to +11% in males and -18 to +13% in females). The difference was positively correlated with the DLBM. FUWW was no better than anthropometrics in equations for predicting FDPA. The FDPA predicted from anthropometrics showed smaller standard errors than when FUWW was used. Neither anthropometrics nor FUWW equations are clearly superior to those previously available.
Organic reactions at high pressure. Preparation of Wittig phosphonium salts at ambient temperature (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganic reactions at high pressure. Preparation of Wittig phosphonium salts at ambient temperatureWilliam G. Dauben, John M. Gerdes, and Richard A. BunceCite this: J. Org. Chem. 1984, 49, 22, 4293–4295Publication Date (Print):November 1, 1984Publication History Published online1 May 2002Published inissue 1 November 1984https://pubs.acs.org/doi/10.1021/jo00196a036https://doi.org/10.1021/jo00196a036research-articleACS PublicationsRequest reuse permissionsArticle Views1927Altmetric-Citations31LEARN 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
Electroporation of Agrobacterium tumefaciens (2003)

Agrobacterium tumefaciens is a soil bacterium that causes tumors on dicotyledonous plants. Virulent strains harbor a large plasmid, the Ti (tumor-inducing) plasmid, which is involved in tumorigenesis. A small segment of this plasmid, the T-DNA, is transferred to the plant cell and becomes integrated into one of the chromosomes in the nucleus. The T-DNA contains genes for the production of phytohormones viz an auxin and a cytokinin. Therefore, expression of the T-DNA in the plant cell leads to tumor formation (for review, see ref. 1). Deletion of the onc genes within the T region of the Ti plasmid results in nononcogenic strains. However, if the 24-bp border repeat, which surrounds the T region in the Ti plasmid, is kept intact, the mutated T-DNA is still delivered to plant cells by Agrobacterium. This natural plant vector system is used for the genetic engineering of plants (for review, see ref. 2). If genes are added to the T region of the Ti plasmid, these are cotransferred to the plant cell. An important finding was that separating the T region from the remaining part of the Ti plasmid did not prevent transfer of the T-DNA to the plant cell (3). On the basis of this principle, the binary vector system was developed. Binary vectors are wide host-range plasmids that are maintained by both E. coli and A. tumefaciens and contain an artificial T region into which genes of interest can be cloned. Traditionally, cloning with binary vectors is done in E. coli. The resulting vector is then introduced into an A. tumefaciens helper strain for delivery of the T-DNA to plant cells.
Asymmetric .ALPHA.-alkylation of cyclohexanone by mediation of a chiral ligand and the leaving-group effect of electrophiles on enantioselectivity. (1989)

By the mediation of a chiral amino ether (4), the asymmetric α-benzylation of cyclohexanone (1) was effected via an achiral lithioenamine (6) to give α-benzylcyclohexanone (3) in up to 52% ee. A dramatic leaving-group effect of electrophiles on enantioselectivity was also observed.
All-trans retinoic acid (ATRA) suppresses transcription of human papillomavirus type 16 (HPV16) in a dose-dependent manner. (2004)

Earlier we found that SiHa cervical squamous carcinoma cells that harbor HPV type 16 respond to ATRA treatment in a dose-dependent manner: high-dose (10(-5)-10(-4) M) but not low-dose (10(-7)-10(-6) M) ATRA induced growth arrest. Growth of HPV-infected cells is highly dependent on the expression of the viral E6/E7 proteins. Thus, targeting expression of the viral E6/E7 genes might influence growth properties of HPV-infected cells. Here, we demonstrated that high-dose ATRA inhibited expression of HPV16 E7 through suppression of the HPV16 promoter (p97) activity. Gelshift assay (EMSA) revealed that binding of the AP-1 transcription factor to an oligonucleotide originated from the HPV type 16 promoter was diminished after high-dose, but not low-dose ATRA treatment. This suggests that high-dose ATRA suppresses HPV 16 promoter activity, at least in part, via a decreased AP-1 binding. Our data might be useful in treatment of cervical dysplasias and/or carcinomas.
Analysis of the Streptococcus downei gtfS gene, which specifies a glucosyltransferase that synthesizes soluble glucans (1990)

The complete nucleotide sequence was determined for the Streptococcus downei (previously Streptococcus sobrinus) MFe28 gtfS gene which specifies a glucosyltransferase (GTF-S) producing water-soluble glucan. A single open reading frame which encodes a mature protein with a molecular weight of 147,408 (1,328 amino acids) and a putative signal peptide 36 or 37 amino acids in length was detected. GTF-S shares extensive sequence similarity with GTF-I (gtfI) from S. downei and GTF-I (gtfB) and GTF-SI (gtfC) from Streptococcus mutans. GTF-S contains a highly conserved enzymatic domain and C-terminal repeated sequences which appear to be involved in glucan binding. Comparison of the deduced GTF-S protein sequence with other sequenced GTF genes of mutans streptococci revealed that these C-terminal repeats occurred in all cases, although the patterns of repeated sequences varied with respect to each other and to the glucan-binding protein of S. mutans. GTF-S contains four C-terminal repeat sequences ranging from 49 to 51 amino acids in length and a partial repeat of 13 amino acids. Nuclear magnetic resonance analysis of the glucan produced by GTF-S revealed that the product consisted of more than 90% alpha-1,6-linked glucosyl residues.