gebhart/patrepeval huggingface dataset:
Rethinking SIMD Vectorization for In-Memory Databases (2015)

Analytical databases are continuously adapting to the underlying hardware in order to saturate all sources of parallelism. At the same time, hardware evolves in multiple directions to explore different trade-offs. The MIC architecture, one such example, strays from the mainstream CPU design by packing a larger number of simpler cores per chip, relying on SIMD instructions to fill the performance gap. Databases have been attempting to utilize the SIMD capabilities of CPUs. However, mainstream CPUs have only recently adopted wider SIMD registers and more advanced instructions, since they do not rely primarily on SIMD for efficiency. In this paper, we present novel vectorized designs and implementations of database operators, based on advanced SIMD operations, such as gathers and scatters. We study selections, hash tables, and partitioning; and combine them to build sorting and joins. Our evaluation on the MIC-based Xeon Phi co-processor as well as the latest mainstream CPUs shows that our vectorization designs are up to an order of magnitude faster than the state-of-the-art scalar and vector approaches. Also, we highlight the impact of efficient vectorization on the algorithmic design of in-memory database operators, as well as the architectural design and power efficiency of hardware, by making simple cores comparably fast to complex cores. This work is applicable to CPUs and co-processors with advanced SIMD capabilities, using either many simple cores or fewer complex cores.
Improvement of Patient Convenience in Treatment with Growth Hormone (1994)

Patient compliance is of vital importance for the outcome of any medical therapy. Compliance is a problem especially in the treatment of non-life-threatening conditions, such as growth retardation in children, where motivation can be low and the rewards delayed. One way to improve compliance is through an improvement in patient convenience. As a result of these considerations as well as the positive experiences reported with insulin pen treatment, an injection pen for growth hormone administration (Nordiject) has been introduced. Results from several patient acceptance studies have shown that the injection pen and the preparation for use in the pen have been found effective and safe with good local tolerability and reduced perception of injection pain. The injection pen was found to simplify the injection procedure and was strongly preferred to conventional syringes and vials. Special attention has been paid to local discomfort and injection pain. A double-blind, randomized cross-over study has shown that 0.9% benzyl alcohol solvent causes statistically significantly less local discomfort that a 0.25% metacresol solvent when used for reconstitution of growth hormone. In another study the 30G needle was compared with 27G, and the use of the 30G needle seems also to give a reduction in injection pain. A further reduction in injection pain can be gained by improving the needle insertion technique. A randomized cross-over study compared two experimental devices, one with manual and one with automatic needle insertion. The results from this study showed a statistically significantly lower injection pain score for the automatic device compared to the manual. The above studies have shown that it is possible to improve patient convenience. Long-term studies will show whether this improvement results in improved compliance and hence a better treatment outcome.
Design of Potent and Selective 2-Aminobenzimidazole-Based p38α MAP Kinase Inhibitors with Excellent in Vivo Efficacy (2005)

We report the design and discovery of a 2-aminobenzimidazole-based series of potent and highly selective p38alphainhibitors. The lead compound 1 had low-nanomolar activity in both ATP competitive enzyme binding and inhibition of TNFalpha release in macrophages. Compound 18 showed excellent pharmacokinetics properties and oral activity in the rat collagen induced arthritis model compared with other p38 reference compounds. A SAR strategy to address CyP3A4 liability is also described.
Herb's bipolar transistors (2001)

The profound influence of Herbert Kroemer's ideas on the development of high-performance bipolar transistors is described. The historical context and subsequent development of innovations such as the drift base, achieved through concentration gradients and later with semiconductor bandgap grading, the use of wide bandgap emitters, concepts of collector-up transistors, and the introduction of new heterojunction materials, are reviewed.
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides (2012)

In the context of the renewed interest of peptides as therapeutics, it is important to have an on-line resource for 3D structure prediction of peptides with well-defined structures in aqueous solution. We present an updated version of PEP-FOLD allowing the treatment of both linear and disulphide bonded cyclic peptides with 9-36 amino acids. The server makes possible to define disulphide bonds and any residue-residue proximity under the guidance of the biologists. Using a benchmark of 34 cyclic peptides with one, two and three disulphide bonds, the best PEP-FOLD models deviate by an average RMS of 2.75 Å from the full NMR structures. Using a benchmark of 37 linear peptides, PEP-FOLD locates lowest-energy conformations deviating by 3 Å RMS from the NMR rigid cores. The evolution of PEP-FOLD comes as a new on-line service to supersede the previous server. The server is available at: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD.
Identification and Characterization of GCP16, a Novel Acylated Golgi Protein That Interacts with GCP170 (2003)

GCP170, a member of the golgin family associated with the cytoplasmic face of the Golgi membrane, was found to have a Golgi localization signal at the NH2-terminal region (positions 137-237). Using this domain as bait in the yeast two-hybrid screening system, we identified a novel protein that interacted with GCP170. The 2.0-kilobase mRNA encoding a 137-amino acid protein of 16 kDa designated GCP16 was ubiquitously expressed. Immunofluorescence microscopy showed that GCP16 was co-localized with GCP170 and giantin in the Golgi region. Despite the absence of a hydrophobic domain sufficient for participating in membrane localization, GCP16 was found to be tightly associated with membranes like an integral membrane protein. Labeling experiments with [3H]palmitic acid and mutational analysis demonstrated that GCP16 was acylated at Cys69 and Cys72, accounting for its tight association with the membrane. A mutant without potential acylation sites (C69A/C72A) was no longer localized to the Golgi, indicating that the acylation is prerequisite for the Golgi localization of GCP16. Although the mutant GCP16, even when overexpressed, had no effect on protein transport, overexpression of the wild type GCP16 caused an inhibitory effect on protein transport from the Golgi to the cell surface. Taken together, these results indicate that GCP16 is the acylated membrane protein, associated with GCP170, and possibly involved in vesicular transport from the Golgi to the cell surface.
Context-based vision system for place and object recognition (2003)

While navigating in an environment, a vision system has to be able to recognize where it is and what the main objects in the scene are. We present a context-based vision system for place and object recognition. The goal is to identify familiar locations (e.g., office 610, conference room 941, main street), to categorize new environments (office, corridor, street) and to use that information to provide contextual priors for object recognition (e.g., tables are more likely in an office than a street). We present a low-dimensional global image representation that provides relevant information for place recognition and categorization, and show how such contextual information introduces strong priors that simplify object recognition. We have trained the system to recognize over 60 locations (indoors and outdoors) and to suggest the presence and locations of more than 20 different object types. The algorithm has been integrated into a mobile system that provides realtime feedback to the user.
Production and functional activity of a recombinant von Willebrand factor-A domain from human complement factor B (1999)

Factor B is a five-domain 90 kDa serine protease proenzyme which is part of the human serum complement system. It binds to other complement proteins C3b and properdin, and is activated by the protease factor D. The fourth domain of factor B is homologous to the type A domain of von Willebrand Factor (vWF-A). A full-length human factor B cDNA clone was used to amplify the region encoding the vWF-A domain (amino acids 229-444 of factor B). A fusion protein expression system was then used to generate it in high yield in Escherichia coli, where thrombin cleavage was used to separate the vWF-A domain from its fusion protein partner. A second vWF-A domain with improved stability and solubility was created using a Cys(267)-->Ser mutation and a four-residue C-terminal extension of the first vWF-A domain. The recombinant domains were investigated by analytical gel filtration, sucrose density centrifugation and analytical ultracentrifugation, in order to show that both domains were monomeric and possessed compact structures that were consistent with known vWF-A crystal structures. This expression system and its characterization permitted the first investigation of the function of the isolated vWF-A domain. It was able to inhibit substantially the binding of (125)I-labelled factor B to immobilized C3b. This demonstrated both the presence of a C3b binding site in this portion of factor B and a ligand-binding property of the vWF-A domain. The site at which factor D cleaves factor B is close to the N-terminus of both recombinant vWF-A domains. Factor D was shown to cleave the vWF-A domain in the presence or absence of C3b, whereas the cleavage of intact factor B under the same conditions occurs only in the presence of C3b.
Characterisation of the growth regulating gene IMP3, a candidate for Silver-Russell syndrome (2002)

A 67 year old man with a clinical diagnosis of attenuated familial adenomatous polyposis (AFAP) and a past history of synchronous colon cancers in the transverse colon was also found to have an intraductal papillary mucinous neoplasm (IPMN) of the pancreas. In addition, several foci of heterotopic gastric oxyntic mucosa were noted in the duodenum, interspersed with flat and polypoid adenomas. The duodenal adenomas showed low grade dysplasia, loss of adenomatous polyposis coli (APC) protein expression, but retention of β&nbsp;catenin staining, localised to the nucleus and cytoplasm. The IPMN in the pancreas showed an identical immunohistochemical profile to the duodenal adenomas. The heterotopic gastric foci in the duodenum were negative for the APC protein, and β&nbsp;catenin staining was membranous in location. Although the patient did not show germline truncating APC mutations or mutations in the MYH gene, the past history, clinical features, and immunohistochemical profile of the various lesions suggest strongly that the IPMN is part of the spectrum of lesions encountered in AFAP. Whether the heterotopic oxyntic gastric mucosa in the duodenum is also related is unclear, but it may represent a forme fruste of fundic gland polyps.
NF-κB in Cellular Senescence and Cancer Treatment (2014)

The NF-κB pathway transcriptionally controls a large set of target genes that play important roles in cell survival, inflammation, and immune responses. While many studies showed anti-tumorigenic and pro-survival role of NF-κB in cancer cells, recent findings postulate that NF-κB participates in a senescence-associated cytokine response, thereby suggesting a tumor restraining role of NF-κB. In this review, we discuss implications of the NF-κB signaling pathway in cancer. Particularly, we emphasize the connection of NF-κB with cellular senescence as a response to chemotherapy, and furthermore, present examples how distinct oncogenic network contexts surrounding NF-κB produce fundamentally different treatment outcomes in aggressive B-cell lymphomas as an example.
A new approach to generating antitumor effectors for adoptive immunotherapy using human adherent lymphokine-activated killer cells. (1988)

Lymphocytes from human peripheral blood incubated with interleukin-2 (IL2) develop lymphokine-activated killer (LAK) activity with the ability to kill a wide variety of tumor cells in a non-major histocompatibility complex-restricted manner. Adoptive immunotherapy with LAK cells and IL2 has been reported to lead to a regression of solid tumors in some patients with advanced malignancies. Aiming to improve the effectiveness of clinical adoptive immunotherapy, we developed a procedure for selective enrichment from human blood mononuclear cells (MNC) of IL2-activated antitumor effector cells. These cells, termed adherent LAK (A-LAK) cells because of their characteristic property of adherence to plastic, demonstrated both higher proliferative potential and greater antitumor cytotoxicity than unseparated MNC. Human A-LAK cells represented only 1 to 4% of IL2-activated MNC at 24 h but expanded from 130- to 1100-fold in 20 days. They comprised a population highly enriched in CD3-Leu19+ effector cells with antitumor activity against fresh human solid tumor cells and established cell lines. A-LAK cells retained antitumor activity for up to 14 days when cultured in the presence of IL2. They also mediated antibody-dependent cytotoxicity. Large-scale generation of A-LAK cells from the blood of patients with cancer proved feasible and should yield populations that are effective in vivo at lower doses than those required with unseparated LAK cells. This offers the potential for improving the antitumor effects, reducing the toxicity, and facilitating the administration of adoptive immunotherapy in humans. A Phase I/II clinical trial utilizing A-LAK cells and IL2 in patients with melanoma and renal cell carcinoma is now in progress.
Chemistry of heterocyclic compounds series. 110. Synthesis of vinyl derivatives of phenanthroline and bipyridine (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of heterocyclic compounds series. 110. Synthesis of vinyl derivatives of phenanthroline and bipyridineGeorge R. Newkome, Garry E. Kiefer, Noboru Matsumura, and Wallace E. PuckettCite this: J. Org. Chem. 1985, 50, 20, 3807–3810Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/jo00220a025https://doi.org/10.1021/jo00220a025research-articleACS PublicationsRequest reuse permissionsArticle Views513Altmetric-Citations11LEARN 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
IgG Fc Receptors (2001)

Since the description of the first mouse knockout for an IgG Fc receptor seven years ago, considerable progress has been made in defining the in vivo functions of these receptors in diverse biological systems. The role of activating Fc gamma Rs in providing a critical link between ligands and effector cells in type II and type III inflammation is now well established and has led to a fundamental revision of the significance of these receptors in initiating cellular responses in host defense, in determining the efficacy of therapeutic antibodies, and in pathological autoimmune conditions. Considerable progress has been made in the last two years on the in vivo regulation of these responses, through the appreciation of the importance of balancing activation responses with inhibitory signaling. The inhibitory FcR functions in the maintenance of peripheral tolerance, in regulating the threshold of activation responses, and ultimately in terminating IgG mediated effector stimulation. The consequences of deleting the inhibitory arm of this system are thus manifested in both the afferent and efferent immune responses. The hyperresponsive state that results leads to greatly magnified effector responses by cytotoxic antibodies and immune complexes and can culminate in autoimmunity and autoimmune disease when modified by environmental or genetic factors. Fc gamma Rs offer a paradigm for the biological significance of balancing activation and inhibitory signaling in the expanding family of activation/inhibitory receptor pairs found in the immune system.
Design of DPSS based fiber bragg gratings and their application in all-optical encryption, OCDMA, optical steganography, and orthogonal-division multiplexing (2014)

The future information infrastructure will be affected by limited bandwidth of optical networks, high energy consumption, heterogeneity of network segments, and security issues. As a solution to all problems, we advocate the use of both electrical basis functions (orthogonal prolate spheroidal basis functions) and optical basis functions, implemented as FBGs with orthogonal impulse response in addition to spatial modes. We design the Bragg gratings with orthogonal impulse responses by means of discrete layer peeling algorithm. The target impulse responses belong to the class of discrete prolate spheroidal sequences, which are mutually orthogonal regardless of the sequence order, while occupying the fixed bandwidth. We then design the corresponding encoders and decoders suitable for all-optical encryption, optical CDMA, optical steganography, and orthogonal-division multiplexing (ODM). Finally, we propose the spectral multiplexing-ODM-spatial multiplexing scheme enabling beyond 10 Pb/s serial optical transport networks.
Organization and regulation of the Corynebacterium glutamicum hom‐thrB and thrC loci (1988)

The genes encoding the three terminal enzymes in the threonine biosynthetic pathway, homoserine dehydrogenase (hom), homoserine kinase (thrB) and threonine synthase (thrC) have been isolated from Corynebacterium glutamicum. The C. glutamicum hom and thrB genes were subcloned on a 3.6 kb SalI-generated chromosomal fragment. The C. glutamicum thrC gene was shown not to be linked to the hom-thrB locus. L-methionine represses the cloned homoserine dehydrogenase and homoserine kinase similar to that of the chromosomally encoded hom and thrB gene products. Northern hybridization analysis demonstrates that this repression is mediated at the level of transcription and that hom-thrB represents an operon in C. glutamicum.
Induction of Vascular Endothelial Growth Factor by Platelet-Activating Factor and Platelet-Derived Growth Factor is Downregulated by Corticosteroids (1997)

Vascular endothelial growth factor (VEGF) is a potent peptide growth factor specific for vascular endothelial cells, which promotes neovascularization and increases vascular permeability in vivo. Enhanced microvascular permeability and edema are common characteristics of inflammatory and neoplastic disorders. Two proinflammatory mediators, platelet-activating factor (PAF) and platelet-derived growth factor (PDGF), are known to contribute to cellular damage and tissue remodeling in a number of lung diseases. To determine whether PAF or PDGF induce VEGF gene expression in primary cultures of human pulmonary fibroblasts and pulmonary vascular smooth-muscle cells (VSMCs), we performed Northern-blot analysis and enzyme-linked immunosorbent assays (EIA). PAF and all three isoforms of PDGF (PDGF-AA, -AB, and -BB) increased VEGF mRNA in a time- and dose-dependent manner. While PAF was shown to increase VEGF mRNA at picomolar concentrations, all PDGF isoforms were effective in inducing VEGF mRNA at nanomolar concentrations. The transcriptional activation was accompanied by increased levels of VEGF protein as determined by EIA in culture medium. These results indicate that VEGF gene expression in VSMCs and fibroblasts is mediated by PAF and/or PDGF isoforms. In a paracrine mode of action, secreted VEGF may then lead to altered endothelial cell functions and vascular hyperpermeability. In the presence of the corticosteroids cortisone, hydrocortisone, dexamethasone, or prednisolone at nanomolar concentrations, this stimulus-dependent transcription of VEGF was abolished. The inhibitory effect of corticosteroids on VEGF expression could explain the clinically well-known antiedematous potency of corticosteroids on a molecular level.
Regulatory mechanisms for the expression of type IV collagenases/gelatinases in murine macrophages. (1994)

The purpose of this study was to determine the regulation of type IV collagenase expression in murine peritoneal macrophages (PEM) after they are incubated with LPS. LPS stimulated the production of the latent forms of 92-kDa (MMP-9) and 72-kDa (MMP-2) type IV gelatinases in a dose-dependent (> 10 ng/ml) and serum-dependent manner. Time course analyses revealed that LPS regulated the expression of MMP-9 and MMP-2 via discordant kinetics. Prolonged treatment of PEM with LPS decreased MMP-9 but not MMP-2 activities. IFN-gamma decreased the production of both gelatinases by PEM responding to LPS. TGF-beta stimulated production of both matrix metalloproteinases but blocked the LPS-mediated secretion of MMP-9. LPS-stimulated MMP-9 production was suppressed by genistein and tyrphostin, two specific tyrosine kinase inhibitors, as well as H-7, a serine/threonine protein kinase inhibitor, but not by HA1004, a relatively selective inhibitor for PKA and PKG. Our data demonstrate that the secretion of MMP-2 and MMP-9 by murine PEM is differentially regulated, suggesting a distinct in vivo role for these two otherwise analogous type IV gelatinases in macrophage-mediated connective tissue destruction at sites of immunologic challenges.
SIGNET: A Neural Network Architecture for Predicting Protein-Protein Interactions (2017)

The study of protein-protein interactions (PPI) is critically important within the field of Molecular Biology, as proteins facilitate key organismal functions including the maintenance of both cellular structure and function. Current experimental methods for elucidating PPIs are greatly hindered by large operating costs, lengthy wait times, as well as low accuracy. The recent development of computational PPI predicting techniques has worked to address many of these issues. Despite this, many of these methods utilize over-engineered features and naive learning algorithms. With the recent advances in Machine Learning and Artificial Intelligence, we attempt to view this problem through a novel, deep learning perspective. We propose a siamese, convolutional neural-network architecture for predicting protein-protein interactions using protein signatures as feature vectors. In comparison to four leading computational methods, we find that our results are comparable to and, in many cases, surpass the results of these methods. The emphasis of the discussion is to show that there is still much room for improvement in the area of PPI prediction using modern deep learning techniques.