gebhart/patrepeval huggingface dataset:
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014)

The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function. To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex. We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain. For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase. This dataset will provide a powerful new resource for understanding the development and function of the brain. To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain.
Organocopper(I) Compounds and Organocuprates in Synthesis (1972)

Organocopper(I) compounds and organocuprates are very versatile reagents the use of which in organic syntheses is in many cases advantageous over that of the usual organometallic compounds. Organocopper(I) compounds and organocuprates have been studied mainly in the last decades and years, respectively. Their use in preparative chemistry is still based on empirical facts and the reaction mechanisms have hitherto been relatively little studied. In this survey, the preparation and reactions of organocopper(l) compounds and organocuprates are discussed. The emphasis is on the conditions that influence the course of the reactions. The choice of the solvent and the addition of salts or complexing agents, as well as the nature of the reaction components play an important role. 1. Organocopper(I) Compounds, Pure or in the Presence of Salts 1.1. Alkylcopper Compounds 1.1.1. Preparation, Stability, and Coupling 1.1.2. Reactions with Carboxylic Acid Chlorides and Halogen Derivatives 1.1.3. 1,4-Additions 1.1.4. Perfluoroalkylcopper Compounds 1.2. Arylcopper Compounds 1.2.1. Preparation and Stability 1.2.2. Reactions with Carboxylic Acid Chlorides and Halogen Derivatives 1.2.3. Reaction Intermediates 1.2.4. 1,4-Additions 1.2.5. Perhaloarylcopper Compounds 1.3. Vinylcopper Compounds 1.4. Alkynylcopper Compounds 1.4.1. Preparation and Stability 1.4.2. Reactions with Carboxylic Acid Chlorides 1.4.3. Reactions with Allyl and Propargyl Halides 1.4.4. Reactions with Aryl and Vinyl Halides 1.4.5. Reactions with 1-Halo-1-alkynes 1.5. Cyclopentadienylcopper 1.6. Conclusion 2. Homocuprates 2.1. Preparation and Stability 2.2. Coupling 2.3. Reactions with Carboxylic Acid Chlorides 2.4. Reactions with Allyl and Propargyl Halides and Esters 2.5. Reactions with Haloarenes and Haloalkenes 2.6. Reactions with Haloalkanes and Halocycloalkanes 2.7. Reactions with Oxiranes 2.8. Reactions with Ketones and 1,4-Additions 2.9. Conclusion
Cytotoxic Necrotizing Factor-1 Contributes to Escherichia coli K1 Invasion of the Central Nervous System (2002)

Escherichia coli K1 invasion of brain microvascular endothelial cells (BMECs) is a prerequisite for penetration into the central nervous system and requires actin cytoskeletal rearrangements. Here, we demonstrate that E. coli K1 invasion of BMECs requires RhoA activation. In addition, we show that cytotoxic necrotizing factor-1 (CNF1) contributes to E. coli K1 invasion of brain endothelial cells in vitro and traversal of the blood-brain barrier in the experimental hematogenous meningitis animal model. These in vitro and in vivo effects of CNF1 were dependent upon RhoA activation as shown by (a) decreased invasion and RhoA activation with the Delta cnf1 mutant of E. coli K1 and (b) restoration of invasion frequency of the Delta cnf1 mutant to the level of the parent E. coli K1 strain in BMECs with constitutively active RhoA. In addition, CNF1-enhanced E. coli invasion of brain endothelial cells and stress fiber formation were independent of focal adhesion kinase and phosphatidylinositol 3-kinase activation. This is the first demonstration that CNF1 contributes to E. coli K1 invasion of BMECs.
Bias in OLAP Queries: Detection, Explanation, and Removal (2018)

On line analytical processing (OLAP) is an essential element of decision-support systems. OLAP tools provide insights and understanding needed for improved decision making. However, the answers to OLAP queries can be biased and lead to perplexing and incorrect insights. In this paper, we propose HypDB, a system to detect, explain, and to resolve bias in decision-support queries. We give a simple definition of a \emph{biased query}, which performs a set of independence tests on the data to detect bias. We propose a novel technique that gives explanations for bias, thus assisting an analyst in understanding what goes on. Additionally, we develop an automated method for rewriting a biased query into an unbiased query, which shows what the analyst intended to examine. In a thorough evaluation on several real datasets we show both the quality and the performance of our techniques, including the completely automatic discovery of the revolutionary insights from a famous 1973 discrimination case.
Impact of Chronic Rhinosinusitis and Endoscopic Sinus Surgery on Bone Remodeling of the Paranasal Sinuses (2008)

In the revision ESS group, soft tissue and bone remodeling may be greater than in the primary ESS group.
Antibodies to Hepatitis B Surface Antigen Potentiate the Response of Human T Lymphocyte Clones to the Same Antigen (1984)

Human t-helper lymphocyte clones specific for hepatitis B virus surface antigen (HBsAg) proliferate on stimulation with HBsAg in vitro. Antibodies specific for HBsAg, but no other antibodies, augment this proliferative response. In the presence of antibodies to HBsAg, the maximum response could be achieved at HBsAg concentrations that were 1 percent of those required in the absence of the antibodies. These findings suggest that antigen-specific antibodies exert regulatory controls on T cells that recognize the same antigens.
Synthesis of a new series of cephalosporins having 3-substituted-ammonio-1-propenyl group as the C-3 side chain. (1990)

The synthesis and antimicrobial activity of eight derivatives of 7-[(Z)-2-(2-aminothiazol-4-yl)- and 7-[(Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-methoxyiminoacetamido] cephalosporins having an (E) or (Z)-3-ammonio-1-propenyl group in the C-3 side chain are described. The (E)-propenyl derivatives were more active than their corresponding Z-isomers and showed well-balanced, broad antibacterial activity against both Gram-positive and Gram-negative bacteria including Pseudomonas aeruginosa.
Inhibition of tyrosine kinase activity of the epidermal growth factor (EGF) receptor by a truncated receptor form that binds to EGF: role for interreceptor interaction in kinase regulation. (1989)

The tyrosine kinase activity of the epidermal growth factor (EGF) receptor is regulated by a truncated receptor of 100 kilodaltons (kDa) that contains the EGF-binding site but not the kinase domain. The inhibition of kinase is not due to competition for available EGF or for the kinase substrate-binding site. Chemical cross-linking studies suggest that the 100-kDa receptor may form a heterodimer with the intact EGF receptor. Structurally related receptor kinases, such as the platelet-derived growth factor receptor, the insulin receptor, and the Neu receptor, were not inhibited by the 100-kDa receptor. The results indicate that (i) the inhibition was specific for the EGF receptor, (ii) the kinase domain had little or no role in determining target specificity, and (iii) the regulation of kinase may be due to a specific interaction of the 100-kDa receptor with the ligand-binding domain of the EGF receptor kinase.
CXCR2 Macromolecular Complex in Pancreatic Cancer: A Potential Therapeutic Target in Tumor Growth (2013)

The signaling mediated by the chemokine receptor CXC chemokine receptor 2 (CXCR2) plays an important role in promoting the progression of many cancers, including pancreatic cancer, one of the most lethal human malignancies. CXCR2 possesses a consensus PSD-95/DlgA/ZO-1 (PDZ) motif at its carboxyl termini, which might interact with potential PDZ scaffold/adaptor proteins. We have previously reported that CXCR2 PDZ motif-mediated protein interaction is an important regulator for neutrophil functions. Here, using a series of biochemical assays, we demonstrate that CXCR2 is physically coupled to its downstream effector phospholipase C-β3 (PLC-β3) that is mediated by PDZ scaffold protein Na(+)/H(+) exchange regulatory factor 1 (NHERF1) into a macromolecular signaling complex both in vitro and in pancreatic cancer cells. We also observe that disrupting the CXCR2 complex, by gene delivery or peptide delivery of exogenous CXCR2 C-tail, significantly inhibits the biologic functions of pancreatic cancer cells (i.e., proliferation and invasion) in a PDZ motif-dependent manner. In addition, using a human pancreatic tumor xenograft model, we show that gene delivery of CXCR2 C-tail sequence (containing the PDZ motif) by adeno-associated virus type 2 viral vector potently suppresses human pancreatic tumor growth in immunodeficient mice. In summary, our results suggest the existence of a physical and functional coupling of CXCR2 and PLC-β3 mediated through NHERF1, forming a macromolecular complex that is critical for efficient and specific CXCR2 signaling in pancreatic cancer progression. Disrupting this CXCR2 complex could represent a novel and effective treatment strategy against pancreatic cancer.
Erythrocyte catalase inactivation (H2O2 production) by ascorbic acid and glucose in the presence of aminotriazole: role of transition metals and relevance to diabetes (1994)

Erythrocytes exposed to ascorbic acid in the presence of aminotriazole undergo a dose- and time-dependent inactivation of endogenous catalase which is proportional to environmental hydrogen peroxide (H2O2) concentrations. The production of H2O2 seems to be dependent upon the availability of transition metal chelatable by o-phenanthroline (OPT), although the kinetics of catalase inactivation and H2O2 production by externally added copper ions in the presence of OPT is complex. Furthermore, although glucose is also able to undergo a transition-metal-catalysed oxidation yielding H2O2, the production of H2O2 by glucose seems to be a minor process by comparison with ascorbic acid oxidation. Indeed, on the basis of these data, transition-metal-catalysed ascorbic acid oxidation is likely to be a more important source of oxidative stress in the diabetic state than hyperglycaemia.
Temporal feature induction for baseball highlight classification (2007)

Most approaches to highlight classification in the sports domain exploit only limited temporal information. This paper presents a method, called temporal feature induction, which automatically mines complex temporal information from raw video for use in highlight classification. The method exploits techniques from temporal data mining to discover a codebook of temporal patterns that encode long distance dependencies and duration information. Preliminary experiments show that using such induced temporal features significantly improves performance of a baseball highlight classification system.
Azacitidine Prolongs Overall Survival Compared With Conventional Care Regimens in Elderly Patients With Low Bone Marrow Blast Count Acute Myeloid Leukemia (2009)

In older adult patients with low marrow blast count (20% to 30%) WHO-defined AML, azacitidine significantly prolongs OS and significantly improves several patient morbidity measures compared with CCR.
Physical interaction between dendritic cells and tumor cells results in an immunogen that induces protective and therapeutic tumor rejection. (1998)

Dendritic cells (DCs) are potent professional APCs capable of presenting Ag in the context of costimulatory signals necessary for T cell activation. Although tumor cells express target Ags, they are generally incapable of stimulating an immune response. We show that the short term physical interaction of DCs and tumor cells, with or without cell fusion, results in rapid, efficient, and stable DC-tumor cell association. Immunization of naive mice with unselected, irradiated DC-tumor cell conjugates induces tumor-specific CD8+ cytotoxic T cells and protection from lethal tumor challenge. Furthermore, the immunogenicity of this cellular vaccine is dependent on the physical interaction of DCs and tumor cells before injection. Immunization with DCs and tumor cells after physical interaction can result in the regression of established tumors and persistent antitumor immunity. These results suggest that immunization with DC-tumor cell vaccines may be a simple, rapid, and potent strategy for tumor immunotherapy.
The Amnesia Atlas. An immersive SenseCam interface as memory-prosthesis (2014)

The Amnesia Atlas constitutes a pilot study for a photographic media interface as memory prosthesis. It utilises the wearable life-logging camera SenseCam to shed light on the importance of photographic imagery and place for memory retrieval. It investigates the relationships of spatiotemporal context on memory encoding and retrieval, utilising immersive 3D visualisation.
A Reconfigurable Built-In Self-Repair Scheme for Multiple Repairable RAMs in SOCs (2006)

This paper presents a reconfigurable built-in self-repair (ReBISR) scheme for multiple repairable RAM cores with different sizes and redundancy organizations (i.e., spare rows/spare columns or spare rows/spare IOs). We also propose an efficient built-in redundancy-analysis (BIRA) algorithm for allocating redundancies for the ReBISR scheme. A reconfigurable BIRA (ReBIRA) circuit is realized to perform the proposed BIRA algorithm for the ReBISR scheme. Experimental results show that the ReBISR scheme can achieve high repair rate (i.e., the ratio of the number of repaired memories to the number of defective memories). The area cost of the reconfigurable BIRA is very small, e.g., the area cost is only about 1.5% if 512times4times256 design parameters and four memory instances (64times2times32, 128times2times64, 256times4times128, and 512times4times256) are considered. Also, the ratio of the redundancy analysis time to the test time is very small, e.g., the ratio for a 512times4times256-bit memory tested by a March-14N algorithm with solid data backgrounds is only about 0.25%
Review Degeneration of the intervertebral disc (2003)

The intervertebral disc is a cartilaginous structure that resembles articular cartilage in its biochemistry, but morphologically it is clearly different. It shows degenerative and ageing changes earlier than does any other connective tissue in the body. It is believed to be important clinically because there is an association of disc degeneration with back pain. Current treatments are predominantly conservative or, less commonly, surgical; in many cases there is no clear diagnosis and therapy is considered inadequate. New developments, such as genetic and biological approaches, may allow better diagnosis and treatments in the future.
Monoclonal Antibody Against Vascular Cell Adhesion Molecule-1 Inhibits Neointimal Formation After Periadventitial Carotid Artery Injury in Genetically Hypercholesterolemic Mice (2000)

Vascular cell adhesion molecule (VCAM)-1 is induced in smooth muscle cells after arterial injury, in which it has been implicated in the recruitment of inflammatory cells to the site of injury. To investigate the effect of hypercholesterolemia on VCAM-1 induction after injury and the role of VCAM-1 in neointimal response to injury, we injured the carotid artery of wild-type and apolipoprotein E null (KO) mice fed normal and high cholesterol chow. We demonstrate a graded response of VCAM-1 induction as well as monocyte/macrophage infiltration by immunohistochemistry 3 days after injury that correlated with increasing circulating cholesterol levels. Three weeks after injury, KO mice fed high cholesterol chow (KO HC group) had a significantly greater neointimal formation compared with wild-type and KO mice fed normal chow (P<0.05). Inhibition of VCAM-1 function in the KO HC group by monoclonal antibody treatment significantly reduced monocyte/macrophage infiltration and neointimal formation. There was reduced alpha-actin expression in KO HC mice 7 days after injury that was partially inhibited by VCAM-1 antibody treatment. Cell migration in an in vitro injury model was partially inhibited by monoclonal VCAM-1 antibody treatment. We propose an additional role for VCAM-1 in smooth muscle cell activation and neointimal formation after injury.
An efficient equivalence checker for combinational circuits (1996)

Article An efficient equivalence checker for combinational circuits Share on Author: Yusuke Matsunaga FUJITSU LABORATORIES LTD, Kawasaki 211-88, Japan FUJITSU LABORATORIES LTD, Kawasaki 211-88, JapanView Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996 Pages 629–634https://doi.org/10.1145/240518.240637Online:01 June 1996Publication History 70citation315DownloadsMetricsTotal Citations70Total Downloads315Last 12 Months3Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Identification of two risk haplotypes for schizophrenia and bipolar disorder in the synaptic vesicle monoamine transporter gene (SVMT) (2007)

The synaptic vesicular monoamine transporter (SVMT) plays a key role in monoaminergic neurotransmission determining the size of neurotransmitter vesicular pools available for exocytotic release. Recently, several lines of evidence have suggested that altered functions of SVMT may be involved in the pathogenesis of certain neuropsychiatric diseases, including psychotic and mood disorders. In the present study, we tested the potential involvement of SVMT gene variants in the etiology of schizophrenia and bipolar disorder. Five different SNPs (T440G, C1368T, T2666C, A2683C, and A745G) were included in the analysis covering a region of about 35 kb along the SVMT gene. Analyses were performed in a case-control sample consisting of 88 bipolar patients, 107 subjects with schizophrenia, and 164 controls. Two risk haplotypes for both schizophrenia and bipolar disorder in SVMT gene were identified. Particularly, 2666T-2683A-745G (TAG) and 2666C-2683C-745A (CCA) combinations were significantly more frequent in both bipolar and schizophrenic patients than in controls. UNPHASED package estimated haplotype effects for all patients yielded relative risks of 4.1 (95%CI: 1.83-9.21) for TAG combination and 2.336 (95%CI: 1.28-4.26) for CCA haplotype. Conversely, 2666T-2683C-745A (TCA) and 2666C-2683A-745G (CAG) haplotypes seemed to protect against these mental disorders, since the estimated frequency in control chromosomes was 12% whilst such haplotypes were not observed in any bipolar or schizophrenic subject (P < 0.0000). Our results strongly suggest that SVMT gene or certain regions of it may constitute a genetic substrate of susceptibility for both schizophrenia and bipolar disorder.
Mutations in the bimC box of Cut7 indicate divergence of regulation within the bimC family of kinesin related proteins (1998)

Members of the bimC family of kinesin related proteins (KRPs) play vital roles in the formation and function of the mitotic spindle. Although they share little amino acid homology outside the highly conserved microtubule motor domain, several family members do contain a 'bimC box', a sequence motif around a p34(cdc2) consensus phosphorylation site in their carboxy-terminal 'tail' region. One family member, Eg5, requires phosphorylation at this site for association with the mitotic spindle. We show that mutations in the Schizosaccharomyces pombe cut7+ gene that change the bimC box p34(cdc2) consensus phosphorylation site at position 1,011 and a neighbouring MAP kinase consensus phosphorylation site at position 1,020 to non-phosphorylatable residues did not affect the ability of S. pombe cut7 genes to complement temperature sensitive cut7 mutants. Phosphorylation site mutants expressed as fusions to green fluorescent protein associated with the mitotic spindle with a localisation indistinguishable from similarly expressed wild-type Cut7. Cells in which cut7.T1011A replaced the genomic copy of cut7+ were viable and formed normal spindles. Deletion of the entire carboxy-terminal tail region did not affect the ability of Cut7 to associate with the mitotic spindle but did inhibit normal spindle formation. Thus, unlike Eg5, neither the p34(cdc2) consensus phosphorylation site in the bimC box nor the entire tail region of Cut7 are required for association with the mitotic spindle.
An electron pair operator approach to coupled cluster wave functions. Application to He2, Be2, and Mg2 and comparison with CEPA methods (1981)

A method for obtaining coupled cluster expansions with double substitutions (CCD) utilizing the electron pair operator approach of self-consistent electron pair (SCEP) theory is presented. A fairly simple operator is developed in this method and its calculation increases the expense over a typical variational configuration expansion only moderately. With this method, large basis set calculations have been performed on the weakly interacting dimers He2, Be2, and Mg2. Comparison calculations have been performed with various types of coupled electron pair approximations (CEPA), which may be viewed as approximations to coupled cluster theory, and with modification of the internal orbitals in the CCD treatment.
Characterization of surface lymphotoxin forms. Use of specific monoclonal antibodies and soluble receptors. (1995)

Lymphotoxin (LT) is a cytokine related to TNF, found in human systems in both secreted and membrane bound forms. The well characterized secreted form is a trimer of a single protein, LT-alpha, whereas the surface form is composed of a complex between two related molecules, LT-alpha and LT-beta. Because there is a distinct receptor for the complex, the membrane form is believed to signal via events different from those elicited by TNF and secreted LT-alpha. By using a battery of anti-LT-alpha and LT-beta mAbs, it is clear that two LT surface forms exist on the surface of PMA-activated II-23 cells, a human T cell hybridoma. Assuming that these surface forms are trimers, a minor form appears early after induction having an apparent stoichiometry of LT-alpha 2/beta 1 and is recognized by one group of anti-LT-alpha mAbs and the p55-TNF receptor. The second and predominant form has an apparent LT-alpha 1/beta 2 composition and is recognized by a second group of pantrophic anti-LT-alpha mAbs and the LT-beta receptor. Neither of the heteromeric forms nor a putative LT-beta homotrimeric form were found to be secreted. The properties of surface LT on the II-23 cell system were similar to those of the surface LT forms on Chinese hamster ovary cells transfected with both LT-alpha and LT-beta genes and a number of lymphoid tumor lines. These experiments point toward the LT-alpha 1/beta 2 complex as the predominant membrane form of LT on the lymphocyte surface, and this complex is the primary ligand for the LT-beta receptor.