gebhart/patrepeval huggingface dataset:
Overcoming the challenges of crossbar resistive memory architectures (2015)

The scalability of DRAM faces challenges from increasing power consumption and the difficulty of building high aspect ratio capacitors. Consequently, emerging memory technologies including Phase Change Memory (PCM), Spin-Transfer Torque RAM (STT-RAM), and Resistive RAM (ReRAM) are being actively pursued as replacements for DRAM memory. Among these candidates, ReRAM has superior characteristics such as high density, low write energy, and high endurance, making it a very attractive cost-efficient alternative to DRAM. In this paper, we present a comprehensive study of ReRAM-based memory systems. ReRAM's high density comes from its unique crossbar architecture where some peripheral circuits are laid below multiple layers of ReRAM cells. A crossbar architecture introduces special constraints on operating voltages, write latency, and array size. The access latency of a crossbar is a function of the data patterns involved in a write operation. These combined with ReRAM's exponential relationship between its write voltage and switching latency provide opportunities for architectural optimizations. This paper makes several key contributions. First, we study the crossbar architecture and describe trade-offs involving voltage drop, write latency, and data pattern. We then analyze microarchitectural enhancements such as double-sided ground biasing and multiphase reset operations to improve write performance. At the architecture level, a simple compression based data encoding scheme is proposed to further bring down the latency. As the compressibility of a block varies based on its content, write latency is not uniform across blocks. To mitigate the impact of slow writes on performance, we propose and evaluate a novel scheduling policy that makes writing decisions based on latency and activity of a bank. The experimental results show that our architecture improves the performance of a system using ReRAM-based main memory by about 44% over a conservative baseline and 14% over an aggressive baseline on average, and has less than 10% performance degradation compared to an ideal DRAM-only system.
Importance of cis-Proline 22 in the Membrane-Binding Conformation of Bovine Prothrombin (1996)

Upon addition of calcium to the metal-free protein, bovine prothrombin displays a conformational change with behavior of a classic trans- to cis-proline isomerization. The change is accompanied by a decrease of the intrinsic protein fluorescence and is essential to creating the membrane-binding conformation of prothrombin. This study showed that an identical conformational change was displayed by a peptide corresponding to residues 1-45 of prothrombin. This peptide contains a single tryptophan that underwent extensive quenching upon calcium addition. The kinetics were slow (t1/2 = 2.7 min at 24 degrees C) and displayed an activation energy of 24 kcal/mol. These properties overlapped precisely with the behavior of bovine prothrombin fragment 1 (residues 1-156). Consistent with studies on prothrombin and other vitamin K-dependent proteins that have been modified or truncated, the 1-45 peptide required about 10-fold higher calcium to elicit these behaviors than did fragment 1. The conformational change was necessary for membrane binding by the 1-45 peptide. The only proline in this sequence is at position 22. This proline is of the trans configuration in a crystallized form of calcium-bovine prothrombin fragment 1 [Soriano-Garcia, M., et al. (1992) Biochemistry 31, 2554]. Unless the protein conformational change is based on another behavior, this study showed that biochemical properties of the protein are inconsistent with structure solutions. Further studies are needed to reconcile structure/function in membrane association. Proline 22 in bovine prothrombin may constitute a useful biochemical marker for the membrane-binding conformation of a vitamin K-dependent protein.
Post-Transplant Lymphoproliferative Disorders (2004)

Post-transplant lymphoproliferative disorder (PTLD) is a life-threatening complication after hematopoietic stem cell or solid organ transplantation. The majority of PTLD is of B-cell origin and associated with Epstein-Barr virus (EBV). During the past decade progress has been made in better understanding the pathogenesis of PTLD, and early detection strategies, such as serial measurement of EBV-DNA load in peripheral blood samples, have assisted in the identification of high-risk patients. In addition, novel immunotherapies have been developed, including the use of monoclonal antibodies and adoptive transfer of EBV-specific T cells. Despite these advances, it remains a major challenge to define indications for preemptive therapies for PTLD and to integrate novel therapeutic approaches with conventional therapies.
Synthesis and pharmacological evaluation of ether and related analogs of .DELTA.8-, .DELTA.9-, and .DELTA.9,11-tetrahydrocannabinol (1991)

The primary goal of this research was to synthesize a series of ether analogues of the cannabinoid drug class and to evaluate their agonist and antagonist pharmacological properties in either the mouse or the rat. Agonist and antagonist activity was evaluated in mice using a multiple-evaluation procedure (locomotor activity, tail-flick latency, hypothermia, ring immobility) and activity in rats determined in a discriminative stimulus paradigm. Additionally, novel analogues were evaluated for their ability to bind to the THC receptor site labeled by 3H-CP-55,940. None of the cannabinoid analogues were capable of attenuating the effects of delta 9-THC (3 mg/kg) in either the rat (doses up to 10 mg/kg) or in the mouse (doses up to 30 mg/kg). It also appears that the compounds with minimal in vivo activity are not mixed agonist/antagonists. These data would suggest that the phenolic hydroxyl is important for receptor recognition (binding) and in vivo potency. Additionally, cannabinoid methyl ethers previously considered inactive have been found to produce limited activity. Lastly, data suggest that delta 9,11-THC is more potent than previous reports indicated, and does possess pharmacological activity.
Structure of a bovine gene for P-450c21 (steroid 21-hydroxylase) defines a novel cytochrome P-450 gene family. (1986)

P-450c21, a cytochrome P-450 enzyme [steroid 21-monooxygenase (steroid 21-hydroxylase), EC 1.14.99.10], mediates the 21-hydroxylation of glucocorticoid and mineralocorticoid hormones in the adrenal gland. The complete sequence of a bovine P-450c21 gene shows it is 3447 base pairs long and contains 10 exons. The intron/exon organization and encoded amino acid sequence indicate that P-450c21 represents a unique family of genes in the P-450 gene superfamily. Primer extension and S1 nuclease protection experiments identified several cap sites for initiation of transcription; the principal cap site produces mRNA with a 5' untranslated region only 11 bases long. S1 nuclease protection experiments confirm that P-450c21 is actively expressed in the adrenal and the testis, an organ not known to secrete 21-hydroxylated steroids.
Mitochondrial DNA Mutation Detection by Electrospray Mass Spectrometry (2006)

ESI-FTICR MS is a rapid, sensitive, and accurate method for the identification and quantification of mtDNA mutations and SNPs.
Recent developments in micromachined silicon (1999)

This paper provides a review, directed at scientists and engineers concerned with microsystems technology, of advances in microelectromechanical systems (MEMS). The emphasis is on silicon technology, where the electrical properties of the material are exploited in circuitry and the mechanical properties are used in sensor and microstructure applications. Developments in surface micromachining are discussed, and applications in sensors, microelectronic devices, vacuum microanalysis systems, microfluidics, and optoelectronic subsystems are reviewed. Some emerging technologies are assessed and promising new research directions are identified.
Phage Display Selection on Whole Cells Yields a Peptide Specific for Melanocortin Receptor 1 (1997)

A phage display system for the selection of peptides binding to heterologously expressed human melanocortin receptor 1 on the surface of insect cells has been established. It could be shown that phage particles displaying the natural ligand alpha-melanocyte-stimulating hormone bind selectively to cells expressing this receptor and that these phages exhibit biological activity on mouse B16F1 melanoma cells. Insect cells were superior to other cell lines tested and have been used to select binders from a small library, in which critical determinants (Phe7-Arg8-Trp9) were kept, whereas the flanking regions where allowed to variate freely. One peptide displaying little similarity with native hormone was found that binds to the receptor also in its free form with an affinity of 7 nM. It showed a remarkable selectivity for this receptor, because it binds to the other melanocortin receptor subtypes with a maximum affinity of 21 microM. This is the first time phage display has been used successfully with G-protein-coupled receptors lacking an extracellular binding domain.
Understanding the New SQL: A Complete Guide (1993)

1 Introduction to SQL-92 2 Getting Started with SQL-92 3 Basic Table Creation and Data Manipulation 4 Basic Data Definition Language (DDL) 5 Values, Basic Functions, and Expressions 6 Advanced Value Expressions: CASE, CAST, and Row Value Expressions 7 Predicates 8 Working with Multiple Tables: The Relational Operators 9 Advanced SQL Query Expressions 10 Constraints, Assertions, and Referential Integrity 11 Accessing SQL from the Real World 12 Cursors 13 Privileges, Users, and Security 14 Transaction Management 15 Connections and Remote Database Access 16 DYNAMIC SQL 17 Diagnostics and Error Management 18 Internationalization Aspects of SQL-92 19 Information Schema 20 A Look to the Future A Designing SQL-92 Databases B A Complete SQL-92 Example C The SQL-92 Annexes: Differences, Implementation-Defined and Implementation-Dependent Features, Deprecated Features, and Leveling D Relevant Standards Bodies E Status Codes F The SQL Standardization Process G The Complete SQL-92 Language
CAMs and Igs: Cell Adhesion and the Evolutionary Origins of Immunity (1987)

The lymphoid system and cells of immunity are as morphologically well defined as those of any complex organ but in addition they show dynamic long-range interactions between the fluid tissues (lymphocytes, monocytes, etc.) and the solid, vascular and generative tissues and organs which they comprise. Given the observation that CAMs are present in epithelial components of lymphoid organs, it appears that, in their ontogeny, the organs of immunity will share a common principle of morphoregulation by CAMs with brains, feathers and other parts of the phenotype. As discussed here, this principle is a regulatory one operating across many levels of organization from the genes to tissues and back again (see Fig. 1). At some early point in the evolution of the immune system, a gene corresponding to an N-CAM precursor must have duplicated to provide a basis for the Ig superfamily with its increasing specializations for recognition and for cellular regulation during the immune response. Lymphocyte cellular families also developed later specializations (along with other leukocytes) for adhesive functions accessory to specific recognition. As far as we can see, the molecules for these accessory functions only remotely resemble CAMs, but closely resemble receptors for matrix molecules and SAMs. What CAMs and Ig superfamily members have in common is an evolutionary path and important roles in mediating complex regulatory responses that arise from cell-cell interactions. In the one case, this regulation leads to morphology, and in the other, to immune recognition. The first depends directly upon pattern (the formation of definite tissue structure); the regulation of the second also depends upon pattern to the extent that its function is dependent upon the morphology of lymphoid organs and vasculature. But although specific immune recognition depends locally upon adhesion through special mechanisms, it does not lead to morphology. One must not therefore impute too much in the physiological sense to the resemblance among brain molecules and molecules of the immune system. CAMs themselves are not directly histotypic at the level of individual differentiated cells but rather are used to link early tissue boundaries in induction and function in a wide variety of different tissues. As a consequence, N-CAM is central to the formation and maintenance of neural tissue but has a much wider tissue distribution and a fundamental role in very early embryogenesis as is the case with other primary CAMs. Thus, the immune system did not evolve from the nervous system, but from a cell adhesion system essential to both.(ABSTRACT TRUNCATED AT 400 WORDS)
Identification and cloning of two overexpressed genes, U21B31/PRAD1 and EMS1, within the amplified chromosome 11q13 region in human carcinomas. (1992)

Amplification of the chromosome 11q13 region is frequently found in human breast cancer and in squamous cell carcinomas of the head and neck, and has been associated with an unfavourable clinical course of disease. The known oncogenes within the amplified 11q13 region, INT2 and HSTF1, are rarely expressed in these tumours, indicating that another, hitherto unidentified, gene or genes confer(s) the biological (prognostic) significance to the amplification of the 11q13 region. To identify the gene or genes, we have constructed a cDNA library from a cell line with an 11q13 amplification and have performed differential cDNA cloning using [32P]dCTP-labelled cDNAs from human squamous cell carcinoma cell lines with and without an 11q13 amplification. We isolated two cDNA clones, U21B31 and U21C8, which recognize two genes amplified and overexpressed in cell lines harbouring an 11q13 amplification. In breast carcinomas and in squamous cell carcinomas amplification of both the U21B31 and the U21C8 gene was found in most tumours with an amplification of the 11q13 region, despite the large distance between both genes. Sequence analysis of the U21C8 cDNA clone revealed no homology to known genes; we call this gene EMS1. The U21B31 cDNA clone corresponded to the 3' end of the PRAD1 proto-oncogene, recently cloned from a parathyroid adenoma. Both gene products are of interest as potential markers to identify tumours with an 11q13 amplification.
Induction of the Angiogenic Phenotype by Hox D3 (1997)

Angiogenesis is characterized by distinct phenotypic changes in vascular endothelial cells (EC). Evidence is provided that the Hox D3 homeobox gene mediates conversion of endothelium from the resting to the angiogenic/invasive state. Stimulation of EC with basic fibroblast growth factor (bFGF) resulted in increased expression of Hox D3, integrin alphavbeta3, and the urokinase plasminogen activator (uPA). Hox D3 antisense blocked the ability of bFGF to induce uPA and integrin alphavbeta3 expression, yet had no effect on EC cell proliferation or bFGF-mediated cyclin D1 expression. Expression of Hox D3, in the absence of bFGF, resulted in enhanced expression of integrin alphavbeta3 and uPA. In fact, sustained expression of Hox D3 in vivo on the chick chorioallantoic membrane retained EC in this invasive state and prevented vessel maturation leading to vascular malformations and endotheliomas. Therefore, Hox D3 regulates EC gene expression associated with the invasive stage of angiogenesis.
Enhancing clinical measures of postural stability with wearable sensors (2012)

About 30% of individuals over the age of 65, and 50% over age 80, fall at least once per year. Fall-related injuries cost the Canadian health care system $2.8 billion annually. Risk for falls in older adults is commonly assessed in the clinical environment using tools such as the Short Physical Performance Battery (SPPB), which include subjective assessments of postural sway while standing under various sensory conditions. This study uses wearable accelerometers and a force plate to quantify measures of postural stability during these tasks. Four participants were asked to maintain quiet stance in six different conditions, while their center of pressure (COP) and accelerations from six accelerometers were recorded. Standard deviations in signals were used as measures of postural sway. The sway observed in all sensors increased with the difficulty of the stance condition. Manipulation of vision and surface stiffness caused greater changes in sway in the AP than ML direction, while changes in stance configuration were more evident in the ML direction. Furthermore, the ankle sensor was the most sensitive in registering changes in sway when manipulating vision and surface stiffness (showing an increase of 236% over baseline values in AP sway with eyes closed and standing on foam), while the thigh was most sensitive to changes in stance width (showing an increase of 336% over baseline values in ML sway in the tandem stance condition). This study contributes in establishing the utility of wearable sensors for quantifying postural stability under various stance configurations in future studies with high-risk older adults.
A small peptide derived from Flt‐1 (VEGFR‐1) functions as an angiogenic inhibitor (2001)

Vascular endothelial growth factor (VEGF) is an angiogenic stimulator which functions through two endothelial specific tyrosine kinase receptors, Flt-1 and Flk-1. In this work, we show that an 11-amino acid peptide derived from the second immunoglobulin-like domain of Flt-1 functions as an angiogenic inhibitor in chick chorioallantoic membrane and inhibited VEGF-induced vascular permeability in Miles' assay without binding to VEGF directly. Circular dichroism and nuclear magnetic resonance analyses indicate that this peptide forms a stable extended structure in solution, presumably beta-sheet structure and is most likely existing as a dimer. Our results suggest that this small peptide functions as an angiogenic inhibitor by inhibiting VEGF function through a non-VEGF binding mechanism.
Two forms of 1B236/myelin-associated glycoprotein, a cell adhesion molecule for postnatal neural development, are produced by alternative splicing. (1987)

The structures of two rat brain-specific 1B236 mRNAs, alternative splice products from a single gene regulated differently during postnatal brain development, were deduced from full-length cDNA clones. The 626- and 582-amino acid-long encoded proteins are indistinguishable from two forms of myelin-associated glycoprotein, a cell adhesion molecule involved in axonal-glial and glial-glial interactions in postnatal brain development, particularly in myelination. The two proteins share a single membrane-spanning domain and a glycosylated N terminus but differ in the structures of their C termini. The N terminus consists of five domains related in sequence to each other and to immunoglobulin-like molecules, especially the neural cell adhesion molecule N-CAM, suggesting a common structure for cell adhesion molecules.
Histological, molecular and functional subtypes of breast cancers (2010)

Increased understanding of the molecular heterogeneity that is intrinsic to the various subtypes of breast cancer will likely shape the future of breast cancer diagnosis, prognosis, and treatment. Advances in the field over the last several decades have been remarkable and have clearly translated into better patient care as evidenced by the earlier detection, better prognosis, and new targeted therapies. There have been two recent advances in the breast cancer research field that have lead to paradigm shifts: first, the identification of intrinsic breast tumor subtypes, which has changed the way we think about breast cancer and second, the recent characterization of cancer stem cells (CSCs), which are suspected to be responsible for tumor initiation, recurrence and resistance to therapy, have opened new exciting avenues to think about breast cancer therapeutic strategies. While these advances constitute major paradigm shifts within the research realm, the clinical arena has yet to adopt and apply our understanding of the molecular basis of the disease to early diagnosis, prognosis and therapy of breast cancers. Here, we will review the current clinical approach to classification of breast cancers, newer molecular-based classification schemes, and potential future of biomarkers representing a functional classification of breast cancer.
Polydeoxyguanine Motifs in a 12-mer Phosphorothioate Oligodeoxynucleotide Augment Binding to the v3 Loop of HIV-1 gpl20 and Potency of HIV-1 Inhibition Independently of G-Tetrad Formation (1996)

Phosphorothioate oligodeoxynucleotides belong to a class of polyanions that bind to the third variable domain (v3) of HIV-1 gp120 and inhibit infectivity of a wide variety of HIV-1 isolates. This potent v3 binding of phosphorothioate oligodeoxynucleotides, which is relatively independent of the nucleotide sequence of the oligodeoxynucleotides, decreases with chain length (below 18-mers) and is low for 8-mers. However, recent studies have observed a nucleotide sequence-dependent augmentation of phosphorothioate oligodeoxynucleotide binding to v3 for 8-mers that contain the S-dG4 motif (e.g., SdT2G4T2) and have suggested that formation of quadruple helical tetraplexes (G-tetrads) is associated with the acquisition of v3 binding ability by small phosphorothioate oligodeoxynucleotides. In the current study, a series of SdG4-containing oligodeoxynucleotides were synthesized with varying tandem length (including the 8-mer SdT2G4T2, the 12-mer SdG4T4G4, and the 28-mer SdG4(T4G4)3) and compared with phosphorothioate oligodeoxynucleotides (with similar lengths or related sequences) for (1) their inhibition of the binding of mAb 9284, which binds to the N-terminal portion of the v3 loop, (2) the values of Kc when these compounds are used as competitors of the rgp120-binding of an alkylating phosphodiester oligodeoxynucleotide probe, and (3) inhibition of HIV-1 infectivity in a cell-cell transmission model. The presence of S-dG4 motifs and the number of tandem motifs augmented v3 binding and anti-HIV-1 infectivity for small (8-mer or 12-mer oligodeoxynucleotides) but did not significantly augment the potency of 28-mers. Whereas tetraplex formation of SdT2G4T2 may contribute to its v3 binding, the 12-mer SdG4T4G4 does not migrate as the tetraplex on nonreducing gels, suggesting that S-dG4 motifs may augment anti-HIV activity by multiple mechanisms.
Ir gene control of the murine secretory IgA response to cholera toxin (1987)

In these experiments we examined the genetic control of the secretory IgA (sIgA) response to cholera toxin (CT) after CT feeding. Inbred, congenic and intra-H-2I region recombinant mouse strains were immunized with intragastric application of 10 micrograms CT on days 0 and 14. Samples of intestinal secretions and plasma were collected 1 week after the second dose and antibodies to CT measured in them by antigen- and isotype-specific enzyme-linked immunosorbent assay. In three different sets of H-2-congenic strains the intestinal IgA anti-CT response clearly depended on the H-2 haplotype rather than on background or IgH genes. H-2b (B10, A.BY/SnJ, C3H.SW) and H-2q (B10.T(6R), DBA/1J) strains were high responders, H-2k (B10.BR, C3H/He), H-2s (A.SW/SnJ) and H-2d (B10.D2) strains were low responders. Within the H-2 complex the intestinal IgA anti-CT response was mapped to the I-A subregion with the use of congenic intra-H-2I region recombinant strains: B10.A(3R) and B10.A(5R) were high responders and B10.A(4R), B10.MBR and B10.GD were low responders. Plasma IgG anti-CT after CT feeding paralleled the sIgA results. Surprisingly, the sIgA and plasma IgG anti-CT responses in individual mice of the various strains tested showed a highly significant positive correlation. We conclude that both the sIgA response and plasma IgG anti-CT response after CT feeding is controlled by the I-A subregion of H-2.