gebhart/patrepeval huggingface dataset:
Hoplite (2017)

We can design an FPGA-optimized lightweight network-on-chip (NoC) router for flit-oriented packet-switched communication that is an order of magnitude smaller (in terms of LUTs and FFs) than state-of-the-art FPGA overlay routers available today. We present Hoplite, an efficient, lightweight, and fast FPGA overlay NoC that is designed to be small and compact by (1) using deflection routing instead of buffered switching to eliminate expensive FIFO buffers and (2) using a torus topology to reduce the cost of switch crossbar. Buffering and crossbar implementation complexities have traditionally limited speeds and imposed heavy resource costs in conventional FPGA overlay NoCs. We take care to exploit the fracturable lookup tables (LUT) organization of the FPGA to further improve the resource efficiency of mapping the expensive crossbar multiplexers. Hoplite can outperform classic, bidirectional, buffered mesh networks for single-flit-oriented FPGA applications by as much as 1.5 × (best achievable throughputs for a 10 × 10 system) or 2.5 × (allocating same amount of FPGA resources to both NoCs) for uniform random traffic. When compared to buffered mesh switches, FPGA-based deflection routers are ≈ 3.5 × smaller (HLS-generated switch) and 2.5 × faster (clock period) for 32b payloads. In a separate experiment, we hand-crafted an RTL version of our switch with location constraints that requires only 60 LUTs and 100 FFs per router and runs at 2.9ns. We conduct additional layout experiments on modern Xilinx and Altera FPGAs and demonstrate wide-channel chip-spanning layouts that run in excess of 300MHz while consuming 10--15% of overall chip resources. We also demonstrate a clustered RISC-V multiprocessor organization that uses Hoplite to help deliver the high processing throughputs of the FPGA architecture to user applications.
Glucagon·Glucagon-like Peptide I Receptor Chimeras Reveal Domains That Determine Specificity of Glucagon Binding (1995)

The binding of glucagon to its hepatic receptor triggers a G-protein-mediated signal that ultimately leads to an increase in hepatic glucose production (gluconeogenesis) and glycogen breakdown (glycogenolysis). In order to elucidate the structural domain(s) of the human glucagon receptor (hGR) involved in the selective binding of glucagon, a series of chimeras was constructed in which various domains of the hGR were replaced by homologous regions from the receptor for the glucoincretin hormone, glucagon-like peptide I (GLP-IR). hGR and GLP-IR are quite similar (47% amino acid identify) yet have readily distinguishable ligand binding characteristics; glucagon binds to the recombinant hGR expressed in COS-7 cells with a Kd that is 1000-fold lower than the Kd for glucagon binding to GLP-IR. In the present study, chimeric receptors were transiently expressed in COS-7 cells and analyzed for glucagon binding. Expression of each receptor chimera was confirmed by immunofluorescence staining using a hGR-specific monoclonal antibody. This report identifies several non-contiguous domains of the hGR that are important for high affinity glucagon binding. Most notable are the membrane-proximal half of the amino-terminal extension, the first extracellular loop, and the third, fourth, and sixth transmembrane domains.
Theoretical Modeling and Implementation of Traveling Wave Sensor Based on PCB Coils (2015)

Based on analyzing characteristics of Rogowski coil, a new type of PCB traveling wave sensor with simple structure, high linearity, and anti-interference ability is proposed. The sensor has fine physical structure, which can effectively resist external electromagnetic interference by anti-interference measurement. In addition, it can greatly improve mutual inductance based on simple combinations. Simulations show that the new PCB traveling wave sensor can validly extract and deliver traveling wave signal and therefore realize fault location and protection accurately.
High-temperature thermometer with fiber optic readout (2005)

Ultra-high temperature measurement is required in many harsh environment applications such as temperature monitoring in combustors and furnaces. This paper presents a novel thermometer, which is capable to measure temperatures above 1000°C with high resolution and accuracy. This sensor functions as a gas thermometer with a fiber optic readout, which will not suffer from blackbody radiation noise. The sensing part has high hardness, good electrical insulation, good wear resistance and does not react with most chemicals. The size of the sensor can be chosen flexibly to satisfy different application requirements. Since no electrical components are involved, the sensor is spark/explosion free and immune to electromagnetic interference (EMI). The sensor structure is simple, easy to fabricate and low cost. Some temperature measurement results in the laboratory are presented.
Axitinib for the treatment of advanced non-small-cell lung cancer (2013)

Several TKI which target angiogenesis pathways have resulted in improved response rates and progression-free survival in NSCLC, but no improvement in overall survival in clinical trials. Axitinib is a more potent inhibitor of vascular endothelial growth factor receptors than other TKI, but this has yet to translate into a clinical benefit. Phase II trials are ongoing, but the published data to date has yet to support a role for axitinib in the treatment algorithm for NSCLC.
Cell Cycle Control of DNA Replication (1996)

The initiation of DNA replication in eukaryotic cells is a highly regulated process that leads to the duplication of the genetic information for the next cell generation. This requires the ordered assembly of many proteins at the origins of DNA replication to form a competent, pre-replicative chromosomal state. In addition to this competent complex, at least two cell cycle regulated protein kinase pathways are required to affect a transition to a post-replicative chromosomal state. Protein kinases required to establish mitosis prevent re-replication of the DNA. As cells exit mitosis, the cell cycle is reset, allowing the establishment of a new, competent replication state.
REPEAT ULTRASOUND GUIDED PROSTATE NEEDLE BIOPSY: USE OF FREE-TO-TOTAL PROSTATE SPECIFIC ANTIGEN RATIO IN PREDICTING PROSTATIC CARCINOMA (1998)

For total PSA in the range of 2 to 15 ng./ml. Hybritech free-to-total PSA ratio appeared to aid in the prediction of cancer on repeat biopsy.
Constitutive phosphoinositide 3-kinase/Akt activation represents a favorable prognostic factor in de novo acute myelogenous leukemia patients (2007)

The phosphoinositide 3-kinase (PI3K/Akt) pathway is activated in acute myelogenous leukemia (AML) and is promising for targeted inhibition. Ninety-two patients with primary AML were analyzed for PI3K/Akt constitutive activation. Fifty percent of the patients presented with constitutive PI3K activation (PI3K (+)). No difference was observed between PI3K (+) and PI3K (-) groups concerning age, sex, white blood cell count, lactate dehydrogenase (LDH) level, bone marrow blast cells, French-American-British (FAB) classification, cytogenetics, RAS or nucleophosmin (NPM) mutations. Slightly more FLT3-ITD was detected in the PI3K (-) group (P = .048). The complete remission rate was similar between the 2 groups. With a median follow-up of 26 months, we observed for PI3K (+) and PI3K (-) patients, respectively, 56% and 33% overall survival (P = .001) and 72% and 41% relapse-free survival (P = .001). Constitutive PI3K/Akt activity is a favorable prognosis factor in AML, even after adjustment for FLT3-ITD, and may confer a particular sensitivity to chemotherapy. A better understanding of the downstream effectors of the PI3K/Akt pathway is needed before targeting in AML.
Relationship of Monocyte Count and Peripheral Arterial Disease (2005)

Monocytes were the only WBC type significantly and independently associated with PAD in a representative sample of the U.S. population after adjustment for other inflammatory markers. These findings reflect the potential role of circulating monocyte counts as markers of atherosclerosis.
Highly Sensitive Determination of microRNA Using Target‐Primed and Branched Rolling‐Circle Amplification (2009)

Abstract Schon ein unterschiedliches Nucleotid in Mikro‐RNAs (miRNAs) wird in einem Assay erfasst, der auf verzweigter Rolling‐Circle‐Amplifizierung (BRCA) und einer Fluoreszenzquantifizierungstechnik beruht. Die Methode diskriminiert miRNA schon ab Konzentrationen von 10 f M und kann miRNA in RNA‐Proben von wenigen Nanogramm bestimmen. magnified image
Redox Trends in Terpyridine Nickel Complexes (2011)

A synthesis has been developed that allows the isolation of four-coordinate [(tpy)Ni-Br] (1, tpy = terpyridine) in high yield. Complex 1 has been structurally characterized, and the X-ray data reveal a square-planar geometry, unlike the known [(tpy')Ni-I] (tpy' = 4,4',4''-tri-tert-butyl-terpyridine) but similar to [(tpy)Ni-CH(3)]. In the solid-state, EPR spectroscopy indicates, however, that unlike [(tpy)Ni-CH(3)], the electronic structure of 1 is a metal-centered, not a ligand-centered radical. Density functional theory (DFT) analyses support this assignment. The preparation of 1 also facilitated the analysis of the redox potentials of a series of terpyridine nickel derivatives. It was found that the overall ligand sphere (one vs two coordinated terpyridine ligands) plays more of a role in determining the redox potentials of these derivatives than do the formal oxidation states of the nickel ions in the solution phase.
Circulating tumor cells and serum tumor biomarkers in small cell lung cancer. (2003)

Lung cancer accounts for approximately 30% of all cancer mortalities in the United States. Small cell lung cancer (SCLC), which is an aggressive malignancy with frequent and early metastases, accounts for about 15% of all of the lung cancer cases with a dismal 5-year survival rate of < 5% with current standard therapies. Early detection of SCLC is challenging, in part due to the lack of adequate serum tumor markers. The goal of this review is to summarize the current knowledge of circulating tumor cells and serum biomarkers in small cell lung cancer. The role of circulating tumor cells in prognostication is controversial, but may be better defined with advancing technologies of detection of such cells with higher precision, and improved clinico-pathological correlations. The current knowledge on the known serum cytokines and tumor biomarkers of SCLC, such as CEA, chromogranin-A and neuron-specific enolase will be presented. Serum cytokines, such as vascular endothelial growth factor (VEGF), stem cell factor (SCF) and hepatocyte growth factor/scatter factor (HGF/SF) are also discussed. New findings in the search for novel diagnostic and therapeutic molecular markers using the emerging genomics and proteomics technologies are emphasized. It is our hope that validation of these new research platforms and technologies will result in improved early detection, prognostication and finally treatment of SCLC with potential novel molecularly-targeted therapeutics.
Growth factor-dependent inhibition of normal hematopoiesis by N-ras antisense oligodeoxynucleotides. (1992)

To determine whether N-ras expression is required at specific stages of the process of in vitro normal human hematopoiesis, adherent- and T lymphocyte-depleted mononuclear marrow cells (A-T-MNC) or highly purified progenitors (CD34+ cells) were cultured in semisolid medium, under conditions that favor the growth of specific progenitor cell types, after exposure to N-ras sense and antisense oligodeoxynucleotides. N-ras antisense, but not sense, oligodeoxynucleotide treatment of A-T-MNC and CD34+ cells resulted in a significantly decreased number of granulocyte/macrophage colony-forming units (CFU-GM) induced by interleukin 3 (IL-3) or granulocyte/macrophage colony-stimulating factor (GM-CSF) and of macrophage colonies (CFU-M) induced by M-CSF, but not of granulocytic colonies induced with G-CSF or IL-5. However, the same treatment significantly inhibited colony formation induced by each of the above factors in combination with IL-3. Megakaryocytic colony (CFU-Meg) formation from A-T-MNC or CD34+ cells in the presence of IL-6 + IL-3 + erythropoietin (Epo) was also markedly decreased after antisense oligodeoxynucleotide treatment. Erythroid colonies derived from A-T-MNC in the presence of Epo (CFU-E) were not inhibited upon antisense treatment, whereas those arising from A-T-MNC or CD34+ cells in the presence of IL-3 + Epo (BFU-E) were markedly affected. These results are consistent with the hypothesis that distinct signal transduction pathways, involving N-ras or not, are activated by different growth factors in different hematopoietic progenitor cells.
Structure−Function Analysis of a Phage Display-Derived Peptide That Binds to Insulin-like Growth Factor Binding Protein 1 (2001)

Highly structured, peptide antagonists of the interaction between insulin-like growth factor 1 (IGF-I) and IGF binding protein 1 (IGFBP-1) have recently been discovered by phage display of naïve peptide libraries [Lowman, H. B., et al. (1998) Biochemistry 37, 8870--8878]. We now report a detailed analysis of the features of this turn-helix peptide motif that are necessary for IGFBP-1 binding and structural integrity. Further rounds of phage randomization indicate the importance of residues contributing to a hydrophobic patch on one face of the helix. Alanine-scanning substitutions confirm that the hydrophobic residues are necessary for binding. However, structural analysis by NMR spectroscopy indicates that some of these analogues are less well folded. Structured, high-affinity analogues that lack the disulfide bond were prepared by introducing a covalent constraint between side chains at positions i and i + 7 or i + 8 within the helix. Analogues based on this scaffold demonstrate that a helical conformation is present in the bound state, and that hydrophobic side chains in this helix, and residues immediately preceding it, interact with IGFBP-1. By comparison of alanine scanning data for IGF-I and the turn-helix peptide, we propose a model for common surface features of these molecules that recognize IGFBP-1.
Complete removal of redundant expressions (1998)

Partial redundancy elimination (PRE), the most important component of global optimizers, generalizes the removal of common subexpressions and loop-invariant computations. Because existing PRE implementations are based on code motion, they fail to completely remove the redundancies. In fact, we observed that 73% of loop-invariant statements cannot be eliminated from loops by code motion alone. In dynamic terms, traditional PRE eliminates only half of redundancies that are strictly partial. To achieve a complete PRE, control flow restructuring must be applied. However, the resulting code duplication may cause code size explosion.This paper focuses on achieving a complete PRE while incurring an acceptable code growth. First, we present an algorithm for complete removal of partial redundancies, based on the integration of code motion and control flow restructuring. In contrast to existing complete techniques, we resort to restructuring merely to remove obstacles to code motion, rather than to carry out the actual optimization.Guiding the optimization with a profile enables additional code growth reduction through selecting those duplications whose cost is justified by sufficient execution-time gains. The paper develops two methods for determining the optimization benefit of restructuring a program region, one based on path-profiles and the other on data-flow frequency analysis. Furthermore, the abstraction underlying the new PRE algorithm enables a simple formulation of speculative code motion guaranteed to have positive dynamic improvements. Finally, we show how to balance the three transformations (code motion, restructuring, and speculation) to achieve a near-complete PRE with very little code growth.We also present algorithms for efficiently computing dynamic benefits. In particular, using an elimination-style data-flow framework, we derive a demand-driven frequency analyzer whose cost can be controlled by permitting a bounded degree of conservative imprecision in the solution.
Structure, function, and biology of SHIP proteins (2000)

One of the “simple” curiosities of life, at least for a biological scientist, is how the growth and development of a complete organism from a single cell is controlled. Part of the answer includes growth factor receptors and their respective ligands, which transduce signals across cell membranes and into the nucleus for transcriptional readout. The molecular nature of these intracellular signals determines the type of signals, the pathways involved, subsequent regulatory interactions, and eventual transcription factor activation/repression. Hematopoietic cell development has been a fruitful system for the
Quantum memory with millisecond coherence in circuit QED (2016)

Significant advances in coherence render superconducting quantum circuits a viable platform for fault-tolerant quantum computing. To further extend capabilities, highly coherent quantum systems could act as quantum memories for these circuits. A useful quantum memory must be rapidly addressable by Josephson-junction-based artificial atoms, while maintaining superior coherence. We demonstrate a superconducting microwave cavity architecture that is highly robust against major sources of loss that are encountered in the engineering of circuit QED systems. The architecture allows for storage of quantum superpositions in a resonator on the millisecond scale, while strong coupling between the resonator and a transmon qubit enables control, encoding, and readout at MHz rates. This extends the maximum available coherence time attainable in superconducting circuits by almost an order of magnitude compared to earlier hardware. Our design is an ideal platform for studying coherent quantum optics and marks an important step towards hardware-efficient quantum computing in Josephson-junction-based quantum circuits.
Magnetic stimulation coil and circuit design (2000)

A detailed analysis of the membrane voltage rise commensurate with the electrical charging circuit of a typical magnetic stimulator is presented. The analysis shows how the membrane voltage is linked to the energy, reluctance, and resonant frequency of the electrical charging circuit. There is an optimum resonant frequency for any nerve membrane depending on its capacitive time constant. The analysis also shows why a larger membrane voltage will be registered on the second phase of a biphasic pulse excitation [1]. Typical constraints on three key quantities voltage, current, and silicone controlled rectifier (SCR) switching time dictate key components such as capacitance, inductance, and choice of turns.
Topical Application of Integrin Antagonists Inhibits Proliferative Retinopathy (2001)

The expression of alphav-integrins is highly selective for angiogenic endothelial cells; ligation inhibition by cyclic RGD peptides prevents pathological neovascularization in tumor or retinopathy models to a large extent. We have previously demonstrated that proliferative retinopathy in a mouse model of retinopathy of prematurity (ROP model) can be reduced by more than 70%. To minimize systemic side effects and unwanted interference with responsive angiogenesis, we investigated topical application of cyclic RGD-peptides. In preliminary experiments, we could exclude any inhibiting effects of the carrier solution containing EDTA, Na2S, mannitol, hydroxyethyl starch, and benzalconium chloride on the inhibitory effect of cyclic RGD peptides. Retinal presence of small molecular-mass integrin antagonists after topical application was confirmed using fluorescein-labeled cyclic RGD peptide. Topical application of the peptide to the eye inhibited proliferative retinopathy in a dose-dependent fashion with a maximum of almost 50%. These results suggest that small molecular-mass peptide antagonists of alphav-type integrins are efficient in inhibiting proliferative retinopathy by topical application.
Rescue of immunoglobulin secretion from human neoplastic lymphoid cells by somatic cell hybridization. (1978)

B leukemia cells from four different patients were hybridized with a mouse myeloma cell line with polyethylene glycol as a fusing agent. The original leukemia cells all expressed immunoglobulin on their surface, but failed to secrete it. Over 200 different human-mouse somatic cell hybrids were obtained; 57% of them secreted human immunoglobulin in large amounts. Human immunoglobulin secretion can be a stable property of these hybrid cells over months of continuous culture. In each case the human immunoglobulin secreted was restricted to the light chain type expressed by the parental B leukemia cell. In addition, these hybrid cells secreted the original mouse myeloma protein and a variety of mixed human-mouse immunoglobulin molecules.
Synthetic gravity modelling - An interpretation tool to integrate seismic and gravity data (1993)

One of the challenges a geophysicist faces today is the integration and calibration of seismic and gravity data. Tools are readily available to calibrate seismic data to wells through the generation of a synthetic seismic trace from a well sonic log. Matching the synthetic seismic trace to the seismic data is the best method to calibrate the reflectors to the known formation tops encountered in a well. Geophysicists know that calibration of their seismic data to a well is critical for an accurate seismic interpretation. Likewise, calibration of the gravity data to known geology is critical for an accurate gravity interpretation. There have been no methods or tools to relate gravity and seismic other than by simple map or profile correlation. The present technique was developed and successfully used on proprietary interpretations by the author for the past seven (7) years.
Electrostatic Potentials inRhodopseudomonas viridisReaction Centers:  Implications for the Driving Force and Directionality of Electron Transfer (1996)

Finite difference solutions to the Poisson equation are used to characterize electrostatic interactions in reaction centers from Rhodopseudomonas viridis. A sizable potential gradient resulting primarily from charged amino acid side chains is found in the protein. This static field favors the observed electron transfers from the primary donor (P) along the L branch of the protein via the bacteriochlorophyll monomer (BL) toward the bacteriopheophytin electron acceptor (HL). The effect of the field is to favor electron transfer to BL by approximately 0.4 eV and to HL by approximately 0.8 eV. The electric field along the M branch is significantly smaller, thus providing a straightforward explanation for the directionality of electron transfer. The large static field in the protein appears to be necessary to overcome the intrinsic cost of charge separation in a low dielectric medium. Electrostatic potentials were calculated for the protein in uniform low dielectric medium and for the protein surrounded by water with and without a membrane. While the calculated site potentials are sensitive to the assumptions about the dielectric response of the protein and surrounding medium, the conclusion that there is a large static field favoring charge separation along the L branch is independent of the detailed model used to describe the system.
Treatment with the immunomodulator FTY720 does not promote spontaneous bacterial infections after experimental stroke in mice (2011)

Our results corroborate the experimental evidence of the protective effect of FTY720 seen in different rodent stroke models. Interestingly, we found no increase in bacterial lung infections even though FTY720 strongly reduces the number of circulating leukocytes.