gebhart/patrepeval huggingface dataset:
FUSE: Front-End User Framework for O/S Abstraction of Hardware Accelerators (2011)

SoCs can be implemented on a single FPGA, offering designers a unique opportunity for Embedded Systems. Instead of defining a fixed architecture early in the design process, the reconfigurable platform allows architectural redesign to meet the system's specific needs. However, the ability to instantiate new modules in the reconfigurable hardware provides a unique set of challenges for integration, particularly to the software (SW) designer. Specifically, the Operating System (OS) cannot automatically abstract these platform changes without redesign. In this paper, we present FUSE, a framework for HW accelerator abstraction that provides: 1) transparency to the SW designer at the application level, and 2) OS support for easy HW accelerator integration. We illustrate FUSE as an API for an embedded Linux OS with POSIX threads on Xilinx's Micro Blaze on a Virtex5. For three different applications and HW accelerators, we achieve performance speedups ranging from 6.4-37×.
Critical reanalysis of the methods that discriminate the activity of CDK2 from CDK1 (2016)

Cyclin dependent kinases 1 and 2 (CDK1 and CDK2) play crucial roles in regulating cell cycle progression from G1 to S, through S, and G2 to M phase. Both inhibition and aberrant activation of CDK1/2 can be detrimental to cancer cell growth. However, the tools routinely employed to discriminate between the activities of these 2 kinases do not have the selectivity commonly attributed to them. Activation of these kinases is often assayed as a decrease of the inhibitory tyrosine-15 phosphorylation, yet the antibodies used cannot discriminate between phosphorylated CDK1 and CDK2. Inhibitors of these kinases, while partially selective against purified kinases, may lack selectivity when applied to intact cells. High levels of cyclin E are often considered a marker of increased CDK2 activity, yet active CDK2 targets cyclin E for degradation, hence high levels usually reflect inactive CDK2. Finally, inhibition of CDK2 does not arrest cells in S phase suggesting CDK2 is not required for S phase progression. Furthermore, activation of CDK2 in S phase can rapidly induce DNA double-strand breaks in some cell lines. The misunderstandings associated with the use of these tools has led to misinterpretation of results. In this review, we highlight these challenges in the field.
Severe achondroplasia with developmental delay and acanthosis nigricans (SADDAN): Phenotypic analysis of a new skeletal dysplasia caused by a Lys650Met mutation in fibroblast growth factor receptor 3 (1999)

We previously discovered a novel missense mutation (Lys650Met) in the tyrosine kinase domain of the fibroblast growth factor receptor 3 (FGFR3) gene in four unrelated individuals with a condition we called "severe achondroplasia with developmental delay and acanthosis nigricans" (SADDAN) [Tavormina et al., 1999: Am. J. Hum. Genet. 64:722-731]. Here we present a more detailed clinical account of the SADDAN phenotype. The FGFR3 Lys650Met mutation results in severe disturbances in endochondral bone growth that approach and overlap those observed in thanatophoric dysplasia, type I. However, this mutation is most often compatible with survival into adulthood. Other unusual bone deformities, such as femoral bowing with reverse (i.e., posterior apex) tibial and fibular bowing and "ram's horn" bowing of the clavicle, are also seen in some patients. In addition to skeletal dysplasia, progressive acanthosis nigricans, and central nervous system structural anomalies, seizures and severe developmental delays are observed in surviving SADDAN patients. Despite its location within the same FGFR3 codon as the thanatophoric dysplasia type II mutation (Lys650Glu) and a similar effect on constitutive activation of the FGFR3 tyrosine kinase, the Lys650Met is not associated with cloverleaf skull or craniosynostosis.
A new gradual hole injection dual-gate LIGBT (1998)

A new shorted-anode lateral insulated gate bipolar transistor (SA-LIGBT), entitled gradual hole injection dual gate LIGBT (GHI-LIGBT), is proposed and fabricated. The new device employs a dual gate and p/sup +/ injector in order to initiate the hole injection gradually from the anode electrode into the drift region so that the negative differential resistance (NDR) regime may be eliminated. The experimental results show that the NDR regime, which may cause undesirable device characteristics, is completely eliminated in the GHI-LIGBT, and the forward voltage drop is reduced by 1 V at the current density of 200 A/cm/sup 2/ in comparison with the conventional SA-LIGBT.
A simple flame ionization detector cell (1963)

A low cost, easily constructed flame ionization detector cell for gas chromatography has been designed and tested. The details of construction are given. The detector output measured with propylene was 3μA mg-1 sec.
Chemokine ligand 2 (CCL2) induces migration and differentiation of subventricular zone cells after stroke (2007)

Ischemic stroke stimulates neurogenesis in the adult rodent brain. The molecules that mediate stroke-induced neurogenesis have not been fully investigated. Using a microarray containing 113 known genes associated with angiogenesis, we analyzed transcriptional profiles in subventricular zone (SVZ) tissue and in cultured neural progenitor cells isolated from the SVZ of adult mice subjected to middle cerebral artery occlusion (MCAo). Among the genes most robustly up-regulated by MCAo were chemokine ligand 2 (CCL2) and chemokine ligand 10 (CXCL10). Consistent with the mRNA data, immunofluorescent staining revealed that MCAo substantially increased the number of CCL2-positive cells in the ipsilateral SVZ and that CCL2-positive cells were positive for both glial fibrillary acidic protein (GFAP) and nestin. In vitro studies showed that incubation of neural progenitor cells with recombinant human CCL2 substantially increased the number of Tuj1-positive cells dose dependently compared with the number in the control group, indicating that CCL2 promotes neuronal differentiation. Blockage of CCL2 with a neutralized antibody against CCL2 abolished the effects of CCL2 on neural progenitor cell migration and differentiation. Treatment of neural progenitor cells with CCL2 did not alter the number of BrdU cells and the number of apoptotic cells compared with those in the control group, suggesting that CCL2 does not affect neural progenitor cell proliferation and cell survival. These data demonstrate that in addition to its role in cell motility, CCL2 plays an important role in neuronal differentiation.
Characterization of the mycoplasma genome. (1984)

Recent advances on the properties of the mycoplasma genome, including size, base composition, replication, extrachromosomal DNA, and transfer of genetic material are briefly reviewed, with emphasis on their phylogenetic implications. The use of cleavage patterns of the mycoplasma genome by restriction endonucleases as "finger-prints" indicating genetic relatedness among strains is discussed. The data support the notion that strains of mycoplasma species of strict host and tissue specificity exhibit marked genetic homogeneity, suggesting a clonal origin for some species. The regions of the mycoplasma genome carrying the ribosomal RNA (rRNA) genes have been studied using restriction endonucleases, cloning, and hybridization procedures. The mycoplasmal rRNA cistrons cross-hybridized among themselves, and with the seven rRNA cistrons of Escherichia coli, demonstrating the marked conservation of structure during evolution of this part of the procaryotic genome. In most of the mollicutes tested so far the number of rRNA cistrons is two, but a few species appear to carry only one rRNA cistron in their genome.
Neural Network Models for Promoter Recognition (1989)

The problem of recognition of promoter sites in the DNA sequence has been treated with models of learning neural networks. The maximum network capacity admissible for this problem has been estimated on the basis of the total of experimental data available on the determined promoter sequences. The model of a block neural network has been constructed to satisfy this estimate and rules have been elaborated for its learning and testing. The learning process involves a small (of the order of 10%) part of the total set of promoter sequences. During this procedure the neural network develops a system of distinctive features (key words) to be used as a reference in identifying promoters against the background of random sequences. The learning quality is then tested with the whole set. The efficiency of promoter recognition has been found to amount to 94 to 99%. The probability of an arbitrary sequence being identified as a promoter is 2 to 6%.
An efficient symbol-level combining scheme for MIMO systems with hybrid ARQ (2009)

This paper proposes a new combining scheme for multiple-input multiple-output (MIMO) systems with hybrid automatic-repeat-request (HARQ). The proposed combining scheme is proved to have the optimal decoding performance. Furthermore, the proposed combining scheme is shown to have low memory requirement and reduced complexity compared to other optimal combining schemes. Simulation results under IEEE 802.16e setting with UMTS channel models verify that the proposed combining scheme achieves the optimal decoding performance and performs much better than other suboptimal combining schemes.
The read-write disturb problem in plated wire memories (1972)

Data illustrating the read-write disturb problem in plated wire memories are reported. It is shown that the application of a dc hard axis field of the order of 1 Oe acting in the same direction as the word pulse can alleviate the disturb. Read-write disturb threshold curves are presented for a variety of pulse sequences incorporating either unipolar or bipolar bit currents. It is found that the second pulse of a bipolar disturb bit current is, for long pulse widths, the most influential. A model, which is based upon an extension of the modified lever mechanism used to explain conventional creep, is proposed. This model can explain all the data. In addition, it predicts that as the bit pulse length is decreased, the bipolar disturb sequence should become less severe. This is observed and, for a pulse width of 50 ns, the disturb threshold moves well above the wall motion current. Finally, a number of methods for increasing operating margins is presented.
Role of phospholamban phosphorylation on Thr17 in cardiac physiological and pathological conditions (2005)

The sarcoplasmic reticulum (SR) Ca(2+)-ATPase (SERCA2a) is under the control of a closely associated SR protein named phospholamban (PLN). Dephosphorylated PLN inhibits the SR Ca(2+) pump, whereas phosphorylation of PLN, at either Ser(16) by PKA or Thr(17) by calmodulin-dependent protein kinase II (CaMKII), reverses this inhibition, thus increasing SERCA2a activity and the rate of Ca(2+) uptake by the SR. This would in turn lead to an increase in the velocity of relaxation, SR Ca(2+) load, and myocardial contractility. Thus, PLN is a major determinant of cardiac contractility and relaxation. Although in the intact heart, beta-adrenoceptor stimulation results in phosphorylation of PLN at both Ser(16) and Thr(17) residues, the role of Thr(17) site has long remained equivocal. In this review, we attempt to highlight the signaling cascade and the physiological relevance of the phosphorylation of this residue in the heart under both physiological and pathological situations.
Bursty impulse noise detection by compressed sensing (2011)

Impulse noise (IN) is one of the major impairments for data transmission over power lines. For power line communications (PLC) systems with bandwidths in the high kHz to MHz range, IN occurs in bursts. As long as those bursts are sufficiently short compared to a signal-processing (e.g. coding) frame, there is hope to successfully mitigate IN. In this paper, we introduce a new IN mitigation technique that is based on the application of block-based compressed sensing (CS). It makes use of null-subcarriers in PLC orthogonal frequency division multiplexing (OFDM) transmission systems and the burst structure of IN to detect the location and the values of IN samples in the received signal. We also devise a semi-analytical error-rate performance evaluation for coded OFDM over IN channels, which allows insights into how CS-based IN detection can be used for improved reliability of transmission. Numerical results for typical PLC transmission settings demonstrate the efficacy of the proposed application of CS for IN detection.
Profile of skin barrier proteins (filaggrin, claudins 1 and 4) and Th1/Th2/Th17 cytokines in adults with atopic dermatitis (2014)

Our data reinforce the role of an altered skin barrier in the pathogenesis of AD. Our results show not only reduced expression of filaggrin and claudin 1 in lesional atopic skin but also inverse correlation of filaggrin expression and disease severity. Moreover, elevation of in situ IL-17 and of circulating interleukin levels in AD emphasize the systemic, inflammatory profile of this defective skin barrier dermatosis.
Effects of nonmineral tissues on measurement of bone mineral content by dual‐photon absorptiometry (1990)

Computer simulations were performed to investigate the effects of nonmineral tissue (overlying soft tissue and nonmineral components of bone) on the measurement of bone mineral content by dual-photon absorptiometry (DPA). Selected experimental studies were performed to test the predictions of the simulations. The results indicate that variations in the composition of nonmineral tissue can significantly affect measurement precision and accuracy at the levels achievable with modern x-ray based absorptiometry systems (0.5%). Thus biological variables may limit further improvements in measurement precision and accuracy. Biological variables also can affect intercalibration of systems that use different radiation sources and/or calibration techniques.
Intracochlear Pressure Changes due to 2 Electrode Types: An Artificial Model Experiment (2016)

Objective To preserve residual hearing in cochlear implant surgery, the electrode design has been refined, and an atraumatic insertion has become one aspect of cochlear implant research. Previous studies have described the effect of insertion speed and opening of the round window membrane on intracochlear pressure changes. The aim of our current study was to observe intracochlear pressure changes due to different cochlear implant electrodes in an artificial cochlear model with stable surrounding factors. Study Design Prospective controlled study. Setting Tertiary referral center. Subjects and Methods The experiments were performed in an artificial cochlear model with a pressure sensor in the apical area. With straight and perimodiolar electrode arrays, 5 insertions with the same insertion speed and 5 insertions over the same time were performed. Results With the perimodiolar high-volume electrode, significantly greater intracochlear fluid pressure changes were observed than with the straight electrode. Compared with the straight electrode, the perimodiolar electrode induces significantly higher pressure peaks (1.12 ± 0.15 vs 0.86 ± 0.05 mm Hg, P = .006) and significantly higher amplitudes (0.38 ± 0.07 vs 0.09 ± 0.07 mm Hg, P < .001). Conclusion The reliable preservation of residual hearing is an important multifactorial challenge in modern cochlear implant surgery. Insertion speed, handling, and electrode design are known to influence the preservation of residual hearing. In our artificial model experiments, we could prove objectively that the volume of the electrodes has a significant influence on the intracochlear pressure changes during cochlear implantation.
Internet Relay Chat: Channel Management (2000)

One of the most notable characteristics of the IRC (Internet Relay Chat) protocol is to allow for users to be grouped in forums, called channels, providing a mean for multiple users to communicate together.
On determining the fundamental matrix : analysis of different methods and experimental results (1993)

The fundamental matrix is a key concept when working with uncalibrated images and multiple viewpoints. It contains all the available geometric information and enables to recover the epipolar geometry from uncalibrated perspective views. This paper addresses the important problem of its robust determination given a number of image point correspondences. We first define precisely this matrix and show clearly how it is related to the epipolar geometry and to the essential matrix introduced earlier by Longuet-Higgins. In particular, we show that this matrix, defined up to a scale factor, must be of rank two. Different parametrizations for this matrix are then proposed to take into account these important constraints and linear and non-linear criteria for its estimation are also considered. We then clearly show that the linear criterion is unable to express the rank and normalization constraints. Using the linear criterion leads definitely to the worst result in the determination of the fundamental matrix. Several examples on real images clearly illustrate and validate this important negative result. To overcome the major weaknesses of the linear criterion, different non-linear criteria are proposed and analyzed in great detail. Extensive experimental work has been performed in order to compare the different methods using a large number of noisy synthetic data and real images. In particular, a statistical method based on variation of camera displacements is used to evaluate the stability and convergence properties of each method.
The D P Wilson Lecture. Research on settlement and metamorphosis of marine invertebrate larvae: Past, present and future (1998)

In 1952, D P Wilson remarked that invertebrate larvae, “... are indeed not helpless, for they are endowed with the power of choice,...”; at settlement. Subsequent efforts have greatly enhanced understanding of the conditions under which larvae metamorphose, altering the conceptual view of this process from “larval choice”; to “developmental induction,”; and aligning studies of invertebrate metamorphosis with those of modern developmental biology. While the precise chemical nature of most metamorphic inducers evades us, elucidation of the phenomena of reception and transduction appears imminent for many larvae. The evidence for receptor cells and molecules specific for inducer substances is convincing for larvae in several phyla, and a generalized picture of stimulation of electrically excitable cells has emerged; larvae from at least eight invertebrate phyla metamorphose in response to augmented K + . To be determined is whether genes specifying receptor proteins for metamorphic inducers share homology and whether metamorphic signals are transduced by the same intracellular pathways across invertebrate phyla. Metamorphic competence can be a developmentally unique condition where non‐growing, non‐feeding larvae are primed to metamorphose when signaled; a genetic explanation for competence merits intense exploration. The acquisition for marine invertebrate larvae of knowledge comparable to that for the genetic basis of timing of photic responses and pupal eclosion in Drosophila will provide material for exciting research in the years ahead. Many species (e.g. the polychaete Hydroides elegans) offer excellent models for laboratory genetic studies of invertebrate settlement and metamorphosis.
Antineoplastic activity of azacarbazoles. III. Synthesis and antitumor evaluation of selected 2-, 3- aza- and diazaanalogues of carbazole. (1986)

Preliminary screening of the antitumor properties of selected azacarbazoles revealed that of all the compounds tested only 2,7-diazacarbazole (compound IX) and 3,6-diazacarbazole (compound XI) caused the inhibition of Sarcoma 180 growth up to 70%. beta- and gamma-Carbolines and their derivatives in presented testing system were inactive. None of the tested compounds displayed marked activity against murine leukemias and was active in the cytotoxicity test of KB cells.
Comparison of PCR-based restriction length polymorphism analysis of urease genes with rRNA gene profiling for monitoring Helicobacter pylori infections in patients on triple therapy (1994)

Multiple isolates of Helicobacter pylori from antral biopsies of nine patients were examined by DNA fingerprinting. Analysis of rRNA gene patterns and HaeIII restriction fragment length polymorphism of PCR-amplified urease genes were compared and used to study colonization before and after failed triple therapy. H. pylori isolates from a single biopsy shared the same HaeIII DNA fingerprint regardless of the isolation method (plate or broth). DNA pattern types of paired strains of H. pylori were distinct between patients and were not grossly affected by treatment except for one patient with an altered strain type. H. pylori infections were generally associated with several subpopulations of strains, evident from the subtypic variation before and after treatment, detectable by both DNA fingerprinting methods. The urease gene patterns also provided evidence that some cultures of H. pylori probably contained a mixture of genomic subtypes. The study suggests that triple therapy has the effect either of inducing minor genomic variations or of changing the proportions of different subtypes of H. pylori. It was concluded that urease gene profiling provides a simple yet reliable method of establishing whether treatment failures are attributable to incomplete eradication of H. pylori.
Crowd Counting Using Group Tracking and Local Features (2010)

In public venues, crowd size is a key indicator of crowd safety and stability. In this paper we propose a crowd counting algorithm that uses tracking and local features to count the number of people in each group as represented by a foreground blob segment, so that the total crowd estimate is the sum of the group sizes. Tracking is employed to improve the robustness of the estimate, by analysing the history of each group, including splitting and merging events. A simplified ground truth annotation strategy results in an approach with minimal setup requirements that is highly accurate.