gebhart/patrepeval huggingface dataset:
Characterization of Scientific Workloads on Systems with Multi-Core Processors (2006)

Multi-core processors are planned for virtually all next-generation HPC systems. In a preliminary evaluation of AMD Opteron Dual-Core processor systems, we investigated the scaling behavior of a set of micro-benchmarks, kernels, and applications. In addition, we evaluated a number of processor affinity techniques for managing memory placement on these multi-core systems. We discovered that an appropriate selection of MPI task and memory placement schemes can result in over 25% performance improvement for key scientific calculations. We collected detailed performance data for several large-scale scientific applications. Analyses of the application performance results confirmed our micro-benchmark and scaling results
The War of the Words: Revamping Operational Terminology for UFOs (1999)

In this study, the correlation between the metabolic profiles of rats undergoing cognition enhancement drug therapy and their associated cognitive behavioral outcomes were investigated. Male Lister Hooded rats were administered either with donepezil, galantamine, or vehicle and subjected to Atlantis watermaze training and novel object recognition tests. An UPLC/MS/MS method was developed to profile 21 neurologically related metabolites in the rat brains. Pharmacologically induced behavioral changes were compared subsequently with the metabolic fluctuations of neurologically related metabolites from multiple neurotransmitter pathways using multivariate and univariate statistical analyses. Significant improvements in cognitive behavioral outcomes were demonstrated in the rats administered with donepezil and galantamine using both AWM training (P < 0.05) and NOR (P < 0.05) tests as compared to those dosed with the vehicle. This corroborated with the significant elevation of eight prominent biomarkers after the cognitive enhancement therapy. An orthogonal partial least-squares discriminant analysis model generated using only the 8 metabolites identified as discriminating the drug-dosed rats from the vehicle-dosed rats gave a Q(2) = 0.566, receiver operator characteristic (ROC) AUC = 1.000, using 7-fold cross validation. Our study suggests that metabolic profiling of rat brain is a potential complementary strategy to the cognitive behavioral tasks for characterizing neurobiological responses to cognition enhancement drug testing.
Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea (2003)

Among Pseudomonas strains isolated from Korean agricultural soils, four strains (Ps 9-14 group: Ps 1-2, Ps 1-10, Ps 5-5 and Ps 9-14T) from the Suwon, Goesan and Samchok regions, three strains (Ps 3-10 group: Ps 2-22, Ps 3-1 and Ps 3-10T) from Umsong Region and four strains (Pss 26 group: Pss 14, Pss 25, Pss 26T and Pss 27) from Jinju Region were identified as three independent groups on the basis of 16S rDNA sequence analysis. While, on the basis of 16S rDNA sequence analysis, Ps 9-14T and Ps 3-10T form a phyletic line with Pseudomonas jessenii CIP 105274T, 'Pseudomonas pavonaceae' IAM 1155 and Pseudomonas graminis DSM 11363T, Pss 26T is grouped with Pseudomonas citronellolis ATCC 13674T and Pseudomonas nitroreducens IAM 1439T. According to DNA-DNA hybridization studies, strain Ps 9-14T shows high DNA relatedness to strain Ps 3-10T (52%) and Pseudomonas migulae CIP 105470T (49%) and strain Ps 3-10T reveals high relatedness to strain Ps 9-14T (48%) and P. jessenii CIP 105274T (45%). Strain Pss 26T shows high relatedness to P. citronellolis LMG 18378T (54%), P. nitroreducens ATCC 33634T (48%) and Pseudomonas aeruginosa LMG 1242T (48%). On the basis of phenotypic and genotypic analyses, three novel species of the genus Pseudomonas are proposed: Pseudomonas koreensis sp. nov. (type strain Ps 9-14T =LMG 21318T =KACC 10848T) for the Ps 9-14 group, Pseudomonas umsongensis sp. nov. (type strain Ps 3-10T =LMG 21317T =KACC 10847T) for the Ps 3-10 group and Pseudomonas jinjuensis sp. nov. (type strain Pss 26T =LMG 21316T =KACC 10760T) for the Pss 26 group.
Fructose-1,6-bisphosphatase Inhibits ERK Activation and Bypasses Gemcitabine Resistance in Pancreatic Cancer by Blocking IQGAP1–MAPK Interaction (2017)

Dysregulation of the MAPK pathway correlates with progression of pancreatic ductal adenocarcinoma (PDAC) progression. IQ motif containing GTPase-activating protein 1 (IQGAP1) is a MAPK scaffold that directly regulates the activation of RAF, MEK, and ERK. Fructose-1,6-bisphosphatase (FBP1), a key enzyme in gluconeogenesis, is transcriptionally downregulated in various cancers, including PDAC. Here, we demonstrate that FBP1 acts as a negative modulator of the IQGAP1-MAPK signaling axis in PDAC cells. FBP1 binding to the WW domain of IQGAP1 impeded IQGAP1-dependent ERK1/2 phosphorylation (pERK1/2) in a manner independent of FBP1 enzymatic activity. Conversely, decreased FBP1 expression induced pERK1/2 levels in PDAC cell lines and correlated with increased pERK1/2 levels in patient specimens. Treatment with gemcitabine caused undesirable activation of ERK1/2 in PDAC cells, but cotreatment with the FBP1-derived small peptide inhibitor FBP1 E4 overcame gemcitabine-induced ERK activation, thereby increasing the anticancer efficacy of gemcitabine in PDAC. These findings identify a primary mechanism of resistance of PDAC to standard therapy and suggest that the FBP1-IQGAP1-ERK1/2 signaling axis can be targeted for effective treatment of PDAC. <i>Cancer Res; 77(16); 4328-41. ©2017 AACR</i>.
Arbitrarily Shaped Motion Prediction for Depth Video Compression Using Arithmetic Edge Coding (2014)

Depth image compression is important for compact representation of 3D visual data in texture-plus-depth format, where texture and depth maps from one or more viewpoints are encoded and transmitted. A decoder can then synthesize a freely chosen virtual view via depth-image-based rendering using nearby coded texture and depth maps as reference. Further, depth information can be used in other image processing applications beyond view synthesis, such as object identification, segmentation, and so on. In this paper, we leverage on the observation that neighboring pixels of similar depth have similar motion to efficiently encode depth video. Specifically, we divide a depth block containing two zones of distinct values (e.g., foreground and background) into two arbitrarily shaped regions (sub-blocks) along the dividing boundary before performing separate motion prediction (MP). While such arbitrarily shaped sub-block MP can lead to very small prediction residuals (resulting in few bits required for residual coding), it incurs an overhead to transmit the dividing boundaries for sub-block identification at decoder. To minimize this overhead, we first devise a scheme called arithmetic edge coding (AEC) to efficiently code boundaries that divide blocks into sub-blocks. Specifically, we propose to incorporate the boundary geometrical correlation in an adaptive arithmetic coder in the form of a statistical model. Then, we propose two optimization procedures to further improve the edge coding performance of AEC for a given depth image. The first procedure operates within a code block, and allows lossy compression of the detected block boundary to lower the cost of AEC, with an option to augment boundary depth pixel values matching the new boundary, given the augmented pixels do not adversely affect synthesized view distortion. The second procedure operates across code blocks, and systematically identifies blocks along an object contour that should be coded using sub-block MP via a rate-distortion optimized trellis. Experimental results show an average overall bitrate reduction of up to 33% over classical H.264/AVC.
An interactive high-level debugger for control-flow optimized programs (1983)

The transformations performed by an optimizing compiler have traditionally impeded interactive debugging in source language terms. A prototype system called Navigator has been developed for debugging optimized programs written in Cedar, an Algol-like language. Navigator can be used to monitor program execution flow in the presence of two optimizations: inline procedure expansion and cross-jumping (merging identical tails of code paths that join). This paper describes the problems that these two optimizations create for debugging and Navigator's solutions to these problems. The selected approach collects extra information during the optimization phases of compilation. At runtime, Navigator uses the additional information to hide the effects of the optimizations from the programmer.
The Human Gene <i>FALL39</i> and Processing of the Cathelin Precursor to the Antibacterial Peptide LL‐37 in Granulocytes (1996)

The peptide FA-LL-37, previously termed FALL-39, was originally predicted from on ORF of a cDNA clone isolated from a human bone marrow library. This peptide was synthesized and found to have antibacterial activity. We have now characterized and sequenced the complete gene for FA-LL-37, termed FALL39. It is a compact gene of 1963 bp with four exons. Exons 1-3 code for a signal sequence and the cathelin region. Exon 4 contains the information for the mature antibacterial peptide. Our results indicate that FALL39 is the only member of the cathelin gene family present in the human genome. Potential binding sites for acute-phase-response factors are identified in the promoter and in intron 2. A possible role for the cytokine interleukin-6 in the regulation of FALL 39 is discussed. Anti-(FA-LL-37) IgG located the peptide in granulocytes and we isolated the mature peptide from these cells after degranulation. Structural analysis determined the mature peptide to be LL-37. To obtain LL-37 for antibacterial assays, synthetic FA-LL-37 was degraded with dipeptidyl-peptidase I. This analysis showed that mature LL-37 is a potent antibacterial peptide.
High-Resolution Quantitative Imaging of Cornea Elasticity Using Supersonic Shear Imaging (2009)

The noninvasive estimation of in vivo mechanical properties of cornea is envisioned to find several applications in ophthalmology. Such high-resolution measurements of local cornea stiffness could lead to a better anticipation and understanding of corneal pathologies such as Keratoconus. It could also provide a quantitative evaluation of corneal biomechanical response after corneal refractive surgeries and a tool for evaluating the efficacy of new cornea treatments such as cornea transplant using femtosecond laser or therapy based on Riboflavin/UltraViolet-A Corneal Cross Linking (UVA CXL). In the very important issue of glaucoma diagnosis and management, the fine tuning corneal elasticity measurement could also succeed to strongly correlate the applanation tonometry with the "true" intra-ocular pressure (IOP). This initial investigation evaluates the ability of ultrafast and high-resolution ultrasonic systems to provide a real-time and quantitative mapping of corneal viscoelasticity. Quantitative elasticity maps were acquired ex vivo on porcine cornea using the supersonic shear imaging (SSI) technique. A conventional 15 MHz linear probe was used to perform conventional ultrasonic imaging of the cornea. A dedicated ultrasonic sequence combines the generation of a remote palpation in the cornea and ultrafast (20,000 frames/s) ultrasonic imaging of the resulting corneal displacements that evolve into a shear wave propagation whose local speed was directly linked to local elasticity. A quantitative high-resolution map (150 microm resolution) of local corneal elasticity can be provided by this dedicated sequence of ultrasonic insonifications. Quantitative maps of corneal elasticity were obtained on ex vivo freshly enucleated porcine corneas. In the cornea, a quite homogenous stiffness map was found with a 190 kPa +/- 32 kPa mean elasticity. The influence of photodynamic Riboflavin/UVA induced CXL was measured. A significant Young's modulus increase was obtained with a mean 890 kPa +/- 250 kPa posttreatment Young's modulus (460% increase), located in the anterior part of the cornea. Simulations based on 3-D time domain finite differences simulation were also performed and found to be in good agreement with ex vivo experiments. The SSI technique can perform real-time, noninvasive, high-resolution, and quantitative maps of the whole corneal elasticity. This technique could be real time and straightforward adapted for a very wide field of in vivo investigations.
True (2000)

Through a glucocorticoid-responsive promoter, glucocorticoids can regulate the transcription of the human papillomavirus (HPV) E6 and E7 viral genes which target the tumour suppressor proteins p53 and Rb respectively. In C4-1 cells, the glucocorticoid dexamethasone up-regulated HPV E6/E7 mRNA and decreased radiation-induced apoptosis. In contrast, dexamethasone had no effect on apoptosis of cells that either lack the HPV genome (C33-a) or in which HPV E6/E7 transcription is repressed by dexamethasone (SW756). Irradiated C4-1 cells showed increased p53 expression, while dexamethasone treatment prior to irradiation decreased p53 protein expression. In addition, p21 mRNA was regulated by irradiation and dexamethasone in accordance with the observed changes in p53. Overall, glucocorticoids decreased radiation-induced apoptosis in cervical carcinoma cells which exhibit increased HPV E6/E7 transcription and decreased p53 expression. Therefore, in HPV-infected cervical epithelial cells, p53-dependent apoptosis appears to depend upon the levels of HPV E6/E7 mRNA.
Probability of miscorrection for Reed-Solomon codes (2002)

The decoder fails to correct an erroneous message to its original untainted version when the number of errors exceeds half the number of appended Reed-Solomon characters. In most cases, the Reed-Solomon algorithm can detect the presence of an excess of errors through built-in filters. However, in a few cases, the message may be corrected to a different code word in which case it is said to be miscorrected. This paper derives a general expression for the probability of miscorrection of an n-character message with a t-error correcting Reed-Solomon code that utilizes a maximum 2/sup m/-character set (GF(2/sup m/)), where 2/sup m/>n, given e errors.
LC/NMR in Natural Products Chemistry (1998)

Efficient detection and rapid characterisation of natural products play an important role for their study in complex biological matrices such as crude plant extracts. Their preliminary identification at the earliest stage of separation is a strategic element for guiding selective isolation procedures. Hyphenated techniques such as high performance liquid chromatography (HPLC) coupled to UV and mass spectrometry (LC/UV/MS) have proved to be extremely useful in combination with biological screening for a rapid survey of natural products. However, these coupled techniques do not allow a full on-line identification, except for some well-known natural products, and complementary on-line spectroscopic information is needed. Thus, HPLC coupled to nuclear magnetic resonance (LC/NMR) represents a potentially interesting complementary technique to LC/UV/MS for detailed on-line structural analysis. Indeed recent progress in NMR technology has given a new impulse to LC/NMR which is now emerging as a powerful analytical tool. The development of efficient solvent suppression techniques enables the measurement of high quality LC/<sup>1</sup>H-NMR spectra, both on-flow and stop-flow, with reversed-phase HPLC conditions. Non-deuterated solvents such as MeOH or MeCN can be used, while water is replaced by D<sub>2</sub>O. In this review, a summary of the basic principles and modes of operation of LC/NMR are briefly described. Selected examples of LC/NMR analyses of natural products in crude p lant extract o r in enriched fractions are presented. They include different ways of using this technique. An overview of the relatively scarce applications with natural products is given. The potential and the limitations of LC/NMR in conjunction with LC/UV/MS for the on-line analysis of plant metabolites are discussed.
Molecular genetics of filamentous fungi: Proceedings of a UCLA symposium held in Keystone, Colorado, April 13-19, 1985 (1985)

Molecular genetics of filamentous fungi: proceedings of a UCLA symposium held in Keystone, Colorado, April 13-19, 1985 , Molecular genetics of filamentous fungi: proceedings of a UCLA symposium held in Keystone, Colorado,... , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
A multiplexed fiber Bragg grating sensor for simultaneous salinity and temperature measurement (2008)

An in-line one-fiber approach to realize simultaneous measurement of salinity and temperature is proposed. The sensor system, which consists of multiplexed polymer-coated fiber Bragg gratings, showed that the polyimide-coated grating responds to variations of both temperature and salinity, while the acrylate-coated grating is only sensitive to the environmental temperature. The experimental results indicated that the temperature sensitivity of the acrylate-coated grating in water was 0.0102nm∕°C for redshifted Bragg wavelength with increasing temperature, and the temperature and the salinity sensitivities of the polyimide-coated grating were 0.0094nm∕°C (redshifted) and 0.0165nm∕M (blueshifted), respectively, which are in excellent agreement with the theoretical analysis.
H/sup ∞/ control of boost converters: comparison to voltage mode, feedforward and current mode controls (2002)

The closed loop characteristics of a boost power converter were examined for different control schemes. The H/sup /spl infin// control was found to exhibit low output impedance over the widest frequency range. The major disadvantage of this control scheme, as compared to the classic ones, is possible static error due to the lower open loop gain at low frequencies. Good agreement was found between simulation results and experimental measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Where Have All the Country Teachers Gone?: And Will They Ever Learn? (1999)

The problem of declining rates of new country teachers who teach music is discussed. It is suggested that concerted efforts to promote the training of teachers in tertiary music courses, particularly for country schools needs to be undertaken.
Design and implementation of Reconfigurable Stream Processor in multimedia applications (2008)

This paper proposed a Reconfigurable Stream Processor applied in multimedia applications. Based on the unique parallel stream processing framework and optimized algorithm mapping method, the reconfigurable processor exploits the parallelism of complex algorithms and provides a high flexibility during run-time to adapt to various applications. The architecture of processor is implemented and verified on the development board of ARM926EJS plus Xilinx Virtex-4XC4VLX80. A H.264 video codec is implemented to verify the reconfigurable architecture, achieving 58%~130% speed boost compared with traditional reconfigurable architectures such as MorphoSys and PACT.
Research and government policy in New Zealand (1993)

Abstract In recent years governments in many countries have set out to alter the way in which their public education systems are resourced, managed and monitored. The process of restructuring is well advanced in New Zealand. This paper explains how radical research and theory in education were used by policy makers to justify the introduction of free market policies and discusses the implications for theory and research in education of the dismantling of the welfare state.
Effective enhancement of low-quality fingerprints with local ridge compensation (2008)

In order to improve performance, image preprocessing for enhancement is essential in a fingerprint recognition system. Most prominent fingerprint enhancement methods perform well for relatively high-quality images but less effectively for low-quality images, especially where the ridge patterns are very noisy and corrupt. To enhance such images, this paper proposes an effective three-step algorithm, a method that locally normalizes input images, computes the local ridge orientation, and then applies a local ridge compensation filter with a rotated window in order to enhance the ridges by matching the local ridge orientation. Experimental results indicate that the proposed method performs better when compared to some noted methods of enhancing low-quality images.
Medical Management of Dry Eye Disease (2008)

Medical management plays a major role in the initial treatment and control of symptoms of dry eye. Empiric evaluation of the effect of the large range of options still has a major role for the management of individual patients.
Capabilities for per Process Tuning of Distributed Operating Systems (2004)

This paper introduces capabilities as a tool to tailor cluster mechanisms usage on a per process basis in a single system image operating system. Using capabilities, processes should only pay the cost in terms of OS resources for the operating system of the mechanisms they want to use. We relate capabilities to policies that are used to try to ensure optimal resource usage across all cluster nodes. Finally, we discuss implementation of these ideas in Kerrighed and describe its usage on a real industrial application.
Improved Splicing of Adeno-Associated Viral (AAV) Capsid Protein-Supplying Pre-mRNAs Leads to Increased Recombinant AAV Vector Production (2008)

Adeno-associated viral (AAV) capsid proteins, thought to be a rate-limiting step in the production of recombinant AAV (rAAV), are translated from spliced mRNAs. Improvement of the native AAV nonconsensus donor sequence increases splicing yet leaves the relative levels of VP1- and VP2/3-encoding mRNAs unchanged, and thus provides a means to increase delivery of correct ratios of AAV capsid proteins. This effect is independent of the AAV serotype used, and occurs whether the rep and cap genes supplied in trans are on the same or separate expression vectors. In the split-vector system, replacement of the more traditionally used cytomegalovirus promoter with that of the AAV5 P41 promoter allowed for even greater levels of splicing, and together with an improved intron donor, led to a 10- to 15-fold increase in the levels of splicing, rAAV production, and transduction compared with levels achieved by traditional cotransfection methods. Thus, the enhancement of splicing presents a useful method to enhance rAAV production via transient transfection.
Pore pressure and fluid detection from compressional - and shear-wave data (2001)

Abstract By analyzing experimental data we show that in many room-dry rocks, the Poisson' s ratio (PR) decreases with decreasing differential pressure (confining minus pore pressure).
Preparation of lisinopril-capped gold nanoparticles for molecular imaging of angiotensin-converting enzyme (2009)

Overexpression of angiotensin-converting enzyme (ACE) has been associated with the pathophysiology of cardiac and pulmonary fibrosis. Moreover, the prescription of ACE inhibitors, such as lisinopril, has shown a favorable effect on patient outcome for patients with heart failure or systemic hypertension. Thus targeted imaging of the ACE would be of crucial importance for monitoring tissue ACE activity as well as the treatment efficacy in heart failure. In this respect, lisinopril-coated gold nanoparticles were prepared to provide a new type of probe for targeted molecular imaging of ACE by tuned K-edge computed tomography (CT) imaging. The preparation involved non-modified lisinopril, using its primary amine group as the anchoring function on the gold nanoparticles surface. The stable lisinopril-coated gold nanoparticles obtained were characterized by UV-vis spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM). Their zeta potential was also measured in order to assess the charge density on the modified gold nanoparticles (GNPs).