gebhart/patrepeval huggingface dataset:
Object storage on CRAQ: high-throughput chain replication for read-mostly workloads (2009)

Massive storage systems typically replicate and partition data over many potentially-faulty components to provide both reliability and scalability. Yet many commerciallydeployed systems, especially those designed for interactive use by customers, sacrifice stronger consistency properties in the desire for greater availability and higher throughput. This paper describes the design, implementation, and evaluation of CRAQ, a distributed object-storage system that challenges this inflexible tradeoff. Our basic approach, an improvement on Chain Replication, maintains strong consistency while greatly improving read throughput. By distributing load across all object replicas, CRAQ scales linearly with chain size without increasing consistency coordination. At the same time, it exposes noncommitted operations for weaker consistency guarantees when this suffices for some applications, which is especially useful under periods of high system churn. This paper explores additional design and implementation considerations for geo-replicated CRAQ storage across multiple datacenters to provide locality-optimized operations. We also discuss multi-object atomic updates and multicast optimizations for large-object updates. 1
Investigation of the Binding Determinants of Phosphopeptides Targeted to the Src Homology 2 Domain of the Signal Transducer and Activator of Transcription 3. Development of a High-Affinity Peptide Inhibitor (2005)

Signal transducer and activator of transcription 3 (Stat3) is a cytosolic transcription factor that relates signals from the cell membrane directly to the nucleus where it, in complex with other proteins, initiates the transcription of antiapoptotic and cell cycling genes, e.g., Bcl-x(L) and cyclin D1. In normal cells Stat3 transduces signals from cytokines such as IL-6 and growth factors such as the epidermal growth factor. Stat3 is constitutively activated in a number of human tumors. Antisense and dominant negative gene delivery result in apoptosis and reduced cell growth, thus this protein is an attractive target for anticancer drug design. As part of our research on the design of Src homology 2 (SH2) directed peptidomimetic inhibitors of Stat3, in this paper we describe structure-activity relationship studies that provide information on the nature of peptide-protein interactions of a high-affinity phosphopeptide inhibitor of Stat3 dimerization and DNA binding, Ac-Tyr(PO3H2)-Leu-Pro-Gln-Thr-Val-NH2, peptide 1. There is a hydrophobic surface on the SH2 domain that can accommodate lipophilic groups on the N-terminus. Of the amino acids tested, leucine provided the highest affinity at pY+1 and its main chain NH is involved with a hydrogen bond with Stat3, presumably Ser636. cis-3,4-Methanoproline is optimal as a backbone constraint at pY+2. The side chain amide protons of Gln are required for high-affinity interactions. The C-terminal dipeptide, Thr-Val, can be replaced with groups ranging in size from methyl to benzyl. We synthesized a phosphopeptide incorporating groups that provided increases in affinity at each position. Thus, hydrocinnamoyl-Tyr(PO3H2)-Leu-cis-3,4-methanoPro-Gln-NHBn, 50, was the highest affinity peptide, exhibiting an IC50 of 125 nM versus 290 nM for peptide 1 in a fluorescence polarization assay.
Effect of VKORC1 Haplotypes on Transcriptional Regulation and Warfarin Dose (2005)

VKORC1 haplotypes can be used to stratify patients into low-, intermediate-, and high-dose warfarin groups and may explain differences in dose requirements among patients of different ancestries. The molecular mechanism of this warfarin dose response appears to be regulated at the transcriptional level.
A planar version of a 4.0 GHz reactively steered adaptive array (1986)

-A planar (two-dimensional) reactively steered adaptive array (RESAA) including a single active microstrip element and eight closely coupled parasitic microstrip elements has been designed and tested. Steering of a null toward a single incident jammer is accomplished by adaptive control of reactive terminations on the parasitic elements using a guided random search algorithm. The planar array can steer a null in both the elevation and azimuth directions with a depth of 30 dB.
Adaptive anisotropic filtering (AAF) for real-time visual enhancement of MPEG-coded video sequences (2002)

Current standards for video compression achieve good performances in terms of data compaction and signal-to-noise ratio of the decoded signal. Nevertheless, there are some known problems concerning the visual quality of reconstructed images, which can be partially solved using appropriate post-processing algorithms. The paper proposes a new adaptive anisotropic filter (AAF) that aims to unify the treatment of different sources of perceptive distortion in MPEG sequences. The process is driven by a local classification of blocks and single pixels of decoded frames, taking into account several parameters (distribution of DCT coefficient energy, presence of sharp variations, spatial position of DCT block boundaries). Experimental results show that the proposed algorithm outperforms existing enhancement approaches, in particular when constraints on complexity and real-time processing are compelling.
Indirect micromanipulation of single molecules in water-in-oil emulsion (2001)

Based on real-time observation and micromanipulation, analytical methods for single DNA molecules have been under development for some time. Precise manipulation, however, is still difficult because single molecules are too small for conventional techniques. We have developed a chemical reaction system that uses water droplets in oil as containers of materials. The water droplets can be manipulated by optical force. The manipulation of the water droplets permits the fusion of two selected droplets. This process corresponds to mixing of different samples. We designate this system as "w/o (water-in-oil emulsion) microreactor system", and each droplet can be thought of as a "microreactor". In this system, single molecules can be manipulated readily, as a molecule can be contained in a microm-sized microreactor. The microreactor utilizes extremely small quantities of samples, therefore, reactions are rapid, as diffusion times in the microreactor are very short. The manipulation technique of the microreactors based on optical force has been applied to induce fusion between microreactors loaded with DNA and YOYO, a fluorescent dye that binds to DNA. This fusion induced a rapid binding of YOYO.
Fluorescence In Situ Hybridization (FISH) Detects Clonal Instability in an Optic Nerve Relapse of Acute Lymphoblastic Leukemia (1998)

Despite antimetabolite therapy, hyperdiploid ALL can rarely recur isolated to an optic nerve. FISH is a useful adjunct for confirming relapse when low numbers of white blood cells are obtained with fine needle aspiration.
Apparatus for high‐precision repetitive sequential optical measurement of living cells (1994)

A system is described which permits the repetitive spectroscopic measurement of individual cells within a population of many cells, while the location of each cell is preserved during various manipulations of the cells and/or their surrounding medium. The central mechanical feature of the system is the cell carrier, a matrix of apertures in which the cells become trapped. The detector electronics operate in a preset photon counting mode, permitting the measurement of low and high light intensities with the same degree of precision. The present instrument configuration is specifically designed for the accurate and precise measurement of the polarization of fluorescence of probes within living cells for application to routine performance of the Cercek SCM test for cancer. With modifications, the apparatus can be applied to a wide range of other clinical and research tasks.
Multifunctional Uniform Nanoparticles Composed of a Magnetite Nanocrystal Core and a Mesoporous Silica Shell for Magnetic Resonance and Fluorescence Imaging and for Drug Delivery (2008)

Magnetic, fluorescent core–shell nanoparticles consist of a single Fe3O4 nanocrystal core and a dye-doped mesoporous silica shell with a poly(ethylene glycol) coating (see picture of TEM images and schematic depictions). These nanoparticles can be used as magnetic resonance and fluorescence imaging agents, and as drug delivery vehicles, thus making them novel candidates for simultaneous cancer diagnosis and therapy. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Efficacy and Adverse Effects of Prophylactic Antiemetics During Patient-Controlled Analgesia Therapy (1999)

Nausea and vomiting are frequent adverse effects of patient-controlled analgesia (PCA) with opioids. To identify the optimal prophylactic antiemetic intervention in this setting, we performed a systematic search for randomized trials (MEDLINE, EMBASE, Cochrane library, reference lists, hand-searching, no language restriction) published up to May 1998 that compared prophylactic antiemetic interventions with placebo or no treatment in the postoperative PCA-setting with opioids. Fourteen placebo-controlled trials (1117 patients) with different regimens of droperidol, ondansetron, hyoscine TTS, tropisetron, metoclopramide, propofol, and promethazine were analyzed. One PCA was with tramadol, all others were with morphine. At 24 h, the cumulative incidence of nausea and vomiting without antiemetics was approximately 50%. Droperidol 0.017-0.17 mg/mg of morphine (0.5-11 mg/d droperidol) was statistically significantly more effective than placebo without evidence of dose-responsiveness; the number needed to treat to prevent nausea compared with placebo was 2.7 (95% confidence interval 1.8-5.2), and that to prevent vomiting was 3.1 (2.3-4.8). Compared with placebo, the incidence of minor adverse effects with droperidol was increased with doses >4 mg/d. Implications: Of 100 patients treated with droperidol added in a patient-controlled analgesia pump with morphine, 30 who would have vomited or been nauseated had they not received droperidol will not suffer these effects. There is no evidence of dose-responsiveness for efficacy with droperidol, but the risk of adverse effects is dose-dependent. There is a lack of evidence for other antiemetics. (Anesth Analg 1999;88:1354-61)
Synthesis and Characterization of Two 111In-Labeled DTPA−Peptide Conjugates (2001)

This report describes the synthesis and characterization of two (111)In-labeled DTPA-peptide conjugates (DTPA-MA and DTPA-BA). It is surprising to find that (111)In(DTPA-MA) and (111)In(DTPA-BA) are more hydrophilic than their corresponding (90)Y analogues, suggesting a different coordination sphere in (111)In and(90)Y complexes of the same DTPA-peptide conjugate. By a reversed phase HPLC method, both (111)In(DTPA-MA) and (111)In(DTPA-BA) showed only one radiometric peak in their respective HPLC chromatogram due to a rapid interconversion of different isomers (particularly cis and trans isomers for (111)In(DTPA-MA); cis-cis, cis-trans, trans-cis, and trans-trans isomers for (111)In(DTPA-BA)). The interconversion of different isomers involves the "wagging" of the diethylenetriamine backbone, "shuffling" of the NO or NO(2) donor sets, and a rapid inversion at the terminal amine-nitrogen atoms.
Central and Opposing Effects of IGF-I and IGF-Binding Protein-3 on Systemic Insulin Action (2006)

IGF-I is recognized as an insulin sensitizer at the liver and muscle, while recent evidence suggests that IGF-binding protein (IGFBP)-3 acts as an insulin antagonist. As there is a paucity of IGF-I receptors in the liver and as the IGF-IGFBP system in the central nervous system is emerging as physiologically relevant, we examined whether the effects of IGF-I and IGFBP-3 on insulin action are mediated through central mechanisms. Intracerebroventricular (ICV) infusion of IGF-I during the insulin clamp (3 mU x kg(-1) x min(-1)) resulted in significant improvement in hepatic insulin action (50%, P < 0.05). In contrast, ICV infusion of IGFBP-3 significantly impaired insulin action at the liver (45% increase in hepatic glucose production, P < 0.01). While IGF-I marginally increased peripheral glucose uptake, IGFBP-3 significantly decreased peripheral glucose uptake (approximately 30%, P < 0.01). As the nuclear localization signal mutant IGFBP-3, which has a normal affinity to IGFs but binds other IGFBP-3 partners poorly and fails to normally internalize, has reduced central activity on metabolism, we conclude that the effects of IGFBP-3 on the hypothalamus involve activity mediated by interfacing with other molecules in addition to IGFs. Marked, opposing, and independent physiological effects of IGF-I and IGFBP-3 through central mechanisms may have implications on potential strategies in specific modulation of peripheral insulin action.
Responses of beneficial Bacillus amyloliquefaciens SQR9 to different soilborne fungal pathogens through the alteration of antifungal compounds production (2014)

Bacillus amyloliquefaciens SQR9 exhibited predominantly antagonistic activities against a broad range of soilborne pathogens. The fungi-induced SQR9 extracts possess stronger antifungal activities compared with SQR9 monoculture extracts. To investigate how SQR9 fine-tunes lipopeptides (LPs) and a siderophore bacillibactin production to control different fungal pathogens, LPs and bacillibactin production and transcription of the respective encoding genes in SQR9 were measured and compared with six different soilborne fungal pathogens. SQR9 altered its spectrum of antifungal compounds production responding to different fungal pathogen. Bacillomycin D was the major LP produced when SQR9 was confronted with Fusarium oxysporum. Fengycin contributed to the antagonistic activity against Verticillium dahliae kleb, Fusarium oxysporum, Fusarium solani, and Phytophthora parasitica. Surfactin participated in the antagonistic process against Sclerotinia sclerotiorum, Rhizoctonia solani, and Fusarium solani. Bacillibactin was up-regulated when SQR9 was confronted with all tested fungi. The reduction in antagonistic activities of three LP and bacillibactin deficient mutants of SQR9 when confronted with the six soilborne fungal pathogens provided further evidence of the contribution of LPs and bacillibactin in controlling fungal pathogens. These results provide a new understanding of specific cues in bacteria-fungi interactions and provide insights for agricultural applications.
Hydrogen-selective sensing at room temperature with ZnO nanorods (2005)

The sensitivity for detecting hydrogen with multiple ZnO nanorods is found to be greatly enhanced by sputter-depositing clusters of Pd on the surface. The resulting structures show a change in room- temperature resistance upon exposure to hydrogen concentrations in N2 of 10–500ppm of approximately a factor of 5 larger than without Pd. Pd-coated ZnO nanorods detected hydrogen down to &amp;lt;10ppm, with relative responses of &amp;gt;2.6% at 10ppm and &amp;gt;4.2% at 500ppm H2 in N2 after a 10min exposure. There was no response at room temperature to O2. Approximately 95% of the initial ZnO conductance after exposure to hydrogen was recovered within 20s by exposing the nanorods to either air or pure O2. This rapid and easy recoverability make the Pd-coated nanorods suitable for practical applications in hydrogen-selective sensing at ppm levels at room temperature with &amp;lt;0.4mW power consumption.
Association of Nocturnal Arrhythmias with Sleep-disordered Breathing (2006)

Individuals with severe sleep-disordered breathing have two- to fourfold higher odds of complex arrhythmias than those without sleep-disordered breathing even after adjustment for potential confounders.
A silent mutation (2939G>A, exon 6; CYP2D6*59) leading to impaired expression and function of CYP2D6 (2006)

We analyzed CYP2D6 in two individuals characterized by impaired sparteine oxidation (intermediate metabolizer phenotype) and genotype 2D62/4 (1661G>C; 2850C>T; 4180G>C) usually associated with normal function. Full genomic sequencing and haplotype analysis confirmed the previously identified silent mutation 2939G>A in exon 6 (former allele variant 2D62J, now termed 2D659), as well as an additional novel 2291G>A change in intron 4. Transient expression in Huh7 hepatoma cells of the entire CYP2D6 gene of constructs carrying either both or only the 2939G>A change resulted in about three-fold reduced levels of mRNA, immunoreactive 2D6 protein and propafenone hydroxylase activity. These data demonstrate profound effects of a silent mutation on expression and function of CYP2D6, resulting in impaired drug oxidation phenotype. The 2939G>A single nucleotide polymorphism in exon 6 was present heterozygously in two individuals out of 308 (0.65%), corresponding to an allele frequency of 0.3%. Genotyping for this mutation thus improves phenotype-genotype correlation for CYP2D6 and may help to predict adverse drug treatment events.
Union Formation and Bargaining Rules in the Labor Market (2005)

This paper analyzes union formation in a model of bargaining between a …rm and several unions. We address two questions: …rst, the optimal con…guration of unions (their number and size) and, second, the impact of the bargaining pattern (simultaneous or sequential). For workers, grouping into several unions works as a price discrimination device which, at the same time, decreases their market power. The analysis shows that optimal union con…guration depends on the rules that regulate the bargaining process (monopoly union, Nash bargaining or right to manage).
Per-pixel camera calibration for 3D range scanning (2005)

Structured-light rangefinder is distinguished from other range scanning systems by its use of off-the-shelf hardware and fast data acquisition. We propose a novel approach to calibrate such a system, namely, calibrate the camera and the projector of the system. This approach handles all types of distortions and produces results in high accuracy. Basically, camera calibration techniques compute the pixel-ray correspondences and represent them by a mathematic model with limited number of parameters. These parametric models, however, cannot model general distortions while distortions not modelled, sometimes, can greatly affect the quality of further applications. The proposed approach computes and maintains a ray database for all pixels explicitly. By trading memory for accuracy, this approach solves the above problem. The resulting ray database can be directly used for 3D point reconstruction using calibration system. It is also useful for model fitting and other operations.
Modulation of endothelial cell activation in sickle cell disease: a pilot study (2001)

The vessel wall endothelium undoubtedly plays a role in the vascular pathobiology of sickle cell disease. This pilot study tested the feasibility of using an inhibitor of nuclear factor (NF)-kappa B, a transcription factor, to modify the endothelial activation state of patients with this vascular disease. For a total of 7 separate drug exposure tests, 3 subjects with sickle cell disease took sulfasalazine (given orally at 1 g every 8 hours), and the activation state of their circulating endothelial cells (CECs) was assessed using immunofluorescence microscopy. Companion studies were also performed using sulfasalazine in sickle transgenic mice to verify its effect simultaneously on both CECs and vessel wall endothelium. Both CECs and tissue vessel wall endothelium in sickle mice have an activated phenotype. In these mice sulfasalazine significantly reduced CEC expression of vascular cell adhesion molecule (VCAM), intracellular adhesion molecule (ICAM), and E-selectin, and it correspondingly reduced expression of these molecules in some tissue vessels. In humans with sickle cell disease, sulfasalazine significantly reduced CEC expression of VCAM, ICAM, and E-selectin, but it did not reduce expression of tissue factor. Addition of a second transcription factor inhibitor, salsalate, did not change this result. This pilot study suggests that endothelial cell activation state can be modified and down-regulated in vivo by sulfasalazine. (Blood. 2001;97:1937-1941)
Multiple oligodeoxyribonucleotide syntheseson a reusable solid-phase CPG support via the hydroquinone-O,O'-diacetic acid (Q-Linker) linker arm (1999)

A strategy for oligodeoxyribonucleotide synthesis on a reusable CPG solid-phase support, derivatized with hydroxyl groups instead of amino groups, has been developed. Ester linkages, through a base labile hydroquinone- O, O '-diacetic acid ( Q-Linker ) linker arm, were used to couple the first nucleoside to the hydroxyl groups on the support. This coupling was rapidly accomplished (10 min) using O -benzotriazol-1-yl- N, N, N ', N '-tetramethyluronium hexafluorophosphate (HBTU) and 1-hydroxybenzotriazole as the activating reagents. Oligodeoxyribonucleotide synthesis was performed using existing procedures and reagents, except a more labile capping reagent, such as chloro-acetic anhydride, methoxyacetic anhydride or t-butylphenoxyacetic anhydride, was used instead of acetic anhydride. After each oligodeoxyribonucleotide synthesis, the product was cleaved from the support with ammonium hydroxide (3 min) and deprotected as usual. Residual linker arms or capping groups were removed by treatment with ammonium hydroxide/methylamine reagent and the regenerated support was capable of reuse. Up to six different oligodeoxyribonucleotide syntheses or up to 25 cycles of nucleoside derivatization and cleavage were consecutively performed on the reusable support. This method may provide a significant cost advantage over conventional single-use solid supports currently used for the manufacture of antisense oligodeoxyribonucleotides.
c‐erbB‐3 protein expression in human breast cancer: comparison with other tumour variables and survival (1994)

c-erbB-3 protein expression was investigated immunohistochemically in a series of 97 malignant breast tumours using the monoclonal antibody RTJ1. Twenty-eight cases (28.8%) showed c-erbB-3 overexpression, 31 cases (32%) showed normal levels of c-erbB-3 and 38 cases (39.2%) were c-erbB-3 negative. c-erbB-3 overexpression was positively but not significantly related to negative lymph node status and survival over a 10-year follow-up period.
Phylogenetic Profiling (2008)

Phylogenetic profiles describe the presence or absence of a protein in a set of reference genomes. Similarity between profiles is an indicator of functional coupling between gene products: the greater the similarity, the greater the likelihood of proteins sharing membership in the same pathway or cellular system. By virtue of this property, uncharacterized proteins can be assigned putative functions, based on the similarity of their profiles with those of known proteins. Profile comparisons, when extended to the entire genome, have the power to reveal functional linkages on a genome-wide scale (the functional "interactome"), elucidating both known and novel pathways and cellular systems.