gebhart/patrepeval huggingface dataset:
Programming Protocol-Independent Packet Processors (2013)

P4 is a high-level language for programming protocol-independent packet processors. P4 works in conjunction with SDN control protocols like OpenFlow. In its current form, OpenFlow explicitly specifies protocol headers on which it operates. This set has grown from 12 to 41 fields in a few years, increasing the complexity of the specification while still not providing the flexibility to add new headers. In this paper we propose P4 as a strawman proposal for how OpenFlow should evolve in the future. We have three goals: (1) Reconfigurability in the field: Programmers should be able to change the way switches process packets once they are deployed. (2) Protocol independence: Switches should not be tied to any specific network protocols. (3) Target independence: Programmers should be able to describe packet-processing functionality independently of the specifics of the underlying hardware. As an example, we describe how to use P4 to configure a switch to add a new hierarchical label.
Efficient indexing of repeated n-grams (2011)

The identification of repeated n-gram phrases in text has many practical applications, including authorship attribution, text reuse identification, and plagiarism detection. We consider methods for finding the repeated n-grams in text corpora, with emphasis on techniques that can be effectively scaled across a cluster of processors to handle very large amounts of text. We compare our proposed method to existing techniques using the 1.5 TB TREC ClueWeb-B text collection, using both single-processor and multi-processor approaches. The experiments show that our method offers an important tradeoff between speed and temporary storage space, and provides an alternative to previous approaches that scales almost linearly in the length of the sequence, is largely independent of n, and provides a uniform workload balance across the set of available processors.
Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma. (2001)

By using a cDNA array representing 14,000 cDNA clusters, we studied the expression profiles in paired clinical hepatocellular carcinoma (HCC) samples and the distal nontumorous liver tissues from the same patients. Despite the significant heterogeneity among the clinical samples, 72 genes (including 30 novel genes) were down-regulated and 84 genes (including 48 novel genes) were up-regulated in >50% of the cancer samples that were identified. The alterations in gene expression levels were confirmed by Northern blot and reverse-transcription PCR in all of 4 randomly selected genes. It was conspicuous that 21 of 38 hepatocarcinoma (HCC) down-regulated genes studied previously were reportedly regulated by a group of liver-enriched transcription factors (LETFs), and 12 of 36 HCC up-regulated genes studied previously were involved in protein translation. Reexamination of the cDNA array data further revealed that most of the genes known to be regulated by LETFs were down-regulated in at least a portion of the HCC samples. Among the LETFs, the expression level of CCAAT/enhancer-binding protein (C/EBP) alpha was down-regulated in cancer, whereas hepatocyte nuclear factor 1 (HNF-1), HNF-3beta, HNF-4alpha, and HNF-4gamma were up-regulated. The expression profiling thus suggested multiple regulatory pathways involved in HCC, especially that related to LETFs.
Hydration of the Fluoride Anion:  Structures and Absolute Hydration Free Energy from First-Principles Electronic Structure Calculations (2004)

A series of first-principles electronic structure calculations have been performed to determine the most stable structures of F-(H2O)n clusters (n = 4, 8, 12, and 16) and the hydration free energy of fluoride anion (F-). The calculated results show that a new, tetrahedrally coordinated fluoride anion hydration structure F-(H2O)4 cluster is lower in Gibbs free energy than the previously considered most stable structure of F-(H2O)4. The first ab initio prediction of potential stable hydration structures for F-(H2O)n clusters (n = 8, 12, and 16) are given. The energetic results show that the tetrahedrally coordinated fluoride anion hydration structure becomes more stable as compared to the other hydration structures with a pyramidal coordination, i.e., a surface ion cluster state, as the cluster size increases from n = 8 to n = 12 to n = 16. This suggests that, with increasing n, the fluoride anion will be internally solvated in large enough F-(H2O)n clusters. These results provide insight into the transition from the hydration structure found in small gas-phase hydrated-anion clusters to the hydration structure observed in aqueous solution. The calculated results show that, for a given n, the bulk solvent effects can qualitatively change the relative thermodynamic stability of different possible isomers of F-(H2O)n clusters and the most stable structure in solution is not necessarily the most stable structure in the gas phase. When n = 16, a pyramidally coordinated fluoride anion hydration structure is the most stable structure in the gas phase, whereas a tetrahedrally coordinated fluoride anion hydration structure has the lowest free energy in solution. The absolute hydration free energy of fluoride anion in aqueous solution, ΔGhyd298(F-), is predicted to be −104.3 ± 0.7 kcal/mol by using a reliable computational protocol of first-principles solvation-included electronic structure calculations. The predicted ΔGhyd298(F-) value of −104.3 ± 0.7 kcal/mol, together with our previously calculated ΔGhyd298(H+) value of −262.4 kcal/mol determined by using the same computational protocol, gives ΔGhyd298(F-) + ΔGhyd298(H+) = −366.7 ± 0.7 kcal/mol in excellent agreement with the value of −366.5 kcal/mol derived from the available experimental data.
Antiinflammatory cannabinoids in diet – towards a better understanding of CB2 receptor action? (2008)

The endocannabinoid system is an ancient lipid signaling network which in mammals modulates neuronal functions, inflammatory processes, and is involved in the aetiology of certain human lifestyle diseases, such as Crohn's disease, atherosclerosis and osteoarthritis. The system is able to downregulate stress-related signals that lead to chronic inflammation and certain types of pain, but it is also involved in causing inflammation-associated symptoms, depending on the physiological context. The cannabinoid type-2 (CB(2)) receptor, which unlike the CB(1) receptor does not induce central side effects, has been shown to be a promising therapeutic target. While CB(1) receptor antagonists/inverse agonists are of therapeutic value, also CB(2) receptor ligands including agonists are of pharmacological interest. Although the endocannabinoid system is known to be involved in the regulation of energy homoeostasis and metabolism (mainly via CB(1) receptors) there was hitherto no direct link between food intake and cannabinoid receptor activation. Our recent finding that beta-caryophyllene, a ubiquitous lipohilic plant natural product, selectively binds to the CB(2) receptor and acts as a full agonist is unexpected. Maybe even more unexpected is that oral administration of this dietary compound exerts potent anti-inflammatory effects in wild type mice but not in CB(2) receptor (Cnr2(-/-)) knockout mice. Like other CB(2) ligands also beta-caryophyllene inhibits the pathways triggered by activation of the toll-like receptor complex CD14/TLR4/MD2, which typically lead to the expression of proinflammatory cytokines (IL-1beta, IL-6; IL-8 and TNFalpha) and promotes a TH(1) immune response. In this addendum, the CB(2) receptor-dependent effect of beta-caryophyllene on LPS-triggered activation of the kinases Erk1/2 and JNK1/2 are further discussed with respect to the possibility that both CB(2) inverse agonists and agonists, independent of their G-protein signaling, may block LPS-triggered activation of MAPKs, leading to inhibition of proinflammatory cytokine expression and attenuation of inflammation.
Contribution of oxygen to attenuation in the solar blind UV spectral region (1989)

The solar blind ultraviolet (SBUV) spectral region covers the interval between 230 and 290 nm. The lower limit of this interval is given by the edge of the Schumann-Runge band and the upper limit is determined by solar radiation penetrating the stratospheric ozone shield. The SBUV region is interesting from the experimental point of view, since the lack of solar background is favorable in such applications as lidar, atmospheric communications, and remote sensing. The present models (LOWTRAN-6) include as atmospheric attenuators in this region ozone absorption and aerosol and molecular scattering. New theoretical calculations of the Herzberg I oxygen band predict significant absorption by O(2). This prediction is confirmed experimentally in this study. Field measurements at 252, 255, and 264 nm are reported over optical paths of up to 2750 m. Results show that LOWTRAN-6 is inadequate in the SBUV region, as indicated by the present extinction measurements.
Closure of abdominal wounds by adhesive strips: a clinical trial. (1975)

In a randomized trial of wound closure in 512 abdominal wounds, wounds were closed with either reinforced Steristrip skin closures or interrupted silk sutures. Comparisons were made of wound pain and discomfort, wound infection, discharge, redness, width, and skin reaction. The causes of peeling of the tapes were assessed. The results showed that tapes were significantly more comfortable and that patients preferred them to sutures (P less than 0.01), but wide scars occurred more often. There was no difference in rates of wound infection and no case of allergy to the tapes was seen. Closure of abdominal wounds by these tapes is a satisfactory procedure that could be used more extensively.
The XML Framework and Its Implications for Corpus Access and Use (2000)

The eXtensible Markup Language (XML) (Bray, et al., 1998) is the emerging standard for data representation and exchange on the World Wide Web. The XML Framework includes very powerful mechanisms for accessing and manipulating XML documents that are likely to significantly impact the way annotated corpora are created and accessed. This paper outlines a few of the possibilities. Introduction The eXtensible Markup Language (XML) (Bray, et al., 1998) is the emerging standard for data representation and exchange on the World Wide Web. At its most basic level XML is a document markup language directly derived from SGML (i.e., allowing tagged text (elements), element nesting, and element references). As such, translation of an SGML encoded document into XML is relatively trivial. However, various features and extensions of XML make it a far more powerful tool for data representation and access than SGML. The following outlines some of these mechanisms and suggests ways in which they can be ...
Pharmacokinetics of Gemtuzumab Ozogamicin, an Antibody‐Targeted Chemotherapy Agent for the Treatment of Patients with Acute Myeloid Leukemia in First Relapse (2001)

The purpose of this study was to characterize the pharmacokinetics of gemtuzumab ozogamicin (Mylotarg; Wyeth-Ayerst Laboratories, St. Davids, PA) in patients with acute myeloid leukemia (AML) in first relapse. Gemtuzumab ozogamicin is an antibody-chemotherapeutic conjugate characterized as antibody-targeted chemotherapy, consisting of an engineered human anti-CD33 antibody (hP67.6) linked to a potent cytotoxic agent, N-acetyl-gamma calicheamicin DMH. The pharmacokinetics of gemtuzumab ozogamicin was evaluated in 59 adult AML patients in first relapse, enrolled in a phase II study. Plasma was collected following each dose at specified times, and the pharmacokinetics was characterized by measures of hP67.6, total calicheamicin derivatives, and unconjugated calicheamicin derivatives. After administration of the first 9 mg/m2 dose of gemtuzumab ozogamicin, the pharmacokinetic parameters (mean +/- SD) of hP67.6 following the first dose were as follows: peak plasma concentration, 2.86 +/- 1.35 mg/L; AUC, 123 +/- 105 mg x h/L; t 1/2, 72.4 +/- 42.0 hours; and clearance, 0.265 +/- 0.229L/h. Increased concentrations were observed after the second dose and are believed to be due to a decrease in clearance by CD33-positive blast cells, a result of the reduced tumor burden following the first dose. The concentration profiles of calicheamicin followed the same time course as hP67.6, evidence that calicheamicin remained conjugated to the antibody and delivered to leukemic cells. No relationship was found between plasma concentration and response at the recommended dose. The pharmacokinetics of gemtuzumab ozogamicin has been characterized in AML patients receiving doses at the proposed therapeutic level.
Modulating intestinal immune responses by lipoteichoic acid-deficient <i>Lactobacillus acidophilus</i> (2012)

These results suggest that the oral administration of the genetically modified strain NCK2025 may be an effective immunotherapeutic approach that reprograms the immune response in colonic inflammatory conditions.
Mapping a New Spontaneous Preterm Birth Susceptibility Gene, IGF1R, Using Linkage, Haplotype Sharing, and Association Analysis (2011)

Preterm birth is the major cause of neonatal death and serious morbidity. Most preterm births are due to spontaneous onset of labor without a known cause or effective prevention. Both maternal and fetal genomes influence the predisposition to spontaneous preterm birth (SPTB), but the susceptibility loci remain to be defined. We utilized a combination of unique population structures, family-based linkage analysis, and subsequent case-control association to identify a susceptibility haplotype for SPTB. Clinically well-characterized SPTB families from northern Finland, a subisolate founded by a relatively small founder population that has subsequently experienced a number of bottlenecks, were selected for the initial discovery sample. Genome-wide linkage analysis using a high-density single-nucleotide polymorphism (SNP) array in seven large northern Finnish non-consanginous families identified a locus on 15q26.3 (HLOD 4.68). This region contains the IGF1R gene, which encodes the type 1 insulin-like growth factor receptor IGF-1R. Haplotype segregation analysis revealed that a 55 kb 12-SNP core segment within the IGF1R gene was shared identical-by-state (IBS) in five families. A follow-up case-control study in an independent sample representing the more general Finnish population showed an association of a 6-SNP IGF1R haplotype with SPTB in the fetuses, providing further evidence for IGF1R as a SPTB predisposition gene (frequency in cases versus controls 0.11 versus 0.05, P = 0.001, odds ratio 2.3). This study demonstrates the identification of a predisposing, low-frequency haplotype in a multifactorial trait using a well-characterized population and a combination of family and case-control designs. Our findings support the identification of the novel susceptibility gene IGF1R for predisposition by the fetal genome to being born preterm.
Spontaneous Self-Assembly of Glycolipid Bilayer Membranes in Sugar-philic Ionic Liquids and Formation of Ionogels (2001)

Ether-containing ionic liquids are developed, which are capable of dissolving carbohydrates such as β-d-glucose, α-cyclodextrin, amylose, agarose, and a glycosylated protein, glucose oxidase. When glycolipids are dispersed in these sugar-philic ionic liquids, stable bilayer membranes are formed. They display reversible thermal transformation from fibrous assemblies to vesicles. Physical gelation of ionic liquids occurs by dissolving amide-group-enriched glycolipids, providing a first example of self-assembling ionogels. The ability to dissolve carbohydrates in ionic liquids and the formation of bilayer membranes, self-assembling gels will open new dimensions in ionic liquid research.
BAC transgenic mice express enhanced green fluorescent protein in central and peripheral cholinergic neurons (2006)

The peripheral nervous system has complex and intricate ramifications throughout many target organ systems. To date this system has not been effectively labeled by genetic markers, due largely to inadequate transcriptional specification by minimum promoter constructs. Here we describe transgenic mice in which enhanced green fluorescent protein (eGFP) is expressed under the control of endogenous choline acetyltransferase (ChAT) transcriptional regulatory elements, by knock-in of eGFP within a bacterial artificial chromosome (BAC) spanning the ChAT locus and expression of this construct as a transgene. eGFP is expressed in ChAT(BAC)-eGFP mice in central and peripheral cholinergic neurons, including cell bodies and processes of the somatic motor, somatic sensory, and parasympathetic nervous system in gastrointestinal, respiratory, urogenital, cardiovascular, and other peripheral organ systems. Individual epithelial cells and a subset of lymphocytes within the gastrointestinal and airway mucosa are also labeled, indicating genetic evidence of acetylcholine biosynthesis. Central and peripheral neurons were observed as early as 10.5 days postcoitus in the developing mouse embryo. ChAT(BAC)-eGFP mice allow excellent visualization of all cholinergic elements of the peripheral nervous system, including the submucosal enteric plexus, preganglionic autonomic nerves, and skeletal, cardiac, and smooth muscle neuromuscular junctions. These mice should be useful for in vivo studies of cholinergic neurotransmission and neuromuscular coupling. Moreover, this genetic strategy allows the selective expression and conditional inactivation of genes of interest in cholinergic nerves of the central nervous system and peripheral nervous system.
Enumeration of Megasphaera elsdenii in rumen contents by real-time Taq nuclease assay (2002)

Megasphaera elsdenii is an important lactate-degrading ruminal bacterium that has been selected for probiotic use to prevent acidosis and enhance starch utilization in grain-fed cattle. The assay developed in this study provides a tool for determining the ability of probiotically-introduced M. elsdenii to establish useful populations in the rumen.
Influence of Lidocaine on Endotoxin-induced Leukocyte-Endothelial Cell Adhesion and Macromolecular Leakage in Vivo (1997)

These results show that lidocaine attenuates endotoxin-induced alterations in leukocyte-endothelial cell adhesion and macromolecular leakage, which suggests that lidocaine may have a therapeutic role in preventing endothelial damage in sepsis.
Evidence that FGF8 signalling from the midbrain-hindbrain junction regulates growth and polarity in the developing midbrain (1997)

The developing vertebrate mesencephalon shows a rostrocaudal gradient in the expression of a number of molecular markers and in the cytoarchitectonic differentiation of the tectum, where cells cease proliferating and differentiate in a rostral to caudal progression. Tissue grafting experiments have implicated cell signalling by the mesencephalic-metencephalic (mid-hindbrain) junction (or isthmus) in orchestrating these events. We have explored the role of Wnt-1 and FGF8 signalling in the regulation of mesencephalic polarity. Wnt-1 is expressed in the caudal mesencephalon and Fgf8 in the most rostral metencephalon. Wnt-1 regulates Fgf8 expression in the adjacent metencephalon, most likely via a secondary mesencephalic signal. Ectopic expression of Fgf8 in the mesencephalon is sufficient to activate expression of Engrailed-2 (En-2) and ELF-1, two genes normally expressed in a decreasing caudal to rostral gradient in the posterior mesencephalon. Ectopic expression of Engrailed-1 (En-1), a functionally equivalent homologue of En-2 is sufficient to activate ELF-1 expression by itself. These results indicate the existence of a molecular hierarchy in which FGF8 signalling establishes the graded expression of En-2 within the tectum. This in turn may act to specify other aspects of A-P polarity such as graded ELF-1 expression. Our studies also reveal that FGF8 is a potent mitogen within the mesencephalon: when ectopically expressed, neural precursors continue to proliferate and neurogenesis is prevented. Taken together our results suggest that FGF8 signalling from the isthmus has a key role in coordinately regulating growth and polarity in the developing mesencephalon.
Protein Prenylation: Genes, Enzymes, Targets, and Functions (1992)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
The Ability of Biomarkers to Predict Systemic Progression in Men with High-Risk Prostate Cancer Treated Surgically Is Dependent on <i>ERG</i> Status (2010)

The objective of this study was to assess the relationship of the tumor protein levels of TOP2A and MIB-1 and ERG status with cancer-specific outcomes in men with high-risk prostate cancer treated by radical prostatectomy (RP). A 150-pair case-control study was designed from RP patients who developed systemic progression (SP) within 6 years of RP (cases) and men who were free of disease at least 8 years after RP (controls). The cases and controls were matched on conventional prognostic clinical parameters. TOP2A and MIB-1 levels were assessed by immunohistochemical methods, and ERG status was assessed by quantitative reverse transcription-PCR. The prognostic abilities of TOP2A and MIB-1 were significantly better in ERG(-) patients, and TOP2A was superior to MIB-1. In receiver operating characteristic analysis, the TOP2A and MIB-1 scores exhibited AUCs of 0.81 and 0.78 for ERG(-) patients, versus 0.67 and 0.68 for ERG(+) patients, respectively. Clinical parameters attained an AUC of 0.65 in ERG(-) patients and 0.54 in ERG(+) patients. When both markers were incorporated into a model for ERG(-) patients, the AUC increased to 0.83, with TOP2A showing a stronger association with SP than MIB-1. The time to SP was significantly associated with TOP2A; higher 5-year SP rates were observed in patients with higher TOP2A protein levels. In addition, although patient numbers are small, the response to adjuvant androgen deprivation therapy is associated with ERG status, showing more significant treatment effect in ERG(+) patients.
Genetic evidence that the retinoid signal is transduced by heterodimeric RXR/RAR functional units during mouse development (1997)

We describe here the analysis of congenital malformations in compound mutant fetuses bearing null alleles in one RXR (alpha, beta or gamma) and one RAR (alpha, beta or gamma) isotype gene. A marked synergy was observed between the effects of mutations in RXR alpha and RARs, as a large number of developmental defects previously found mainly in RAR single and compound mutants were recapitulated in specific RXR alpha/RAR compound mutants. Several malformations were seen only in one type of RXR alpha/RAR mutant combination, whereas others were seen in several types of RXR alpha/RAR double mutants. No synergy was observed between the effects of mutations of either RXR beta or RXR gamma mutations and those of any of the RAR mutations. These genetic data suggest that RXR/RAR heterodimers are the functional units transducing the retinoid signal for a large number of RA-dependent processes, and furthermore, that RXR alpha is the main RXR implicated in the developmental functions of RARs. The significance of these observations is discussed with respect to the problem of functional specificity and redundancy among retinoid receptors in vivo.