gebhart/patrepeval huggingface dataset:
End-to-end packet delay and loss behavior in the internet (1993)

We use the measured round trip delays of small UDP probe packets sent at regular time intervals to analyze the end-to-end packet delay and loss behavior in the Internet. By varying the interval between probe packets, it is possible to study the structure of the Internet load over different time scales. In this paper, the time scales of interest range from a few milliseconds to a few minutes. Our observations agree with results obtained by others using simulation and experimental approaches. For example, our estimates of Internet workload are consistent with the hypothesis of a mix of bulk traffic with larger packet size, and interactive traffic with smaller packet size. We observe compression (or clustering) of the probe packets, rapid fluctuations of queueing delays over small intervals, etc. Our results also show interesting and less expected behavior. For example, we find that the losses of probe packets are essentially random unless the probe traffic uses a large fraction of the available bandwidth. We discuss the implications of these results on the design of control mechanisms for the Internet.
Six of 12 Relapsed or Refractory Indolent Lymphoma Patients Treated 10 Years Ago with 131I-Tositumomab Remain in Complete Remission (2011)

Optimal patient benefit might be obtained in indolent lymphoma when administering radioimmunotherapy up-front in combination with chemotherapy and rituximab treatment. However, these results show that radioimmunotherapy alone achieved long-lasting remissions in 6 of 12 (50%) indolent lymphoma patients in relapse after 1 or multiple chemotherapies.
Apolipoprotein E Suppresses the Type I Inflammatory Response In Vivo (2005)

Apolipoprotein E (apoE) is synthesized in the liver and in macrophages, and it has antiatherogenic properties that are mediated, at least in part, through the regulation of plasma cholesterol homeostasis. Previous data suggest that apoE also has antiinflammatory properties that may contribute to protection against atherosclerosis independent of its role in lipid metabolism. In this study, apoE knockout and C57BL/6 mice were stimulated with low-dose lipopolysaccharide (LPS) and other Toll-like receptor (TLR) agonists. We show that apoE modulates the systemic type I inflammatory response in vivo. The proinflammatory cytokines tumor necrosis factor alpha, interleukin (IL)-6, IL-12, and interferon-gamma were upregulated to a significantly greater extent in apoE-deficient mice than in wild-type mice at both the mRNA and protein levels following administration of LPS. In contrast, hypercholesterolemic low-density lipoprotein receptor/apobec-1 double knockout mice had a similar cytokine response as wild-type mice, eliminating hypercholesterolemia as a cause for the exaggerated cytokine response. Importantly, reconstitution of apoE expression in the liver of apoE-deficient mice normalized the LPS-induced plasma protein levels of IL-12p40. Furthermore, there was selective upregulation of plasma IL-12 in apoE knockout mice by a TLR3 agonist, poly I:C, but not by other TLR agonists, CpG oligonucleotide or Toxoplasma gondii antigen. This implies that apoE selectively regulates TLR4- and TLR3-mediated signaling of IL-12 production. These results indicate that apoE modulates the T helper-1-type immune response in vivo by modulating IL-12 production.
A SYSTEM PARTITIONING AND OPTIMIZATION APPROACH TO TARGET CASCADING (1999)

This article presents a rigorous but practical methodology for addressing the target cascading process. Under this concept, product design can be viewed as a four-step process: (i) specify overall product targets; (ii) propagate product targets to system, subsystem and component “sub-targets”; (iii) design system, subsystems and components to achieve their respective subtargets; and (iv) verify that the resulting product meets overall product targets. The goal of the target cascading process is that systems, subsystems and components operate together in the desired way (i.e., they are compatible and consistent). A mathematically rigorous decisionmaking methodology that takes advantage of hierarchical system partitioning and coordination and analytical models can be a valuable tool for both engineers and managers. The main benefits of target cascading are reduction in product design-cycle time, avoidance of design iterations late in the development process, and increased likelihood that physical prototypes will be closer to production quality. Target setting also allows outsourcing the design of a particular subsystem or component after providing the supplier with the corresponding set of targets.
Electrical Stimulation of Sphenopalatine Ganglion for Acute Treatment of Cluster Headaches (2010)

Sphenopalatine ganglion stimulation can be effective in relieving acute severe CH pain and associated autonomic features. Chronic long-term outcome studies are needed to determine the utility of SPG stimulation for management and prevention of CH.
Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant (1997)

NAD(+)-dependent malic enzyme was cloned from the Escherichia coli genome by PCR based on the published partial sequence of the gene. The enzyme was overexpressed and purified to near homogeneity in two chromatographic steps and was analyzed kinetically in the forward and reverse directions. The Km values determined in the presence of saturating cofactor and manganese ion were 0.26 mM for malate (physiological direction) and 16 mM for pyruvate (reverse direction). When malic enzyme was induced under appropriate culture conditions in a strain of E. coli that was unable to ferment glucose and accumulated pyruvate, fermentative metabolism of glucose was restored. Succinic acid was the major fermentation product formed. When this fermentation was performed in the presence of hydrogen, the yield of succinic acid increased. The constructed pathway represents an alternative metabolic route for the fermentative production of dicarboxylic acids from renewable feedstocks.
p38 Mitogen-activated Protein Kinase Activates Peroxisome Proliferator-activated Receptor α (2001)

The expression of enzymes involved in fatty acid beta-oxidation (FAO), the principal source of energy production in the adult mammalian heart, is controlled at the transcriptional level via the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARalpha). Evidence has emerged that PPARalpha activity is activated as a component of an energy metabolic stress response. The p38 mitogen-activated protein kinase (MAPK) pathway is activated by cellular stressors in the heart, including ischemia, hypoxia, and hypertrophic growth stimuli. We show here that PPARalpha is phosphorylated in response to stress stimuli in rat neonatal cardiac myocytes; in vitro kinase assays demonstrated that p38 MAPK phosphorylates serine residues located within the NH(2)-terminal A/B domain of the protein. Transient transfection studies in cardiac myocytes and in CV-1 cells utilizing homologous and heterologous PPARalpha target element reporters and mammalian one-hybrid transcription assays revealed that p38 MAPK phosphorylation of PPARalpha significantly enhanced ligand-dependent transactivation. Cotransfection studies performed with several known coactivators of PPARalpha demonstrated that p38 MAPK markedly increased coactivation specifically by PGC-1, a transcriptional coactivator implicated in myocyte energy metabolic gene regulation and mitochondrial biogenesis. These results identify PPARalpha as a downstream effector of p38 kinase-dependent stress-activated signaling in the heart, linking extracellular stressors to alterations in energy metabolic gene expression.
The Length of and Nonhydrophobic Residues in the Transmembrane Domain of Dengue Virus Envelope Protein Are Critical for Its Retention and Assembly in the Endoplasmic Reticulum (2010)

The morphogenesis of many enveloped viruses, in which viral nucleocapsid complex interacts with envelope (E) protein, is known to take place at various sites along the secretory pathway. How viral E protein retains in a particular intracellular organelle for assembly remains incompletely understood. In this study, we investigated determinants in the E protein of dengue virus (DENV) for its retention and assembly in the endoplasmic reticulum (ER). A chimeric experiment between CD4 and DENV precursor membrane/E constructs suggested that the transmembrane domain (TMD) of E protein contains an ER retention signal. Substitutions of three nonhydrophobic residues at the N terminus of the first helix (T1) and at either the N or C terminus of the second helix of the TMD with three hydrophobic residues, as well as an increase in the length of T1, led to the release of chimeric CD4 and E protein from the ER, suggesting that short length and certain nonhydrophobic residues of the TMD are critical for ER retention. The analysis of enveloped viruses assembled at the plasma membrane and of those assembled in the Golgi complex and ER revealed a trend of decreasing length and increasing nonhydrophobic residues of the TMD of E proteins. Taken together, these findings support a TMD-dependent sorting for viral E proteins along the secretory pathway. Moreover, similar mutations introduced into the TMD of DENV E protein resulted in the increased production of virus-like particles (VLPs), suggesting that modifications of TMD facilitate VLP production and have implications for utilizing flaviviral VLPs as serodiagnostic antigens and vaccine candidates.
Metagenomic Analysis of the Human Distal Gut Microbiome (2006)

The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.
Robotic excavation in construction automation (2002)

This article presents some results of the autonomous excavation project conducted at the Australian Centre for Field Robotics (ACFR) with a focus on construction automation. The application of robotic technology and computer control is one key to construction industry automation. Excavation automation is a multidisciplinary task, encompassing a broad area of research and development. The ultimate goal of the ACFR excavation project is to demonstrate fully autonomous execution of excavation tasks in common construction, such as loading a truck or digging a trench. A number of difficult theoretical and practical problems must be solved to achieve this objective. The problems fall into three main groups: excavation planning, sensing and estimation, and control.
HPLC Analysis of Fluorescently Labeled Glycans (2003)

The study of the glycan chains (oligosaccharides) of glycoproteins presents a number of analytical problems that generally make their analysis more difficult than that of the peptides to which they are attached. A number of different analytical techniques have been applied to the study of glycans. Definitive characterization has traditionally been performed using nuclear magnetic resonance spectroscopy (NMR) and this still remains the only way to unequivocally assign the structure to novel glycans. But the techniques do require relatively large amounts of material (in the milligram range). In addition, access to the sophisticated equipment and the expertise required for the interpretation of data mean that the technique is available only to specialized dedicated laboratories. Another technique, which has also been applied extensively to studies of glycan structure, is that of mass spectrometry in various forms. A number of structures have been solved by means of fast atom bombardment (FAB-MS) (1,2) although generally further information from linkage analysis by gas chromatography-MS of permethylated alditol acetates (PMAA [3-5]) or by use of specific exoglycosidase enzymes (6) is required. Other techniques for mass spectrometric analysis are becoming more widely used as a result of recent developments in instrumentation (7-9). Both matrix-assisted laser desorption mass spectrometry with time-of-flight detection (8) (MALDI-TOF) and electrospray coupled to post source decay (9) to produce fragmentation ions are now becoming routinely used. The instrumentation is still expensive, however, and requires skilled operation and interpretation. There are also still problems with optimization and contamination of samples. Another technique that is also used is capillary electrophoresis, which can offer rapid characterization but that can also be difficult to optimize (10). Polyacrylamide gel electrophoresis of fluorescently labeled glycans, a technique that requires no expensive instrumentation or specialized expertise, may also be used for screening or profiling. Although this is very useful for routine screening of a large number of samples, detailed characterization or sequencing of complex mixtures is problematic.
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach (2012)

Advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. Genotyping-by-sequencing (GBS) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. GBS uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. Here we present a GBS approach for species that currently lack a reference genome sequence. We developed a novel two-enzyme GBS protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified SNPs and tags. We were able to map over 34,000 SNPs and 240,000 tags onto the Oregon Wolfe Barley reference map, and 20,000 SNPs and 367,000 tags on the Synthetic W9784 × Opata85 (SynOpDH) wheat reference map. To further evaluate GBS in wheat, we also constructed a de novo genetic map using only SNP markers from the GBS data. The GBS approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. Development of the sequenced reference genome(s) will in turn increase the utility of GBS data enabling physical mapping of genes and haplotype imputation of missing data. Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs.
Dynamic threshold pass-transistor logic for improved delay at lower power supply voltages (1999)

We have investigated circuit options to surpass the 1 V power-supply limitation predicted by traditional scaling guidelines. By modulating the body bias, we can dynamically adjust the threshold voltage to have different on- and off-state values. Several dynamic threshold voltage MOSFET (DTMOS) logic styles were analyzed for ultralow-power use-from 1.5 down to 0.5 V. Since ordinary pass-transistor logic degrades as the voltages are reduced, we investigated the effects that a dynamic threshold has on various styles of pass-transistor logic. Three different pass-transistor restoration schemes were simulated with the various DTMOS techniques. Results indicate that controlling the body bias can provide a substantial speed increase and that such techniques are useful over a large range of supply voltages. Process complexity and other tradeoffs associated with DTMOS logic variations are also discussed.
Statistical considerations in seed purity testing for transgenic traits (2001)

Abstract Recent advances in agricultural biotechnology have produced many new crop varieties with valuable transgenic traits. These varieties are being, and will continue to be, marketed alongside conventional non-transgenic varieties. As a result, seed purity in commercial seed lots is of particular importance to both seed consumers and seed producers. A key step in the seed production process is the design of sampling and testing procedures used to evaluate seed lot purity. However, due to uncertainties in such methods, there is always a risk of incorrectly rejecting or accepting a seed lot. This paper discusses factors that should be considered when designing and implementing seed purity testing procedures to manage this misclassification risk – especially with regard to the presence or absence of transgenic traits. Many sources of uncertainty in both seed lot sampling and in the assay methods are described, and recommendations for reducing their impact are provided. This paper also explains the statistical concepts of misclassification risk as it affects seed producers and seed consumers. Sampling plans and formulas for determining the sample sizes necessary to control these misclassification errors when accepting or rejecting seed lots are also provided. Both simple, single-stage testing plans and the, often more efficient, double-stage testing plans are described. Testing seed pools rather than individual seeds is introduced as another way of adding efficiency to the testing process. Formulas are given for determining, from a seed sample, the confidence limits for the actual purity level of a commercial lot.
CSF Neurofilament Light Chain Levels in Primary Progressive MS: Signs of Axonal Neurodegeneration (2018)

<b>Objectives:</b> Elevated neurofilament light chain (NFL) levels within the cerebrospinal fluid (CSF) are a biomarker representing axonal neurodegeneration in rapid progressive neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). It is unclear to what extent the levels of NFL increase in the CSF (CSF-NFL) in a chronic neuroinflammatory process with axonal neurodegeneration, as found in primary progressive multiple sclerosis (PPMS). <b>Methods:</b> We used a multicenter approach to statistically compare CSF-NFL levels between PPMS patients (<i>n</i> = 50), ALS patients (<i>n</i> = 50), and healthy controls (<i>n</i> = 50). Clinical findings, including disease duration, expanded disability status scale (EDSS), electrophysiological recordings such as visual evoked potentials or spinal and cerebral MRI, and previously administered treatment were selected as experimental parameters retrospectively. <b>Results:</b> Median [range] CSF-NFL concentrations in PPMS patients were significantly higher than in the controls [1724 (799-4275) pg/ml vs. 1202 (612-2934) pg/ml, <i>p</i> = 0.015], and significantly lower compared to ALS patients [1724 (799-4275) pg/ml vs. 10238 (2610-35138) pg/ml, <i>p</i> < 0.001]. There was no correlation between CSF-NFL and disease duration (<i>p</i> = 0.5), EDSS (<i>p</i> = 0.2) or treatment (<i>p</i> = 0.3). <b>Conclusion:</b> We conclude that CSF-NFL may mirror the proposed slow axonal degeneration in PPMS, but does not reflect the disease severity.
Novel all optical light modulation based on complex refractive index changes of organic dye-doped polymer film upon photoexcitation (1996)

A novel all-optical light modulation has been proposed based on photoinduced changes of an imaginary part of complex refractive index in guided wave geometry. Very fast and repeated modulation of a reading beam (reflected intensity) was demonstrated at the incident angle corresponding to a sharp guided wave resonance using phthalocyanine-doped poly(vinyl alcohol) film as a photoresponsive layer and a nanosecond pulsed laser as a writing beam. Such responses were mainly due to the formation and decay of excited triplet phthalocyanine. The rise and fall time was markedly improved as compared with previous systems based on photothermal changes of the refractive index.
Evaluation of Trapping and Vacuuming Compared with Low-Impact Insecticide Tactics for Managing German Cockroaches in Residences (1997)

Journal Article Evaluation of Trapping and Vacuuming Compared with Low-Impact Insecticide Tactics for Managing German Cockroaches in Residences Get access Walid Kaakeh, Walid Kaakeh Center for Urban and Industrial Pest Management, Department of Entomology, Purdue University, West Lafayette, IN 47907-1158 Search for other works by this author on: Oxford Academic PubMed Google Scholar Gary W. Bennett Gary W. Bennett Center for Urban and Industrial Pest Management, Department of Entomology, Purdue University, West Lafayette, IN 47907-1158 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 90, Issue 4, 1 August 1997, Pages 976–982, https://doi.org/10.1093/jee/90.4.976 Published: 01 August 1997 Article history Received: 15 November 1996 Accepted: 18 February 1997 Published: 01 August 1997
The Arabidopsis Abscisic Acid Response Gene ABI5 Encodes a Basic Leucine Zipper Transcription Factor (2000)

The Arabidopsis abscisic acid (ABA)-insensitive abi5 mutants have pleiotropic defects in ABA response, including decreased sensitivity to ABA inhibition of germination and altered expression of some ABA-regulated genes. We isolated the ABI5 gene by using a positional cloning approach and found that it encodes a member of the basic leucine zipper transcription factor family. The previously characterized abi5-1 allele encodes a protein that lacks the DNA binding and dimerization domains required for ABI5 function. Analyses of ABI5 expression provide evidence for ABA regulation, cross-regulation by other ABI genes, and possibly autoregulation. Comparison of seed and ABA-inducible vegetative gene expression in wild-type and abi5-1 plants indicates that ABI5 regulates a subset of late embryogenesis-abundant genes during both developmental stages.
Small Molecule-Assisted, Line-Independent Maintenance of Human Pluripotent Stem Cells in Defined Conditions (2012)

Human pluripotent stem cells (hPSCs) are conventionally grown in a mouse feeder cell-dependent manner. Chemically defined culture conditions are, however, desirable not only for potential medically oriented applications but also for investigating mechanisms of self-renewal and differentiation. In light of the rather high complexity and cost of existing defined hPSC culture systems, we have systematically evaluated over 20 potential media ingredients. Only components that reproducibly gave beneficial effects were ultimately combined to yield a simple and cost-effective formulation termed FTDA. This xeno-free medium is based on mimicking self-renewal factor activities present in mouse embryonic fibroblast-conditioned medium, at minimal dosages. Additionally, small molecule inhibitors of BMP and WNT signaling served to specifically suppress typical types of spontaneous differentiation seen in hPSC cultures. FTDA medium was suitable for the generation of human induced pluripotent stem cells and enabled robust long-term maintenance of diverse hPSC lines including hard-to-grow ones. Comparisons with existing defined media suggested reduced spontaneous differentiation rates in FTDA. Our results imply that using supportive factors at minimal concentrations may still promote robust self-renewal and preserve pluripotency of hPSCs.