gebhart/patrepeval huggingface dataset:
Topology Discovery in Heterogeneous IP Networks: The NetInventory System (2004)

Knowledge of the up-to-date physical topology of an IP network is crucial to a number of critical network management tasks, including reactive and proactive resource management, event correlation, and root-cause analysis. Given the dynamic nature of today's IP networks, keeping track of topology information manually is a daunting (if not impossible) task. Thus, effective algorithms for automatically discovering physical network topology are necessary. Earlier work has typically concentrated on either 1) discovering logical (i.e., layer-3) topology, which implies that the connectivity of all layer-2 elements (e.g., switches and bridges) is ignored, or 2) proprietary solutions targeting specific product families. In this paper, we present novel algorithms for discovering physical topology in heterogeneous (i.e., multi-vendor) IP networks. Our algorithms rely on standard SNMP MIB information that is widely supported by modern IP network elements and require no modifications to the operating system software running on elements or hosts. We have implemented the algorithms presented in this paper in the context of the NetInventory topology-discovery tool that has been tested on Lucent's own research network. The experimental results clearly validate our approach, demonstrating that our tool can consistently discover the accurate physical network topology with reasonably small running-time requirements even for fairly large network configurations.
Genetic analysis of ethylene responses in Arabidopsis thaliana. (1991)

The plant hormone ethylene mediates a number of developmental processes and responses to environmental stress in higher plants. Our research efforts over the last three years have been focused on developing an understanding of the molecular basis of ethylene action in plants. To this end, we have isolated mutants in Arabidopsis thaliana with altered responses to ethylene. One such mutant, designated etr, shows no measurable responses to ethylene and has reduced ethylene binding in leaf tissue indicating that the mutation may directly affect the ethylene receptor. We have genetically mapped the etr mutation and by chromosome walking have isolated an 18 kb fragment of genomic DNA that contains the mutant gene. Sequence analysis of cDNAs which map to the 18 kb fragment has produced a candidate for the ETR gene which codes for a putative transmembrane protein kinase. Sequence analysis indicates a domain composed of 9 copies of a 23 amino acid leucine-rich repeat unit and a domain containing a serine/threonine type protein kinase. These two domains are separated by a single 24 amino acid hydrophobic domain. A model is presented that describes the possible mechanism of action of the protein kinase with respect to ethylene-mediated responses in plants.
Bamboo: A fast descriptor based on AsymMetric pairwise BOOsting (2014)

A robust hash, or content-based fingerprint, is a succinct representation of the perceptually most relevant parts of a multimedia object. A key requirement of fingerprinting is that elements with perceptually similar content should map to the same fingerprint, even if their bit-level representations are different. In this work we propose BAMBOO (Binary descriptor based on AsymMetric pairwise BOOsting), a binary local descriptor that exploits a combination of content-based fingerprinting techniques and computationally efficient filters (box filters, Haar-like features, etc.) applied to image patches. In particular, we define a possibly large set of filters and iteratively select the most discriminative ones resorting to an asymmetric pair-wise boosting technique. The output values of the filtering process are quantized to one bit, leading to a very compact binary descriptor. Results show that such descriptor leads to compelling results, significantly outperforming binary descriptors having comparable complexity (e.g., BRISK), and approaching the discriminative power of state-of-the-art descriptors which are significantly more complex (e.g., SIFT and BinBoost).
Risk factors for venous thrombosis: prevalence, risk, and interaction. (1997)

Annually, 1 in 1,000 individuals is affected by venous thrombosis. Risk factors that are known to increase the risk of thrombosis may be either genetic or acquired, or have a combined origin. Many of these risk factors are very frequent, among which several have been recently identified, such as resistance to activated protein C by factor V Leiden, hyperhomocysteinemia, high levels of factors VIII, as well as the classical acquired risk factors, such as surgery and malignancies. When the prevalence of risk factors is high, it becomes likely that in some individuals two or more risk factors will be present simultaneously. The question "What happens to the risk in these circumstances?" is one involving interaction, also known as effect modification or synergy. In this article we review the prevalence and risk estimates for the various genetic and acquired risk factors for venous thrombosis, discuss the concept of interaction, and give an overview of the evidence for interaction of these risk factors.
Peimine impairs pro-inflammatory cytokine secretion through the inhibition of the activation of NF-κB and MAPK in LPS-induced RAW264.7 macrophages (2013)

In the previous study, we found that peimine has good anti-inflammatory effects in vivo. However, the anti-inflammatory mechanism of peimine remains unclear. We, therefore, assessed the effects of peimine on inflammatory cytokines in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. We found that peimine (0-25 mg/L) significantly inhibited tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-1β, and increased IL-10 production. Furthermore, peimine significantly inhibited the phosphorylation of p38, ERK and c-jun N-terminal kinase (JNK) as well as decreased p65 and IκB. The present results indicate that peimine inhibits the production of inflammatory cytokines induced by LPS through blocking MAPKs and NF-κB signaling pathways.
A <i>Phex</i> mutation in a murine model of X-linked hypophosphatemia alters phosphate responsiveness of bone cells (2011)

Mutations in the PHEX gene cause X-linked hypophosphatemia (XLH). Hypophosphatemia in XLH results from increased circulating levels of a phosphaturic hormone, fibroblast growth factor 23 (FGF23), which inhibits renal phosphate reabsorption and 1,25-dihydroxyvitamin D (calcitriol) synthesis. The current standard therapy for XLH--high-dose phosphate and calcitriol--further increases FGF23 concentrations, suggesting that patients with XLH may have an altered response to extracellular phosphate. To test for the presence of abnormal phosphate responsiveness, we compared serum biochemistries and femoral Fgf23 mRNA expression between wild-type mice, murine models of XLH (Phex(K496X)) and hyperphosphatemic tumoral calcinosis (Galnt3(-/-)), and Galnt3/Phex double-mutant mice. Phex mutant mice had not only increased Fgf23 expression but also reduced proteolytic cleavage of intact Fgf23 protein, resulting in markedly elevated intact Fgf23 levels and consequent hypophosphatemia. In contrast, despite markedly increased Fgf23 expression, Galnt3 knockout mice had significantly high proteolytic cleavage of Fgf23 protein, leading to low intact Fgf23 concentrations and hyperphosphatemia. Galnt3/Phex double-mutant mice had an intermediate biochemical phenotype between wild-type and Phex mutant mice, including slightly elevated intact Fgf23 concentrations with milder hypophosphatemia. Despite the hypophosphatemia, double-mutant mice attempted to reduce serum phosphate back to the level of Phex mutant mice by upregulating Fgf23 expression as much as 24-fold higher than Phex mutant mice. These data suggest that Phex mutations alter the responsiveness of bone cells to extracellular phosphate concentrations and may create a lower set point for "normal" phosphate levels.
Immunoglobulin Concentrations in Duodenal Fluid of Infants and Children (1980)

The immunoglobulin content of duodenal fluid in children at different ages has not as yet been determined, while that of serum, feces, and saliva has been well established. In 92 normal infants, children, and young adults on whom duodenal intubation was performed, duodenal fluid IgA, IgM, and IgG levels were measured. From these data, a developmental profile of immunoglobulins in duodenal fluid from 2 weeks of life to 19 years was obtained. Duodenal fluid IgA, IgM, and IgG appeared to maintain rather constant levels. The grand mean IgA level was lower than the mean IgG level (12.7 +/- 0.8 vs 29.1 +/- 2.5 mg/g of protein). Secretory component was detected in all duodenal fluids. IgG concentrations were greater than those of IgM (29.1 +/- 2.5 vs 13.2 +/- 1.4 mg/g of protein) over all age ranges. The developmental patterns of all immunoglobulins appeared to be different from those observed in serum or saliva with the exception of duodenal fluid IgA, which has a pattern similar to that of salivary IgA.
HIV neutralizing IgA in exposed seronegative subjects recognise an epitope within the gp41 coiled-coil pocket. (2000)

Human immunodeficiency virus (HIV)-specific IgA can be detected in cervical secretions, saliva, and sera of HIV-infected and HIV-uninfected individuals with a known exposure to the virus. IgA from HIV-uninfected exposed seronegative individuals (ESN) neutralize in vitro primary strains of HIV-1. We analyzed the epitopes of HIV recognized by serum HIV-specific IgA of ESN individuals to identify the antigenic correlates of HIV neutralization in exposed-uninfected subjects, and to verify whether different epitopes would be recognized by HIV-specific IgA of ESN and of HIV-infected patients. Results confirmed that HIV-neutralizing IgA are detected in sera of ESN and showed that neutralization of primary HIV strains is mediated by the recognition of different epitopes in HIV-infected patients and ESN. Thus, whereas IgA of HIV+ individuals recognize epitopes expressed both within gp120 and gp41, IgA of ESN exclusively bind to gp41-expressed epitopes. Epitope mapping revealed that the epitope recognized by serum IgA of ESN on gp41 is restricted to aa 581-584 (LQAR) and corresponds to coiled coil pocket in the alpha helic region. In contrast, the epitope seen by IgA of HIV-infected patients on gp41 is identified by two regions; the first is contained within the cystein loop (aa 589-618), the second correspond to C terminal region in the extra membrane region of gp 41 (aa 642-673). Thus, we have identified and characterized the epitopes that mediate neutralization of HIV in individuals in whom infection does not occur despite multiple exposures to the virus. These results have important implications for the development of a new therapy against HIV infection.
Automatic page turner machine for high-speed book digitization (2013)

In recent years, there has been an increasing demand to digitize a huge number of books. A promising new approach for meeting this demand, called Book Flipping Scanning, has been proposed. This is a new style of scanning in which all pages of a book are captured while a user continuously flips through the pages without stopping at each page. Although this new technology has had a tremendous impact in the field of book digitization, page turning is still done manually, which acts as a bottleneck in the development of high-speed book digitization. Against this background, this paper proposes a newly designed high-speed, high-precision book page turner machine. Our machine turns the pages in a contactless manner by utilizing the elastic force of the paper and an air blast. This design enables high-speed performance that is ten times faster than conventional approaches and, in addition, causes no obstruction in the digitization process. This paper reports the evaluation of the proposed machine using various types of paper with different qualities. Our machine achieved almost 100% success rate when turning pages at around 300 pages/min, showing that it is a promising technology for turning pages at high-speed and with high precision.
Neospora caninum Calcium-Dependent Protein Kinase 1 Is an Effective Drug Target for Neosporosis Therapy (2014)

Despite the enormous economic importance of Neospora caninum related veterinary diseases, the number of effective therapeutic agents is relatively small. Development of new therapeutic strategies to combat the economic impact of neosporosis remains an important scientific endeavor. This study demonstrates molecular, structural and phenotypic evidence that N. caninum calcium-dependent protein kinase 1 (NcCDPK1) is a promising molecular target for neosporosis drug development. Recombinant NcCDPK1 was expressed, purified and screened against a select group of bumped kinase inhibitors (BKIs) previously shown to have low IC50s against Toxoplasma gondii CDPK1 and T. gondii tachyzoites. NcCDPK1 was inhibited by low concentrations of BKIs. The three-dimensional structure of NcCDPK1 in complex with BKIs was studied crystallographically. The BKI-NcCDPK1 structures demonstrated the structural basis for potency and selectivity. Calcium-dependent conformational changes in solution as characterized by small-angle X-ray scattering are consistent with previous structures in low Calcium-state but different in the Calcium-bound active state than predicted by X-ray crystallography. BKIs effectively inhibited N. caninum tachyzoite proliferation in vitro. Electron microscopic analysis of N. caninum cells revealed ultra-structural changes in the presence of BKI compound 1294. BKI compound 1294 interfered with an early step in Neospora tachyzoite host cell invasion and egress. Prolonged incubation in the presence of 1294 interfered produced observable interference with viability and replication. Oral dosing of BKI compound 1294 at 50 mg/kg for 5 days in established murine neosporosis resulted in a 10-fold reduced cerebral parasite burden compared to untreated control. Further experiments are needed to determine the PK, optimal dosage, and duration for effective treatment in cattle and dogs, but these data demonstrate proof-of-concept for BKIs, and 1294 specifically, for therapy of bovine and canine neosporosis.
Soil carbon measurements using inelastic neutron scattering (2000)

Soil carbon sequestration is a whole new area of energy related research that provides a fundamentally new approach for dealing with climate change resulting from the substantial increase in CO/sub 2/ concentration in the atmosphere. Carbon sequestration in soil is recognized to play a major role in allowing fossil fuels to remain a vital component of the national energy mix. At present soil carbon is measured by taking core samples and involves extensive laboratory work. We propose a novel nondestructive in situ method for carbon analysis using the Inelastic Neutron Scattering (INS) (n,n'/spl gamma/) reaction. The feasibility of detecting carbon in soil was demonstrated using a clinical in vivo body composition facility, located in the Medical Department at BNL. A D-T generator, operated at 55 kV, irradiated 12"/spl times/12"/spl times/14" aluminum boxes filled with 70 lb. Clean sand and mixtures of sand with 2%, 5% and 10% carbon powder by weight. The spectra were acquired for 1 hr and subsequently the carbon peaks were analyzed using the trapezoidal method for peak extraction. The results demonstrate that the proposed method is suitable for carbon analysis in soil, and it should allow sequential sampling of soil carbon within a soil volume of about 0.5 m/sup 3/ with an error of about 1% or less. It is expected that, with final optimization, changes of about 1% in the soil carbon content would be observable with sufficient confidence levels.
Data Personalization: a Taxonomy of User Profiles Knowledge and a Profile Management Tool (2008)

ABSTRACT. The goal of data personalization is to facilitate the expression of the need of a particular user and to enable him to obtain relevant information when he accesses an information system. The relevance of the information is defined by a set of criteria and preferences specific to each user or community of users. The data describing the users &apos; interests and preferences is often gathered in the form of profiles. The content of a profile varies according to the target application and to its context (databases, information retrieval, digital libraries, multimedia applications). This paper elaborates a taxonomy of the most important knowledge composing a profile and proposes a generic model that can be instantiated and adapted for each specific application. The model is supported by a profile management tool (PMT) which also allows matching of profiles, aggregation of profiles and knowledge derivation from profiles. The last section of the paper lists some research challenges related to data personalization as identified in the APMD project initiated within the French Research Program on Data Masses 1. 1.
Characterization of a Novel Fucose-Regulated Promoter (P<sub><i>fcsK</i></sub>) Suitable for Gene Essentiality and Antibacterial Mode-of-Action Studies in<i>Streptococcus pneumoniae</i> (2003)

The promoter of the Streptococcus pneumoniae putative fuculose kinase gene (fcsK), the first gene of a novel fucose utilization operon, is induced by fucose and repressed by glucose or sucrose. When the streptococcal polypeptide deformylase (PDF) gene (def1, encoding PDF) was placed under the control of P(fcsK), fucose-dependent growth of the S. pneumoniae (P(fcsK)::def1) strain was observed, confirming the essential nature of PDF in this organism. The mode of antibacterial action of actinonin, a known PDF inhibitor, was also confirmed with this strain. The endogenous fuculose kinase promoter is a tightly regulated, titratable promoter which will be useful for target validation and for confirmation of the mode of action of novel antibacterial drugs in S. pneumoniae.
LARGE-SCALE MANUFACTURING OF ALL FOUR 2′-DEOXYNUCLEOSIDES VIA NOVEL STRATEGIES INCLUDING A CHEMO-ENZYMATIC PROCESS (2001)

A chemical synthesis of 2-deoxyribose-1-phosphate 2 and its enzymatic conversion into purine 2'-deoxynucleosides (dNus) are shown. Besides the chemo-enzymatic process for purine dNus, a modified process for practical dC preparation is also established. Consequently, a series of practical manufacturing processes of all four dNus have been realized via novel strategies.
Tensile Property Improvements of Spinodal Cu-15Ni-8Sn by Two-Phase Heat Treatment (1982)

A heat treatment has been developed which produces significant improvements in the tensile properties of Cu-15Ni-8Sn spinodal alloy. The treatment involves solution heat treatment in the two-phase region rather than the single-phase region normally used. After quenching and aging, increased strength and ductility of the alloy over single phase solution heat-treated and aged values were found. The mechanical properties obtained were superior to any previously observed for material of the compositions studied in the solution treated, quenched, and aged condition. Also, the alloys’ transformation kinetics were greatly slowed by the two phase heat-treatment. It is suggested that the increase in strength and slow kinetics of transformation observed are caused by grain size effects and by grain boundary modifications. Resistivity data and etching response corroborate these arguments.
Realization of multirate digital filters with powers‐of‐two coefficients (1992)

Abstract With a view to reducing the amount of hardware in the lowpass filter (LPF), bandpass filter (BPF), and band‐elimination filter (BEF) processing important in digital signal processing, this paper presents a method for configuration of the multirate digital filters with powers‐of‐two coefficients only. The proposed filters are constructed with the sampling rate increaser, the reference LPF and the sampling rate decreaser. The reference LPF consists of the stopband‐forming filter and the pass‐band compensating filter. The stopband‐forming filter consists of a cascade of RRSs while the linear phase FIR or IIR configuration is used for the passband‐compensating filter. First, a method of configuration is presented for the reference LPF based on the sampling rate increaser with powers‐of‐two coefficients. Next, it is shown that the multirate LPF, HPF (high‐pass filter), BPF and BEF with an arbitrary cutoff frequency can be constructed easily from the reference LPF. The present method is particularly effective for narrowband LPF and HPF. Since no multiplier is used, they have zero coefficient sensitivity. It is shown by means of a design example that the present method is effective in reducing the amount of hardware.
The determination of traces of beryllium in human and rat urine samples by gas chromatography (1970)

The toxic nature of beryllium necessitates the use of a sensitive method for its detection. Present methods are not entirely satisfactory and the use of gas chromatography for the detection and determination of beryllium has been advocated. In the procedure described, beryllium is isolated by solvent extraction in the form of a volatile, thermally stable chelate with trifluoroacetylacetone, and is then determined by gas chromatography with an electron-capture detector. Results are presented for the determination of aqueous beryllium solutions and for beryllium contained in urine. Satisfactory results were obtained with both direct solvent extraction and solvent extraction after wet oxidation of the sample. The rate of excretion of beryllium by rats was measured by this method. The procedure is rapid, reliable and sensitive; the limit of detection is l ng ml–1.
Fault tolerant three-phase AC motor drive topologies; a comparison of features, cost, and limitations (2003)

This paper compares the many fault tolerant three-phase AC motor drive topologies that have been proposed to provide output capacity for the inverter faults of switch short or open-circuits, phase-leg short-circuits, and single-phase open-circuits. Also included is a review of the respective control methods for fault tolerant inverters including two-phase and unipolar control methods. The output voltage and current space in terms of dq components is identified for each topology and fault. These quantities are then used to normalize the power capacity of each system during a fault to a standard inverter during normal operation. A silicon overrating cost factor is adopted as a metric to compare the relative switching device costs of the topologies compared to a standard three-phase inverter.
HAMR Media Design in Optical and Thermal Aspects (2013)

In a heat-assisted magnetic recording (HAMR) system, the thermal performances of recording medium are very critical for recording density because the track density and bit density are dominated by thermal spot size in the cross-track direction and temperature gradient in the down-track direction. The optical intensity and its distribution generated by the near field optical transducer serve as a heat source to heat the medium. Therefore, the medium optical response to the transducer is also very important for the medium's thermal response. In this paper, based on the structure required by the magnetic performance, the effects of the medium structures on its optical and thermal performances are studied. The results show that a thinner interlayer (MgO layer) is beneficial to the medium's performance. However, the seed layer (NiTa layer) deteriorates the performance seriously. Small in-plane thermal conductivity (good isolation) of the granular recording layer is also very important for the thermal performance of the medium. However, the out-plane thermal conductivity is not very critical in certain ranges.