gebhart/patrepeval huggingface dataset:
Role of zinc-binding- and hemopexin domain-encoded sequences in the substrate specificity of collagenase and stromelysin-2 as revealed by chimeric proteins. (1993)

The relationship of enzyme structure to substrate specificity for the matrix metalloproteinases interstitial collagenase and stromelysin-2 has been investigated by analysis of the cleavage specificity of recombinant human collagenase-stromelysin-2 hybrid proteins and C terminally truncated collagenase and stromelysin-2. Two series of chimeric proteins were devised by progressive substitution of exon-encoded domains. The recombinant proteins were expressed in COS-7 cells as protein A-fusion proteins and purified on an IgG affinity matrix. Treatment with 4-amino-phenylmercuric acetate released active metalloproteinase of the sizes predicted for the chimeric proteins. Active forms of both the chimeric protein series and the short form enzymes expressed both casein- and gelatin-degrading activities. Like stromelysin, the catalytic activity of stromelysin-2 was contained in the N-terminal domain (encoded by exons 1-5) and was apparently independent of the C-terminal domain (encoded by exons 6-10). Only full-length collagenase displayed a triple helicase (collagenolytic) activity; no combination of N- or C-terminal collagenase domains fused with stromelysin-2 domains had such activity. This suggests that the triple helicase activity is a composite of elements derived from both halves of the collagenase molecule. C terminally truncated collagenase (exons 1-5) and a hybrid of collagenase exons 1-5 and stromelysin-2 exons 6-10 cleaved denatured type I collagen (gelatin) to generate diagnostic peptides in gelatin fingerprint assays. When exon 5 (the exon encoding the zinc-binding domain) was derived from stromelysin-2, the enzyme specificity in the fingerprint assay changed to that of native stromelysin-2. In contrast, when exon 5 was derived from collagenase, the specificity reflected that of the parent enzyme. Our data also suggest that mismatching of exons 2 and 5 destabilizes the enzyme, presumably by altering the geometry of the propeptide-zinc-binding site interaction. We conclude that the loss of triple helicase collagenolytic activity is not accompanied by a shift to the broad specificity characteristic of stromelysin. Rather, the zinc-binding domain confers a distinct cleavage specificity on each metalloproteinase.
Imaging of Ultra-Weak Photon Emission in a Rheumatoid Arthritis Mouse Model (2013)

Ultra-weak photon emission (UPE) of a living system received scientific attention because of its potential for monitoring increased levels of reactive oxygen species (ROS) in the pathogenesis of rheumatoid arthritis (RA). In this study, a highly sensitive cryogenic charge-coupled device (CCD) camera was used to monitor in a RA mouse model the photon emission both without and with luminol. For that purpose, arthritis was induced in mice utilizing a repeated co-administration of type II collagen with lipopolysaccharide. Quantitative imaging of ultra-weak photon emission of the front and back paws of the animals was initiated 70 days after the first injection. All of the animals were measured once without luminol and once again immediately after luminol injection. Data illustrated a higher UPE intensity after initiating arthritis by CII-injection of the animals. The increase in UPE intensity was measured with and without using luminol indicating that this imaging technology may be useful for the future study of human RA.
Construction and Characterization of a <i>recA</i> Mutant of <i>Thiobacillus ferrooxidans</i> by Marker Exchange Mutagenesis (2000)

To construct Thiobacillus ferrooxidans mutants by marker exchange mutagenesis, a genetic transfer system is required. The transfer of broad-host-range plasmids belonging to the incompatibility groups IncQ (pKT240 and pJRD215), IncP (pJB3Km1), and IncW (pUFR034) from Escherichia coli to two private T. ferrooxidans strains (BRGM1 and Tf-49) and to two collection strains (ATCC 33020 and ATCC 19859) by conjugation was analyzed. To knock out the T. ferrooxidans recA gene, a mobilizable suicide plasmid carrying the ATCC 33020 recA gene disrupted by a kanamycin resistance gene was transferred from E. coli to T. ferrooxidans ATCC 33020 by conjugation under the best conditions determined. The two kanamycin-resistant clones, which have retained the kanamycin-resistant phenotype after growth for several generations in nonselective medium, were shown to have the kanamycin resistance gene inserted within the recA gene, indicating that the recA::Omega-Km mutated allele was transferred from the suicide plasmid to the chromosome by homologous recombination. These mutants exhibited a slightly reduced growth rate and an increased sensitivity to UV and gamma irradiation compared to the wild-type strain. However, the T. ferrooxidans recA mutants are less sensitive to these physical DNA-damaging agents than the recA mutants described in other bacterial species, suggesting that RecA plays a minor role in DNA repair in T. ferrooxidans.
Recurrent urinary tract infections in women: diagnosis and management. (2010)

Recurrent urinary tract infections, presenting as dysuria or irritative voiding symptoms, are most commonly caused by reinfection with the original bacterial isolate in young, otherwise healthy women with no anatomic or functional abnormalities of the urinary tract. Frequency of sexual intercourse is the strongest predictor of recurrent urinary tract infections in patients presenting with recurrent dysuria. In those who have comorbid conditions or other predisposing factors, recurrent complicated urinary tract infections represent a risk for ascending infection or urosepsis. Escherichia coli is the most common organism in all patient groups, but Klebsiella, Pseudomonas, Proteus, and other organisms are more common in patients with certain risk factors for complicated urinary tract infections. A positive urine culture with greater than 102 colony-forming units per mL is the standard for diagnosing urinary tract infections in symptomatic patients, although culture is often unnecessary for diagnosing typical symptomatic infection. Women with recurrent symptomatic urinary tract infections can be treated with continuous or postcoital prophylactic antibiotics; other treatment options include self-started antibiotics, cranberry products, and behavioral modification. Patients at risk of complicated urinary tract infections are best managed with broad-spectrum antibiotics initially, urine culture to guide subsequent therapy, and renal imaging studies if structural abnormalities are suspected.
Fast Camera Calibration for the Analysis of Sport Sequences (2005)

Semantic analysis of sport sequences requires camera calibration to obtain player and ball positions in real-world coordinates. For court sports like tennis, the marker lines on the field can be used to determine the calibration parameters. We propose a real-time calibration algorithm that can be applied to all court sports simply by exchanging the court model. The algorithm is based on (1) a specialized court-line detector, (2) a RANSAC-based line parameter estimation, (3) a combinatorial optimization step to localize the court within the set of detected line segments, and (4) an iterative court-model tracking step. Our results show real-time calibration of, e.g., tennis and soccer sequences with a computation time of only about 6 ms per frame.
Distributed paging and registration in wireless networks (2005)

The success of current and future wireless networks depends on their ability to provide connections to mobile terminals anywhere and at any time. It is therefore of crucial importance that wireless networks are able to quickly and efficiently locate mobile users at the time of an incoming call, which is achieved in current networks through a combination of paging and registration. In this article we present novel distributed paging and registration procedures that are naturally suited to future distributed wireless network architectures. In addition, the distributed nature of these strategies allows us to effectively balance the paging and registration traffic and the required signal processing throughout the network and alleviate any potential overloads of individual base stations.
Recalage elastique d'images angiographiques (1987)

Une methode automatique est proposee pour la mise en correspondance d'images peu structurees. Destinee au recalage d'images angiographiques, elle est tolerantre a de fortes dissimilarites locales, liees a la presence de produit radioopaque. Elle permet une estimation precise des deplacements locaux autorisant une correction par un modele elastique
Understanding Latency Variation in Modern DRAM Chips (2016)

Long DRAM latency is a critical performance bottleneck in current systems. DRAM access latency is defined by three fundamental operations that take place within the DRAM cell array: (i) activation of a memory row, which opens the row to perform accesses; (ii) precharge, which prepares the cell array for the next memory access; and (iii) restoration of the row, which restores the values of cells in the row that were destroyed due to activation. There is significant latency variation for each of these operations across the cells of a single DRAM chip due to irregularity in the manufacturing process. As a result, some cells are inherently faster to access, while others are inherently slower. Unfortunately, existing systems do not exploit this variation. The goal of this work is to (i) experimentally characterize and understand the latency variation across cells within a DRAM chip for these three fundamental DRAM operations, and (ii) develop new mechanisms that exploit our understanding of the latency variation to reliably improve performance. To this end, we comprehensively characterize 240 DRAM chips from three major vendors, and make several new observations about latency variation within DRAM. We find that (i) there is large latency variation across the cells for each of the three operations; (ii) variation characteristics exhibit significant spatial locality: slower cells are clustered in certain regions of a DRAM chip; and (iii) the three fundamental operations exhibit different reliability characteristics when the latency of each operation is reduced. Based on our observations, we propose Flexible-LatencY DRAM (FLY-DRAM), a mechanism that exploits latency variation across DRAM cells within a DRAM chip to improve system performance. The key idea of FLY-DRAM is to exploit the spatial locality of slower cells within DRAM, and access the faster DRAM regions with reduced latencies for the fundamental operations. Our evaluations show that FLY-DRAM improves the performance of a wide range of applications by 13.3%, 17.6%, and 19.5%, on average, for each of the three different vendors' real DRAM chips, in a simulated 8-core system. We conclude that the experimental characterization and analysis of latency variation within modern DRAM, provided by this work, can lead to new techniques that improve DRAM and system performance.
How Much Can Colorless, Directionless and Contentionless (CDC) of ROADM Help Dynamic Lightpath Provisioning? (2012)

We evaluate the impact of the colorless, directionless, and contentionless features of ROADM on dynamic lightpath service provisioning. It is found that colorless plays the most significant role in improving lightpath blocking performance.
The Basics of Triangulation Sensors (1998)

riangulation sensors fall into the general category of noncontact height or range measurement devices. A triangulation sensor may provide the same information as a linear variable differential transformer or contact probe, but without touching the object to be measured. The sensors work by projecting a beam of light onto the object of interest and calculating the distance from a reference point by determining where the reflected light falls on a detector (see Figure 1). As the point of light falling on the object moves closer to or farther from the reference point, the spot position on the detector changes. Sensor Types Triangulation sensors are either diffuse or specular. The need for two types of sensors arises from differing reflectance characteristics of materials
Anaerobic Biological Treatment Processes (1971)

The anaerobic biological processes that produce methane are reviewed. The organisms catalyzing these reactions are a morphologically diverse collection of obligate anaerobes. Commensal and symbiotic with other anaerobes, they reduce or dismutate H2, formate, acetate, methanol, and other fermentation products to CO2 and methane, completing the anaerobic cycle. Five species have been isolated and characterized so far. Methane is generated mainly either from CO2 or from substrate methyl groups, probably via methyl vitamin B12 derivatives.
Deadline-aware bandwidth sharing by allocating switch buffer in data center networks (2016)

Most of today's data center applications are sensitive to latency. In this paper, a Deadline-aware bandwidth Sharing mechanism by Allocating switch Buffer (DSAB) is proposed to satisfy the deadline requirements of flows. As the existing work SAB does, DSAB also leverages the feature that the buffer size of a switch port is usually much larger than the product of bandwidth and round trip delay in data center networks. The basic idea of DSAB is to allocate switch buffer to deadline-sensitive flows in priority and the remaining buffer is fairly allocated to background flows. However, this method will possibly lead to bandwidth wastage in topologies with multiple bottlenecks. Therefore, enlightened by the pre-authorization method in credit card systems, we propose a Pre-Authorization (PA) algorithm to address this problem. The PA algorithm allows switches take back the extra allocated bandwidth by adding a bandwidth confirmation phase after the bandwidth request phase. End hosts and switch functions of DSAB is implemented in Linux kernel and NetFPGA platform, respectively. The results of experiments conducted in a real small testbed indicate that DSAB can indeed satisfy the deadline requirements of deadline-sensitive flows by allocating switch buffer to them in priority.
Development of the Internet of Things in China (2011)

Along with address of the conception of Smarter Planet,the development of the Internet of Things(IOT) has attracted highly attention of academia,industry,and news media.There are still many open issues in the definition,internal principles,architectures and system models of IOT.This paper concluded some concepts in the Internet of Things and analyzed the key factors which confined the development of the Internet of Things.Then the author gave the solutions of these issues and explored the future of the Internet of Things in China.
<i>In planta</i>imaging of Δ9-tetrahydrocannabinolic acid in<i>Cannabis sativa L.</i>with hyperspectral coherent anti-Stokes Raman scattering microscopy (2013)

Nature has developed many pathways to produce medicinal products of extraordinary potency and specificity with significantly higher efficiencies than current synthetic methods can achieve. Identification of these mechanisms and their precise locations within plants could substantially increase the yield of a number of natural pharmaceutics. We report label-free imaging of Δ⁹-tetrahydrocannabinolic acid (THCa) in Cannabis sativa L. using coherent anti-Stokes Raman scattering microscopy. In line with previous observations we find high concentrations of THCa in pistillate flowering bodies and relatively low amounts within flowering bracts. Surprisingly, we find differences in the local morphologies of the THCa-containing bodies: organelles within bracts are large, diffuse, and spheroidal, whereas in pistillate flowers they are generally compact, dense, and have heterogeneous structures. We have also identified two distinct vibrational signatures associated with THCa, both in pure crystalline form and within Cannabis plants; at present the exact natures of these spectra remain an open question.
Characterization of fretting fatigue in self‐piercing riveted aluminium alloy sheets (2006)

ABSTRACT A study was conducted to characterize fretting fatigue in self‐piercing riveted single‐lap joints of aluminium alloy 5754 sheets. The experimental results showed that fretting occurred at three different positions in the joint. It was established that fretting led to surface work‐hardening and crack initiation as well as early stage crack propagation. Crack initiated at the surface of the riveted sheets as a result of high stress concentration and propagated oblique to the mating surface under the effect of fretting fatigue. The depth of damage due to fretting depended on the applied load and the cycle time. Microhardness measurements allowed the estimation of the depth of damage due to fretting. These results were observed to correlate well with the length of crack propagation.
Targeting the Replication of Adenoviral Gene Therapy Vectors to Lung Cancer Cells: The Importance of the Adenoviral E1b-55kD Gene (1999)

It has been proposed that an adenovirus with the E1b-55kD gene deleted has a selective advantage in replicating in cancer cells that have mutations in the p53 gene (Bischoff et al., 1996). We have explored this hypothesis in several lung cancer cell lines, and evaluated potential mechanisms that might regulate the replication of Ad338, an E1b-55kD-deleted virus, with the objective of developing a rational approach for targeting gene therapy to lung tumors. Our data show that Ad338 replicates poorly in three lung cancer cell lines with various p53 mutations (H441, H446, and Calu1), yet this virus replicates to a high level in a lung cancer cell line with wild-type p53 (A549) and in a normal lung fibroblast line (IMR90). Viral DNA replication, expression of viral proteins, and shutoff of host cell proteins were not important variables in limiting the replication of the E1b-55kD-deleted virus. However, the cell lines resistant to host cell protein shutoff were also the most resistant to the cytopathic effect induced by mutant and wild-type virus and the only cells to survive for 8 days following infection. The E1b-55kD protein clearly has an important role in viral replication beyond its interaction with p53. Thus, an E1b-55kD-deleted virus cannot be used to specifically target viral replication to p53-mutated lung cancer cells.
The toxicity of cochliodinol, an antibiotic metabolite of <i>Chaetomium</i> spp. (1970)

Cochliodinol is a phenol of unknown structure and a metabolite of Chaetomium cochliodes and C. globosum. It inhibited the growth of some species of several genera of microfungi at concentrations of 1–10 μg/ml. The germination of spores of Botrytis allii and Fusarium moniliforme was also inhibited, at similar concentrations. Cochliodinol forms stable, insoluble salts with strong bases but the triethanolamine salt is appreciably soluble in water. Solutions of this salt inhibit the growth of many species of bacteria. The growth of several strains of Pseudomonas aeruginosa isolated from the local general hospital was inhibited at 30 μg/ml. Cytopathological effects were not observed in cultures of HeLa cells at 5 μg/ml and preliminary toxicity tests in young turkeys and rats did not reveal symptoms of acute toxicity.
Raman amplifier-based long-distance remote, strain and temperature sensing system using an erbium-doped fiber and a fiber Bragg grating (2004)

We demonstrate a novel, Raman amplifier-based long-distance sensing system for simultaneous measurement of temperature and strain using a combined sensing probe of an erbium-doped fiber (EDF) and a fiber Bragg grating. By recycling residual Raman pump power for generation of amplified spontaneous emission in the EDF after distributed Raman amplification in the transmission fiber, the overall system configuration was significantly simplified without requiring any additional broadband light source. We obtain a remote sensing operation of simultaneous temperature and strain measurement at a location of 50 km. High quality of sensing signals with a ~ 11 dB signal-to-noise ratio (SNR) is readily achieved even after the 50 km transmission with distributed Raman amplification.
The effect of detector performance on high count rate PET imaging with a tomograph based on position-sensitive detectors (1988)

Emission-computed tomography systems using large position-sensitive detectors must handle high event rates per detector during dynamic studies. To determine the ability of their positron-emission tomograph (PET) to perform high-count-rate scans, the authors have studied detector performance up to single rates in excess of 2 million counts per second per detector. To evaluate the quality of images resulting from data acquired at these rates, signal-to-noise ratio analyses were applied to both simulated and experimental high-count-rate images of a cold-spot phantom. Changes in image quality were quantitated, allowing the testing of combinations of high-count-rate event processing techniques to produce optimal high-count-rate images. It was found that severe image degradation occurs when the centroid positioning algorithm is used, due to the long tails in the detector point speed function that result at high count rates. Image quality is greatly improved when the local centroid event-positioning algorithm is used to eliminate the tails. Further improvements are possible with shorter integration time and an upper-level energy discriminator set at 600 keV, close to the photopeak.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Low-Dose Chlorambucil in the Treatment of Generalized Granuloma annulare (1979)

5 of 6 adults with generalized granuloma annulare responded favorably to therapy with low-dose chlorambucil. 5 of the patients had lesions that were recurrent and long-standing and that resisted conventional modalities of therapy. Low-dose chlorambucil may be effective in a short-term therapy program but should be used only in patients with persistent, widespread, or unusual forms of generalized granuloma annulare. The program requires close patient and hematologic supervision.
A Hybrid Silk/RADA-Based Fibrous Scaffold with Triple Hierarchy for Ligament Regeneration (2012)

While silk-based microfibrous scaffolds possess excellent mechanical properties and have been used for ligament tissue-engineering applications, the microenvironment in these scaffolds is not biomimetic. We hypothesized that coating a hybrid silk scaffold with an extracellular matrix (ECM)-like network of self-assembling peptide nanofibers would provide a biomimetic three-dimensional nanofibrous microenvironment and enhance ligament tissue regeneration after bone marrow-derived mesenchymal stem cell (BMSC)-seeding. A novel scaffold possessing a triple structural hierarchy comprising macrofibrous knitted silk fibers, a silk microsponge, and a peptide nanofiber mesh was developed by coating self-assembled RADA16 peptide nanofibers on a silk microfiber-reinforced-sponge scaffold. Compared with the uncoated control, RADA-coated scaffolds showed enhanced BMSC proliferation, metabolism, and fibroblastic differentiation during the 3 weeks of culture. BMSC-seeded RADA-coated scaffolds showed an increasing temporal expression of key fibroblastic ECM proteins (collagen type I and III, tenascin-C), with a significantly higher tenascin-C expression compared with the controls. BMSC-seeded RADA-coated scaffolds also showed a temporal increase in total collagen and glycosaminoglycan production (the amount produced being higher than in control scaffolds) during 3 weeks of culture, and possessed 7% higher maximum tensile load compared with the BMSC-seeded control scaffolds. The results indicate that the BMSC-seeded RADA-coated hybrid silk scaffold system has the potential for use in ligament tissue-engineering applications.