gebhart/patrepeval huggingface dataset:
Regulatory region of the gene for the ompA protein, a major outer membrane protein of <i>Escherichia coli</i> (1980)

The ompA protein, an outer membrane protein required for conjugation, is one of the most abundant proteins in Escherichia coli. The structural gene for the ompA protein cloned in a plasmid vector, pMF21, conferred sensitivity to ompA protein-specific phages. We have determined the DNA sequence of a fragment of 533 base pairs encompassing the regulatory region of the ompA gene: the promoter region, the 5'-untranslated region, and the region corresponding to the signal peptide for this secretory protein. The promoter region has a sequence that is remarkably homologous with the lac and gal promoters. Particularly, both the ompA and gal promoters have the same octanucleotide sequence, T-C-A-C-A-C-T-T, in their RNA polymerase recognition site, which has been shown to be involved in the binding of cyclic AMP receptor protein to the gal promoter. Analogous with the observations in the gal operon, a specific RNA transcript was produced only when glycerol, a DNA-destabilizing agent, was added to a cell-free system directed by a DNA fragment of the ompA gene. These data indicate that the ompA mRNA has an untranslated region at the 5' end of about 140 nucleotides. In this region there are two additional initiation codons (II and III) besides the initiation codon (I) for the pro-ompA protein. AUG-III is located 30 bases upstream from AUG-I and accompanies a ribosome-binding site. Therefore, AUG-III is likely to begin the synthesis of a pentapeptide. The termination codon for the peptide overlaps with AUG-II, so that the ribosomes could reinitiate from AUG-II without being released from the mRNA. This reinitiation leads to the synthesis of a heptapeptide. The termination codon for this peptide also overlaps with AUG-I, which initiates the production of the pro-ompA protein. Because AUG-I also has an adjacent ribosome-binding site, the tandem repeat of initiation codons and ribosome-binding sites may be an important mechanism for facilitating the rate of initiation of translation. Extensive secondary structures exist in the 5' end as well as in the coding region of the ompA mRNA, which may also play a role in the function of the mRNA.
DRP: An Efficient Directional Routing Protocol for Mobile Ad Hoc Networks (2006)

This paper addresses the issue of routing in mobile ad hoc networks (MANETs) using directional antennas. Existing directional routing schemes either assume a complete network topology beforehand or simply use omni-directional routing schemes to forward packets in underlying directional environment. In this paper, we propose a Directional Routing Protocol (DRP) for MANETs. DRP is an on-demand directional routing protocol which assumes a cross layer interaction between routing and MAC layer and is inspired by Dynamic Source Routing (DSR) protocol. The main features of DRP include an efficient route discovery mechanism, establishment and maintenance of directional routing and directional neighbor tables (DRT and DNT, respectively), and novel directional route recovery mechanisms. We have implemented DRP on top of MDA; a MAC protocol for directional antennas and have compared its performance with the DSR protocol over both omni-directional and directional antenna models. Our results show that DRP considerably improves the packet delivery ratio, decreases the end to end packet latency, has lesser routing overhead, and is robust to link failures.
Controlled slew rate output buffer (2003)

A controlled-slew-rate output buffer has been designed that controls transition edges of an output signal. Thus, AC transients at switching times can be substantially reduced. This eventually reduces switching noise. The theoretical simulations and experimental verifications of this output buffer are presented. A comparison in terms of noise reduction and speed tradeoffs between a controlled and a conventional noncontrolled-slew-rate output buffer is outlined. A test circuit was developed in a 1.25- mu m 10 K gate array double-metal CMOS process. The test chip evaluation shows that the magnitude of output ringing in both transition edges is reduced on the controlled slew rate output buffer. The cost of reducing switching noise is sacrificing some speed performance. A TTL input level test shows controlled slew rate output buffers coupled less switching noise to the power buses than the noncontrolled version.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Poor predictive value of broad-range PCR for the detection of arthroplasty infection in 92 cases (2005)

The PCR technique cannot be recommended for the routine detection of prosthetic infection. The large number of false positive results may represent sample contamination, or bacterial presence related to low-virulence organisms, low bacterial load, or a strong host immune response.
Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva (2016)

Exosomes are small extracellular vesicles containing microRNAs and mRNAs that are produced by various types of cells. We previously used ultrafiltration and size-exclusion chromatography to isolate two types of human salivary exosomes (exosomes I, II) that are different in size and proteomes. We showed that salivary exosomes contain large repertoires of small RNAs. However, precise information regarding long RNAs in salivary exosomes has not been fully determined. In this study, we investigated the compositions of protein-coding RNAs (pcRNAs) and long non-protein-coding RNAs (lncRNAs) of exosome I, exosome II and whole saliva (WS) by next-generation sequencing technology. Although 11% of all RNAs were commonly detected among the three samples, the compositions of reads mapping to known RNAs were similar. The most abundant pcRNA is ribosomal RNA protein, and pcRNAs of some salivary proteins such as S100 calcium-binding protein A8 (protein S100-A8) were present in salivary exosomes. Interestingly, lncRNAs of pseudogenes (presumably, processed pseudogenes) were abundant in exosome I, exosome II and WS. Translationally controlled tumor protein gene, which plays an important role in cell proliferation, cell death and immune responses, was highly expressed as pcRNA and pseudogenes in salivary exosomes. Our results show that salivary exosomes contain various types of RNAs such as pseudogenes and small RNAs, and may mediate intercellular communication by transferring these RNAs to target cells as gene expression regulators.
Use of non-radioactive probes for mRNA detection by in situ hybridization: interests and applications in the central nervous system. (1995)

Non-radioactive probes for in situ hybridization (ISH) are now widely used to detect mRNAs in the central nervous system (CNS) using light and electron microscopy. Many different protocols for the detection of biotinylated or digoxigenin-labelled probes are now available. The advantages and inconveniences of the use of the non-radioactive probes are reviewed in the current work. These aspects are illustrated by some results from first-hand experience in the field of ISH to analyse gene expression and neuronal phenotypes in the hypothalamus and the basal ganglia. A very sensitive procedure for the simultaneous detection of two mRNAs with cRNA probes have been detailed and using in particular digoxigenin-labelled probes.
Effect of radiation and tirapazamine (SR-4233) on three melanoma cell lines (1998)

In this study the response of three melanoma cell lines to single doses of radiation, to the bioreductive drug tirapazamine (SR-4233) and to the combination of radiation and tirapazamine was determined. Tirapazamine is a bioreductive drug with specific cytotoxicity in hypoxic conditions. Three melanoma cell lines (MM576, MM96L and murine B16-F10) were exposed to increasing concentrations of tirapazamine to assess cytotoxicity under aerobic and hypoxic conditions. Also, clonogenic survival after single doses of 4 MV X-rays was determined under aerobic and hypoxic conditions, with and without 20 microM tirapazamine. Tirapazamine was an effective hypoxic cytotoxin in the three cell lines. The concentrations of tirapazamine causing equal cell kill were 1000 mM for aerobic cells and 50 mM for hypoxic cells. The oxygen enhancement ratios for single X-ray doses were between 2 and 3 for all the cell lines. Addition of 20 microM tirapazamine to hypoxic cells 1 h before irradiation produced the same radiosensitivity as aerobic cells. Tirapazamine had a minimal effect on the radiosensitivity of aerobic cells. Since melanomas are known to contain hypoxic cells which may reduce their radiosensitivity, these in vitro results have demonstrated the potential of tirapazamine to overcome the radioresistance of hypoxia and give encouragement for further studies.
Biomarkers of ovulation, endometrial receptivity, fertilisation, implantation and early pregnancy progression (2006)

Increasing interest in early preconception and periconception exposures and human developmental outcomes has led to studies that monitor subjects from before conception to gestation, birth and childhood. Monitoring ovulation, endometrial receptivity, fertilisation, implantation and gestation requires the non-invasive collection of biological information and samples, and the measurement of biochemical and biological markers (biomarkers) that are associated with the aforementioned physiological events. This paper describes some of the key features of biomarkers needed for epidemiological studies, identifies some existing and potential biomarkers and available measurement devices, and suggests some directions for identification and development of new biomarkers that might be employed in longitudinal studies involving the analysis of female reproductive function and of embryonic development.
Specificity of circulating and tissue-bound autoantibodies in Goodpasture syndrome. (1996)

Goodpasture syndrome is an often fatal autoimmune disease associated with glomerulonephritis and/or pulmonary hemorrhage. The clinical manifestations of this disease correlate well with the presence of circulating antiglomerular basement membrane (GBM) autoantibodies. The primary target antigen in glomerular and alveolar basement membranes is thought to be the alpha 3 chain of type IV collagen. Nearly all that is known about anti-GBM antibodies in humans comes from work on unbound circulating antibody. We recently had the unique and rare opportunity to obtain early postmortem antibody and tissues from a patient who died with catastrophic Goodpasture syndrome. The specificity of circulating, kidney-bound and lung-bound autoantibodies from this patient was evaluated against a variety of purified basement membrane constituents. The results indicate that the primary target for the circulating and tissue-bound autoantibodies is the NC1 domain of the alpha 3(IV) chain of type IV collagen. Additionally, all the antibodies recognize a cryptic epitope/s on the alpha 3(IV)NC1 hexamer. Furthermore, tissue-bound and circulating antibodies compete with one another for overlapping epitopes on the antigen. These findings demonstrate that circulating autoantibodies in Goodpasture syndrome are highly representative of those bound to organ tissues, strengthening the notion that pathogenic autoantibodies are targeted to the alpha 3(IV)NC1 collagen, and that previous reports of findings in the circulation may be applicable to tissue injury.
Salt tolerance of <i>Arabidopsis thaliana</i> requires maturation of <i>N</i> -glycosylated proteins in the Golgi apparatus (2008)

Protein N-glycosylation in the endoplasmic reticulum (ER) and in the Golgi apparatus is an essential process in eukaryotic cells. Although the N-glycosylation pathway in the ER has been shown to regulate protein quality control, salt tolerance, and cellulose biosynthesis in plants, no biological roles have been linked functionally to N-glycan modifications that occur in the Golgi apparatus. Herein, we provide evidence that mutants defective in N-glycan maturation, such as complex glycan 1 (cgl1), are more salt-sensitive than wild type. Salt stress caused growth inhibition, aberrant root-tip morphology, and callose accumulation in cgl1, which were also observed in an ER oligosaccharyltransferase mutant, staurosporin and temperature sensitive 3a (stt3a). Unlike stt3a, cgl1 did not cause constitutive activation of the unfolded protein response. Instead, aberrant modification of the plasma membrane glycoprotein KORRIGAN 1/RADIALLY SWOLLEN 2 (KOR1/RSW2) that is necessary for cellulose biosynthesis occurred in cgl1 and stt3a. Genetic analyses identified specific interactions among rsw2, stt3a, and cgl1 mutations, indicating that the function of KOR1/RSW2 protein depends on complex N-glycans. Furthermore, cellulose deficient rsw1-1 and rsw2-1 plants were also salt-sensitive. These results establish that plant protein N-glycosylation functions beyond protein folding in the ER and is necessary for sufficient cell-wall formation under salt stress.
The Kirton Adaptation-Innovation Inventory (1999)

The Kirton Adaptation- Innovation Inventory (KAI) is designed to measure propensity to innovate versus propensity to adapt, a personality dimension claimed significant for understanding and building organizational effectiveness This article presents a series of validity checks for the KAI, reports two serendipitous findings, then tests Kirton's hypothesis that a team composed of extreme adapters or extreme innovators is less effective than a team balanced on this dimension
Audio-frequency magnetotellurics with a grounded electric dipole source (1975)

Abstract The conventional audio-frequency magnetotelluric method has been useful in problems of shallow exploration to depths of a few kilometers. Because the natural sources are unpredictable in strength and direction, we have examined the possibility of doing magnetotelluric sounding utilizing the ratio of horizontal electric field to horizontal magnetic field from a controlled source. The source chosen for this study was a grounded electric dipole. The equations for the electric and magnetic fields around this antenna as a function of range and azimuth have been calculated for a half-space and for a one-layered earth. These calculations were checked for the half-space case with an analog model and in the field at the Bonneville Salt Flats. In addition, layered cases were calculated, and a field example near Timmins, Ont., studied.Provided the distance of the observation point from the source is three skin depths (relative to the greatest resistivity in the section) or more, the conventional magnetotelluric interpretations can be applied. If the observations are closer than this, it is possible to use sets of type curves for the analysis. Such curves have been calculated.Lateral variations were studied in a model tank and by studying a massive sulfide deposit near Gooderham in Ontario.
Are insects resistant to plant proteinase inhibitors? (1995)

Six species of Lepidoptera were evaluated for their susceptibility to serine proteinase inhibitors from cabbage. Trypsin and chymotrypsin activity from larval Pieris rapae and Pieris napi were not significantly inhibited (0–18%), in vitro, by cabbage proteinase inhibitors, while the serine proteinase activity in the midguts of larval Plutella xylostella was moderately inhibited (40–50%), and Trichoplusia ni, Lymantria dispar, and Helicoverpa zea were substantially inhibited (55–85%) by cabbage proteinase inhibitors. These results suggest that the growth and development of the latter three species should be reduced following ingestion of these inhibitors. However, chronic ingestion of cabbage proteinase inhibitors only reduced the growth and development of T. ni. This lack of biological activity of the proteinase inhibitors against the other two species was explained by a shift in the relative proportion of digestive enzymes in response to ingestion of proteinase inhibitors. Following ingestion of cabbage proteinase inhibitors, the predominant trypsin-like enzyme(s) in the midgut of larval L. dispar and H. zea were resistant to inhibition by cabbage trypsin inhibitors (13–18% inhibited), while the trypsin(s) in T. ni was moderately susceptible (37% inhibited). These results were confirmed for H. zea and T. ni feeding on proteinase inhibitors in tomato foliage. This is the first demonstration of adaptation to proteinase inhibitors, and has important implications for gene regulation and physiological plasticity.
AC-power-signal-biased LED modulation method for ubiquitous visible light communication (2012)

We propose and demonstrate an AC-power-signal-biased light-emitting-diode (LED) modulation. To minimize the signal distortion, the message signal is up-converted to a carrier of 400 KHz and 60 Hz AC-power signal are combined using our developed bias tee circuit. Measurement result shows a bit error rate (BER) below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-8</sup> at a transmission distance of 2 m. This technique is energy-efficient and compatible with AC LED, since AC to DC converter is not needed.
Automatic Deployment of Specification-based Intrusion Detection in the BACnet Protocol (2017)

Specification-based intrusion detection (SB-ID) is a suitable approach to monitor Building Automation Systems (BASs) because the correct and non-compromised functioning of the system is well understood. Its main drawback is that the creation of specifications often require human intervention. We present the first fully automated approach to deploy SB-ID at network level. We do so in the domain of BASs, specifically, the BACnet protocol (ISO 16484-5). In this protocol, properly certified devices are demanded to have technical documentation stating their capabilities. We leverage on those documents to create specifications that represent the expected behavior of each device in the network. Automated specification extraction is crucial to effectively apply SB-ID in volatile environments such as BACnet networks, where new devices are often added, removed, or replaced. In our experiments, the proposed algorithm creates specifications with both precision and recall above 99.5%. Finally, we evaluate the capabilities of our detection approach using two months (80GB) of BACnet traffic from a real BAS. Additionally, we use synthetic traffic to demonstrate attack detection in a controlled environment. We show that our approach not only contributes to the practical feasibility of SB-ID in BASs, but also detects stealthy and dangerous attacks.
A proposal management of the legacy network environment using OpenFlow control plane (2012)

The Future Internet will arise from the convergence of new network concepts and combine technologies, services, media and content. It will offer flexibility and diversity with scalable content and services that are accessible through a wide range of interfaces and devices. However, the biggest challenge now is how to enable and test the proposed approaches so that they can be validated without sacrificing the current production infrastructure. The OpenFlow protocol allows production networking environments such as campus networks, metropolitan networks or R&D networks, to be used as experimental infrastructure hosting, future Internet architectures, software and protocols, in parallel with the production traffic. During rollout, there is a practical problem that arises with Legacy networks that do not support OpenFlow and need to be replaced/upgraded or refined by means of costly network re-engineering. This paper proposes a new OpenFlow architecture with new components, capable of managing Legacy-non-OpenFlow elements by offering a new solution that facilitates the management of Legacy technologies and allows them to be employed in FI experimentation environment and increase the number of experiment with the Legacy Network Environment using OpenFlow control.
Chained Iron Microparticles for Directionally Controlled Actuation of Soft Robots (2017)

Magnetic field-directed self-assembly of magnetic particles in chains is useful for developing directionally responsive materials for applications in soft robotics. Using materials with greater complexity allows advanced functions, while still using simple device architectures. Elastomer films containing chained magnetic microparticles were prepared through solvent casting and formed into magnetically actuated lifters, accordions, valves, and pumps. Chaining both enhances actuation and imparts a directional response. Cantilevers used as lifters were able to lift up to 50 times the mass of the polymer film. We introduce the "specific torque", the torque per field per mass of magnetic particles, as a figure of merit for assessing and comparing the performance of lifters and related devices. Devices in this work generated specific torques of 68 Nm/kgT, which is significantly higher than in previously reported actuators. Applying magnetic fields to folded accordion structures caused extension and compression, depending on the accordion's orientation. In peristaltic pumps comprised of composite tubes containing embedded chains, magnetic fields caused a section of the tube to pinch closed where the field was applied. These results will facilitate both the further development of soft robots based on chained magnetic particles and efforts to engineer materials with higher specific torque.
Who rated what: a combination of SVD, correlation and frequent sequence mining (2007)

KDD Cup 2007 focuses on predicting aspects of movie rating behavior. We present our prediction method for Task 1 “Who Rated What in 2006” where the task is to predict which users rated which movies in 2006. We use the combination of the following predictors, listed in the order of their efficiency in the prediction: • The predicted number of ratings for each movie based on time series prediction, also using movie and DVD release dates and movie series detection by the edit distance of the titles. • The predicted number of ratings by each user by using the fact that ratings were sampled proportional to the margin. • The low rank approximation of the 0–1 matrix of known user–movie pairs with rating. • The movie–movie similarity matrix. • Association rules obtained by frequent sequence mining of user ratings considered as ordered itemsets. By combining the predictions by linear regression we obtained a prediction with root mean squared error 0.256; the first runner up result was 0.263 while a pure all zeroes prediction already gives 0.279, indicating the hardness of the task.
Connexin 43 expression and proliferation of human limbal epithelium on intact and denuded amniotic membrane. (2002)

These data indicate that denudation of the devitalized amniotic epithelium to expose its basement membrane might be a microenvironmental cue to promote TAC differentiation. The model system described herein is ideal for future exploration of the exact mechanistic operation in the microenvironmental niche that maintains the "stemness" of limbal SCs as well as in the signal that promotes corneal TAC differentiation.
The design of a fault tolerant GEQRNS processing element for linear systolic array DSP applications (2002)

In this work the design of a Galois Enhanced Quadratic Residue Number System processor is presented, which can be used to construct linear systolic arrays. The processor architecture has been, optimized to perform multiply-accumulate type operations on complex operands. The processor is also shown to have a high degree of tolerance to manufacturing defects and faults which occur during operation. A prototype integrated circuit has been fabricated in 1.5 /spl mu/m CMOS technology, which is shown to operate at 40 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Bacteria in the pathogenesis of inflammatory bowel disease (2006)

Molecular techniques are giving us better insight into the gut microbiota in inflammatory bowel disease that should translate into improved therapies.