gebhart/patrepeval huggingface dataset:
Regular step arrays on silicon (1998)

Highly regular arrays of steps are produced on vicinal Si(111)7×7. The step edges are atomically straight for up to 2×104 lattice sites. The terraces are single domain, which produces a minimum kink width of 2.3 nm (half a 7×7 unit cell) and thus a high barrier for creating kinks. Criteria for obtaining optimum step arrays are established, such as the miscut [≈1° towards (1̄1̄2)] and an annealing sequence which passes through step bunching regions quickly.
Removal of Pathogenic Autoantibodies by Immunoadsorption (2005)

Autoimmune diseases result from disrupted tolerance to self-antigens and subsequent damage to tissues and organs. In several diseases, specific autoantibodies have been either proved or suspected to play a role in this process. Consequently, several strategies have been devised in an attempt to discard the destructive immunoglobulins. Currently, both nonselective and epitope-specific methods are applied in several diseases. In this review, we provide a summary of the available data on elimination of pathogenic autoantibodies and discuss the advantages and pitfalls of the different approaches.
Proline oxidase, encoded by p53-induced gene-6, catalyzes the generation of proline-dependent reactive oxygen species. (2001)

The p53-dependent initiation of apoptosis is accompanied by the induction of proline oxidase (POX), a mitochondrial enzyme catalyzing the conversion of proline to pyrroline-5-carboxylate with the concomitant transfer of electrons to cytochrome c. However, the contribution of increased POX activity to apoptosis, if any, remains unknown. Using Adriamycin to initiate p53-dependent apoptosis, we showed that the expression of POX is up-regulated in a time- and dose-dependent manner in a human colon cancer cell line (LoVo). In cells expressing POX, the addition of proline increases reactive oxygen species (ROS) generation in a concentration-dependent manner; glutamate, a downstream product of proline oxidation, had no effect. Induction of POX was dependent on the p53 status of the cell. In the conditionally immortalized murine colonic epithelial cell line YAMC, where the p53 phenotype can be modulated by temperature, proline oxidase expression and ROS production could only be induced when the cells were phenotypically p53-positive. To confirm that the observed ROS production was not secondary to some other effect of p53, we also conditionally expressed POX in a p53-negative colon cancer line. Again, we found a proline-dependent ROS increase with POX expression. We hypothesize that proline oxidation supports the generation of ROS by donating reducing potential to an electron transport chain altered either by p53-dependent mechanisms or by overexpression of POX.
Critical Flicker Frequency in Traumatic Brain Injury (2008)

Primary Objective: To determine whether critical flicker frequency (CFF) thresholds are elevated in individuals with traumatic brain injury (TBI) and correlated with the degree of motion and light sensitivity. \nMethods and procedures: The foveal CFF threshold was assessed in individuals with TBI (n=18) having varying degrees of light and motion sensitivity. Mean CFF values were obtained using the ascending and descending psychophysical method of limits with binocular viewing at 40 cm. A rating-scale questionnaire was used to assess the degree of light sensitivity and motion sensitivity. These parameters were also assessed in a visually-normal cohort. \nMain outcomes and results: CFF in the TBI group was not significantly different across age groups from the visually- normal cohort. However, mean CFF among the TBI subjects was significantly higher for the “light sensitive” and “motion sensitive” subgroups when compared to the “not light sensitive” and “not motion sensitive” subgroups. The majority of TBI subjects had both light and motion sensitivity.\nConclusion: An elevated CFF among a subgroup of TBI subjects may be related to the symptoms of light and motion sensitivity that many TBI patients experience. Underlying mechanisms involving disinhibition of the magnocellular pathway as a result of brain injury may be causal of the hypersensitivity to light and motion. CFF thresholds can potentially aid clinicians in determining methods of treatment for TBI patients.
A low-cost real-time stereo vision system for looking at people (2002)

Real-time computer vision systems that observe the actions of people have received increasing attention as they are important for a broad range of applications. Examples are intelligent man-machine interfaces or intelligent rooms that have the capability to understand the actions of their inhabitants. In this paper we present the design of a stereo vision system for the precise and robust real time tracking of human hands and heads that unlike previous systems uses low-cost industry standard components. The system uses color and motion information to find the human. Using previously calibrated cameras the 3D positions of hands and head are calculated. Because of its client-server architecture the system is scalable to an arbitrary number of cameras and application processes. Experimental results for the performance of the system are given.
IMPORTING CHANGE: CANADIAN COMPETITION AND THE U.S. FLORICULTURE INDUSTRY (2008)

During the last century American agriculture has undergone a massive transformation from an industry dominated by a large number of small family-owned farms to an industry characterized by a fewer larger scale, heavily-capitalized enterprises. In this paper, we analyze the shifting geography of production with respect to the U.S. floriculture industry. The ongoing transformation of the floriculture industry is being driven by two interrelated phenomena. One is growing Canadian imports, particularly from Ontario. Canadian producers benefit from a fortuitous location with respect to major American markets, operate on a larger scale, enjoy a more favorable institutional setting, and until recently, profited from a favorable exchange rate. Another transformative process has been increasing sales of floricultural products by mass merchandisers in the U.S. The “big box ” stores favor large scale operations, including Canadian exporters, due to larger scale demand and more complex sales agreements. As a result of these transformative changes, the U.S. floriculture industry will likely move to a dual market structure, consisting of large scale producers, who can supply the “big boxes ” and compete effectively with foreign imports, and another segment of small scale producers who will have to carve out local markets based on higher quality customer service and/or being responsive to specialized consumer demands.
179. In Vivo Delivery of DNA or siRNA Formulated into Nanoparticles with Linear PEI (2006)

One of the most promising non-viral vectors is the cationic polymer polyethylenimine (PEI), a well-known cell culture transfection reagent. In particular, the latest generation of linear PEI is more efficient than the first generation of branched polymers. Various delivery routes of small size defined PEI polyplexes formulated in a 5% glucose solution can be used (intravenous, intracerebral, intraperitoneal, intracardiac, instillation …). Intravenous injection (IV) is the route of choice in many gene therapy applications. Among the different routes of IV injection tested (caudal, jugular and retro-orbital), the retro-orbital route appears to be the simplest and the most efficient one to deliver the gene of interest in the organs studied (i.e. lung, liver, spleen, heart and kidney). The purpose of our work was to compare different parameters of DNA injection complexed with L-PEI injected by retro-orbital route. Different amount of pCMVLuc plasmid was injected complexed with in vivo-jetPEI™ in 22–24 grams OF1 female mice. Among the DNA quantity injected (10 μg to 70 μg) at N/P ratio of 8, we have shown that the quantity of 40 or 50 μg gives the most efficient plasmid expression. For this amount, the best result was obtained by injecting 400 or 600 μl instead of 200 μl. As the efficiency and the cytotoxicity depend on the molecular weight of the polymer, we compared different polymer length and showed that the commercial in vivo-jetPEI™ by being noncytotoxic is the most efficient in gene delivery. The pharmacokinetic and organ distribution profile was also determined with 40 μg of plasmid between 6 and 72 hours after the injection of the plasmid. Taken together, our data showed that the IV retro-orbital injection is the route of choice to inject plasmid DNA complexed with linear polyethylenimine. Moreover, we have also explored the promising potential of in vivo-jetPEI™ to deliver active siRNAs injected by retro-orbital route and shown that in vivo-jetPEI™ can deliver siRNAs silencing a co-transfected target gene expressed in lungs after intravenous injection in mice.
Indium-Mediated Allylation of the <i>N</i>,<i>N</i>-Dimethyl Glyoxal Mono-Hydrazone: One-Pot Synthesis of Bis-Homoallyl, and of Homoallyl-Alkyl 1,2-Diols (1999)

Hydrazones behave as highly reactive species in the allylation under Barbier conditions. Nucleophilic addition of an alkyllithium to the carbonyl moiety of the glyoxal mono-hydrazone followed by indium-mediated allylation, leads in high yields to bis-functionalized 1,2-diols in a one-pot two-step reaction.
Solid state recrystallization: a promising technique for the growth of semiconductor materials (2003)

Abstract Experimental results related to the growth by solid state recrystallization of different semiconductors such as HgCdTe, HgMnTe, CdTe, ZnSe and ZnS are reported and reviewed. The importance of the initial texture and of the deviation from stoichiometry is stressed and the essential role of metal vacancies is emphasized.
Identification of<i>Bilophila wadsworthia</i>by specific PCR which targets the taurine:pyruvate aminotransferase gene (2006)

The bile-resistant, strictly anaerobic bacterium Bilophila wadsworthia is found in human faecal flora, in human infections and in environmental samples. A specific PCR primer set for the gene encoding the first metabolic enzyme in the degradative pathway for taurine in B. wadsworthia, taurine:pyruvate aminotransferase (tpa), was developed and tested. In addition, enrichment cultures were started from faecal samples of primates and felines and shown to contain B. wadsworthia. These were subcultured on agar media and then identified by PCR fingerprinting. PCR for tpa was successful in all positive enrichment cultures and showed no amplification signal in a variety of other bacterial species. Therefore, this PCR method could be a promising tool for rapid detection of B. wadsworthia in biological samples.
Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf (2003)

Estimating protein-protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute-solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson-Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras-Raf obtained in this study of -8.3 kcal mol(-1) is in good agreement with the experimental result of -9.6 kcal mol(-1), however, further probing the transferability of the applied protocol that led to this result is necessary.
Overexpression of Endothelial Nitric Oxide Synthase Improves Endothelium-Dependent Vasodilation in Arteries Infused with Helper-Dependent Adenovirus (2012)

Adenoviral vectors (Ad) are useful tools for in vivo gene transfer into endothelial cells. However, endothelium-dependent vasodilation is impaired after Ad infusion, and this impairment is not prevented by use of advanced-generation "helper-dependent" (HD) Ad that lack all viral genes. We hypothesized that endothelium-dependent vasodilation could be improved in Ad-infused arteries by overexpression of endothelial nitric oxide synthase (eNOS). We tested this hypothesis in hyperlipidemic, atherosclerosis-prone rabbits because HDAd will likely be used for treating and preventing atherosclerosis. Moreover, the consequences of eNOS overexpression might differ in normal and atherosclerosis-prone arteries and could include atherogenic effects, as reported in transgenic mice. We cloned rabbit eNOS and constructed an HDAd that expresses it. HDAdeNOS increased NO production by cultured endothelial cells and increased arterial eNOS mRNA in vivo by ∼10-fold. Compared to arteries infused with a control HDAd, HDAdeNOS-infused arteries of hyperlipidemic rabbits had significantly improved endothelium-dependent vasodilation, and similar responses to phenylephrine and nitroprusside. Moreover, infusion of HDAdeNOS had local atheroprotective effects including large, significant decreases in intimal lipid accumulation and arterial tumor necrosis factor (TNF)-α expression (p≤0.04 for both). HDAdeNOS infusion yields a durable (≥2 weeks) increase in arterial eNOS expression, improves vasomotor function, and reduces artery wall inflammation and lipid accumulation. Addition of an eNOS expression cassette improves the performance of HDAd, has no harmful effects, and may reduce atherosclerotic lesion growth.
Impact strength of polymers: 1. The effect of thermal treatment and residual stress (1976)

Abstract The effect of thermal annealing and quenching on the notched Izod impact strength of several polymers has been studied. Primary emphasis was placed on polycarbonate, but ABS, PVC, polysulfone, and polymethylmethacrylate were also studied. It was determined that residual stresses created by thermal quenching from above the glass transition temperature can have a great effect on impact strength for the polycarbonate, PVC, and polysulfone polymers studied. In fact, it is shown that the thickness transition observed in impact strength for polycarbonates is governed by the residual stresses and not by thickness. In polycarbonates, quenched sheets up to 3/8 in. in thickness have shown impact strengths of 18 ft‐lb/in. whereas sheets 1/8 in. in thickness can be embrittled by annealing, showing an impact strength of 2 ft‐lb/in. However, it has been shown that this embrittlement results from the absence of residual stress. Residual stresses having maximum values up to 3000 psi (in Compression) have been determined at the polycarbonate sheet surface using birefringence measurement techniques. The existence of these compressive stresses is postulated to restrict the extent of craze growth at the notch tip, and the impact specimen can yield rather than fail in a brittle manner if the stress state is sufficient.
Optical character recognition based on nonredundant correlation measurements (1979)

The essence of character recognition is a comparison between the unknown character and a set of reference patterns. Usually, these reference patterns are all possible characters themselves, the whole alphabet in the case of letter characters. Obviously, N analog measurements are highly redundant, since only K = log(2)N binary decisions are enough to identify one out of N characters. Therefore, we devised K reference patterns accordingly. These patterns, called principal components, are found by digital image processing, but used in an optical analog computer. We will explain the concept of principal components, and we will describe experiments with several optical character recognition systems, based on this concept.
Partial identification of spirochaetes from two dairy cows with digital dermatitis by polymerase chain reaction analysis of the 16S ribosomal RNA gene (1997)

Specimens taken postmortem from typical lesions of digital dermatitis in two dairy cows were tested by the polymerase chain reaction (PCR) for the presence of a spirochaetal 16S rRNA gene. Seven different assays detected the gene in the samples from both cows. Two of the PCR products were sequenced and a comparison of the nucleotide sequences revealed that the spirochaete belonged to the genus Treponema and was closely related to Treponema denticola. A PCR specific for the detection of the digital dermatitis-associated treponeme was developed.
CHD1L: a novel oncogene (2013)

Comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer and - 140 driver genes have been identified, but not all of them have been extensively investigated. CHD1L (chromodomain helicase/ATPase DNA binding protein 1-like gene) or ALC1 (amplified in liver cancer 1) is a newly identified oncogene located at Chr1q21 and it is amplified in many solid tumors. Functional studies of CHD1L in hepatocellular carcinoma and other tumors strongly suggested that its oncogenic role in tumorigenesis is through unleashed cell proliferation, G1/S transition and inhibition of apoptosis. The underlying mechanisms of CHD1L activation may disrupt the cell death program via binding the apoptotic protein Nur77 or through activation of the AKT pathway by up-regulation of CHD1L-mediated target genes (e.g., ARHGEF9, SPOCK1 or TCTP). CHD1L is now considered to be a novel independent biomarker for progression, prognosis and survival in several solid tumors. The accumulated knowledge about its functions will provide a focus to search for targeted treatment in specific subtypes of tumors.
Coumalic Acid (2003)

Abstract Coumalic acid reactant: 200 g. (1.49 moles) of powdered malic acid product: coumalic acid
Lempel-Ziv compression of structured text (2004)

We describe a novel Lempel-Ziv approach suitable for compressing structured documents, called LZCS, which takes advantage of redundant information that can appear in the structure. The main idea is that frequently repeated subtrees may exist and these can be replaced by a backward reference to their first occurrence. The main advantage is that compressed documents generated by LZCS are easy to display, access at random, and navigate. In a second stage, processed documents can be further compressed using some semiadaptive technique, so that random access and navigability remain possible. LZCS is especially efficient to compress collections of highly structured data, such as XML forms, invoices, e-commerce and web-service exchange documents. The comparison against structure-based and standard compressors shows that LZCS is a competitive choice for this type of documents, while the others are not well-suited to support navigation or random access.
Lire: lucene image retrieval (2008)

LIRe (Lucene Image Retrieval) is a light weight open source Java library for content based image retrieval. It provides common and state of the art global image features and offers means for indexing and retrieval. Due to the fact that it is based on a light weight embedded text search engine, it can be integrated easily in applications without relying on a database server.
A compact, high power, sub-millimeter-wave Extended Interaction Klystron (2008)

This presentation describes the performance of a recently developed 218 GHz extended interaction klystron (EIK) amplifier producing 7W CW and weighing less than 4.3 kg.
The DNase activity of RNase T and its application to DNA cloning (1999)

RNase T is one of eight distinct 3'-->5' exoribonucleases present in Escherichia coli. The enzyme plays an important role in stable RNA metabolism, including tRNA end turnover and 3' maturation of most stable RNAs because it is the only RNase that can efficiently remove residues near a double-stranded (ds) stem. In the course of study of its specificity and mechanism, we found that RNase T also has single-strand-specific DNase activity. Purified RNase T degrades both single-stranded (ss)RNA and ssDNA in a non-processive manner. However, in contrast to its action on RNA, RNase T binds ssDNA much more tightly and shows less sequence specificity. As with RNA, DNA secondary structure strongly affects its degradation by RNase T. Thus, RNase T action on a dsDNA with a single-stranded 3'-extension efficiently generates blunt-ended DNA. This property of RNase T suggested that it might be a useful enzyme for blunt-ended DNA cloning. We show here that RNase T provides much higher cloning efficiency than the currently used mung bean nuclease.
Studies on transmissible gastroenteritis of swine. II. Selected characteristics of a cytopathogenic virus common to five isolates from transmissible gastroenteritis. (1966)

Five cell culture isolates from transmissible gastroenteritis (TGE) of swine have been studied. There is a cytopathogenic virus common to all of these isolates. Some of the characteristics of this virus, such as its size, approximately 100 mmicro, its relative sensitivity to ether, lability at pH 2, pH 3, and pH 10, and its heat lability suggest that it may be a member of the myxovirus class. Concurrent research in this laboratory indicates that this cytopathogenic virus is not the only virus involved in the etiology of TGE, but it appears to be associated with many of the outbreaks of TGE which have been studied by this laboratory.
Data Jackets for Synthesizing Values in the Market of Data (2013)

In order to make a social environment where analysts and decision makers in active businesses and sciences can be provided with data they need, we discuss why we should and how we can (re)design an environment called the market of data, where each user or provider of data can externalize and share the value of each part of data so that one can buy/sell it in a reasonable condition, e.g., for a reasonable price or as open source if it may give merits to people in general rather than to particular segments who can pay. Presenting one way to go, that is called Innovators’ Marketplace on Data Jackets, we show a vision for the systematic design of the market of data where existing tools and new technologies are configured, such as the visualization of the relation among databases/datasets for aiding stakeholders’ communication about possible use scenarios of data. By this, this paper calls for potential contributors in the future to the market of data.