gebhart/patrepeval huggingface dataset:
S100 Family Members and Trypsinogens Are Predictors of Distant Metastasis and Survival in Early-Stage Non-Small Cell Lung Cancer (2004)

Distant metastasis is the predominant cause of death in early-stage non-small cell lung cancer (NSCLC). Currently, it is impossible to predict the occurrence of metastasis at early stages and thereby separate patients who could be cured by surgical resection alone from patients who would benefit from additional chemotherapy. In this study, we applied a comparative microarray approach to identify gene expression differences between early-stage NSCLC patients whose cancer ultimately did or did not metastasize during the course of their disease. Transcriptional profiling of 82 microarrays from two patient groups revealed differential expression of several gene families including known predictors of metastasis (e.g., matrix metalloproteinases). In addition, we found S100P, S100A2, trypsinogen C (TRY6), and trypsinogen IVb (PRSS3) to be overexpressed in tumors that metastasized during the course of the disease. In a third group of 42 patients, we confirmed the induction of S100 proteins and trypsinogens in metastasizing tumors and its significant correlation with survival by real-time quantitative reverse transcription-PCR. Overexpression of S100A2, S100P, or PRSS3 in NSCLC cell cultures led to increased transendothelial migration, corroborating the role of S100A2, S100P, and PRSS3 in the metastatic process. Taken together, we provide evidence that expression of S100 proteins and trypsinogens is associated with metastasis and predicts survival in early stages of NSCLC. For the first time, this implicates a role of S100 proteins and trypsinogens in the metastatic process of early-stage NSCLC.
Understanding the Risk of Futures Exchange: Evidence from SHFE (2009)

Based on the descriptive analysis of China futures trading mechanism and the structure of China futures exchange, this paper defines the risk of futures exchange as uncertainties in the futures market that cause the futures exchange to suffer loss due to the default of its members. Several risk factors such as price fluctuations, market monopoly, capital sufficiency and market manipulation can be identified when the development of China futures market is more closely observed. By setting up a risk-warning model for China futures exchange through multivariate analysis using data from SHFE, an empirical study indicates that as the most important risk factor the price fluctuation has a great influence on China futures exchange. The effectiveness of the risk-warning model is supported by the analysis results from the latest data.
Regulated activity of the IgH intron enhancer (Eμ) in the T lymphocyte lineage (1995)

The activity of the IgH (E mu) enhancer in the T lymphocyte lineage has been investigated using both transgenic mice and transfection studies. Thymocyte fractionation experiments indicate that a transgene consisting of the bacterial chloramphenicol acetyl transferase (CAT) gene, linked to E mu and the SV40 early promoter (E mu-CAT), is expressed only in thymocytes with a mature medullary phenotype and not in immature cells. Transfection of this same construct into two thymoma cell lines representing different stages of thymocyte development mimics the pattern of activity observed in vivo. Further transfection experiments suggest that this pattern of expression might be attributed to the differential activity of the E2E3 and octanucleotide motifs of E mu during development. In contrast, an Ig lambda transgene (linked to E mu and an Ig V lambda promoter) is expressed in the majority of thymocytes. We envisage that the different patterns of expression of the two transgenes reflect interactions between their respective promoters and the factors which are bound to E mu at different stages of thymocyte development. Although differing in their pattern of expression within the thymus, the two transgenes share the property of extinction in peripheral T lymphocytes. These results indicate that the expression of E mu-linked transgenes in the thymus cannot simply be explained by activation of the enhancer in a lymphoid progenitor cell prior to B/T lineage divergence. Rather, the enhancer (or components of it) must be independently activated (and inactivated) during T lymphocyte development. Furthermore, this activity is consistent with the developmental timing of Ig DH-JH rearrangements in these cells.
<title>Micromachined pipettes integrated in a flow channel for single DNA molecule study by optical trapping</title> (2000)

We have developed a micromachined flow cell consisting of a flow channel integrated with micropipettes. The flow cell is used in combination with an optical trap set-up (optical tweezers) to study mechanical and structural properties of (lambda) -DNA molecules. The flow cell was realized using silicon micromachining including the so-called buried channel technology to fabricate the micropipettes, the wet etching of glass to create the flow channel, and the powder blasting of glass to create the fluid connections. The volume of the flow cell is 2 (mu) l. The pipettes have a length of 130 micrometer, a width of 5 - 10 micrometer, a round opening of 1 micron and can be processed with different shapes. Using this flow cell we stretched single molecules ((lambda) -DNA) showing typical force-extension curves also found with conventional techniques.
<title>Ship silhouette recognition using principal components analysis</title> (1997)

We report on an evaluation study of a ship classifier based on the principal components analysis (PCA). A set of ship profiles are used to build a covariance matrix which is diagonalized using the Karhunen-Loeve transform. A subset of the principal components corresponding to the highest eigenvalues are selected as the ship features space. The recognition process consists in projecting a profile on this eigen-subspace and performing a similarity measure. We have measured the recognition performance of the classifier using various sets of range-profile signatures of ship silhouette images and simulated synthetic aperture radar images of ships under various aspect angles. It is found that the PCA-based ship classifier design offers good class discriminacy when trained with a limited number of ship classes under an aspect angle range of 60 degrees about the ship side view. Additional tests are however necessary to validate the classifier on large data sets and real images.
Minimal non-orthogonality rate 1 space-time block code for 3+ Tx antennas (2002)

We propose a full rate space-time block code for 3+ Tx antennas. The code is chosen to minimize the non-orthonormality that arises from increasing the rate above the maximum allowed by orthogonality. A linear decoding based on iterative interference cancellation between parts of the code approaches the maximal likelihood decoding performance.
Treatment of Hypersensitive Teeth Using Neodymium:Yttrium-Aluminum-Garnet Lasers: A Comparison of the Use of Various Settings in an in Vivo Study (1997)

The spectrum of the methods available to treat hypersensitive teeth is very great. The chances for success in the use of these different therapies are equally variable. Faced with the already successful effort of the Nd:YAG laser in the treatment of exposed tooth necks, the effectiveness of the use of different settings of the Nd:YAG laser on exposed dentine was examined in this clinical study. In the case of comparison of the therapy success of the laser settings amongst one another, no significant difference could be found. This leads us to a conclusion, that laser irradiation is therapeutically effective at very low settings.
What's Gonna Happen to the Class of 2010? (2001)

First, I live in a college town. The land-grant university, some light industry, and an active group of downtown merchants make up our community. We also have a Super Wal-Mart, open 24 hours and that says it all. Second, I'm the father of a nine-year-old son, Nate. I enjoy being a dad, and it has come with some unexpected rewards. I don't have to feel guilty about buying Cap'n Crunch, I have been known to play Nintendo until the wee hours of the morning, and I also know the names of at least a dozen Pokemon characters. Nate includes me in activities of his Cub Scout pack, takes me on bike rides, and allows me to be seen at school occasionally. From time to time, undergraduates ask me if Nate will enroll in Agricultural Education or join the FFA. While I haven't lost any sleep over this question, I hope he will be interested in at least trying the program. Certainly, his second grade teacher has cultivated his interest in agriculture. Thanks to her, what my son lacks in exposure to production agriculture is being made up for in lessons on tissue culture, wildlife study, and seed germination experiments. When Nate is 14 he will be putting together a high school schedule. If you want him to enroll in your program, don't offer him tissue culture, because he has already done that. While I can convince him to try at least one freshman level agriculture course, I'm not so sure about his classmates. You will have to offer them something special too, or they will cast their lot with one of the other enticing electives. Over the last few years I have come to appreciate other dads. There is an unwritten dad-club, a club you automatically belong to because your son is a Cub Scout or t-ball player. In this club, dads usually stand around and either brag on their sons or explain that their son's bad behavior is from his mother's influence. You also get to find out a lot about the others dads in the club. These dads want things for their sons. Mostly the things they want are positive experiences. Can your agricultural education program offer my son positive experiences? Here's what I saw last week: sec Monday night we had a Cub Scout den meeting at Tyler's house. Tyler's dad arranged a woodworking activity for the boys where they all learned to use a handsaw, band saw, hand drill and the proper technique in using sandpaper. I said this activity was at Tyler's house, but I should have explained that it was in Tyler's dad's woodworking shop; a virtual showroom of up-to-date woodworking equipment. Tyler's dad works at a company that makes stereo speakers, but his love is woodworking. I left wondering if Tyler's dad would encourage him to enroll in Ag. sec On Tuesday night we had coach-pitch baseball. …
Selective pulmonary vasodilation by inhaled nitric oxide is due to hemoglobin inactivation. (1993)

The presence of hemoglobin, even in extremely small amounts, restricts the vasodilating effect of inhaled nitric oxide gas to the pulmonary circulation.
A layerless additive manufacturing process based on CNC accumulation (2011)

Purpose Most current additive manufacturing (AM) processes are layer based. By converting a three‐dimensional model into two‐dimensional layers, the process planning can be dramatically simplified. However, there are also drawbacks associated with such an approach such as inconsistent material properties and difficulty in embedding existing components. The purpose of this paper is to present a novel AM process that is non‐layer based and demonstrate its unique capability. Design/methodology/approach An AM process named computer numerically controlled (CNC) accumulation has been developed. In such a layerless AM process, a fiber optic‐cable connected with an ultraviolet (UV) LED and related lens is served as an accumulation tool. The cable is then merged inside a tank that is filled with UV‐curable liquid resin. By controlling the on/off state of the UV‐LED and the multi‐axis motion of the cable, a physical model can be built by selectively curing liquid resin into solid. Findings It is found that the cured resin can be safely detached from the accumulation tool by applying a Teflon coating on the tip of the fiber‐optic cable, and controlling an appropriate gap between the cable and the base. The experimental results verified the curing and attaching force models. Research limitations/implications A proof‐of‐concept testbed has been developed based on a curing tool that has a diameter around 2 mm. The relatively large tool size limits the geometry resolution and part quality of the built parts. Originality/value By incorporating multi‐axis tool motion, the CNC accumulation process can be beneficial for applications such as plastic part repairing, addition of new design features, and building around inserts.
Protein motifs 5. Zinc fingers. (1995)

The term zinc finger was first used to describe a 30-residue, repeated sequence motif found in an unusually abundant Xenopus transcription factor. It was proposed that each motif is folded around a central zinc ion to form an independent minidomain and that adjacent zinc fingers are combined as modules to make up a DNA-binding domain with the modules "gripping" the DNA (hence the term finger). We now know that these proposals were correct and that these DNA-binding motifs are found in many eukaryotic DNA-binding proteins. More recently, crystal structures of three different complexes between zinc finger domains and their target DNA binding sites have revealed a remarkably simple mode of interaction with DNA. The simplicity of the zinc finger structure, and of its interaction with DNA, is a very striking feature of this protein domain. After the discovery of the zinc finger motif, patterns of potential zinc ligands have been found in several other proteins, some of which also bind to DNA. Structural studies of these domains have revealed how zinc can stabilize quite diverse protein architectures. In total, 10 such small zinc-binding domains have been studied structurally. These form a diverse collection, but each in turn has been termed a zinc finger motif-although clearly what they have in common is only their zinc-binding property, which stabilizes an apparently autonomously folded unit.
Molecular mass measurement of intact ribonucleic acids via electrospray ionization quadrupole mass spectrometry (1995)

The use of electrospray ionization mass spectrometry for the accurate determination of molecular masses of polynucleotides and small nucleic acids is developed. The common problem of gas phase cation adduction that is particularly prevalent in the mass spectrometric analysis of nucleic acids is reduced through the use of ammonium acetate precipitations and by the addition of chemical additives that compete for adduct ions in solution. The addition of chelating agents such as trans-1,2-diaminocyclohexane-N,N,N,',N'-tetraacetic acid to remove divalent metal ions and triethylamine to displace monovalent cations from the analyte, in conjunction with ammonium acetate precipitation, reduces cation adduction to levels that permit accurate mass analysis (mass errors of less than 0.01%) without further complex cleanup procedures. The potential utility of accurate mass measurements of small ribonucleic acids is discussed.
Inhibition of S-adenosylmethionine decarboxylase and diamine oxidase activities by analogues of methylglyoxal bis(guanylhydrazone) and their cellular uptake during lymphocyte activation (1984)

Several congeners of methylglyoxal bis(guanylhydrazone) were tested for their ability to inhibit eukaryotic putrescine-activated S-adenosylmethionine decarboxylase (EC 4.1.1.50) and intestinal diamine oxidase (EC 1.4.3.6). All the compounds tested, namely methylglyoxal bis(guanylhydrazone), ethylglyoxal bis(guanylhydrazone), dimethylglyoxal bis(guanylhydrazone) and the di-N"-methyl derivative of methylglyoxal bis(guanylhydrazone), were strong inhibitors of both yeast and mouse liver adenosylmethionine decarboxylase activity in vitro. The enzyme from both sources was most powerfully inhibited by ethylglyoxal bis(guanylhydrazone). All the diguanidines likewise inhibited diamine oxidase activity in vitro. The maximum intracellular concentrations of the ethyl and dimethylated analogues achieved in activated lymphocytes were only about one-fifth of that of the parent compound. However, both derivatives appeared to utilize the polyamine-carrier system, as indicated by competition experiments with spermidine.
Modular PROTAC Design for the Degradation of Oncogenic BCR‐ABL (2015)

Proteolysis Targeting Chimera (PROTAC) technology is a rapidly emerging alternative therapeutic strategy with the potential to address many of the challenges currently faced in modern drug development programs. PROTAC technology employs small molecules that recruit target proteins for ubiquitination and removal by the proteasome. The synthesis of PROTAC compounds that mediate the degradation of c-ABL and BCR-ABL by recruiting either Cereblon or Von Hippel Lindau E3 ligases is reported. During the course of their development, we discovered that the capacity of a PROTAC to induce degradation involves more than just target binding: the identity of the inhibitor warhead and the recruited E3 ligase largely determine the degradation profiles of the compounds; thus, as a starting point for PROTAC development, both the target ligand and the recruited E3 ligase should be varied to rapidly generate a PROTAC with the desired degradation profile.
Altered distribution of platelet-activating factor-acetylhydrolase activity between LDL and HDL as a function of the severity of hypercholesterolemia (2002)

Platelet-activating factor-acetylhydrolase (PAF-AH) is a lipoprotein-associated phospholipase A2 capable of hydrolyzing platelet-activating factor (PAF) and oxidatively modified phospholipids. We studied the plasma- and lipoprotein-associated PAF-AH activity in patients with primary hypercholesterolemia. Thirty-eight unrelated patients with heterozygous familial hypercholesterolemia (HeteroFH), five patients with homozygous FH (HomoFH), and 33 patients with primary non-FH hypercholesterolemia (NonFH) participated in the study. In all patient groups the plasma PAF-AH activity was significantly elevated compared with 33 normolipidemic controls, the HomoFH having the highest and the NonFH patients showing the lowest enzyme activity. Gradient ultracentrifugation studies showed that this increase is not only due to the elevation in the plasma LDL but also to the increase in the PAF-AH activity associated with each LDL subfraction, being more profound in the small-dense LDL-5. Unlike LDL, no difference in the HDL-associated PAF-AH activity was observed among all groups. Consequently, an altered distribution of enzyme activity among apolipoprotein B (apoB)- and apolipoprotein A-I (apoA-I)-containing lipoproteins is observed in hypercholesterolemic patients, resulting in a significant decrease in the ratio of the HDL-associated PAF-AH to the total plasma enzyme activity compared with controls. This reduction is proportional to the increase of the plasma LDL-cholesterol (LDL-C) levels and consequently to the severity of the hypercholesterolemia. Thus, the ratio of HDL-associated PAF-AH-total plasma enzyme activity may be useful as a potential marker of atherogenicity in subjects with primary hypercholesterolemia.
RNA VIRUS MUTATIONS AND FITNESS FOR SURVIVAL (1997)

RNA viruses exploit all known mechanisms of genetic variation to ensure their survival. Distinctive features of RNA virus replication include high mutation rates, high yields, and short replication times. As a consequence, RNA viruses replicate as complex and dynamic mutant swarms, called viral quasispecies. Mutation rates at defined genomic sites are affected by the nucleotide sequence context on the template molecule as well as by environmental factors. In vitro hypermutation reactions offer a means to explore the functional sequence space of nucleic acids and proteins. The evolution of a viral quasispecies is extremely dependent on the population size of the virus that is involved in the infections. Repeated bottleneck events lead to average fitness losses, with viruses that harbor unusual, deleterious mutations. In contrast, large population passages result in rapid fitness gains, much larger than those so far scored for cellular organisms. Fitness gains in one environment often lead to fitness losses in an alternative environment. An important challenge in RNA virus evolution research is the assignment of phenotypic traits to specific mutations. Different constellations of mutations may be associated with a similar biological behavior. In addition, recent evidence suggests the existence of critical thresholds for the expression of phenotypic traits. Epidemiological as well as functional and structural studies suggest that RNA viruses can tolerate restricted types and numbers of mutations during any specific time point during their evolution. Viruses occupy only a tiny portion of their potential sequence space. Such limited tolerance to mutations may open new avenues for combating viral infections.
Peregrine (2013)

Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost. We report the development of a new RNA-Seq library preparation technique that produces representative, strand-specific RNA-Seq libraries from small amounts of starting material in a fast, simple and cost-effective manner. Additionally, we have developed a new quantitative PCR-based assay for precisely determining the number of PCR cycles to perform for optimal enrichment of the final library, a key step in all SGS library preparation workflows.
The clinical application of linagliptin in Asians (2015)

Asia has a growing diabetic population. Linagliptin, a member of dipeptidyl peptidase-4 inhibitor class, is unique in its nonlinear pharmacokinetics with the characteristics of rapid attainment of steady state, little accumulation, predominantly nonrenal route of elimination, prolonged terminal half-life, and sustained inhibition of dipeptidyl peptidase-4 enzyme. No clinically relevant difference in pharmacokinetics was observed between Asians and non-Asians. The management of type 2 diabetes is increasingly challenging with the progression of disease, especially with the requirements of minimal hypoglycemia, weight gain, fluid retention, and other adverse effects. Linagliptin was efficacious and well-tolerated in Asian type 2 diabetes patients with or without renal or hepatic dysfunctions, comparable to that in Caucasians. This review will focus on the usage of linagliptin in clinical studies in Asians.
Autofluorescence of normal and malignant bronchial tissue (1991)

In vivo autofluorescence spectra were obtained in 5 patients with carcinoma in situ, 26 patients with invasive tumors, and 1 patient with severe dysplasia. Significant spectral differences were observed between pre-cancerous, cancerous, and normal bronchial tissues. This difference may afford a method to image and/or detect early lung cancer by using tissue autofluorescence alone.
Organometallic methods for the synthesis and functionalization of azaindoles (2007)

Azaindoles (also called pyrrolopyridines) constitute essential subunits in many pharmaceutically important compounds. The synthesis of azaindoles has been a great synthetic challenge for chemists. Many classical methods for indole synthesis (such as Fischer and Madelung cyclizations) often cannot be effectively applied to the synthesis of the corresponding azaindoles. In recent years, advances in organometallic chemistry have enabled a number of novel and efficient methodologies for azaindole formation as well as for the further functionalization of azaindole templates. In this tutorial review, we have surveyed the recent development of organometallic chemistry-based methods for azaindole synthesis.