gebhart/patrepeval huggingface dataset:
Evaluation of Colon Cancer–Specific Antigen 2 as a Potential Serum Marker for Colorectal Cancer (2008)

Our initial study shows that CCSA-2 is a potential serum-based marker for colon cancer detection with high sensitivity and specificity.
Chemopreventive effect of phosphodieasterase-4 inhibition in benzo(a)pyrene-induced murine lung cancer model (2014)

In vivo experiments in the benzo(a)pyrene-induced model of lung cancer show that PDE4 inhibition significant inhibits lung carcinogenesis. Our results provide evidence that PDE4 inhibitors may be suitable for the prevention of the lung cancer in high-risk groups, for example, heavy smokers and patients with COPD.
A Model of Human Tumor Dormancy: An Angiogenic Switch From the Nonangiogenic Phenotype (2006)

This model provides a conceptual framework and a reproducible in vivo system to study unresolved central questions in cancer biology regarding the initiation, reversibility, and molecular regulation of the timing of the angiogenic switch.
Bioadhesive properties of pegylated nanoparticles (2005)

The design of bioadhesive nanoparticles (NPs) for targeting specific sites within the gut remains a major challenge. One possible strategy to solve this problem may be the use of pegylated NPs. In general, these carriers display different bioadhesive properties to nondecorated NPs. Thus, pegylated NPs show a higher ability to interact with the small intestine mucosa rather than with the stomach. However, the type of surface conformation of polyethylene glycol chains appears to have a great influence on the behaviour of these NPs. Theoretically, the traditional 'brush' polyethylene glycol corona would facilitate the penetration of the pegylated particles through the mucus layer and the subsequent adhesive interaction with the mucosa, which would promote their absorption by intestinal enterocytes. On the contrary, pegylated NPs with a 'loop' conformation would increase the time of residence of the adhered fraction of particles in the mucosa.
Synchronization control of coded video streams: Algorithms and implementation. (1997)

In this thesis, we propose to blend the intra-media synchronization control of coded video streams with the decoding process. We present a client based application level buffer control scheme for coded video to maintain stream continuity, avoid data overflow and underflow conditions and compensate for possible clock drifts at the client. The control policy, referred to as the Predecoder Synchronization Controller (PSC), uses buffer occupancy as its main control parameter. Based on high and low buffer occupancy thresholds, overflow threats and starvation threats are detected. Time contraction (selective frame drop) and expansion concepts (selective frame repeat) are used to prevent these data overflow and starvation threats to become real conditions, respectively. PSC algorithms are specified for both Motion JPEG and MPEG. In the case of starvation or overflow threats, the PSC was found to smoothen the stream, avoiding long frame freeze and abrupt scene change situations, by creating localized variations in the rate of displayed stream. A prototype implementation of both MJPEG and MPEG PSCs was also carried out. (Abstract shortened by UMI.)
Comparing the defence-related gene expression changes upon root-knot nematode attack in susceptible versus resistant cultivars of rice (2016)

Rice is one of the major staple food crops in the world and an excellent model system for studying monocotyledonous plants. Diseases caused by nematodes in rice are well documented and among them, root-knot nematode (RKN), Meloidogyne graminicola, causes extensive yield decline. It is therefore necessary to identify novel sources of natural resistance to RKN in rice and to investigate the rice-RKN interaction in detail to understand the basal plant defence mechanisms and nematode manipulation of the host physiology. To this end, six different cultivars of rice were initially screened for RKN infection and development; Pusa 1121 and Vandana were found to be most susceptible and resistant to RKN infection, respectively. In order to investigate the role of major hormone-regulated plant defence pathways in compatible/incompatible rice-RKN interaction, some well-identified marker genes involved in salicylate/jasmonate/ethylene pathway were evaluated for their differential expression through qRT-PCR. In general, our study shows a remarkable discrepancy in the expression pattern of those genes between compatible and incompatible rice-RKN interaction. As most information on the molecular interplay between plants and nematodes were generated on dicotyledonous plants, the current study will strengthen our basic understanding of plant-nematode interaction in the monocot crops, which will aid in defining future strategies for best plant health measures.
Molecular Recognition at the Exterior Surface of a Zwitterionic Telomer Brush (2010)

3-Sulfo-N,N-dimethyl-N-(2'-methacryloyloxyethyl)propanaminium inner salt (SPB) was polymerized on a glass plate with a surface-confined initiator of atom transfer radical polymerization (ATRP) having a 2-bromoisobutyryl group. The glass plate modified with a brush of sulfobetaine telomer (PSPB) was highly hydrophilic and showed a strong resistance against nonspecific adsorption of proteins such as lysozyme and albumin. Through the polymerization from the free surface of PSPB chain by ATRP, furthermore, N-methacryloyloxysuccinimide (MAOSu) residues were introduced, and the incubation of the telomer (PSPB-b-PMAOSu)-modified glass chip with a lectin (concanavalin A, Con A) gave a glass chip covered with the Con-A-modified PSPB brush. The Con A fixed to the zwitterionic telomer brush pursued specific binding of mannose residues accumulated on the surface of Au colloidal particles, resulting in the increase in absorbance at 550 nm ascribable to localized surface plasmon resonance, while the nonspecific adsorption of proteins to the surface of the glass chip was still largely suppressed. The present results indicate usefulness of the zwitterionic telomer surface with antibiofouling properties as a scaffold for specific sensing devices.
A Multicenter, Placebo-controlled Trial of Melatonin for Sleep Disturbance in Alzheimer's Disease (2003)

Based on actigraphy as an objective measure of sleep time, melatonin is not an effective soporific agent in people with Alzheimer's disease.
Knee injury and Osteoarthritis Outcome Score (KOOS) - validation and comparison to the WOMAC in total knee replacement. (2003)

The Knee injury and Osteoarthritis Outcome Score (KOOS) is a valid, reliable, and responsive outcome measure in total joint replacement. In comparison to the WOMAC, the KOOS improved validity and may be at least as responsive as the WOMAC.
Syndecan-1 expression is up-regulated in pancreatic but not in other gastrointestinal cancers (2000)

Syndecan-1 belongs to the syndecan family of cell surface transmembrane heparan-sulfate proteoglycans, which participate in cell proliferation, cell migration and cell-matrix interactions. Decreased expression of syndecan-1 has been observed in some gastrointestinal malignancies, and it is thought that high levels of syndecan-1 correlate with the maintenance of epithelial morphology and inhibition of invasiveness. In our study, we characterized the expression of syndecan-1 in normal, chronic pancreatitis and primary and metastatic human pancreatic cancer tissues, in cultured pancreatic cancer cell lines and in esophageal, gastric, colon, and liver cancers. Pancreatic cancer cell lines expressed syndecan-1 mRNA and protein at variable levels. In addition, these cells also released syndecan-1 into the culture medium. Pancreatic cancer tissues markedly over-expressed syndecan-1 mRNA in comparison with both chronic pancreatitis (2.4-fold increase, p < 0.01) and normal pancreatic samples (10.6-fold increase, p < 0.01). There was no difference in syndecan-1 mRNA expression between early and advanced tumors. By in situ hybridization and immunohistochemistry, syndecan-1 expression was evident at relatively low levels in the ductal cells and less frequently in acinar cells of the normal pancreas. In chronic pancreatitis, syndecan-1 was present at low to moderate levels in areas with atrophic acinar cells and ductular complexes. In contrast, in pancreatic cancer tissues, syndecan-1 was present at moderate to high levels in the majority of the cancer cells within the tumor mass and also in metastatic lesions of pancreatic tumors. Syndecan-1 mRNA levels in other gastrointestinal malignancies (esophageal, gastric, colon and liver cancers) were not significantly different from the levels observed in the corresponding normal samples. Together, our findings suggest that syndecan-1 expression by pancreatic cancer cells may be of importance in the pathobiology of this disorder and that its role in pancreatic cancer seems to be different from that in other gastrointestinal malignancies.
VSV-G-Enveloped Vesicles for Traceless Delivery of CRISPR-Cas9 (2018)

The method of delivery of CRISPR-Cas9 into target cells is a strong determinant of efficacy and specificity in genome editing. Even though high efficiency of Cas9 delivery is necessary for optimal editing, its long-term and high levels of expression correlate with increased off-target activity. We developed vesicles (VEsiCas) carrying CRISPR-SpCas9 ribonucleoprotein complexes (RNPs) that are efficiently delivered into target cells through the fusogenic glycoprotein of the vesicular stomatitis virus (VSV-G). A crucial step for VEsiCas production is the synthesis of the single guide RNA (sgRNA) mediated by the T7 RNA polymerase in the cytoplasm of producing cells as opposed to canonical U6-driven Pol III nuclear transcription. In VEsiCas, the absence of DNA encoding SpCas9 and sgRNA allows rapid clearance of the nuclease components in target cells, which correlates with reduced genome-wide off-target cleavages. Compared with SpCas9 RNPs electroporation, which is currently the method of choice to obtain transient SpCas9 activity, VEsiCas deliver the nuclease with higher efficiency and lower toxicity. We show that a wide variety of cells can be edited through VEsiCas, including a variety of transformed cells, induced pluripotent stem cells (iPSCs), and cardiomyocytes, in vivo. VEsiCas is a traceless CRISPR-Cas9 delivery tool for efficient and safe genome editing that represents a further advancement toward the therapeutic use of the CRISPR-Cas9 technology.
Dendrimers in medical nanotechnology (2009)

Dendrimers are a class of highly branched synthetic polymers that form spherical macromolecules that can be reliably synthesized to a specific physical size in a highly reproducible manner. Dendrimers of different generations are chemically related to each other, allowing the study of molecular size without the interfering variable of different chemical structures.
Discrimination of wine using taste and smell sensors (1998)

The taste-smell sensory fusion was conducted by combining a taste sensor array using lipid/polymer membranes and a smell sensor array using conducting polymer elements. Responses to different brands of wine were investigated and a clear discrimination among different samples was obtained by processing the data from either type of sensors. The effect of the aging process on the quality of wine was also studied. It was found that the system can discriminate among differently aged samples of the same red wine. The information provided by one type of array is independent of that provided by the other and their combination enhances the overall information available concerning the sample being measured. This suggests that the sensory fusion can be a powerful way to improve the performance of sensor technologies currently available.
Iridium Complex-Catalyzed Allylic Amination of Allylic Esters (2001)

Iridium complex-catalyzed allylic amination of allylic carbonates was studied. The solvent strongly affected the catalytic activity. The use of a polar solvent such as EtOH is essential for obtaining the products in high yield. The reaction of (E)-3-substituted-2-propenyl carbonate and 1-substituted-2-propenyl carbonate with pyrrolidine in the presence of a catalytic amount of [Ir(COD)Cl](2) and P(OPh)(3) (P/Ir = 2) gave a branch amine with up to 99% selectivity. Both secondary and primary amines could be used for this reaction. When a primary amine was used, selective monoallylation occurred. No diallylation product was obtained. The reaction of 1,1-disubstituted-2-propenyl acetate with amines exclusively gave an alpha,alpha-disubstituted allylic amine. This reaction provides an alternative route to the addition of an organometallic reagent to ketimines for the preparation of such amines. The reaction of (Z)-3-substituted-2-propenyl carbonate with amines gave (Z)-linear amines with up to 100% selectivity. In all cases, no (E)-linear amine was obtained. The selectivities described here have not been achieved in similar palladium complex-catalyzed reactions.
Antibody modeling assessment (2011)

A blinded study to assess the state of the art in three-dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high-resolution x-ray Fab crystal structures covering a wide range of antigen-binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x-ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 Å. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 Å. H3 prediction yielded rmsd values around 3.0 Å for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments.
Optical limiter using a lead phthalocyanine (1993)

The performance of an optical limiter based on Pb-tetrakis(cumylphenoxy)phthalocyanine, a robust organic material with a large χ(3) and figure of merit, χ(3)/α0, is described. In an f/5 limiter with a sample transmission of 0.68, the threshold for limiting was 8±2 nJ and the dynamic range was greater than a factor of 103. The threshold for the PbPc(CP)4 limiter was ∼15 times smaller and the high intensity transmission ∼4–5 times lower than an equivalent limiter based on a thermal nonlinearity.
Influence of Physical Properties of Biomaterials on Cellular Behavior (2011)

Increasing mesh size of the hydrogels resulted in an increase in cellular proliferation exhibiting the strong correlation between mesh size and cell growth, while mesh size had a differential effect on ECM accumulation and expression of cartilage specific markers.
A New Mouse Myeloma Cell Line that Has Lost Immunoglobulin Expression but Permits the Construction of Antibody-Secreting Hybrid Cell Lines (1979)

We have isolated a subclone of the mouse myeloma cell line P3-X63-Ag8 that does not express immunoglobulin heavy or light chains. This clone X63-Ag8.653 can be used for efficient fusion with antibody-forming cells to obtain hybrid cell lines producing pure monoclonal antibodies. Screening of hybrid cell lines for specificity and immunoglobulin classes was done with a modified enzyme-linked immunosorbent assay.
Metabolism of ent-Kaurene to Gibberellin A12-Aldehyde in Young Shoots of Normal Maize (1992)

Young shoots of normal maize (Zea mays L.) were used to determine both the stepwise metabolism of ent-kaurene to gibberellin A(12)-aldehyde and the endogenous presence of the members in this series. Each of the five steps in the sequence was established by feeds of 17-(13)C, (3)H-labeled kauranoids to cubes from the cortex of elongating internodes, to homogenates from the cortex of elongating internodes, and/or to homogenates from dark-grown seedlings. The (13)C-metabolites were identified by Kovats retention indices (KRI) and full-scan capillary gas chromatography-mass spectrometry (GC-MS). Five substrates and the final product in this sequence were shown to be native by the isotopic dilution of 17-(13)C, (3)H-labeled substrates added as internal standards to extracts obtained from elongating internodes. Evidence for the isotopic dilution was obtained by KRI and full-scan capillary GC-MS. Thus, we document the presence in young maize shoots of the metabolic steps, ent-kaurene --> ent-kaurenol --> ent-kaurenal --> ent-kaurenoic acid --> ent-7 alpha-hydroxykaurenoic acid --> gibberellin A(12)-aldehyde.
Generation of a mouse mutant by oligonucleotide-mediated gene modification in ES cells (2006)

Oligonucleotide-mediated gene targeting is emerging as a powerful tool for the introduction of subtle gene modifications in mouse embryonic stem (ES) cells and the generation of mutant mice. However, its efficacy is strongly suppressed by DNA mismatch repair (MMR). Here we report a simple and rapid procedure for the generation of mouse mutants using transient down regulation of the central MMR protein MSH2 by RNA interference. We demonstrate that under this condition, unmodified single-stranded DNA oligonucleotides can be used to substitute single or several nucleotides. In particular, simultaneous substitution of four adjacent nucleotides was highly efficient, providing the opportunity to substitute virtually any given codon. We have used this method to create a codon substitution (N750F) in the Rb gene of mouse ES cells and show that the oligonucleotide-modified Rb allele can be transmitted through the germ line of mice.
Pushing the boundaries of molecular replacement with maximum likelihood (2001)

The molecular-replacement method works well with good models and simple unit cells, but often fails with more difficult problems. Experience with likelihood in other areas of crystallography suggests that it would improve performance significantly. For molecular replacement, the form of the required likelihood function depends on whether there is ambiguity in the relative phases of the contributions from symmetry-related molecules (e.g. rotation versus translation searches). Likelihood functions used in structure refinement are appropriate only for translation (or six-dimensional) searches, where the correct translation will place all of the atoms in the model approximately correctly. A new likelihood function that allows for unknown relative phases is suitable for rotation searches. It is shown that correlations between sequence identity and coordinate error can be used to calibrate parameters for model quality in the likelihood functions. Multiple models of a molecule can be combined in a statistically valid way by setting up the joint probability distribution of the true and model structure factors as a multivariate complex normal distribution, from which the conditional distribution of the true structure factor given the models can be derived. Tests in a new molecular-replacement program, Beast, show that the likelihood-based targets are more sensitive and more accurate than previous targets. The new multiple-model likelihood function has a dramatic impact on success.
DNA Sequencing: From Experimental Methods to Bioinformatics (1997)

What is DNA Sequencing? Chemical degradation (Maxam and Gilbert) method. Chain termination (Sanger dideoxy) method. Instrumentation and reagents. Template preparation. Gel electrophoresis. Non-radioactive methods. Troubleshooting. Confirmatory sequencing. Sequencing PCR products. Strategies for new sequence determination. Introduction to Bioinformatics and the Internet. Sequence databases. Sequence alignment and database searches. Sequencing projects and Contig analysis. Protein function prediction. Protein structure prediction. Appendices.
Safety evaluation and risk assessment of electronic cigarettes as tobacco cigarette substitutes: a systematic review (2014)

Electronic cigarettes are a recent development in tobacco harm reduction. They are marketed as less harmful alternatives to smoking. Awareness and use of these devices has grown exponentially in recent years, with millions of people currently using them. This systematic review appraises existing laboratory and clinical research on the potential risks from electronic cigarette use, compared with the well-established devastating effects of smoking tobacco cigarettes. Currently available evidence indicates that electronic cigarettes are by far a less harmful alternative to smoking and significant health benefits are expected in smokers who switch from tobacco to electronic cigarettes. Research will help make electronic cigarettes more effective as smoking substitutes and will better define and further reduce residual risks from use to as low as possible, by establishing appropriate quality control and standards.
Methane drainage with cross-measure boreholes on a retreat longwall face (1983)

Methane drainage by cross-measure boreholes on retreat longwall faces can be a viable alternative to the vertical gob degas boreholes under favorable circumstances. The research was done in a mine working Pittsburgh Coal seam in Northern West Virginia under U.S.B.M. Co-operative Agreement No. 14-09-0050-3252. The study was the first application of this technique to Pittsburgh coal seam. A total of fourteen, small diameter, inclined boreholes were drilled over a retreat longwall panel from gate roads, to intersect the overlying coal seams. All boreholes were manifolded to a pipeline and the gob gas was extracted by an exhaust fan on surface. The methane capture ratio was poor at 7 to 18% at various stages of the longwall panel. A vertical gob degas borehole captured an additional 20% gas. Poor results were due to premature failures of the cross-measure boreholes leading to air leakage. For better performance the boreholes should be drilled from a point 30 to 45 m from longwall pillar over the largest chain pillar, the standpipe should be grouted for at least 6 m, and the entry containing boreholes and the pipeline must be supported to ensure access for maintenance, and optimization of methane capture. Coursing the ventilation airmore » around longwall such that it forces methane-migration towards cross-measure boreholes can further improve methane capture. The optimum vertical inclination is 45/sup 0/ + or - 10/sup 0/.« less
CD-Search: protein domain annotations on the fly (2004)

We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST(R) heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi.