gebhart/patrepeval huggingface dataset:
Immunohistochemical biomarkers for bladder cancer prognosis (2011)

Urothelial carcinoma of the bladder (UCB) is an especially complex and heterogeneous disease with a broad spectrum of histologic findings and potentially lethal behavior. Despite advances in surgical techniques, as well as intravesical and systemic therapies, up to 30% of patients with non-muscle-invasive UCB and 50% of patients with muscle-invasive UCB experience disease progression, recurrence, and eventual death. Standard prognostic features, such as pathologic stage and grade, have limited ability to predict the outcomes of this heterogeneous population. Current risk-stratification algorithms using clinical and pathologic parameters are limited in their prognostic ability. Molecular medicine holds the promise that clinical outcomes will be improved by more accurate prognostication and directing therapy towards the mechanisms and targets associated with the growth of an individual patient's tumor. Immunohistochemical analysis of biomarker expression has provided insight into the molecular pathogenesis of UCB and offers the potential for improving clinical decision making. Numerous candidate immunohistochemical biomarkers for patients with UCB have been identified, with those relating to the cell cycle and apoptosis/cell proliferation being the most extensively studied. The present review discusses the most promising immunohistochemical biomarkers. Special attention is paid to recent data from a multi-institutional collaboration that has implemented a regulated, phased biomarker discovery and validation pathway. Because UCB tumorigenesis and progression is a process involving multiple genetic and epigenetic alterations, multiple biomarkers need to be integrated into a prognostic signature to accurately predict outcomes. There is no doubt that biomarkers will eventually guide our clinical decision making regarding follow-up scheduling and treatment choice.
ChemInform Abstract: Synthesis of Highly Substituted Symmetrical 1,3‐Dienes via Tandem Carbocupration and Organocuprate Oxidation. (2011)

Abstract A one‐pot tandem carbocupration/oxidation of alkynyl esters provides rapid access to highly substituted symmetrical 1,3‐dienes [cf.
Security and Performance Comparison of ONOS and ODL controllers (2019)

Informational Report
Expression and Characterization of the Human c- myc DNA-Binding Protein (1985)

In an effort to study in detail the nature of the protein product of the human protooncogene c-myc, we have expressed the gene at high levels in Escherichia coli. The c-myc coding region was taken from a full-length cDNA clone and inserted into a vector designed to express foreign gene products efficiently in E. coli. Pulse-labeling experiments indicated that the rate of expression of c-myc in this thermoinducible expression system is very efficient. The product was relatively stable and accumulated to approximately 10% of total cellular protein. A purification protocol was devised which allowed the c-myc protein to be readily purified in quantities sufficient for detailed biochemical and physical analyses. A high-titer polyclonal antiserum was raised against the pure protein and shown to immunoprecipitate the p110gag-myc fusion protein of MC-29-infected quail cells. This antiserum also selectively detects a protein with an apparent molecular weight of 64,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis from a Burkitt lymphoma cell line. We conclude that this 64-kilodalton protein is the human c-myc gene product since the E. coli-made protein exhibits an equivalent molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, even though its calculated molecular weight is 49,000. Furthermore, we demonstrate that the bacterially made human c-myc protein is a DNA-binding protein and that it exhibits a high nonspecific affinity for double-stranded DNA.
Analytical method of a multilayered meander-line polarizer plate with normal and oblique plane-wave incidence (1987)

Simple empirical formulas for perpendicular and parallel polarization susceptances for a meander-line grating plate are given. The numerical results compared favorably with experimental data and published data. Simple transmission-line model in terms of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</tex> -type mode and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H</tex> -type mode for multilayered meander-line polarizer plate is presented for plane wave incidence at normal and oblique angles. Numerical results for design examples are given for practical application.
Enhanced Growth of β-C 3N 4 Crystallites at a High Substrate Temperature (1998)

The growth of β-C 3 N 4 crystallites is studied at various substrate temperatures by an inductively-coupled plasma sputtering method using 500 W of radio frequency power to enhance the gas dissociation. The crystallites deposited are demonstrated to be β-C 3 N 4 phase rather than other phases from the transmission electron diffraction and the X-ray photoelectron spectroscopy results. Upon increasing the substrate temperature from 400°C to 800°C, β-C 3 N 4 crystallite size increases from 0.02 µm to 0.2 µm, but the [N]/[C] atomic ratio in the film decreases slightly from 1.0 to 0.85, suggesting that the film contains larger β-C 3 N 4 crystallites in a less nitrogenated amorphous carbon matrix at a higher temperature. The film deposited at 800°C exhibits a highly spotty transmission electron diffraction pattern and contains a high percentage (90%) of sp 3 C-N bonding as estimated from X-ray photoelectron spectroscopy. The results suggest that a high substrate temperature enhances the formation of β-C 3 N 4 crystallites at a high degree of gas dissociation.
Calorie restriction does not elicit a robust extension of replicative lifespan inSaccharomyces cerevisiae (2014)

Calorie restriction (CR) is often described as the most robust manner to extend lifespan in a large variety of organisms. Hence, considerable research effort is directed toward understanding the mechanisms underlying CR, especially in the yeast Saccharomyces cerevisiae. However, the effect of CR on lifespan has never been systematically reviewed in this organism. Here, we performed a meta-analysis of replicative lifespan (RLS) data published in more than 40 different papers. Our analysis revealed that there is significant variation in the reported RLS data, which appears to be mainly due to the low number of cells analyzed per experiment. Furthermore, we found that the RLS measured at 2% (wt/vol) glucose in CR experiments is partly biased toward shorter lifespans compared with identical lifespan measurements from other studies. Excluding the 2% (wt/vol) glucose experiments from CR experiments, we determined that the average RLS of the yeast strains BY4741 and BY4742 is 25.9 buds at 2% (wt/vol) glucose and 30.2 buds under CR conditions. RLS measurements with a microfluidic dissection platform produced identical RLS data at 2% (wt/vol) glucose. However, CR conditions did not induce lifespan extension. As we excluded obvious methodological differences, such as temperature and medium, as causes, we conclude that subtle method-specific factors are crucial to induce lifespan extension under CR conditions in S. cerevisiae.
Peptidyl - tRNA hydrolase and RNase activities In cell fractions of rat liver used in in vitro reconstitution of rough membrane (1975)

Peptidyl-tRNA hydrolase and RNase activities have been studied in those fractions of rat liver, which are used in in vitro reconstitution of rough membrane, because these enzymes may interfere with the in vitro reconstitution. It was found that smooth membrane has an active peptidyl-tRNA hydrolase, while the other fractions tested, polyribosomes, rough membrane, stripped rough membrane and the post-microsomal supernatant had no, or very low, peptidyl-tRNA hydrolase activity. Polyribosomes, rough and stripped rough membrane have RNase activity; this activity could be completely inhibited by rat liver RNase inhibitor. It is shown that RNase inhibitor is an obligatory component in in vitro experiments, in which rough membrane is reconstituted from stripped rough membrane, ribosomes and mRNA.
Fabrication of bio-fiber based Eichhornia crassipes /Al 2 O 3 particles hybrid biocomposites and investigation of important properties (2023)

The need for environmentally friendly composite materials that meet the necessary criteria is growing. Making novel environmentally acceptable composites with hybrid Eichhornia crassipes (EGs)/Al 2 O 3 particles is an option. This paper aims to investigate the thermal, tensile strength, and flexural strength properties of a polyester composite filled with hybrid EG/Al 2 O 3 particles. The tensile strength, flexural strength, and morphology of EGs/Al 2 O 3 hybrid composite will be investigated in this work. The hot pressed for 60 minutes at 170°C procedure was used to shape the hybrid composite. EGs/Al 2 O 3 particles content was altered from 0:25 to 5:20, 10:15 to 15:10, 20:5, and 25:0 (vol.%). The results reveal that when the EGs content of the composite is in the range of 10–15% (vol.%), the tensile and bending strength of the composite increases. The EGI (15% EGs:10% Al 2 O 3 ) and EGH (10% EGs:10% Al 2 O 3 ) composites had the highest tensile and bending strengths, with 38.697 and 77.786 MPa, respectively. The boost in strength is thought to be due to Al 2 O 3 acting as a cursor in the composite, preventing fracture progression. The scanning electron microscope (SEM) fracture morphology reveals a strong and tight interfacial connection between the EGs, Al 2 O 3 , and polyester layers. In addition, when the EGs grew, the composites’ thermal characteristics improved. According to the findings, the EGs/ Al 2 O 3 particle hybrid composite can be used in automotive applications.
Copper nanowire based transparent conductive films with high stability and superior stretchability (2014)

The unique partly-embedding structure makes the copper nanowire-based film a transparent conductive electrode, with mechanical robustness and great anti-oxidation stability.
An evaluation of climate and runoff variability and associated livelihood risks in the Mzingwane Catchment Limpopo Basin Zimbabwe (2006)

Climate change occurs over relatively long time scales, although some acceleration in changes can also be seen in data of the last twenty years. The reasons for the current changes in the climatological variables might be anthropogenic (e.g. greenhouse gas emission) or natural (e.g. solar variability etc.), or most likely a combination of both reasons. An increasing body of evidence shows that greenhouse gas emissions are changing our climate significantly. Climate change is projected to substantially reduce available water (as reflected by projected runoff from a catchment) in many of the waterscarce areas of the world A statistical analysis was carried out of over fifty years of precipitation, temperature and runoff data from several locations in the Mzingwane Catchment – the portion of the Limpopo Basin that falls within Zimbabwe. The trends show declines in precipitation and runoff and increases in maximum and minimum temperatures, across the catchment. The trends observed are comparable to those predicted from some of the global circulation models (GCMs) based on the Intergovernmental Panel on Climate Change Special Report on Emission Scenarios (IPCC (SRES)). Regression analyses show the relationships between climate variability and change and decreasing runoff. The trends observed have major livelihood implications. Zimbabwe’s second largest city, Bulawayo, and some other urban and mining centres, obtain water from the Upper Mzingwane subcatchment, and the long term reliability of this supply is threatened. The majority of the population in the Mzingwane Catchment are smallholder farmers, dependant largely on rainfed agriculture. Reduced and erratic precipitation threatens their future yields. Mitigating the impact of climate change requires a package of strategies including (i) water demand management in the urban centres, (ii) a major investment in soil water conservation strategies for smallholder farmers, (iii) expansion of recycling by large water users, and (iv) development of alternative livelihood strategies.
Image Analysis Using Mathematical Morphology (1987)

For the purposes of object or defect identification required in industrial vision applications, the operations of mathematical morphology are more useful than the convolution operations employed in signal processing because the morphological operators relate directly to shape. The tutorial provided in this paper reviews both binary morphology and gray scale morphology, covering the operations of dilation, erosion, opening, and closing and their relations. Examples are given for each morphological concept and explanations are given for many of their interrelationships.
Congenital adrenal hyperplasia and lower urinary tract symptoms (2005)

Patients with a diagnosis of CAH are more likely to have significant urinary symptoms than normal controls. At present it is not clear whether this is a result of surgery or an effect of CAH. In at least two-thirds of patients surgery did not achieve the objective of reducing urinary symptoms.
Postsynaptic synucleins mediate vesicular exocytosis of endocannabinoids (2021)

Abstract Two seemingly unrelated questions have long motivated studies in neuroscience: How are endocannabinoids, among the most powerful modulators of synaptic transmission, released from neurons? What are the physiological functions of synucleins, key contributors to Parkinson’s Disease? Here, we report an unexpected convergence of these two questions: Endocannabinoids are released via vesicular exocytosis from postsynaptic neurons by a synuclein-dependent mechanism. Specifically, we find that deletion of all synucleins selectively blocks all endocannabinoid-dependent synaptic plasticity; this block is reversed by postsynaptic expression of wildtype but not of mutant α-synuclein. Loading postsynaptic neurons with endocannabinoids via patch-pipette dialysis suppressed presynaptic neurotransmitter release in wildtype but not in synuclein-deficient neurons, suggesting that the synuclein deletion blocks endocannabinoid release. Direct optical monitoring of endocannabinoid release confirmed the requirement of synucleins. Given the role of synucleins in vesicular exocytosis, the requirement for synucleins in endocannabinoid release indicates that endocannabinoids are secreted via exocytosis. Consistent with this hypothesis, postsynaptic expression of tetanus-toxin light chain, which cleaves synaptobrevin SNAREs, also blocked endocannabinoid-dependent plasticity and release. The unexpected finding that endocannabinoids are released via synuclein-dependent exocytosis assigns a function to synucleins and resolves a longstanding puzzle of how neurons release endocannabinoids to induce synaptic plasticity.
Photoinitiated copolymerization of acrylamide and styrene in oil‐in‐water microemulsion (1997)

This article describes the copolymerization of acrylamide with styrene in oil-in-water microemulsion, using dodecyl betaine as emulsifier and α-hydroxy-α,α-dimethyl acetophenone or α,α-dimethoxy-phenyl acetophenone as photoinitiator. Results indicated that the photoinitiation of polymerization occurs at the interface between the oil phase and the water phase and that the polymerization occurs in the microemulsion droplet. Particle size increased with increasing polymerization time. The copolymer chain consisted of isolated acrylamide units randomly distributed among styrene groups. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 66: 2543–2549, 1997
DiMeX: A Text Mining System for Mutation-Disease Association Extraction (2016)

The number of published articles describing associations between mutations and diseases is increasing at a fast pace. There is a pressing need to gather such mutation-disease associations into public knowledge bases, but manual curation slows down the growth of such databases. We have addressed this problem by developing a text-mining system (DiMeX) to extract mutation to disease associations from publication abstracts. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic patterns to extract mutation-disease associations. DiMeX achieves high precision and recall with F-scores of 0.88, 0.91 and 0.89 when evaluated on three different datasets for mutation-disease associations. DiMeX includes a separate component that extracts mutation mentions in text and associates them with genes. This component has been also evaluated on different datasets and shown to achieve state-of-the-art performance. The results indicate that our system outperforms the existing mutation-disease association tools, addressing the low precision problems suffered by most approaches. DiMeX was applied on a large set of abstracts from Medline to extract mutation-disease associations, as well as other relevant information including patient/cohort size and population data. The results are stored in a database that can be queried and downloaded at http://biotm.cis.udel.edu/dimex/. We conclude that this high-throughput text-mining approach has the potential to significantly assist researchers and curators to enrich mutation databases.
Mechanical B ehavior of Irradiated M etals. (2022)

Abstract not provided.
Electron-Lattice Systems in Weak Gravitation: The Schiff Dessler Problem (2009)

The behavior of composite matter in external fields can be very revealing. The quantum mechanical problem of a material object (test mass) placed in a uniform (weak) gravitational field, g, was considered by many authors starting with Schiff [Phys. Rev. 151, 1067 (1966)]. Depending on the theoretical treatment opposing results of gravity induced (electric) field have been reported. In the Schiff model [L.I. Schiff, PRB, 1, 4649 (1970)] the field is predicted to be oriented anti-parallel (with reference to g). On the other hand it is found to be parallel in the elastic lattice model [A. J. Dessler et al, Phys.Rev, 168, 737, (1968); Edward Teller, PNAS, 74, 2664 (1977)]. Surprisingly, modern researchers have largely overlooked this interesting contradiction. Here an experimental test is suggested. We also reason that advanced density functional type calculations can provide valuable guidance.
Structure and Function of the Estrogen Receptor (1993)

The hormone binding domain of the estrogen receptor is required not only for binding estradiol but also to form stable homodimers of the protein and mediate transcriptional activation by the receptor. Residues that are essential for estrogen binding are also involved in dimerization, suggesting that the hormone-binding pocket is at or near the dimer interface. Distinct hydrophobic and charged residues are essential for hormone-dependent transcriptional activation, and these appear to be conserved by other members of the nuclear receptor family. We have found that the pure antiestrogens ICI 164384 and ICI 182780 increase the turnover of the receptor compared with that in the presence of estradiol. Because it is likely that the pure antiestrogens bind to a similar region of the receptor as that of estradiol, we propose that they inhibit receptor dimerization by means of their 7 alpha alkyl-amide extension. It appears that as a consequence nuclear uptake is inhibited and the receptor more rapidly degraded in the cytoplasm.
Improved Grain Boundary Conductivity By Post Annealing: Minimizing Vacancy Depletion through Non-Equilibrium Distribution of Immobile Species (2014)

A one dimensional model has been used to study the thermodynamics of defects in ionic crystals. It is found that space charge layer near grain boundary contributes to grain boundary resistance. Quenching less mobile ions to a distribution equilibrated at higher annealing temperatures increases point defect concentrations, which leads to a smaller grain boundary resistance. EIS measurement confirmed the model, and it is found that post annealing at higher temperatures helps to improve ionic transport through grain boundary.
Maintaining Monodispersity in a Microbubble Population Formed by Flow-Focusing (2008)

The dynamic processes impacting the size distributions of lipid-encapsulated microbubbles formed by flow-focusing were observed by video optical microscopy. Parameters studied included the filling gas, gas saturating the surrounding solution, and microbubble size (initial size 2-12 microm) to simulate typical laboratory conditions. Typically, dissolution or growth, followed by Ostwald ripening at a collection cover glass, were observed and quantified. However, in the case of small nitrogen-filled microbubbles surrounded by an air-saturated solution, Ostwald ripening was avoided for at least 9 h. These bubbles had a final size distribution of 1.5 +/- 0.1 microm. This work suggests that lipid-encapsulated microbubbles formed by flow-focusing should be given sufficient time to reach a terminal size before coming into contact with each other. These long-lived mondisperse microbubbles should be of interest in ultrasound contrast agents, microfabrication, food, and research applications.
Dna methylating activity in murine lymphoma cells xenogenized by triazene derivatives (1987)

We investigated whether epigenetic rather than mutational events may be involved in the induction of novel immunogenicity ("xenogenization") in murine lymphoma treated with triazene derivatives. To this end, we assessed the DNA methylation pattern of tumor cells during the course of in vivo or in vitro xenogenization by 2 triazenes, and compared it with the changes induced by the DNA hypomethylating agent 5-azacytidine (5-aza). While all of the tested agents were able to increase tumor cell immunogenicity, their effects on DNA methylating activity were opposite. In particular, the novel immunogenicity conferred by 5-aza treatment correlated well with the extent of hypomethylation induced, whereas xenogenization by triazenes was accompanied by a limited increase in DNA methylating activity. Interestingly, the antimutagenic compound quinacrine, which is known to block the xenogenizing activity of triazenes, was incapable of hypermethylating effects, whereas the hypermethylating agent cytosine arabinoside (ara-C) was apparently unable to interfere with the induction of novel immunogenicity by triazenes.
High Molecular-Weight Thermoplastic Polymerization of Kraft Lignin Macromers with Diisocyanate (2014)

A high molecular-weight thermoplastic lignin-based polymer was successfully synthesized by adjusting the degree of polymerization while inducing linear growth of lignin macromers via methylene diphenyldiisocyanate. The thermoplastic lignin-urethane polymer was desirably achieved in a narrow range of reaction conditions of 2.5 to 3.5 h at 80 oC in this study, and the molecular weight of the resulting lignin-based polyurethanes (LigPU) reached as high as 912,000 g/mole, which is far above any reported values of lignin-based polymer derivatives. The thermal stability of LigPU was greatly improved by the urethane polymerization, giving the initial degradation temperature (T2%) at 204 °C, which should be compared with T2% = 104 °C of the pristine lignin. This was due to the fact that the OH groups in the lignin macromers, having low bond-dissociation energy, were replaced by the urethane bonds. In dielectric analysis, the synthesized LigPU exhibited a softening transition at 175 °C corresponding to a combinatorial dual process of the dry Tg,dry of the lignin macromers and the softening of methylenediphenyl urethane chains. This work clearly demonstrated that a high molecular weight of thermoplastic LigPU could be desirably synthesized, broadening the lignin application for value added and eco-friendly products through common melt processes of polymer blend or composites.