gebhart/patrepeval huggingface dataset:
Novel oncolytic adenoviruses targeted to melanoma: specific viral replication and cytolysis by expression of E1A mutants from the tyrosinase enhancer/promoter. (2002)

Malignant melanoma is characterized by growing incidence, early metastasis, and a lack of effective treatment for advanced disease, suggesting a pressing need for novel therapeutic approaches. Conditionally replicative adenoviruses (CRAds) constitute a new and promising strategy for cancer treatment that has been rapidly translated into clinical trials. We engineered novel melanoma-targeted CRAds, AdTyrdelta24 and AdTyrdelta2delta24, by replacing the adenoviral E1A promoter with a cassette containing a polyA sequence and a human tyrosinase enhancer/promoter construct (hTyr2E/P). The small size of this cassette allows retention of the E3 region within these CRAds, which was shown to enhance viral spread and oncolysis. In addition, we introduced mutations (delta24 and delta2delta24) into the viral E1A gene, which attenuate adenoviral replication in quiescent cells. The cell cycle pathways mediating this attenuation are defective in melanoma cells. By analysis of E1A expression, we prove fidelity of hTyr2E/P in the adenoviral genome and in the context of viral replication when an upstream polyA was included. We further show efficient cytotoxicity of AdTyrdelta24 and AdTyrdelta2delta24 in melanoma cell lines and a 100-1000-fold attenuation in cell lines derived from various nonmelanocytic tissues. Virus replication and progeny production of these viruses were similarly selective, resulting in 200-800-fold higher virus yields in melanoma cells versus control cells, thus establishing viral cytolysis and spread as the cause of the observed cell killing. Cytotoxicity of AdTyrdelta24 for normal fibroblasts and keratinocytes was strongly attenuated, and this virus caused selective killing of melanoma cells but not surrounding keratinocytes in a coculture system. Progeny production and cytotoxicity of AdTyrdelta24 in melanoma cells were similar to matching viruses containing the stronger cytomegalovirus enhancer/promoter instead of hTyr2E/P. Furthermore, AdTyrdelta24 showed a cytopathic effect similar to the wild-type E1A containing AdTyrwt and only minimally reduced compared with wild-type adenovirus. We conclude that the generated CRAds AdTyrdelta24 and AdTyrdelta2delta24 constitute novel targeted agents for gene therapy and viral oncolysis of metastatic melanoma.
Dirichlet process mixture models made scalable and effective by means of massive distribution (2019)

Clustering with accurate results have become a topic of high interest. Dirichlet Process Mixture (DPM) is a model used for clustering with the advantage of discovering the number of clusters automatically and offering nice properties like, e.g., its potential convergence to the actual clusters in the data. These advantages come at the price of prohibitive response times, which impairs its adoption and makes centralized DPM approaches inefficient. We propose DC-DPM, a parallel clustering solution that gracefully scales to millions of data points while remaining DPM compliant, which is the challenge of distributing this process. Our experiments, on both synthetic and real world data, illustrate the high performance of our approach on millions of data points. The centralized algorithm does not scale and has its limit on 100K data points, where it needs more than 7 hours. In this case, our approach needs less than 30 seconds.
Cataloging coding sequence variations in human genome databases (2008)

Background: With the recent growth of information on sequence variations in the human genome, predictions regarding the functional effects and relevance to disease phenotypes of coding sequence variations are becoming increasingly important. The aims of this study were to catalog protein-coding sequence variations (CVs) occurring in genetic variation databases and to use bioinformatic programs to analyze CVs. In addition, we aim to provide insight into the functionality of the reference databases. Methodology and Findings: To catalog CVs on a genome-wide scale with regard to protein function and disease, we investigated three representative databases; the Human Gene Mutation Database (HGMD), the Single Nucleotide Polymorphisms database (dbSNP), and the Haplotype Map (HapMap). Using these three databases, we analyzed CVs at the protein function level with bioinformatic programs. We proposed a combinatorial approach using the Support Vector Machine (SVM) to increase the performance of the prediction programs. By cataloging the coding sequence variations using these databases, we found that 4.36 % of CVs from HGMD are concurrently registered in dbSNP (8.11 % of CVs from dbSNP are concurrent in HGMD). The pattern of substitutions and functional consequences predicted by three bioinformatic programs was significantly different among concurrent CVs, and CVs occurring solely in HGMD or in dbSNP. The experimental results showed that the proposed SVM combination noticeably outperformed the individual prediction programs.
Influence of Simple Electrolytes on the Orientational Ordering of Thermotropic Liquid Crystals at Aqueous Interfaces (2011)

We report orientational anchoring transitions at aqueous interfaces of a water-immiscible, thermotropic liquid crystal (LC; nematic phase of 4'-pentyl-4-cyanobiphenyl (5CB)) that are induced by changes in pH and the addition of simple electrolytes (NaCl) to the aqueous phase. Whereas measurements of the zeta potential on the aqueous side of the interface of LC-in-water emulsions prepared with 5CB confirm pH-dependent formation of an electrical double layer extending into the aqueous phase, quantification of the orientational ordering of the LC leads to the proposition that an electrical double layer is also formed on the LC-side of the interface with an internal electric field that drives the LC anchoring transition. Further support for this conclusion is obtained from measurements of the dependence of LC ordering on pH and ionic strength, as well as a simple model based on the Poisson-Boltzmann equation from which we calculate the contribution of an electrical double layer to the orientational anchoring energy of the LC. Overall, the results presented herein provide new fundamental insights into ionic phenomena at LC-aqueous interfaces, and expand the range of solutes known to cause orientational anchoring transitions at LC-aqueous interfaces beyond previously examined amphiphilic adsorbates.
Digital Video Processing—1980 (1980)

The end objective of the engineering portion of the motion picture and television industries is to provide the tools for effective visual communication. Advances in engineering technology have brought the film and videotape media progressively closer together during the past decade. The digital technology of the 80s will make further and significant strides toward the eventual creation of one highly versatile electronic motion picture communications tool.
Modeling of $V_{\rm th}$ Shift in nand Flash-Memory Cell Device Considering Crosstalk and Short-Channel Effects (2008)

A threshold-voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) shift of sub-100-nm NAND flash-memory cell transistors was modeled systematically, and the modeling was verified by comparing with the data from measurement and 3-D device simulation. The V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> shift of the NAND flash-memory cell was investigated by changing parameters such as gate length, width, drain voltage, dielectric material between cells, space between cells, lightly doped-drain depth, and adjacent-cell bias. The proposed model covers two dominant device physics: capacitance coupling effect between adjacent cells and short-channel effect. Our model showed an accurate prediction of the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> shift of NAND flash-memory array and a good agreement with the data from simulation and measurement.
Controlling Height with Temperature (1998)

Temperature management has emerged as an important tool for plant height control in greenhouse production systems. This is particularly important in vegetable transplant production where chemical controls for plant height are limited or not legal. Plant height is a function of the number of nodes and the length of each internode, and both are strongly influenced by greenhouse temperatures. Node number, or formation rate, is primarily a function of the average greenhouse temperature, increasing as the average temperature increases. Internode length is strongly influenced by the relationship between the day and night temperature, commonly referred to as DIF (day temperature - night temperature). As DIF increases, so does internode length in most plant species studied. Although the nature and magnitude of temperature effects vary with species, cultivar, and environmental conditions, these two basic responses can be used to modify transplant growth. Although data are limited, controlling transplant height with temperature does not appear to adversely influence plant establishment or subsequent yield.
Quality Control in Manufacturing of Electrospun Nanofiber Composites (2003)

Introduction The extremely small fiber size and low mass of nanofiber composites makes quality control measurement very difficult. Most commercially available contact measurement equipment cannot work with the nanofiber composite without altering its characteristics. Generally, non-contacting optical methods are not effective because the wavelength of the light used is greater than the diameter of the nanofibers. Non-contact Gamma or Beta gauges lack the necessary resolution. Research methods such as Scanning Electron Microscopy (SEM) are not practical in a production setting. Large-scale production of nanofiber composites requires unique quality control (QC) methods. Figures 1a, 1b, and 1c show examples of nanofiber composites manufactured by Donaldson. As Donaldson Company’s nanofiber production has increased to over 10,000 m per day during the last 20 years, QC methods have been developed to address these needs. Four evaluation tools that have been developed for commercial production of nanofibers will be described. These evaluation tools focus on: uniformity of nanofiber distribution, fiber size distribution, durability of fiber layer in the composite, and environmental resistance.
Estimation of sequential circuit activity considering spatial and temporal correlations (2002)

We present an exact and an approximate method for estimating signal activity at the internal nodes of sequential logic circuits. The methodology takes spatial and temporal correlations of logic signals into consideration. Given the state transition graph (STG) of a finite state machine (FSM), we create an extended state transition graph (ESTG), where the temporal correlations of the input signals are explicitly represented. From the graph we derive the equations to calculate exact signal probabilities and activities. For large circuits an approximate method for calculating the activities by unrolling the next state logic is proposed. Experimental results show that if temporal and spatial correlations are not considered, the switching activities of the internal nodes can be off by more than 40% compared to simulation based techniques. However, the results of the approximate method proposed in the paper is within 5% of logic simulation results.
Hepatitis C Virus Subgenomic Replicon Requires an Active NS3 RNA Helicase (2005)

Mutations were introduced into the NS3 helicase region of a hepatitis C virus (HCV) Con1 subgenomic replicon to ascertain the role of the helicase in viral replication. One new replicon lacked two-thirds of the NS3 helicase (Deltahel), and six others contained one of the following six amino acid substitutions in NS3: R393A, F438A, T450I, E493K, W501A, and W501F. It has been previously reported that purified R393A, F438A, and W501A HCV helicase proteins do not unwind RNA but unwind DNA, bind RNA, and hydrolyze ATP. On the other hand, previous data suggest that a W501F protein retains most of its unwinding abilities and that purified T450I and E493K HCV helicase proteins have enhanced unwinding abilities. In a hepatoma cell line that has been cured of HCV replicons using interferon, the T450I and W501F replicons synthesized both negative-sense and positive-sense viral RNA and formed colonies after selection with similar efficiencies as the parent replicon. However, the Deltahel, R393A, F438A, and W501A replicons encoded and processed an HCV polyprotein but did not synthesize additional viral RNA or form colonies. Surprisingly the same phenotype was seen for the E493K replicon. The inability of the E493K replicon to replicate might point to a role of pH in viral replication because a previous analysis has shown that, unlike the wild-type NS3 protein, the helicase activity of an E493K protein is not sensitive to pH changes. These results demonstrate that the RNA-unwinding activity of the HCV NS3 helicase is needed for RNA replication.
Progesteron in der Mitch: Radioimmunologische Bestimmung, Beziehungen zur Gelbkörperfunktion and Milchfettkonzentration (1973)

Inhalt Ein spezifisches und hock empfindliches radioimmunologisches Verfahren zur Bestimmung von Progesteron in der Mitch wurde entwickelt, das auch den Zuverlässigkeitskriterien entspricht. 0,2 ml Mitch reichen als Ausgangsmenge aus, um über vorhandene odor fehlende Gelbkörperfunktion bei der Kuh zu informieren. Parallelmessungen im Blutplasma und Mitch ergaben synchron verlaufende Progesteronkonzentrationen während des Zyklus and der Früngravidität. Bezüglich der Stichproben ist zu berücksichtigen, daβ der Milchfettgehalt die aktuelle Progesteronkonzentration in der Mitch beeinflussen kann. Die Praktikabilität des Verfahrens zur routinemäβigen Diagnostik der Frühträchtigkeit sowie von klinischen Fällen bei der Kuh wird weiter untersucht. Contents (Progesterone in milk: determination by radioimmunoassay, relations to corpus luteum function and milk fat concentrations) A Specific and highly sensitive radioimmunoassay, also meeting the other reliability criteria, for the determination of progesterone in milk is described. Milk samples of 0,2 ml are sufficient to inform about presence or absence of a corpus luteum function in the cow. Concentrations in milk and peripheral plasma revealed an identical secretion pattern for progesterone during the oestrous cycle and early pregnancy. Concerning the drawing of the milk sample it is necessary to realize that the milk fat content can influence the actual progesterone concentration. The practicability of the procedure to diagnose routinely early pregnancy or clinical cases in cows is under further research.
The importance of proper weighting methods (1993)

The importance of good weighting methods in information retrieval --- methods that stress the most useful features of a document or query representative --- is examined. Evidence is presented that good weighting methods are more important than the feature selection process and it is suggested that the two need to go hand-in-hand in order to be effective. The paper concludes with a method for learning a good weight for a term based upon the characteristics of that term.
Expression of IL-23R and IL-17 and the pathology and prognosis of urinary bladder carcinoma (2018)

Expression of interleukin-23 receptor (IL-23R) and IL-17 in urinary bladder carcinoma (UBC) was investigated to explore the correlations with prognosis. IL-23/IL-17 axis significantly inhibited the development of inflammatory bowel disease. Thirty patients with UBC were enrolled in Zhengzhou Central Hospital Affiliated to Zhengzhou University from September 2013 to September 2014. Tumor tissue and adjacent healthy tissue were collected, and the levels of IL-23R and IL-17 mRNA were detected by RT-PCR. Thirty healthy people were also selected to serve as normal control group. Serum levels of IL-23R and IL-17 in serum of UBC patients and normal controls were detected by ELISA, and the correlations with clinical features of UBC were analyzed. Pearson's correlation analysis was used to analyze the correlation between IL-23R and IL-17 protein expression. Follow-up study was performed by phone or during patient's visit to out-patient department. Overall survival (OS) and disease-free survival (DFS) curves were plotted by Kaplan-Meier method to analyze the correlation between expression of IL-23R and IL-17 and survival time. ROC curve was used to detect the diagnostic values of IL-23R and IL-17 protein for UBC. Levels of IL-23R and IL-17 mRNA in UBC tissue were 3.26 and 2.65 times higher than those in adjacent tissue (P<0.05), and serum levels of IL-23R and IL-17 protein in UBC patients were significantly higher than those in normal control group. Protein expression levels of IL-23R and IL-17 were correlated with clinical stage and lymph node metastasis in UBC patients (P<0.05), and Cox hazard model showed that L-23R and IL-17 expression may be independent factors for UBC (P<0.05), and high expression levels of IL-23R and IL-17 significantly shortened the OS and DFS (P<0.05). Serum levels of IL-23R and IL-17 can be used to effectively diagnose clinical stage and lymph node metastasis of UBC patients, and the combined diagnosis has a higher sensitivity and specificity than the diagnosis using a single factor. These findings indicated that expression levels of IL-23R and IL-17 were increased in tumor tissue and serum of UBC patients, and the increased expression levels of IL-23R and IL-17 were correlated with poor prognosis. Detection of IL-23R and IL-17 levels has certain clinical significance in the diagnosis and prognosis of UBC.
A pulsed finite-difference time-domain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges (2000)

We combine the finite-difference time-domain method with pulse response techniques in order to calculate the light scattering properties of biological cells over a range of wavelengths simultaneously. The method we describe can be used to compute the scattering patterns of cells containing multiple heterogeneous organelles, providing greater geometric flexibility than Mie theory solutions. Using a desktop computer, we calculate the scattering patterns for common homogeneous models of biological cells and also for more complex representations of cellular morphology. We find that the geometry chosen significantly impacts scattering properties, emphasizing the need for careful consideration of appropriate theoretical models of cellular scattering and for accurate microscopic determination of optical properties.
Anterior Cruciate Ligament Reconstruction With Amnion Biological Augmentation (2018)

Anterior cruciate ligament (ACL) ruptures are common and unfortunate injuries for many athletes. The standard therapy for ACL rupture is ACL reconstruction with either autograft, harvested from hamstring or patellar tendon, or allograft tendon from a tissue donor. Advances in tissue engineering have produced interventions to augment the healing process and may have applications when it comes to ACL reconstruction. In this Technical Note and accompanying video, we describe a simple technique to implant an amnion matrix graft with a tendon graft during ACL reconstruction. This procedure uses the proposed anti-inflammatory, scaffolding, and stem cell-producing effects of the amniotic membrane to biologically augment the healing process of an ACL reconstruction.
Recombinant expression of<i>Streptococcus pneumoniae</i>capsular polysaccharides in<i>Escherichia coli</i> (2016)

Currently, Streptococcus pneumoniae is responsible for over 14 million cases of pneumonia worldwide annually, and over 1 million deaths, the majority of them children. The major determinant for pathogenesis is a polysaccharide capsule that is variable and is used to distinguish strains based on their serotype. The capsule forms the basis of the pneumococcal polysaccharide vaccine (PPV23) that contains purified capsular polysaccharide from 23 serotypes, and the pneumococcal conjugate vaccine (PCV13), containing 13 common serotypes conjugated to CRM197 (mutant diphtheria toxin). Purified capsule from S. pneumoniae is required for pneumococcal conjugate vaccine production, and costs can be prohibitively high, limiting accessibility of the vaccine in low-income countries. In this study, we demonstrate the recombinant expression of the capsule-encoding locus from four different serotypes of S. pneumoniae within Escherichia coli. Furthermore, we attempt to identify the minimum set of genes necessary to reliably and efficiently express these capsules heterologously. These E. coli strains could be used to produce a supply of S. pneumoniae serotype-specific capsules without the need to culture pathogenic bacteria. Additionally, these strains could be applied to synthetic glycobiological applications: recombinant vaccine production using E. coli outer membrane vesicles or coupling to proteins using protein glycan coupling technology.
Synthesis of New Amphiphilic Diblock Copolymers and Their Self-Assembly in Aqueous Solution (2005)

Amphiphilic diblock copolymers composed of poly(butyl acrylate) as the hydrophobic block with a low glass transition temperature and of six different hydrophilic blocks (one anionic, one cationic, and four nonionic hydrophilic blocks) are prepared via reversible addition fragmentation chain transfer (RAFT) polymerization. The nonionic hydrophilic blocks comprise in addition to the classical poly(dimethylacrylamide), the thermally sensitive poly(N-acryloylpyrrolidine), and a comb-type polymer made of a poly(ethylene glycol acrylate) macromonomer, as well as a new strongly hydrophilic sulfoxide polymer. The “living” character of the polymerizations is supported by very low polydispersity indexes and a good correlation between the molar masses obtained and the theoretically expected ones. Two distinct glass transition temperatures were found by differential scanning calorimetry for the block copolymers, suggesting the immiscibility of the blocks in bulk. The self-assembling properties of the amphiphilic diblock copolymers in aqueous and organic media were studied by nuclear magnetic resonance spectroscopy and dynamic light scattering, as a function of the polarity of the hydrophilic blocks, the ratio of the lengths of the two blocks, and the overall molar mass of the diblock copolymers. Micellelike aggregates with diameters from 25 to 100 nm in water are found, as well as inverse micelles in organic solvents. The length of the hydrophobic block seems to be the main factor governing the size of the aggregates in water. The aggregates are very stable upon dilution and temperature cycles. For large hydrophobic blocks, big structures are observed in addition to small micelles initially after the dispersion in water. As the big aggregates disappear slowly, the micellization process seems thermodynamically favored. If two populations of micelles made from different block copolymers are brought together, “mixed” micelles are formed. The implicit exchange of polymers proves the dynamic character of the micellar systems based on poly(butyl acrylate) as hydrophobic block.
Modeling the Whole Firm: The Effect of Multiple Inputs and Financial Intermediation on Bank Deposit Rates (2004)

Empirical studies of price competition typically analyze the direct effects of market structure, cost, and local demand on prices; this approach has been applied widely to studies of bank deposit rates. However, the theory of the banking firm suggests that substitutability between sources of deposits and conditions in the bank loan market should also affect the pricing of retail deposits. This paper develops a theoretical model to incorporate these effects, and tests the predictions empirically using institution-level deposit rate data from Bank Rate Monitor. The results suggest that the cost of large-scale deposits affects how banks price retail deposits, and that conditions in lending markets feed back into retail deposit rates.