gebhart/patrepeval huggingface dataset:
Reactions of 1,5-π-cyclization of gem-difluoro-substituted azomethine ylides involving an aromatic ring (2006)

Reactions of N-(5-R-furan-2-ylmethylidene)anilines with difluorocarbene proceeds through intermediate azomethine ylides suffering 1,5-π-cyclization to yield 6,6-difluorocyclopropa[b]furo[2,3-c]pyrrole and/or 4,4,6,6-tetrafluorocyclopropa[b]furo[2,3-c]pyrrole. The heating of these compounds without solvent resulted in high yields of 2,5-disubstituted 7-fluoro-4,5-dihydrofuro[3,2-c]pyridin-4(5H)-ones.
Integrating expression-based drug response and SNP-based pharmacogenetic strategies into a single comprehensive pharmacogenomics program (2000)

In the third millennium, competitive advantage in drug development will derive from expertise in two areas: 1) the ability to prioritize and triage hits from a combinatorial chemistry/high-throughput screening experiment and pursue only those hits most likely to succeed through clinical development, and 2) the ability to identify those patients capable of mounting a therapeutic response with minimal toxic effects. Pharmacogenomics, the branch of genomics addressing molecular pharmacology and toxicology, is anticipated to streamline drug development by addressing these issues. Pharmacogenomics includes two separate disciplines: expression pharmacogenomics and pharmacogenetics. Typically, they are regarded as unique fields and are pursued independently from each other. Here, we describe a pharmacogenomic strategy that combines and integrates both fields to create a single robust program. GeneCalling, a rapid, comprehensive differential transcript expression profiling technique, is applied to rodent models of drug response to identify novel markers predictive of drug efficacy and toxicity. SeqCalling, a high-throughput transcript sequencing strategy with a coding region bias, has identified 120,000 novel human single nucleotide polymorphisms (SNPs). Novel pharmacogenetic candidates are then identified by searching the human orthologs of rodent drug response genes for SeqCalling SNPs that can be pursued in systematic genotype screens to verify clinical correlations. In this manner, GeneCalling expression pharmacogenomics identifies markers capable of triaging leads from hits and SeqCalling converts a subset of these markers into pharmacogenetic correlates capable of identifying appropriately responsive patients. Drug Dev. Res. 49:54–64, 2000. © 2000 Wiley-Liss, Inc.
Recognition of shapes by editing their shock graphs (2004)

This paper presents a novel framework for the recognition of objects based on their silhouettes. The main idea is to measure the distance between two shapes as the minimum extent of deformation necessary for one shape to match the other. Since the space of deformations is very high-dimensional, three steps are taken to make the search practical: 1) define an equivalence class for shapes based on shock-graph topology, 2) define an equivalence class for deformation paths based on shock-graph transitions, and 3) avoid complexity-increasing deformation paths by moving toward shock-graph degeneracy. Despite these steps, which tremendously reduce the search requirement, there still remain numerous deformation paths to consider. To that end, we employ an edit-distance algorithm for shock graphs that finds the optimal deformation path in polynomial time. The proposed approach gives intuitive correspondences for a variety of shapes and is robust in the presence of a wide range of visual transformations. The recognition rates on two distinct databases of 99 and 216 shapes each indicate highly successful within category matches (100 percent in top three matches), which render the framework potentially usable in a range of shape-based recognition applications.
Adiponectin: A Novel Adipokine Linking Adipocytes and Vascular Function (2004)

Cardiovascular disease accounts for an overwhelming proportion of the morbidity and mortality suffered by patients with obesity and type 2 diabetes mellitus, and recent work has elucidated several potential mechanisms by which increased adiposity enhances cardiovascular risk. Excess adipose tissue, especially in certain compartments, leads to reduced insulin sensitivity in metabolically responsive tissues, which is frequently associated with a set of cardiovascular risk factors, including hyperinsulinemia, hypertension, dyslipidemia, and glucose intolerance. Increasing attention has also been paid to the direct vascular effects of plasma proteins that originate from adipose tissue, especially adiponectin, which exhibits potent antiinflammatory and antiatherosclerotic effects. This brief review will summarize recent work on the vascular actions of adiponectin, which complements the growing body of information on its insulin-sensitizing effects in glucose and lipid metabolism. Adiponectin is now a recognized component of a novel signaling network among adipocytes, insulin-sensitive tissues, and vascular function that has important consequences for cardiovascular risk.
Identification of HLA-A2-restricted CTL epitopes of a novel tumour-associated antigen, KIF20A, overexpressed in pancreatic cancer (2010)

KIF20A is a novel promising candidate for anticancer immunotherapeutic target for pancreatic cancers.
<title>Complexity analysis of the emerging MPEG-4 standard as a basis for VLSI implementation</title> (1998)

A complexity analysis of the video part of the emerging ISO/IEC MPEG-4 standard was performed as a basis for HW/SW partitioning for VLSI implementation of a portable MPEG-4 terminal. While the computational complexity of previously standardized video coding schemes was predictable for I-, P- and B-frames over time, the support of arbitrarily shaped visual objects as well as various coding options within MPEG-4 introduce now content dependent computational requirements with significant variance. In this paper the result of a time dependent complexity analysis of the encoding and decoding process of a binary shape coded video object (VO) and the comparison with a rectangular shaped VO is given for the complete codec as well as for the single tools of the encoding and decoding process. It is shown, that the average MB complexity per arbitrary shaped P-VOP depicts significant variation over time for the encoder and minor variations for the decoder.
Electrochemical sensing based on printable temporary transfer tattoos (2012)

The realization of epidermal chemical sensing requires a fabrication methodology compatible with the non-planarity and irregularities of the human anatomy. This communication describes the development of printed temporary transfer tattoo (T3) electrochemical sensors for physiological and security monitoring of chemical constituents leading to the demonstration of 'electronic skin'.
Signal Transduction in Maize and Arabidopsis Mesophyll Protoplasts (2001)

Plant protoplasts show physiological perceptions and responses to hormones, metabolites, environmental cues, and pathogen-derived elicitors, similar to cell-autonomous responses in intact tissues and plants. The development of defined protoplast transient expression systems for high-throughput screening and systematic characterization of gene functions has greatly contributed to elucidating plant signal transduction pathways, in combination with genetic, genomic, and transgenic approaches.
Using background modes for testing, debugging and emulation of microcontrollers (2002)

The Background Mode of operation for the M68HC16 and M68300 families of microcontrollers has provided a method whereby an external host development system can take control of the microcontroller causing it to execute certain elementary commands. As shown here, a more complex system can be built using the Background Mode as a base to form an inexpensive, yet capable, emulation system. The addition of a bus state analyzer and appropriate software can further enhance a host development system's usefulness without significantly impacting the complexity of the emulation/debugging system. Most importantly, the Background Debug Mode allows the actual microcontroller in the target system to emulate itself providing, perhaps, the most accurate form of emulation.
Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures (2000)

We report a new tandem mass spectrometric approach for the improved identification of polypeptides from mixtures (e.g., using genomic databases). The approach involves the dissociation of several species simultaneously in a single experiment and provides both increased speed and sensitivity. The data analysis makes use of the known fragmentation pathways for polypeptides and highly accurate mass measurements for both the set of parent polypeptides and their fragments. The accurate mass information makes it possible to attribute most fragments to a specific parent species. We provide an initial demonstration of this multiplexed tandem MS approach using an FTICR mass spectrometer with a mixture of seven polypeptides dissociated using infrared irradiation from a CO2 laser. The peptides were added to, and then successfully identified from, the largest genomic database yet available (C. elegans), which is equivalent in complexity to that for a specific differentiated mammalian cell type. Additionally, since only a few enzymatic fragments are necessary to unambiguously identify a protein from an appropriate database, it is anticipated that the multiplexed MS/MS method will allow the more rapid identification of complex protein mixtures with on-line separation of their enzymatically produced polypeptides.
Plasmonic-Based Electrochemical Impedance Spectroscopy: Application to Molecular Binding (2011)

Plasmonic-based electrochemical impedance spectroscopy (P-EIS) is developed to investigate molecular binding on surfaces. Its basic principle relies on the sensitive dependence of surface plasmon resonance (SPR) signal on surface charge density, which is modulated by applying an ac potential to a SPR chip surface. The ac component of the SPR response gives the electrochemical impedance, and the dc component provides the conventional SPR detection. The plasmonic-based impedance measured over a range of frequency is in quantitative agreement with the conventional electrochemical impedance. Compared to the conventional SPR detection, P-EIS is sensitive to molecular binding taking place on the chip surface and less sensitive to bulk refractive index changes or nonspecific binding. Moreover, this new approach allows for simultaneous SPR and surface impedance analysis of molecular binding processes.
A New Biological Matrix for Septal Occlusion (2003)

The ideal septal occluder scaffold should promote the healthiest and most complete healing response possible while eventually facilitating the full resorption of the material, leaving "native" tissue behind. An excellent biocompatibility of the scaffold tissue is a prerequisite for quick, complete, and firm ingrowth of the device, optimizing outcomes and minimizing the potential for complications. Intestinal collagen layer (ICL) is a highly purified (acellular) bioengineered type-1 collagen derived from porcine submucosa. It is gradually resorbed by the host organism and subsequently replaced by the host tissue. CardioSEAL occluders were modified by substituting the conventional polyester fabric for an intestinal collagen layer (ICL). Percutaneous transcatheter closure of interventionally created atrial septal defects was performed in lambs using these modified occluders. A complete pathomorphological investigation including histology was carried out after 2, 4, and 12 weeks follow-up. Standard CardioSEAL implants served as a control group. After 2 weeks in vivo the devices were already covered completely by neo-endothelium. Compared with the conventional synthetic scaffold, ICL devices showed a quicker endothelialization, decreased thrombogenicity, and superior biocompatibility with no significant cellular infiltration observed in the histology of explants with ICL fabrics. After 3 months in vivo the collagen layer remained mechanically intact, but began to show the first histological signs of mild disintegration, gradual resorption, and remodeling. In conclusion, short-term results from preliminary in vivo experiments using a bioengineered collagen matrix as the occluder tissue scaffold showed excellent biocompatibility. This resulted in superior overall results: quicker endothelialization, a decreased thrombogenicity, and decreased immunological host response.
Functional Myc-Max heterodimer is required for activation-induced apoptosis in T cell hybridomas. (1994)

T cell hybridomas respond to activation signals by undergoing apoptotic cell death, and this is likely to represent comparable events related to tolerance induction in immature and mature T cells in vivo. Previous studies using antisense oligonucleotides implicated the c-Myc protein in the phenomenon of activation-induced apoptosis. This role for c-Myc in apoptosis is now confirmed in studies using a dominant negative form of its heterodimeric binding partner, Max, which we show here inhibits activation-induced apoptosis. Further, coexpression of a reciprocally mutant Myc protein capable of forming functional heterodimers with the mutant Max can compensate for the dominant negative activity and restore activation-induced apoptosis. These results imply that Myc promotes activation-induced apoptosis by obligatory heterodimerization with Max, and therefore, by regulating gene transcription.
Oxidative Kerogen Degradation: A Potential Approach to Hydraulic Fracturing in Unconventionals (2019)

Oil and gas production from shale formations has proven to be economical because of advances in hydraulic fracturing but remains very challenging in part because of the presence of the ductile, polymer nature of the hydrocarbon source material, kerogen. This organic matter is intertwined among silicates, aluminosilicates, and other minerals as fine laminae that weave among the shale rock fabric, adding soft mechanical cohesion to the material. A potential solution has been developed, a new type of reactive fracturing fluid composed of strong oxidizers such as bromate (BrO3–), which could mitigate the adverse effects of the polymeric nature of kerogen on the hydraulic conductivity of the fractured shale formation. High-resolution scanning electron microscopy of kerogen-rich shale samples before and after fluid treatment demonstrates notable porosity enhancement evident by cracks forming in the macerals and augmenting the volumetric porosity. The stability of the reactive components at elevated reservoir temperatures in addition to the demonstrated results suggest the potential for measureable improvements in hydraulic conductivity and hence in the ultimate recovery of oil and gas from future hydraulic fracturing operations.
PHAEODACTYLUM TRICORNUTUM MICROALGAE GROWTH RATE IN HETEROTROPHIC AND MIXOTROPHIC CONDITIONS (2009)

The Brazilian National Program for Biofuel Production has been encouraging diversification of feedstock for biofuel production. One of the most promising alternatives is the use of microalgae biomass for biofuel production. The cultivation of microalgae is conducted in aquatic systems, therefore microalgae oil production does not compete with agricultural land. Microalgae have greater photosynthetic efficiency than higher plants and are efficient fixing CO2. The challenge is to reduce production costs, which can be minimized by increasing productivity and oil biomass. Aiming to increase the production of microalgae biomass, mixotrophic cultivation, with the addition of glycerol has been shown to be very promising. During the production of biodiesel from microalgae there is availability of glycerol as a side product of the transesterification reaction, which could be used as organic carbon source for microalgae mixotrophic growth, resulting in increased biomass productivity. In this paper, to study the effect of glycerol in experimental conditions, the batch culture of the diatom Phaeodactylum tricornutum was performed in a 2-liter flask in a temperature and light intensity controlled room. During 16 days of cultivation, the number of cells per ml was counted periodically in a Neubauer chamber. The calculation of dry biomass in the control experiment (without glycerol) was performed every two days by vacuum filtration. In the dry biomass mixotrophic experiment with glycerol concentration of 1.5 M, the number of cells was assessed similarly in the 10th and 14th days of cultivation. Through a volume element methodology, a mathematical model was written to calculate the microalgae growth rate. Was used an equation that describes the influence of irradiation and concentration of nutrients in the growth of microalgae. A simulation time of 16 days was used in the computations, with initial concentration of 0.1 g l-1. In order to compare simulation data with experimental data, we calculated the dry weight in 8 points in the course of sixteen days. In this way, it was possible to assess graphically biomass concentration versus time through the experiments and by numerical simulation. It was identified that the simulation results were consistent with the experiments and that the addition of glycerol greatly influenced the growth of microalgae. In the present analysis, the glycerol added increased 30% in biomass.
Chromosomal alterations in squamous cell carcinomas of the head and neck: Window to the biology of disease (2001)

Cytogenetic endpoints may be useful tools for dissecting clinical differences in tumor behavior and response to therapy. Numerous studies are underway to examine the biology of and genetic alterations in SCCHN that will lead to additional markers for use as rapid, noninvasive screening methods for individuals at high risk for primary or recurrent SCCHN. Our goal is to minimize morbidity and mortality from SCCHN by identifying useful predictors of disease and recurrence risk and response to therapy to implement earlier detection and more effective prevention and/or treatment strategies.
Exploration of subsite binding specificity of human cathepsin D through kinetics and rule‐based molecular modeling (1993)

The family of aspartic proteinases includes several human enzymes that may play roles in both physiological and pathophysiological processes. The human lysosomal aspartic proteinase cathepsin D is thought to function in the normal degradation of intracellular and endocytosed proteins but has also emerged as a prognostic indicator of breast tumor invasiveness. Presented here are results from a continuing effort to elucidate the factors that contribute to specificity of ligand binding at individual subsites within the cathepsin D active site. The synthetic peptide Lys-Pro-Ile-Glu-Phe*Nph-Arg-Leu has proven to be an excellent chromogenic substrate for cathepsin D yielding a value of kcat/Km = 0.92 x 10(-6) s-1 M-1 for enzyme isolated from human placenta. In contrast, the peptide Lys-Pro-Ala-Lys-Phe*Nph-Arg-Leu and all derivatives with Ala-Lys in the P3-P2 positions are either not cleaved at all or cleaved with extremely poor efficiency. To explore the binding requirements of the S3 and S2 subsites of cathepsin D, a series of synthetic peptides was prepared with systematic replacements at the P2 position fixing either Ile or Ala in P3. Kinetic parameters were determined using both human placenta cathepsin D and recombinant human fibroblast cathepsin D expressed in Escherichia coli. A rule-based structural model of human cathepsin D, constructed on the basis of known three-dimensional structures of other aspartic proteinases, was utilized in an effort to rationalize the observed substrate selectivity.
Theme identification in human-human conversations with features from specific speaker type hidden spaces (2014)

This paper describes a research on topic identification in a real-world customer service telephone conversations between an agent and a customer. Separate hidden spaces are considered for agents, customers and the combination of them. The purpose is to separate semantic constituents from the speaker types and their possible relations. Probabilities of hidden topic features are then used by separate Gaussian classifiers to compute theme probabilities for each speaker type. A simple strategy, that does not require any additional parameter estimation, is introduced to classify themes with confidence indicators for each theme hypothesis. Experimental results on a real-life application show that the use of features from speaker type specific hidden spaces capture useful semantic contents with significantly superior performance with respect to independent word-based features or a single set of features. Experimental results also show that the proposed strategy makes it possible to perform surveys on collections of conversations by automatically selecting processed samples with high theme identification accuracy.
Benchmarking Database Systems A Systematic Approach (1983)

This paper describes a customized database and a comprehensive set of queries that can be used for sys-tematic benchmarking of relational database systems. Designing this database and a set of carefully tuned bench-marks represents a first attempt in developing a scientific methodology for performance evaluation of database management systems. We have used this database to perform a comparative evaluation of the database machine DIRECT, the &amp;amp;quot;university &amp;amp;quot; and &amp;amp;quot;commercial &amp;amp;quot; versions of the INGRES database system, the relational database sys-tem ORACLE, and the IDM 500 database machine. We present a subset of our measurements (for the single user case only), that constitute a preliminary performance evaluation of these systems. NOTE TO THE READER It is important for the reader to recognize that the results presented in this paper represent the performance of the various database systems at ONE point in time and that new releases of the various systems will undoubtably perform differently. The objective of this research was not to make a definitive statement as to which is the best relational database system on the market today. Rather, our goal was to develop a standard set of benchmarks that could be used by database system designers for evaluating changes to their systems and by users for selecting the system which best suits their needs. It is also imperative that the reader understands that the results presented in no way measure the performance of the various systems in a multiuser environment. We are currently developing a methodology for benchmarking database systems in this environment.
Recommendations for the Standardization and Interpretation of the Electrocardiogram (2007)

This statement provides a concise list of diagnostic terms for ECG interpretation that can be shared by students, teachers, and readers of electrocardiography. This effort was motivated by the existence of multiple automated diagnostic code sets containing imprecise and overlapping terms. An intended outcome of this statement list is greater uniformity of ECG diagnosis and a resultant improvement in patient care. The lexicon includes primary diagnostic statements, secondary diagnostic statements, modifiers, and statements for the comparison of ECGs. This diagnostic lexicon should be reviewed and updated periodically.