gebhart/patrepeval huggingface dataset:
Air-Stable Conversion of Separated Carbon Nanotube Thin-Film Transistors from p-Type to n-Type Using Atomic Layer Deposition of High-κ Oxide and Its Application in CMOS Logic Circuits (2011)

Due to extraordinary electrical properties, preseparated, high purity semiconducting carbon nanotubes hold great potential for thin-film transistors (TFTs) and integrated circuit applications. One of the main challenges it still faces is the fabrication of air-stable n-type nanotube TFTs with industry-compatible techniques. Here in this paper, we report a novel and highly reliable method of converting the as-made p-type TFTs using preseparated semiconducting nanotubes into air-stable n-type transistors by adding a high-κ oxide passivation layer using atomic layer deposition (ALD). The n-type devices exhibit symmetric electrical performance compared with the p-type devices in terms of on-current, on/off ratio, and device mobility. Various factors affecting the conversion process, including ALD temperature, metal contact material, and channel length, have also been systematically studied by a series of designed experiments. A complementary metal-oxide-semiconductor (CMOS) inverter with rail-to-rail output, symmetric input/output behavior, and large noise margin has been further demonstrated. The excellent performance gives us the feasibility of cascading multiple stages of logic blocks and larger scale integration. Our approach can serve as the critical foundation for future nanotube-based thin-film macroelectronics.
Markers of Intestinal Inflammation, Not Bacterial Burden, Correlate With Clinical Outcomes in Clostridium difficile Infection (2013)

Persistent diarrhea in CDI correlates with intestinal inflammation and not fecal pathogen burden. These findings suggest that modulation of host response, rather than adjustments to antimicrobial regimens, might be a more effective approach to patients with unremitting disease.
Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes (2003)

Micro-RNAs are a class of small non-coding regulatory RNAs that impair translation by imperfect base pairing to mRNAs. For analysis of their cellular function we injected different miRNA-specific DNA antisense oligonucleotides in Drosophila embryos. In four cases we observed severe interference with normal development, one had a moderate impact and six oligonucleotides did not cause detectable phenotypes. We further used the miR-13a DNA antisense oligonucleotide as a PCR primer on a cDNA library template. In this experimental way we identified nine Drosophila genes, which are characterised by 3' untranslated region motifs that allow imperfect duplex formation with miR-13 or related miRNAs. These genes, which include Sos and Myd88, represent putative targets for miRNA regulation. Mutagenesis of the target motif of two genes followed by transfection in Drosophila Schneider 2 (S2) cells and subsequent reporter gene analysis confirmed the hypothesis that the binding potential of miR-13 is inversely correlated with gene expression.
Holographic photopolymerization for fabrication of electrically switchable inorganic-organic hybrid photonic structures (2003)

Holography offers a versatile, rapid and volume scalable approach for making large area, multi-dimensional, organic PBGs; however, the small refractive index contrast of organics prevents formation of a complete band-gap. The introduction of inorganic nanoparticles to the structure provides a possible solution. In contrast to the multiple steps (exposure, development and infiltration) necessitated by lithographic-based holography (e.g. photoresists), holographic photopolymerization of monomer-nanoparticle suspensions enables one-step fabrication of multidimensional organic-inorganic photonic band gap (PBG) structures with high refractive index contrast. The PBGs are formed by segregation of semiconductor nanocrystals during polymerization of the polymer network. Addition of CdSe/ZnS polymerization of the highly cross-linked polymer network. Addition of CdSe/ZnS quantum dots or ZnO nanocrystals to the H-PDLCs formulation results in phase segregation of the nanoparticles into the liquid crystal rich lamellae, producing photonic structures with high diffraction efficiencies that may be modulated by application of an external electric field.
Design and Synthesis of N-Maleimido-Functionalized Hydrophilic Polymers via Copper-Mediated Living Radical Polymerization:  A Suitable Alternative to PEGylation Chemistry (2005)

A series of alpha-functional maleimide polymethacrylates (M(n) = 4.1-35.4 kDa, PDi = 1.06-1.27) have been prepared via copper-catalyzed living radical polymerization (LRP). Two independent synthetic protocols have been successfully developed and the polymers obtained in multigram scale, with an 80-100% content of maleimide reactive chain ends, depending on the method employed. A method for the synthesis of amino-terminated polymers, starting from Boc-protected amino initiators, has also been developed, as these derivatives are key intermediates in one of the two processes studied in the present work. The alternative synthetic pathway involves an initiator containing a maleimide unit "protected" as a Diels-Alder adduct. After the polymerization step, the maleimide functionality has been reintroduced by retro-Diels-Alder reaction, by simply refluxing those polymers in toluene for 7 h. These maleimido-terminated materials, poly(methoxyPEG((475))) methacrylates and poly(glycerol) methacrylates, differ for both the nature and size of the polymer side branches and showed an excellent solubility in water, a property that made them an ideal candidate for the synthesis of new polymer-(poly)peptide biomaterials. These functional polymers have been successfully employed in conjugation reactions in the presence of thiol-containing model substrates, namely, reduced glutathione (gamma-Glu-Cys-Gly) and the carrier protein, bovine serum albumin (BSA), in 100 mM phosphate buffer (pH 6.8-7.4) and ambient temperature.
Quantification of hepatitis C virus by TaqMan PCR: Comparison with HCV amplicor monitor assay (1999)

The quantitation of serum levels of hepatitis C virus RNA in chronic hepatitis C has been regarded as one of the most important indicators for the outcome of interferon therapy. A new method was used for quantitating the copy number of hepatitis C virus RNA using TaqMan polymerase chain reaction and for comparing the ability and usefulness of this assay with Amplicor Monitor assay in 138 patients. The detection range of hepatitis C virus RNA by TaqMan polymerase chain reaction was from 2 x 10(3) to 2 x 10(8) copies/ml. Hepatitis C virus RNA was detectable in 128 cases (92.8%) and undetectable in 10 cases (7.2%) by this method. The RNA levels measured by Amplicor Monitor assay correlated significantly with those measured by TaqMan polymerase chain reaction assay and the sensitivity of the two assays was almost equal. Thus, TaqMan polymerase chain reaction assay appears sufficiently sensitive for the evaluation of hepatitis C virus RNA and would be useful for the diagnosis and management of hepatitis C virus infection.
Pattern Recognition in Coupled Chemical Kinetic Systems (1993)

A network of open, bistable reaction systems coupled by mass transfer is simulated. The mass transfer rates are determined by a Hebb-type rule, and the programmable network can store patterns of high and low concentrations in each bistable system. In a parallel computation, the network recognizes patterns similar, but not necessarily identical, to stored patterns.
Substrate-dependent changes of the oxidative O-dealkylation mechanism of several chemical and biological oxidizing systems (1996)

The O-dealkylation mechanisms of a series of alkyl aryl ethers, mediated by several chemical and biological oxidizing systems, i.e. Cu2+–ascorbic acid–O2, γ-radiolysis and rat liver microsomes-NADPH/O2, were examined. In every oxidizing system, the O-dealkylation mechanisms changed dramatically depending on the nature of the substrates. In the Cu2+–ascorbic acid–O2 system and γ-radiolysis, electron density at the ipso-position and the ease of H atom abstraction from the alkyl moiety of the substrates were critical to determine the O-dealkylation mechanism. In the cytochrome P450-dependent monooxygenases, the determinant was whether or not the substrate has a phenolic hydroxy group at an ortho- or para-position relative to the alkoxy group. The results have led us to propose a new O-dealkylation mechanism involving the initial formation of a phenoxyl radical.
Binary mutation testing through dynamic translation (2012)

This paper presents a novel mutation based testing method through binary mutation. For this, a table of mutants is derived by control flow analysis of a disassembled binary under test. Mutations are injected at runtime by dynamic translation. Thus, our approach neither relies on source code nor a certain compiler. As instrumentation is avoided, testing results correspond to the original binary. In addition to high-level language faults, the proposed approach captures target specific faults related to compiling and linking. We investigated the software of an automotive case study. For this, a taxonomy of mutation operators for the ARM instruction set is proposed. Our experimental results prove 100% accuracy w.r.t. confidence metrics provided by conventional testing methods while avoiding significant mutant compilation overhead. Further speed up is achieved by an efficient binary mutation testing framework that relies on extending the open source software emulator QEMU.
Mechanistic Basis of Enzyme-Targeted Drugs (2005)

Enzymes offer unique opportunities for drug design that are not available to cell surface receptors, nuclear hormone receptors, ion channels, transporters, and DNA. Here, we review the variety of inhibition mechanisms for enzyme-targeted drugs, and establish an enzyme target database for drugs currently marketed in the United States. From an analysis of the FDA Orange Book, there are 317 marketed drugs that work by inhibiting an enzyme. These drugs inhibit 71 enzymes, including 48 human, 13 bacterial, five viral, four fungal, and one protozoal enzyme. Among the 317 drugs, 65% either undergo reactive chemistry in the active site of the target enzyme or contain a structural motif related to the substrate. Among the 71 enzyme targets, 25 are irreversibly inhibited by drugs, and 19 of the 25 irreversibly inhibited enzymes are covalently modified by the drug. In two additional cases, the drug forms a covalent complex with the substrate, and in three more cases, the drug traps a covalent enzyme-substrate intermediate. Four of the 71 enzymes are inhibited by transition-state analogues. Moreover, advanced methods for determining transition-state structure now offer the opportunity for direct drug design without resorting to expensive random testing campaigns. A full appreciation of enzyme mechanisms sets enzymes apart as a specialized class of targets for highly directed drug design.
A Concise Synthesis of the Pyrroloquinoline Nucleus of the Makaluvamine Alkaloids (1997)

Abstract A concise five step synthesis of the pyrroloquinoline related to makaluvamine, and discorhabdine from 1,2-dimethoxy-3,5-dinitrobenzene is developed.
Transcriptional Analysis of Essential Genes of the Escherichia coli Fatty Acid Biosynthesis Gene Cluster by Functional Replacement with the Analogous Salmonella typhimurium Gene Cluster (1998)

The genes encoding several key fatty acid biosynthetic enzymes (called the fab cluster) are clustered in the order plsX-fabH-fabD-fabG-acpP-fabF at min 24 of the Escherichia coli chromosome. A difficulty in analysis of the fab cluster by the polar allele duplication approach (Y. Zhang and J. E. Cronan, Jr., J. Bacteriol. 178:3614-3620, 1996) is that several of these genes are essential for the growth of E. coli. We overcame this complication by use of the fab gene cluster of Salmonella typhimurium, a close relative of E. coli, to provide functions necessary for growth. The S. typhimurium fab cluster was isolated by complementation of an E. coli fabD mutant and was found to encode proteins with > 94% homology to those of E. coli. However, the S. typhimurium sequences cannot recombine with the E. coli sequences required to direct polar allele duplication via homologous recombination. Using this approach, we found that although approximately 60% of the plsX transcripts initiate at promoters located far upstream and include the upstream rpmF ribosomal protein gene, a promoter located upstream of the plsX coding sequence (probably within the upstream gene, rpmF) is sufficient for normal growth. We have also found that the fabG gene is obligatorily cotranscribed with upstream genes. Insertion of a transcription terminator cassette (omega-Cm cassette) between the fabD and fabG genes of the E. coli chromosome abolished fabG transcription and blocked cell growth, thus providing the first indication that fabG is an essential gene. Insertion of the omega-Cm cassette between fabH and fabD caused greatly decreased transcription of the fabD and fabG genes and slower cellular growth, indicating that fabD has only a weak promoter(s).
Inhibitors of Bacterial Efflux Pumps as Adjuvants in Antibacterial Therapy and Diagnostic Tools for Detection of Resistance by Efflux (2010)

Abstract: Active efflux is a wide-spread mechanism for bacterial resistance to antibiotics, which contributes to poor intrinsic susceptibility, cross-resistance to structurally diverse classes of drugs, or selection of other mechanisms of resistance. Thus, inhibition of efflux pumps appears to be (i) a promising strategy for restoring the activity of existing antibiotics, and (ii) a useful method to detect the presence of efflux determinants in clinical isolates. Structurally dissimilar classes of inhibitors have been patented in the last decade, some are analogues of antibiotic substrates [tetracyclines, quinolones or aminoglycosides] and others are new chemical entities [including substituted indoles, ureas, aromatic amides, piperidinecarboxylic acids, alkylamino- or alkoxyquinolines, peptidomimetics, and pyridopyrimidines]. Their spectrum of activity, in terms of companion antibiotics and bacteria, differ significantly. Narrow spectrum inhibitors are of prime interest as diagnostic tools, while broad spectrum inhibitors are expected for adjuvant therapies. Apart from (i) a peptidomimetic inhibitor of Mex pumps in Pseudomonas aeruginosa (MC-04,124), for which efficacy was evaluated in
Triplex DNA Finally Comes of Age (1991)

Researchers in several labs are exploring the use of triplex DNA to produce a new type of molecular scissors for cutting DNA. Even the best of the restriction enzymes that are currently used for that purpose cut at many sites, mincing the genome into a multitude of small bits that are hard to separate and analyze. But triplex-based scissors may be able to cut at one or a few sites, giving a much more manageable collection of large DNA pieces. Such scissors would be a great help in mapping and sequencing the human genome and in isolating individual genes.
A Self- and Mutually Injection-Locked Radar System for Monitoring Vital Signs in Real Time With Random Body Movement Cancellation (2016)

This paper presents a system for monitoring vital signs that is based on a self- and mutually injection-locked radar architecture. To detect vital signs with reduced body motion artifacts, the system uses two voltage-controlled oscillators that are self-injection locked to themselves and mutually injection locked to each other. Additionally, the system uses two different gain antennas. These features cancel out most of the body motion artifacts while preserving the vital sign signals. In the experiments, more than 85% of the body motion artifacts are removed, so the vital sign signals can be accurately monitored in real time.
Integration of representation into goal-driven behavior-based robots (1992)

An architecture that integrates a map representation into a reactive, subsumption-based mobile robot is described. This fully integrated reactive system removes the distinction between the control program and the map. The method was implemented and tested on a mobile robot equipped with a ring of sonars and a compass, and programmed with a collection of simple, incrementally designed behaviors. The robot performs collision-free navigation, dynamic landmark detection, map construction and maintenance, and path planning. Given any known landmark as a goal, the robot plans and executes the shortest known path to it. If the goal is not reachable, the robot detects failure, updates the map, and finds an alternate route. The topological representation primitives are designed to suit the robot's sensors and its navigation behavior, thus minimizing the amount of stored information. Distributed over a collection of behaviors, the map itself performs constant-time localization and linear-time path planning. The approach is qualitative and robust.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene Amplification and Overexpression of Aurora-C in Breast and Prostate Cancer Cell Lines (2012)

Human aurora kinases are three highly conserved serine/threonine kinases with regulatory function in chromosome alignment, chromosome segregation, and cytokinesis during cell cycle progression and their overexpression associates with malignant transformation and proliferation of cancer cells. Aurora genes are located at loci that are commonly altered in cancers. Aurora-A has oncogenic activity while Aurora-B does not. Aurora-C is only detected in mammals with involvement in meiosis. Oncogenic activity of Aurora-C is still in dispute. We evaluated the expression of three Aurora kinases by real-time RT-PCR in well-known breast and prostate cancer cell lines. Cell cycle was studied with flow cytometry. In both more invasive cell lines' p53-null cells, PC-3 and MDA-MB-231, an increase in mRNA expression of three Aurora kinases, especially Aurora-C, was observed. Genomic DNA was examined for gene amplification and aneuploidy as a mechanism of overexpression. At DNA level, only Aurora-C showed gene amplification in breast cancer cell lines (p < 0.005). Here we provide evidence for the first time of Aurora-C overexpression and gene amplification.
Nutrition Intervention Trials in Linxian, China: Supplementation With Specific Vitamin/Mineral Combinations, Cancer Incidence, and Disease-Specific Mortality in the General Population (1993)

The results on their own are not definitive, but the promising findings should stimulate further research to clarify the potential benefits of micronutrient supplements.
LNA (LOCKED NUCLEIC ACID) AND THE DIASTEREOISOMERIC α-L-LNA: CONFORMATIONAL TUNING AND HIGH-AFFINITY RECOGNITION OF DNA/RNA TARGETS (2001)

The remarkable binding properties of LNA (Locked Nucleic Acid) and alpha-L-LNA (the alpha-L-ribo configured diastereoisomer of LNA) are summarized, and hybridization results for LNA/2'-O-Me-RNA chimera and LNAs with a "dangling" nucleotide are introduced. In addition, results from NMR investigations on the furanose conformations of the individual nucleotide monomers in different duplexes are presented. All these data are discussed with focus on the importance of conformational steering of unmodified nucleotides in partly modified LNA and alpha-L-LNA sequences in relation to the unprecedented binding properties of LNA and alpha-L-LNA.
Scaling Pharmacodynamics from In Vitro and Preclinical Animal Studies to Humans (2009)

An important feature of mechanism-based pharmacokinetic/pharmacodynamic (PK/PD) models is the identification of drug- and system-specific factors that determine the intensity and time-course of pharmacological effects. This provides an opportunity to integrate information obtained from in vitro bioassays and preclinical pharmacological studies in animals to anticipate the clinical and adverse responses to drugs in humans. The fact that contemporary PK/PD modeling continues to evolve and seeks to emulate systems level properties should provide enhanced capabilities to scale-up pharmacodynamic data. Critical steps in drug discovery and development, such as lead compound and first in human dose selection, may become more efficient with the implementation and further refinement of translational PK/PD modeling. In this review, we highlight fundamental principles in pharmacodynamics and the basic expectations for in vitro bioassays and traditional allometric scaling in PK/PD modeling. Discussion of PK/PD modeling efforts for recombinant human erythropoietin is also included as a case study showing the potential for advanced systems analysis to facilitate extrapolations and improve understanding of inter-species differences in drug responses.
Bankruptcy Law, Economics of Corporate and Personal (2008)

Bankruptcy is the legal process whereby financially distressed firms, individuals, and occasionally governments resolve their debts. The bankruptcy process for firms plays a central role in economics, because competition tends to drive inefficient firms out of business, thereby raising the average efficiency level of those remaining. Bankruptcy also has an important economic function for individual debtors, since it provides them with partial consumption insurance and supplements the government- provided safety net. This article discusses the economic objectives of bankruptcy and surveys theoretical and empirical research on corporate and personal bankruptcy.
High expression of ets-1 gene in human thymocytes and immature T leukemic cells. (1988)

The cellular ets-1 gene homologous to the 5' region of the v-ets sequence of the E26 retrovirus codes for a 6.8-kb mRNA that is translated into a 51-kDa protein in human cells. A survey of mRNA from human tissues showed the thymus as the tissue with the highest level of ets-1 transcription, within other hematopoietic organs and tissues, including spleen, fetal liver, lymph nodes, bone marrow, and peripheral lymphocytes exhibiting low or undetectable levels of hybridization. A high level of ets-1 expression was found in murine thymocyte mRNA as well. Investigation of the ets-1 expression levels in human leukemic samples showed that primary malignant T cells (T-ALLs), corresponding to intrathymic stages of maturation, have a much higher level of ets-1 mRNA than malignant T lymphoid cells with a mature phenotype, such as adult T cell leukemias (ATLs). T-ALLs were also higher in ets-1 expression than the other lymphoid (pre-T-ALL, c-ALL, pre-B-ALL) malignant cells analyzed. Insignificant amounts of the specific ets-1 mRNA were detected in several acute myeloid leukemias representing various degrees of maturation. The elevated ets-1 mRNA in thymocytes suggests a biological role for the ets-1 product in these cells that could be explored to investigate ets-1 function. Finally, the exhibited expression of ets-1 in lymphoid cells and absence from malignant myeloid cells makes it a candidate marker for phenotyping human hematopoietic tumors.