gebhart/patrepeval huggingface dataset:
Molecular Markers Associated with Water Use Efficiency and Leaf Ash in Soybean (1996)

Water use efficiency (WUE) is an important trait that has been associated with drought tolerance of crop plants, and leaf ash (LASH) generally related to WUE. A restriction fragment length polymorphism (RFLP) map was constructed from a soybean [ Glycine max (L.) Merr.] population of 120 F4‐derived lines from a cross of ‘Youngș × PI416937. The purpose of this research was to identify quantitative trait loci (QTL) associated with WUE and LASH in 36‐d‐old, greenhouse‐grown plants. The experimental design was a randomized complete block with six replications. Significant ( P &lt; 0.01) phenotypic differences were detected among the lines for both traits. A total of four and six independent RFLP markers were associated with WUE and LASH and if combined each group of markers would explain 38 and 53% of the variability in the respective traits. One marker locus (cr497‐1), on USDA Linkage Group J, explained 13.2% of the variation in WUE indicating the presence of a major QTL. The LASH was negatively correlated with WUE ( r = −0.40**), and two QTL were associated with both WUE and LASH. For each of these QTL, the allele for increased WUE was associated with reduced LASH.
Cytotoxicity of surface-functionalized silicon and germanium nanoparticles: the dominant role of surface charges (2013)

Although it is frequently hypothesized that surface (like surface charge) and physical characteristics (like particle size) play important roles in cellular interactions of nanoparticles (NPs), a systematic study probing this issue is missing. Hence, a comparative cytotoxicity study, quantifying nine different cellular endpoints, was performed with a broad series of monodisperse, well characterized silicon (Si) and germanium (Ge) NPs with various surface functionalizations. Human colonic adenocarcinoma Caco-2 and rat alveolar macrophage NR8383 cells were used to clarify the toxicity of this series of NPs. The surface coatings on the NPs appeared to dominate the cytotoxicity: the cationic NPs exhibited cytotoxicity, whereas the carboxylic acid-terminated and hydrophilic PEG- or dextran-terminated NPs did not. Within the cationic Si NPs, smaller Si NPs were more toxic than bigger ones. Manganese-doped (1% Mn) Si NPs did not show any added toxicity, which favors their further development for bioimaging. Iron-doped (1% Fe) Si NPs showed some added toxicity, which may be due to the leaching of Fe(3+) ions from the core. A silica coating seemed to impart toxicity, in line with the reported toxicity of silica. Intracellular mitochondria seem to be the target for the toxic NPs since a dose-, surface charge- and size-dependent imbalance of the mitochondrial membrane potential was observed. Such an imbalance led to a series of other cellular events for cationic NPs, like decreased mitochondrial membrane potential (ΔΨm) and ATP production, induction of ROS generation, increased cytoplasmic Ca(2+) content, production of TNF-α and enhanced caspase-3 activity. Taken together, the results explain the toxicity of Si NPs/Ge NPs largely by their surface characteristics, provide insight into the mode of action underlying the observed cytotoxicity, and give directions on synthesizing biocompatible Si and Ge NPs, as this is crucial for bioimaging and other applications in for example the field of medicine.
Pacific Northwest GridWise? Testbed Demonstration Projects; Part I. Olympic Peninsula Project (2008)

This report describes the implementation and results of a field demonstration wherein residential electric water heaters and thermostats, commercial building space conditioning, municipal water pump loads, and several distributed generators were coordinated to manage constrained feeder electrical distribution through the two-way communication of load status and electric price signals. The field demonstration took place in Washington and Oregon and was paid for by the U.S. Department of Energy and several northwest utilities. Price is found to be an effective control signal for managing transmission or distribution congestion. Real-time signals at 5-minute intervals are shown to shift controlled load in time. The behaviors of customers and their responses under fixed, time-of-use, and real-time price contracts are compared. Peak loads are effectively reduced on the experimental feeder. A novel application of portfolio theory is applied to the selection of an optimal mix of customer contract types.
Speech Coding Algorithms: Foundation and Evolution of Standardized Coders (2003)

Overview of Speech Coding -- Classification of Speech Coders -- Speech Production and Modeling -- Some Properties of the Human Auditory System -- Speech Coding Standards -- About Algorithms -- Signal Processing Techniques -- Pitch Period Estimation -- All-Pole and All-Zero Filters -- Stochastic Processes and Models -- Power Spectral Density -- Periodogram -- Autoregressive Model -- Autocorrelation Estimation -- Other Signal Models -- Linear Prediction -- The Problem of Linear Prediction -- Linear Prediction Analysis of Nonstationary Signals -- Examples of Linear Prediction Analysis of Speech -- The Levinson-Durbin Algorithm -- The Leroux-Gueguen Algorithm -- Long-Term Linear Prediction -- Synthesis Filters -- Practical Implementation -- Moving Average Prediction -- Scalar Quantization -- Uniform Quantizer -- Optimal Quantizer -- Quantizer Design Algorithms -- Algorithmic Implementation -- Pulse Code Modulation and its Variants -- Uniform Quantization -- Nonuniform Quantization -- Differential Pulse Code Modulation -- Adaptive Schemes -- Vector Quantization -- Optimal Quantizer -- Quantizer Design Algorithms -- Multistage VQ -- Predictive VQ -- Other Structured Schemes -- Scalar Quantization of Linear Prediction Coefficient -- Spectral Distortion -- Quantization Based on Reflection Coefficient and Log Area Ratio -- Line Spectral Frequency -- Quantization Based on Line Spectral Frequency -- Interpolation of LPC -- Linear Prediction Coding -- Speech Production Model -- Structure of the Algorithm -- Voicing Detector.
Microfluidics-based systems biology (2006)

Systems biology seeks to develop a complete understanding of cellular mechanisms by studying the functions of intra- and inter-cellular molecular interactions that trigger and coordinate cellular events. However, the complexity of biological systems causes accurate and precise systems biology experimentation to be a difficult task. Most biological experimentation focuses on highly detailed investigation of a single signaling mechanism, which lacks the throughput necessary to reconstruct the entirety of the biological system, while high-throughput testing often lacks the fidelity and detail necessary to fully comprehend the mechanisms of signal propagation. Systems biology experimentation, however, can benefit greatly from the progress in the development of microfluidic devices. Microfluidics provides the opportunity to study cells effectively on both a single- and multi-cellular level with high-resolution and localized application of experimental conditions with biomimetic physiological conditions. Additionally, the ability to massively array devices on a chip opens the door for high-throughput, high fidelity experimentation to aid in accurate and precise unraveling of the intertwined signaling systems that compose the inner workings of the cell.
Executable use cases: requirements for a pervasive health care system (2004)

Many software experts argue that when we design a new system, we should create an explicit description of the environment in which the proposed system is to be used. The argument becomes crucial for pervasive computing, which aims to tightly integrate systems into their environments and into the work processes they're to support. However, prototypes typically provide an explicit representation only of the system itself. Executable use cases, on the other hand, can also describe the environment. EUCs are designed to: narrow the gap between informal ideas about requirements and the formalization that eventually and inevitably emerges during system implementation; and spur communication between users and system developers. Iterative prototyping is a feasible starting point to pursue these goals. But EUCs encompass both iterative prototyping and explicit environment descriptions in terms of workflow modeling. This article describes a case study in which developers used EUCs to prototype an electronic patient record system for hospitals in Aarhus, Denmark.
Effect of phosphorothioate modification of oligodeoxynucleotides on specific protein binding. (1994)

Phosphorothioate modification of internucleoside linkages is widely used to prevent degradation of oligodeoxynucleotide (ODN) therapeutic agents in serum and cells. This modification generally increases ODN potency, but in many instances it is associated with an increase of poorly understood nonspecific effects. In this study, we have found that both cellular retention and nonspecific protein binding are dependent upon the extent of the oligonucleotide's modification. Flow cytometry of cells treated with fluorescein-labeled single-stranded (ss) or double-stranded (ds) ODNs demonstrated that fully phosphorothioate-modified ODNs exhibit much greater cellular association than 3'-terminally modified ODNs (with three 3'-terminal phosphorothioate linkages). Additionally, gel shift assays with either ss- or ds-probes showed that fully phosphorothioate-modified ODNs also exhibit much greater cytoplasmic and nuclear protein binding than either 3'-terminally modified or unmodified ODNs. However, gel shift competition assays showed that transcription factor binding by fully phosphorothioate-modified ds-ODNs was completely nonspecific relative to 3'-terminally modified and unmodified ds-ODNs. These results suggest that the benefits derived from full phosphorothioate modification of ODNs may be negated by increases of nonspecific protein binding and associated sequence-independent effects.
A Revolution in biotechnology (1989)

Foreword John Kendrew 1. Heredity, genes and DNA Jean L. Marx 2. Synthesis without cells Ethan S. Simon, Alan Akiyama and George Whitesides 3. Microorganisms as producers of feedstock chemicals Randolph T. Hatch and Ralph Hardy 4. Gene cloning opens up a new frontier in health L. Patrick Gage 5. The microbial production of biochemicals Saul L. Neidleman 6. Single-cell proteins John H. Litchfield 7. Bacterial leaching and biomining David Woods and Douglas E. Rawlings 8. Bacteria and the environment Tamar Barkay, Deb Chatterjee, Stephen Cuskey, Ronald Walter, Fred Genthren and A. W. Bourquin 9. Biological nitrogen fixation Andrew W. B. Johnston 10. Plant cell and tissue culture Edward C. Cocking 11. Improving crop plants by the introduction of isolated genes Jozef Schell, Bruno Gronenborn and Robert T. Fraley 12. Monoclonal antibodies and their applications Jean L. Marx 13. Site-directed antibodies in biology and medicine Thomas M. Shinnick and Richard A. Lerner 14. New methods for the diagnosis of genetic diseases Yuet Wai Kan 15. The prospect of gene therapy for human hereditary diseases Jean L. Marx 16. Biotechnology, international competition and regulatory strategies Joseph G. Perpich Glossary Index.
PCS 1900 MHz duplexer using thin film bulk acousticresonators (FBARs) (1999)

An ultra-miniature duplexer (5 × 8 × 2.2 mm3) consisting of two FBAR filters and nine passive components operating at 1900 MHz is described. The minimum insertion loss for the Tx and Rx bands is better than –3 dB. Isolation between the Tx and Rx ports exceeds 50 dB over most of the Tx band and 46 dB in the Rx band. The FBAR filters handle up to 2 W throughout the passband.
The distinct surface of human blood dendritic cells, as observed after an improved isolation method. (1990)

Prior studies have identified a subset of dendritic cells in human blood, as well as their stimulatory function for T-cell-mediated immune responses. However research has been limited by difficulties in isolation, since dendritic cells make up only 0.1-1% of blood mononuclear cells. We present a protocol that reliably yields preparations that are greater than 80-90% pure. The method relies on the sequential depletion of the major cell types in blood and simultaneously provides T cells, monocytes, and B plus natural killer cells for comparison with dendritic cells. The last step in the procedure is the removal of residual contaminants on the basis of expression of a CD45R epitope. The enrichment of dendritic cells is evident by three criteria, each of which is related to the surface of these antigen-presenting cells. (i) All dendritic cells are motile, constantly forming large lamellipodia or veils. (ii) When analyzed with a large panel of monoclonal antibodies and the FACS, the cells express high levels of all known polymorphic major histocompatibility complex gene products, as well as a distinct combination of receptors and adhesion molecules. Unlike monocytes, for example, dendritic cells lack Fc receptors and the colony-stimulating factor 1 receptor (c-fms) but express much higher levels of ICAM-1 and LFA-3 adhesins. (iii) In functional assays, dendritic cells are at least 100 times more potent than monocytes or lymphocytes in stimulating the primary mixed leukocyte reaction. These properties help make the trace subset of dendritic cells more amenable to further functional and clinical studies.
Candidate's Thesis: Polymer Chemotherapy for Head and Neck Cancer (2000)

The study results indicate that polymer chemotherapy is effective against a variety of SCCs of the head and neck, both in vitro and in vivo, and may become a useful therapeutic option for head and neck cancer.
Degradative acetolactate synthase of Bacillus subtilis: purification and properties (1975)

A degradative acetolactate synthase (acetolactate pyruvate-lyase [carboxylating], EC 4.1.3.18) from Bacillus subtilis has been partially purified and characterized. The synthesis of the enzyme was induced by growth of cells in minimal medium plus isobutyrate or acetate. The enzyme was partially purified by ammonium sulfate fractionation, gel filtration, and hydroxyapatite chromatography. The pH optimum of the purified enzyme was 7.0 in phosphate buffer. When assayed in phosphate buffer (pH 7.0), activity was stimulated by acetate and inhibited by sulfate. When assayed in acetate buffer (pH 5.8), activity was inhibited both by sulfate and phosphate. Michaelis-Menten kinetics was observed when the enzyme was assayed in phosphate buffer (pH 6.0 or 7.0), and inhibition by sulfate was competitive and activation by acetate was noncompetitive. When assayed in acetate buffer (pH 5.8), nonlinear Lineweaver-Burk plots were obtained; inhibition by phosphate appeared to be competitive and that by sulfate was of the mixed type. The approximate molecular weight of the purified enzyme was 250,000 as determined by gel filtration.
Synthesis of 3H and 14C labelled SCH 48461 (1996)

3H-Sch 47949, racemic 3H-Sch 48461, was prepared at a specific activity of 40 mCi/mmole by Pt catalysed exchange with tritiated water. 3H-Sch 48461 was prepared at a specific activity of 64.6 Ci/mmole by a Pd/C catalysed reduction of an olefinic intermediate. 14C-Sch 48461 was prepared in 8 steps from 14C-potassium cyanide with an overall radiochemical yield of 18.5%.
Resistance Studies with Daptomycin (2001)

We studied the in vitro emergence of resistance to daptomycin using three methods: spontaneous resistance incidence, serial passage in the presence of increasing drug concentrations, and chemical mutagenesis. No spontaneously resistant mutants were obtained for any organism tested (<10(-10) for Staphylococcus aureus, <10(-9) for Staphylococcus epidermidis, <10(-9) for Enterococcus faecalis, <10(-9) for Enterococcus faecium, <10(-8) for Streptococcus pneumoniae). Population analysis demonstrated that bacterial susceptibility to daptomycin is heterogeneous. Assay results were sensitive to calcium concentration and culture density, both of which can affect apparent resistance rates. Stable S. aureus mutants were isolated by both serial passage in liquid media and chemical mutagenesis. The daptomycin MICs for these isolates were 8- to 32-fold higher than for the parental strain. Many mutants with high MICs (>12.5 microg/ml) had significant growth defects but did not display phenotypes typical of S. aureus small colony variants. The voltage component (Delta psi) of the bacterial membrane potential was increased in three independent resistant isolates. In vivo data showed that some daptomycin-resistant mutants had lost significant virulence. For other mutants, the degree of in vitro resistance was greater than the change in in vivo susceptibility. These results suggest that infection with some daptomycin-resistant organisms may still be easily treatable.
Alkali-Silica Reactivity: Effect of Alkali in Aggregate on Expansion (1986)

Tests were performed on samples of alkali-bearing aggregates to determine amounts of alkali that could be removed by leaching in Ca(OH)2 solution and water at 38°C (100°F) and 80°C (176°F). Additional tests were made on one reactive aggregate which was first subjected to leaching and then used to make mortar bars for testing in accordance with ASTM C 227. Leach periods of 7, 28, 90, and 180 days were used. Results show that alkali present within concrete aggregate particles may participate in alkali-silica reactivity. Alkali levels much greater than those present in high-alkali cements can be leached from non-reactive as well as reactive aggregate materials. It is suggested that ion-exchange processes possibly augmented by partial dissolution of the aggregate, facilitate leaching of alkali. Removal of alkali from aggregates, prior to their use in mortar bars, was shown to reduce expansions. Expansions were progressively reduced as greater amounts of alkali were leached from aggregates prior to their use with low- as well as high-alkali cements. Applicability of these findings to concrete in service is discussed.
Characterization of the -2,8-polysialyltransferase from Neisseria meningitidis with synthetic acceptors, and the development of a self-priming polysialyltransferase fusion enzyme (2007)

Glycoconjugates containing polysialic acid have many biological activities and represent target molecules for therapeutic interventions. Enzymatic synthesis of these glycoconjugates should give access to these important molecules to evaluate their potential. The polysialyltransferases from both Neisseria meningitidis and Escherichia coli were cloned and expressed as recombinant proteins in E. coli. We have used synthetic acceptors to probe the acceptor requirement of these enzymes and to examine the basic enzymology. The minimum number of sialic acid residues (Neu5Ac) on the acceptor for activity in vitro was shown to be 2 for both enzymes, but a large increase in activity was seen if the acceptor had three Neu5Ac residues. The polysialyltransferase from N. meningitidis generated longer reaction products than the enzyme from E. coli on FCHASE acceptors. Examination of the products showed them to be a heterogeneous mixture, but products with >50 Neu5Ac residues could be seen using capillary zone electrophoresis analyses. In addition we made fusion proteins of these polysialyltransferase enzymes with the bifunctional alpha-2,3/alpha-2,8-sialyltransferase from Campylobacter jejuni to create self priming polysialyltransferases. These bifunctional sialyltransferases utilized various synthetic disaccharide acceptors with a terminal galactose, and we demonstrate here that the PST enzyme from N. meningitidis and its fusion protein with the C. jejuni sialyltransferase can be used to create polysialic acid on O-linked glycopeptides.
Retracted: Novel approaches for gene‐specific interference via manipulating actions of microRNAs: Examination on the pacemaker channel genes HCN2 and HCN4 (2007)

Recent evidence has suggested microRNAs as viable therapeutic targets for a wide range of human disease. However, lack of gene-specificity of microRNA actions may hinder this application. Here we developed two new approaches, the gene-specific microRNA mimic and microRNA-masking antisense approaches, to explore the possibility of using microRNA's principle of actions in a gene-specific manner. We examined the value of these strategies as rational approaches to develop heart rate-reducing agents and "biological pacemakers" by manipulating the expression of the cardiac pacemaker channel genes HCN2 and HCN4. We showed that the gene-specific microRNA mimics, 22-nt RNAs designed to target the 3'untranslated regions (3'UTRs) of HCN2 and HCN4, respectively, were efficient in abrogating expression and function of HCN2 and HCN4. The gene-specific microRNA mimics repressed protein levels, accompanied by depressed f-channel conductance and the associated rhythmic activity, without affecting mRNA levels of HCN2 and HCN4. Meanwhile, we also designed the microRNA-masking antisense based on the miR-1 and miR-133 target sites in the 3'UTRs of HCN2 and HCN4 and found that these antisense oligodeoxynucleotides markedly enhanced HCN2/HCN4 expression and function, as reflected by increased protein levels of HCN2/HCN4 and If conductance, by removing the repression of HCN2/HCN4 expression induced by endogenous miR-1/miR-133. The experimental examination of these techniques and the resultant findings not only indicate feasibility of interfering miRNA action in a gene-specific fashion but also may provide a new research tool for studying function of miRNAs. The new approaches also have the potential of becoming alternative gene therapy strategies.
Estimation of Bacterial Densities by Means of the "Most Probable Number" (1950)

THIS PAPER attempts to give a simple account of the concept of the most probable number (m.p.n.) of organisms in the dilution method. The concept is quite old, going back to McCrady (4) in 1915, and has been discussed by various writers from time to time, so that little of what I shall present is new. In addition, some advice is given on the planning of dilution series. The dilution method is a means for estimating, without any direct count, the density of organisms in a liquid. It is used principally for obtaining bacterial densities in water and milk. The method consists in taking samples from the liquid, incubating each sample in a suitable culture medium, and observing whether any growth of the organism has taken place. The estimation of density is based on an ingenious application of the theory of probability to certain assumptions. For a biologist, it is more important to be clear about these assumptions than about the details of the mathematics, which are rather intricate.
Effects of MYCN Antisense Oligonucleotide Administration on Tumorigenesis in a Murine Model of Neuroblastoma (2003)

Decreased expression of hMYCN protein is achievable with the use of AS oligonucleotide treatment, even in the presence of hMYCN oncogene amplification. Antisense strategies targeting the hMYCN oncogene in vivo decrease mouse neuroblastoma tumorigenesis. Investigation of their clinical effect in children with neuroblastoma is warranted.