gebhart/patrepeval huggingface dataset:
Heterodimeric DNA-binding dyes designed for energy transfer: stability and applications of the DNA complexes (1993)

Spectroscopic studies of the complexes of double-stranded (ds) DNA with the polymethylene-amine linked heterodimers thiazole orange-thiazole blue, thiazole orange-ethidium, and fluorescein-ethidium, in each case show efficient energy transfer from donor to acceptor chromophores (Benson, S.C., Singh, P. and Glazer, A.N. (1993) accompanying manuscript). A quantitative assay of the stability of such complexes during gel electrophoresis is presented. The off-rate of dye from complexes formed at an initial dsDNA bp:dye ratio > or = 10:1 follows strict first-order kinetics. The t0.5 values for the dissociation of a series of related dyes provide a quantitative criterion for the design of DNA-binding fluorophores. Complexes of dsDNA with the monomeric propidium and cyanine dyes, [1-(9-amino-4,7-diazanonyl)-3,8-diamino-6-phenyl-phenanthridinium bromide trihydrobromide] and (N,N'-tetramethyl-1,3-propanediamino)propyl thiazole orange [4-[3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidenyl]-1-(4 ,4,8-trimethyl-4,8-diazanonyl)-quinolinium diiodide], are much more stable than those with their widely used counterparts, ethidium and thiazole orange. Applications of the new dyes in post-staining of gels and in the multiplex detection of DNA restriction fragments are presented.
Quantitative 13C NMR Analysis of Lignins with Internal Standards (2001)

Novel protocols for acquiring quantitative (13)C NMR spectra of lignins have been developed using the internal reference compounds 1,3,5-trioxane and pentafluorobenzene. Trioxane offers a convenient internal standard for collecting inverse gated proton decoupled (13)C NMR spectra for lignins, whereas pentafluorobenzene can be used to provide information on the amount of methine carbon using the DEPT experiment. In each case, the internal reference compounds provide single, un-overlapped sharp signals in the middle of the spectral region, permitting facile integration. These integrals could be used to determine the amounts of different structural features of lignins, expressed in absolute units of millimoles per gram. The optimum parameters for these experiments were validated for a variety of spectrometer platforms, and standard errors were determined for different spectral areas using lignin model compounds and "standard" lignins. In addition, the data derived for the International Round Robin "standard" lignins showed good agreement with the data from quantitative (31)P NMR spectroscopy and published data, obtained by independent laboratories using independent methods of analysis.
Recurrent Clostridium Difficile Disease: Epidemiology and Clinical Characteristics (1999)

Recurrent CDAD is a persistent disease that may result in prolonged hospital stays, additional medical costs, and rare serious complications.
Noninvasive urinary miRNA biomarkers for early detection of pancreatic adenocarcinoma. (2015)

Currently, the majority of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) present with locally invasive and/or metastatic disease, resulting in five-year survival of less than 5%. The development of an early diagnostic test is, therefore, expected to significantly impact the patient's prognosis. In this study, we successfully evaluated the feasibility of identifying diagnostic cell free microRNAs (miRNAs) for early stage PDAC, through the analysis of urine samples. Using Affymetrix microarrays, we established a global miRNA profile of 13 PDAC, six chronic pancreatitis (CP), and seven healthy (H) urine specimens. Selected differentially expressed miRNAs were subsequently investigated using an independent technique (RT-PCR) on 101 urine samples including 46 PDAC, 29 CP and 26 H. Receiver operating characteristic (ROC) and logistic regression analyses were applied to determine the discriminatory potential of the candidate miRNA biomarkers. Three miRNAs (miR-143, miR-223, and miR-30e) were significantly over-expressed in patients with Stage I cancer when compared with age-matched healthy individuals (P=0.022, 0.035 and 0.04, respectively); miR-143, miR-223 and miR-204 were also shown to be expressed at higher levels in Stage I compared to Stages II-IV PDAC (P=0.025, 0.013 and 0.008, respectively). Furthermore, miR-223 and miR-204 were able to distinguish patients with early stage cancer from patients with CP (P=0.037 and 0.036). Among the three biomarkers, miR-143 was best able to differentiate Stage I (n=6) from healthy (n=26) with area under the curve (AUC) of 0.862 (95% CI 0.695-1.000), with sensitivity (SN) of 83.3% (95% CI 50.0-100.0), and specificity (SP) of 88.5% (95% CI 73.1-100.0). The combination of miR-143 with miR-30e was significantly better at discriminating between these two groups, achieving an AUC of 0.923 (95% CI 0.793-1.000), with SN of 83.3% (95% CI 50.0-100.0) and SP of 96.2% (95% CI 88.5-100.0). In this feasibility study, we demonstrate for the first time the utility of miRNA biomarkers for non-invasive, early detection of PDAC in urine specimens.
The Extracellular Matrix of Animals (2002)

[reaction: see text] The reaction of the vinyl oxirane 1 derived from D-glucal with a series of O-nucleophiles (alcohols, phenol, and diacetone D-glucose) affords the corresponding 2-unsaturated beta-O-glycosides in a completely stereoselective way (syn 1,4-addition pathway). Epoxide 1 is generated in situ by treatment of the corresponding hydroxy mesylate 2 with t-BuOK in anhydrous benzene.
10-Gb/s transmission of 1.55-μm directly modulated signal over 100 km of negative dispersion fiber (2001)

The largest transmission distance (100 km) ever reported for a commercially available 10-Gb/s 1.55-μm directly modulated signal over a single fiber link without using any dispersion compensation is demonstrated. The achieved dispersion-length product for a Q-factor greater than 9.4 dB (bit-error rate less than 10/sup -15/) was about 750 ps/nm. The fiber that enabled such long transmission distance with high dispersion tolerance is a nonzero dispersion-shifted fiber that has negative dispersion in the entire usable bandwidth (1280-1620 nm) and is optimized for operation with directly modulated lasers. The excellent single-channel transmission performance that we achieved can be expected also from wavelength-division-multiplexed systems with channels across the erbium-doped fiber amplifier bands.
Development of Metal-Based Microelectrode Sensor Platforms by Chemical Vapor Deposition (2001)

A novel approach to the fabrication of metal mircoelectrodes is described that employs chemical vapor deposition (CVD) techniques and electrode modification strategies. Two specific examples for the fabrication of copper and silver microelectrodes are described, which utilize a combination of CVD coating, electroetching and electroplating. Initially, a 25 μm diameter tungsten wire is concentrically coated with an insulating layer of silica with excellent adhesion between the two surfaces. Tungsten metal is then readily removed by electrochemical etching in hydroxide solution to afford a well-defined microcavity at the electrode tip. For the purpose of demonstrating the concept of introducing specific selectivity into the device as well as fabricating well-defined metal microelectrodes, copper and silver were electrodeposited into the microcavity from aqueous solutions of the respective cations. Both modified electrodes were characterized by electrochemistry and microscopy, and subsequently used as electrochemical sensors for the detection of glucose and chloride ions. This methodology offers a facile approach to the development of highly selective microsensors with well-defined electrode sensing elements.
Mitigating the Impact of Process Variations on Processor Register Files and Execution Units (2006)

Design variability due to die-to-die and within-die process variations has the potential to significantly reduce the maximum operating frequency and the effective yield of high-performance microprocessors in future process technology generations. One serious manifestation of this increased variability is a reduction in the mean frequency of fabricated chips due to fluctuations in device characteristics causing reduced circuit performance. In this paper, we propose to mitigate the impact of variations through variable-latency register files and execution units which are key architectural components that may encounter variability problems. We also illustrate the importance of closing the gap in expected delay of these distinct structures. A post fabrication test and configuration strategy is proposed. We find that 23% mean frequency improvement with an average IPC loss of 3% (and never exceeding 5% for worst case chips) is possible for the 65nm technology node by properly adopting the proposed schemes
Combinatorial mixing of microfluidic streams (2004)

We have devised a microfluidic mixer design that produces all the mixture combinations of a given number of dilutions of the input compounds. As proof of the concept, we present a device that generates four titrations of two dye solutions, blue and yellow, and combinatorially mixes the blue titrations with the yellow titrations to deliver the sixteen mixture combinations in separate outlet microchannels. Our device features four different flow levels made by stacking nine laser-cut Mylar laminates. The fluidic network has a symmetric design that guarantees that the flow rates are the same at all the outlets, with deviations attributable to imperfections in the fabrication, assembly, or perfusion processes. Design rules for scaling up the number of compounds and/or dilutions are presented. The mixing scheme has broad applicability in high-throughput combinatorial testing applications such as drug screening, cell-based biochemical assays, lab-on-a-chip devices, and biosensors.
Synthesis of a diamine dithiol bifunctional chelating agent for incorporation of technetium-99m into biomolecules (1990)

The synthesis of a bifunctional chelating agent (BCA), 1, based on the diaminedithiol (DADT) ligand system, is described. The six-step synthetic sequence has been accomplished in 16% overall yield, affording 1, which contains a thiolactone as a reactive moiety, which permits direct coupling to nucleophiles without the formation of byproducts. The reactivity of 1 toward benzylamine and subsequent labeling of the ligand with technetium-99m has been evaluated as a model for preparation of various bioconjugates. Both coupling and exchange labeling occur in high yield under mild conditions, and competition reactions with diethylenetriaminepentaacetic acid (DTPA) indicate the superior stability of the technetium-99m-DADT complex. Preparation of BCA 1 thus provides a new avenue into technetium-labeled radiopharmaceuticals.
Anatomic, Intrinsic, and Synaptic Properties of Dorsal and Ventral Division Neurons in Rat Medial Geniculate Body (1999)

Anatomic, intrinsic, and synaptic properties of dorsal and ventral division neurons in rat medial geniculate body. Presently little is known about what basic synaptic and cellular mechanisms are employed by thalamocortical neurons in the two main divisions of the auditory thalamus to elicit their distinct responses to sound. Using intracellular recording and labeling methods, we characterized anatomic features, membrane properties, and synaptic inputs of thalamocortical neurons in the dorsal (MGD) and ventral (MGV) divisions in brain slices of rat medial geniculate body. Quantitative analysis of dendritic morphology demonstrated that tufted neurons in both divisions had shorter dendrites, smaller dendritic tree areas, more profuse branching, and a greater dendritic polarization compared with stellate neurons, which were only found in MGD. Tufted neuron dendritic polarization was not as strong or consistent as earlier Golgi studies suggested. MGV and MGD cells had similar intrinsic properties except for an increased prevalence of a depolarizing sag potential in MGV neurons. The sag was the only intrinsic property correlated with cell morphology, seen only in tufted neurons in either division. Many MGV and MGD neurons received excitatory and inhibitory inferior colliculus (IC) inputs (designated IN/EX or EX/IN depending on excitation/inhibition sequence). However, a significant number only received excitatory inputs (EX/O) and a few only inhibitory (IN/O). Both MGV and MGD cells displayed similar proportions of response combinations, but suprathreshold EX/O responses only were observed in tufted neurons. Excitatory and inhibitory postsynaptic potentials (EPSPs and IPSPs) had multiple distinguishable amplitude levels implying convergence. Excitatory inputs activated alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptors the relative contributions of which were variable. For IN/EX cells with suprathreshold inputs, first-spike timing was independent of membrane potential unlike that of EX/O cells. Stimulation of corticothalamic (CT) and thalamic reticular nucleus (TRN) axons evoked a GABAA IPSP, EPSP, GABAB IPSP sequence in most neurons with both morphologies in both divisions. TRN IPSPs and CT EPSPs were graded in amplitude, again suggesting convergence. CT inputs activated AMPA and NMDA receptors. The NMDA component of both IC and CT inputs had an unusual voltage dependence with a detectable DL-2-amino-5-phosphonovaleric acid-sensitive component even below -70 mV. First-spike latencies of CT evoked action potentials were sensitive to membrane potential regardless of whether the TRN IPSP was present. Overall, our in vitro data indicate that reported regional differences in the in vivo responses of MGV and MGD cells to auditory stimuli are not well correlated with major differences in intrinsic membrane features or synaptic responses between cell types.
A guide to successful synthesis design (2005)

Preface.Glossary and Abbreviations.1 Organic Synthesis: General Remarks.1.1 Introduction.1.2 Synthesis Design.1.3 Hard and Soft Acids and Bases.1.4 The Curtin-Hammett Principle.2 Stereoelectronic Effects and Reactivity.2.1 Hyperconjugation with r Bonds.2.2 Hyperconjugation with Lone Electron Pairs.2.3 Hyperconjugation and Reactivity.2.4 Conclusion.3 The Stability of Organic Compounds.3.1 Introduction.3.2 Strained Bonds.3.3 Incompatible Functional Groups.3.4 Conjugation and Hyperconjugation of Incompatible Functional Groups.3.5 Stability Toward Oxygen.3.6 Detonations.4 Aliphatic Nucleophilic Substitutions: Problematic Electrophiles.4.1 Mechanisms of Nucleophilic Substitution.4.2 Structure of the Leaving Group.4.3 Structure of the Electrophile.5 The Alkylation of Carbanions.5.1 Introduction.5.2 The Kinetics of Deprotonations.5.3 Regioselectivity of Deprotonations and Alkylations.5.4 The Stability of Carbanions.6 The Alkylation of Heteroatoms.6.1 Alkylation of Fluoride.6.2 Alkylation of Aliphatic Amines.6.3 Alkylation of Anilines.6.4 Alkylation of Alcohols.6.5 Alkylation of Phenols.6.6 Alkylation of Amides.6.7 Alkylation of Carbamates and Ureas.6.8 Alkylation of Amidines and Guanidines.6.9 Alkylation of Carboxylates.7 The Acylation of Heteroatoms.7.1 Problematic Carboxylic Acids.7.2 Problematic Amines.7.3 Problematic Alcohols.8 Palladium-catalyzed C-C Bond Formation.8.1 Introduction.8.2 Chemical Properties of Organopalladium Compounds.8.3 Mechanisms of Pd-catalyzed C-C Bond Formation.8.4 Homocoupling and Reduction of the Organyl Halide.8.5 Homocoupling and Oxidation of the Carbon Nucleophile.8.6 Transfer of Aryl Groups from the Phosphine Ligand.8.7 ipso- vs cine-Substitution at Vinylboron and Vinyltin Derivatives.8.8 Allylic Arylation and Hydrogenation as Side Reactions of the Heck Reaction.8.9 Protodemetalation of the Carbon Nucleophile.8.10 Sterically Hindered Substrates.8.11 Cyclometalation.8.12 Chelate Formation.9 Cyclizations.9.1 Introduction.9.2 Baldwins Cyclization Rules.9.3 Structural Features of the Chain.9.4 Ring Size.9.5 Heterocycles.10 Monofunctionalization of Symmetric Difunctional Substrates.10.1 Introduction.10.2 Monofunctionalization of Dicarboxylic Acids.10.3 Monofunctionalization of Diols.10.4 Monofunctionalization of Diamines.10.5 Monoalkylation of C,H-Acidic Compounds.10.6 Monoderivatization of Dihalides.Index.
Characterization of dentin and enamel by use of optical coherence tomography (1999)

Optical coherence tomographic images of human dentin and enamel are obtained by use of polarization-sensitive optical coherence tomography. A birefringence effect in enamel (lambda = 856 nm) and light propagation along dentinal tubules are observed. The group index of refraction for both dentin and enamel was measured at 1.50 +/- 0.02 and 1.62 +/- 0.02, respectively.
Specific Suppression of Human CD4+ Th Cell Responses to Pig MHC Antigens by CD8+CD28− Regulatory T Cells (1998)

Evidence that T cells can down-regulate the immune response by producing or consuming certain cytokines or by lysing APCs or Th cells has been provided in various systems. However, the generation and characterization of suppressor T cell lines have met with limited success. Here we show that xenospecific suppressor T cells can be generated by in vitro stimulation of human T cells with pig APCs. Similar to allospecific suppressors, these xenospecific suppressor T cells carry the CD8+CD28- phenotype and react to MHC class I Ags expressed by the APCs used for priming. TCR spectratyping of T suppressor cells showed oligoclonal usage of TCR-Vbeta families, indicating that xenostimulation of CD8+CD28- T cells results in Ag-driven selection of a limited Vbeta repertoire. Xenospecific T suppressor cells prevent the up-regulation of CD154 molecules on the membrane of Th cells, inhibiting their ability to react against the immunizing MHC class II xenoantigens. The mechanism of this suppression, therefore, appears to be blockade of CD154/CD40 interaction required for efficient costimulation of activated T cells.
Computer Modeling of Atomic Force Microscopy Force Measurements:  Comparisons of Poisson, Histogram, and Continuum Methods (1998)

A computer model of the AFM pull-off process was used to test the Poisson method for calculating bond forces and to compare the Poisson and histogram methods of finding single-molecule bond-rupture forces. The Poisson method appeared to work well, producing accurate individual bond-rupture forces even in the presence of moderate to large amounts of different types of variations or noise, while the histogram method only produced good results at low noise levels, even with large sample sizes. Three cases were found where use of the Poisson model could lead to inaccurate measurement of individual bond forces, the most important being related to the bond-formation probability, which must be low (ideally <5%) for accurate results. The Johnson−Kendall−Roberts (JKR) continuum method was also examined. Poisson and JKR methods are not expected to produce similar results, but are complementary, and if used together may produce accurate measurements of both individual bond-rupture forces and bond-formation probabilities, even if neither method alone is successful.
Sequence-specific DNA binding by Myc proteins. (1991)

Myc proteins have a tripartite carboxyl-terminal domain containing specific amino acid sequence motifs: a basic motif, a helix-loop-helix motif, and a leucine heptad repeat. Similar sequence motifs have been identified in several eukaryotic transcription factors and were shown to facilitate protein-DNA and protein-protein interactions. By using recombinant v-Myc proteins obtained by bacterial expression of full-length or partially deleted avian v-myc alleles, the functional relevance of these sequence motifs for Myc protein oligomerization and for DNA binding was investigated. All recombinant v-Myc proteins that have retained the carboxyl-terminal domain dimerize and specifically bind to double-stranded DNA containing the palindromic core sequence CACGTG. This and a closely related DNA sequence element have been defined previously as part of the binding sites for human transcription factors USF and TFE3, which specifically bind to the adenovirus major late promoter or the muE3 motif within the immunoglobulin heavy-chain enhancer, respectively. It is shown that a 61-amino-acid peptide sequence containing only the bipartite basic motif/helix-loop-helix domain of Myc is necessary and sufficient for dimerization and sequence-specific DNA binding of v-Myc recombinant proteins.
Subjective and objective assessment of acoustical and overall environmental quality in secondary school classrooms (2008)

A subjective survey on perceived environmental quality has been carried out on 51 secondary-school classrooms, some of which have been acoustically renovated, and acoustical measurements were carried out in eight of the 51 classrooms, these eight being representative of the different types of classrooms that are the subject of the survey. A questionnaire, which included items on overall quality and its single aspects such as acoustical, thermal, indoor air and visual quality, has been administered to 1006 students. The students perceived that acoustical and visual quality had the most influence on their school performance and, with the same dissatisfaction for acoustical, thermal and indoor air quality, they attributed more relevance, in the overall quality judgment, to the acoustical condition. Acoustical quality was correlated to speech comprehension, which was correlated to the speech transmission index, even though the index does not reflect all the aspects by which speech comprehension can be influenced. Acoustical satisfaction was lower in nonrenovated classrooms, and one of the most important consequences of poor acoustics was a decrease in concentration. The stronger correlation between average noise disturbance scores and L(A max) levels, more than L(Aeq) and L(A90), showed that students were more disturbed by intermittent than constant noise.
HERCULES-a system for high-level synthesis (1988)

This paper presents an approach to high-level synthesis of VLSI processors and systems. Synthesis consists of two phases: behavioral synthesis, which involves implementation-independent representations, and structural synthesis, that relates to the transformation of a behavior into an implementation. We describe HERCULES, a system for high-level synthesis developed at Stanford University. In particular, we address the hardware description problem, behavioral synthesis and optimization using a method called the reference stack, and the mapping of behavior onto a structure. We present a model for control based on sequencing graphs that supports multiple threads of execution flow, allowing varying degree of parallelism in the resulting hardware. Results are then presented for three examples: MC6502, Intel8251 and FRISC, a 16-bit microprocessor.
Cellular Uptake and Efflux of Azithromycin, Erythromycin, Clarithromycin, Telithromycin, and Cethromycin (2005)

Macrolide antibiotics have an outstanding ability to concentrate within host cells, particularly phagocytes. In the study described in this paper five different macrolide antibiotics were compared regarding the uptake and release kinetics in human peripheral blood polymorphonuclear neutrophils (PMNs) and three different cell lines, two phagocytic cell lines (RAW 264.7 and THP-1) and an epithelial cell line (MDCK). Based on the results obtained, the substances tested could be clustered into different groups. Azithromycin constituted the first group, characterized by rapid and nonsaturable uptake into phagocytic cells and a high degree of retention in the preloaded cells. The second group included erythromycin and clarithromycin. These two substances do not exhibit cell specificity; consequently, they are taken up to a similar extent and are released by all cell types studied. Ketolides constituted the last group. Their uptake was saturable in cells of monocytic lineage as well as in nondifferentiated cells of myeloid lineage, and they were rapidly released from all the cell lines studied. However, in PMNs, ketolide uptake was not saturable; and unlike telithromycin, cethromycin rapidly egressed from the loaded cells.