gebhart/patrepeval huggingface dataset:
Effect of the finite extinction ratio of an electro-optic modulator on the performance of distributed probe-pump Brillouin sensorsystems (2003)

The effect of the finite extinction ratio of an electro-optic modulator (EOM) on the Brillouin frequency measurement of a distributed Brillouin-based fiber optic sensor is studied. An EOM with a finite extinction ratio limits the application of Brillouin optical time domain analysis in a distributed Brillouin-based fiber optic sensor. This results in confusion in specifying the location of the strained region and in error in detecting the Brillouin frequency and hence in strain and temperature measurement.
Watson: Anticipating and Contextualizing Information Needs (1999)

In this paper, we introduce a class of systems called Information Management Assistants (IMAs). IMAs automatically discover related material on behalf of the user by serving as an intermediary between the user and information retrieval systems. IMAs observe users interact with everyday applications and then anticipate their information needs using a model of the task at hand. IMAs then automatically fulfill these needs using the text of the document the user is manipulating and a knowledge of how to form queries to traditional information retrieval systems (e.g., Internet search engines, abstract databases, etc.). IMAs automatically query information systems on behalf of users as well as provide an interface by which the user can pose queries explicitly. Because IMAs are aware of the user&amp;apos;s task, they can augment their explicit query with terms representative of the context of this task. In this way, IMAs provide a framework for bringing implicit task context to bear on servicing expli...
Rearrangement and amplification of c-abl sequences in the human chronic myelogenous leukemia cell line K-562. (1983)

Structural rearrangements of specific cellular sequences (c-onc genes) homologous to acute transforming retrovirus oncogenes (v-onc genes) have been recently described in various malignancies. Here we show that human cellular sequences (c-abl) homologous to the transforming sequences of the mouse Abelson leukemia virus (v-abl) are amplified some 4- to 8-fold in K-562, a Philadelphia chromosome-positive cell line derived from a patient with chronic myelogenous leukemia in blast crisis. Restriction analysis of K-562 and other human DNA samples reveals a significant rearrangements of the c-abl sequences in this cell line. In addition, investigation of v-abl-related cytoplasmic RNA reveals relatively high levels of these sequences in K-562 compared to other normal and leukemia cells. We have also observed that lambda light chain constant region immunoglobulin genes are amplified in K-562, whereas kappa light chain sequences exhibit no amplification. These results are discussed within the context of the possibility that these Philadelphia chromosome-positive cells exhibit a reciprocal translocation involving chromosome 9 (containing c-abl) and chromosome 22 (containing the lambda light chain genes).
Amyloid &#946; -Protein Assembly as a Therapeutic Target of Alzheimers Disease (2008)

Alzheimer's disease (AD), the most common neurodegenerative disorder in the aged, is characterized by the cerebral deposition of fibrils formed by the amyloid beta-protein (Abeta), a 40-42 amino acid peptide. The folding of Abeta into neurotoxic oligomeric, protofibrillar, and fibrillar assemblies is hypothesized to be the key pathologic event in AD. Abeta is formed through cleavage of the Abeta precursor protein by two endoproteinases, beta-secretase and gamma-secretase, that cleave the Abeta N-terminus and C-terminus, respectively. These facts support the relevance of therapeutic strategies targeting Abeta production, assembly, clearance, and neurotoxicity. Currently, no disease-modifying therapeutic agents are available for AD patients. Instead, existing therapeutics provide only modest symptomatic benefits for a limited time. We summarize here recent efforts to produce therapeutic drugs targeting Abeta assembly. A number of approaches are being used in these efforts, including immunological, nutraceutical, and more classical medicinal chemical (peptidic inhibitors, carbohydrate-containing compounds, polyamines, "drug-like" compounds, chaperones, metal chelators, and osmolytes), and many of these have progressed to phase III clinical trails. We also discuss briefly a number of less mature, but intriguing, strategies that have therapeutic potential. Although initial trials of some disease-modifying agents have failed, we argue that substantial cause for optimism exists.
Monoaryloxide Pyrrolide (MAP) Imido Alkylidene Complexes of Molybdenum and Tungsten That Contain 2,6-Bis(2,5-R2-pyrrolyl)phenoxide (R = i-Pr, Ph) Ligands and an Unsubstituted Metallacyclobutane on Its Way to Losing Ethylene (2013)

We report the synthesis of Mo and W MAP complexes that contain O-2,6-(2,5-R<sub>2</sub>-pyrrolyl)<sub>2</sub>C<sub>6</sub>H<sub>3</sub> (2,6-dipyrrolylphenoxide or ODPP<sup>R</sup>) ligands in which R = i-Pr, Ph. W(NAr)(CH-t-Bu)(Pyr)(ODPP<sup>Ph</sup>) (<b>4a</b>; Ar = 2,6-disopropylphenyl, Pyr = pyrrolide) reacts readily with ethylene to yield a metallacyclobutane complex, W(NAr)(C<sub>3</sub>H<sub>6</sub>)(Pyr)(ODPP<sup>Ph</sup>) (<b>5</b>). The structure of <b>5</b> in the solid state shows that it is approximately a square pyramid with the WC<sub>4</sub> ring spanning apical and basal positions. This SP' structure, which has never been observed as an actual intermediate, must now be regarded as an integral feature of the metathesis reaction.
Self-Assembled Monothiol-Terminated Hyperbranched Polyglycerols on a Gold Surface:  A Comparative Study on the Structure, Morphology, and Protein Adsorption Characteristics with Linear Poly(ethylene glycol)s (2008)

Monothiol-terminated hyperbranched polyglycerols (HPGs) were synthesized by ring-opening polymerization of glycidol from partially deprotonated 2,2'-dihydroxyethane disulfide as the initiator and subsequent reduction of the disulfide group. Two molecular weights of HPG thiols were synthesized. The molecular weights of the polymers were determined by MALDI-TOF analysis, and the presence of thiol was verified by Ellman's assay. The self-assembly of HPG thiols on gold was studied and compared with that of linear poly(ethylene glycol) (PEG) thiols utilizing various surface analysis techniques. Monothiol-functionalized HPGs readily adsorbed to a gold surface and formed highly uniform thin films on the surface. The graft density of the HPG layer decreased with an increase in the molecular weight of the polymer. The amount of polymer on the surface increased with increasing incubation concentration and saturated above 6 g/L polymer concentration. Generally, HPG thiols gave lower graft density compared to linear PEG thiols of similar molecular weight. AFM morphological studies showed that HPG thiols form more uniform and smooth surface films compared to PEG thiols. Incubation of a polymer-coated surface (HPG thiols and PEG thiols) with bovine serum albumin and immunoglobulin showed that the high molecular weight hyperbranched polyglycerol was more resistant to protein adsorption than linear PEG of similar molecular weight or lower molecular weight HPG. The protein adsorption decreased with increasing graft density of the HPG chains on the surface. Our results show that HPG could be a good alternative to PEG in the development of nonfouling functional surfaces.
Surface-Enhanced Resonance Raman Scattering as a Novel Method of DNA Discrimination (2000)

Die DNA-Analyse erfordert oft einen Trennungsschritt; gerade dieser Schritt lässt sich vermeiden, indem oberflächenverstärkte Resonanz-Raman-Streuung (SERRS) zur Analyse eingesetzt wird. Mit dieser Methode kann man in einer Mischung bei niedrigen Konzentrationen zwischen zwei markierten Oligonucleotidsträngen unterscheiden, auch bei verschiedenen Verhältnissen. Sie ist ähnlich empfindlich wie Fluoreszenzmethoden, aber im Unterschied zu diesen mit üblichen Geräten in jedem Labor durchführbar.
Quantitative assay of the lytic action of immune lymphoid cells on 51-Cr-labelled allogeneic target cells in vitro; inhibition by isoantibody and by drugs. (1968)

The in vitro cytotoxic effect of spleen cells of mice immunized by tumour allografts was studied by measuring target cell inactivation as a function of release of radioactive label ((51)Cr) or loss of cloning efficiency. When sensitized lymphoid cells were incubated with target cells at a ratio of 100:1, up to 90 per cent of the incorporated label was released within 6–9 hours, while the number of clone-forming cells was reduced by up to 99 per cent in the same time period. Isoantiserum from the graft recipients, as well as its 19S and 7S fractions, protected target cells against the toxic effect of the spleen cells, but a lipoprotein antigen isolated from the tumour cells failed to inhibit the cytotoxic reaction. Target cell lysis as measured by specific release of (51)Cr was partially inhibited by actinomycin-D and by cycloheximide at concentrations which effectively blocked DNA-dependent RNA and protein synthesis.
A method to establish pure fibroblast and endothelial cell colony cultures from murine bone marrow. (1990)

Studies on the effect of the microenvironment on hematopoiesis would benefit from the availability of pure populations of nontransformed cells of each of the stromal cell types. The adherent murine bone marrow stromal cell population in this study consisted of fibroblasts, endothelial cells, and macrophages. Fibroblasts were segregated from the phagocytic endothelial cells and macrophages by allowing the phagocytic cells to ingest magnetic beads, with subsequent exposure to a magnetic field, effecting cell separation. Pure colony cultures of fibroblasts and endothelial cells were formed by varying the bead-to-cell ratio and incubation period of the cells. For complete purification of the fibroblasts, subsequent passaging was also necessary. Near confluent growth of each type was obtained with subsequent passages and sustained culture. The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) was used to enhance endothelial cell growth. We were not able to obtain pure populations of bone marrow macrophages in near confluent culture. The three cell types were identified by cellular morphology, acid and alkaline phosphatase staining, binding with the lectins Ulex europaeus and Bandeiraea simplicifolia, and the capacity to stain for the factor VIII-related antigen (von Willebrand's Factor).
B-cell prolymphocytic leukemia: a specific subgroup of mantle cell lymphoma (2014)

B-cell prolymphocytic leukemia (B-PLL) is a rare mature B-cell malignancy that may be hard to distinguish from mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL). B-PLL cases with a t(11;14) were redefined as MCL in the World Health Organization 2008 classification. We evaluated 13 B-PLL patients [7 being t(11;14)-positive (B-PLL+) and 6 negative (B-PLL-)] and compared them with MCL and CLL patients. EuroFlow-based immunophenotyping showed significant overlap between B-PLL+ and B-PLL-, as well as between B-PLL and MCL, whereas CLL clustered separately. Immunogenotyping showed specific IGHV gene usage partly resembling MCL. Gene expression profiling showed no separation between B-PLL+ and B-PLL- but identified 3 subgroups. One B-PLL subgroup clustered close to CLL and another subgroup clustered with leukemic MCL; both were associated with prolonged survival. A third subgroup clustered close to nodal MCL and was associated with short survival. Gene expression profiles of both B-PLL+ and B-PLL- showed best resemblance with normal immunoglobulin M-only B-cells. Our data confirm that B-PLL+ is highly comparable to MCL, indicate that B-PLL- also may be considered as a specific subgroup of MCL, and suggest that B-PLL is part of a spectrum, ranging from CLL-like B-PLL, to leukemic MCL-like B-PLL, to nodal MCL-like B-PLL.
Near-field scanning optical microscopy of photonic crystal nanocavities (2003)

Near-field scanning optical microscopy was used to observe high-resolution images of confined modes and photonic bands of planar photonic crystal (PPC) nanocavities fabricated in active InGaAsP material. We have observed the smallest optical cavity modes, which are intentionally produced by fractional edge dislocation high-Q cavity designs. The size of the detected mode was roughly four by three lattice spacings. We have also observed extended dielectric-band modes of the bulk PPC surrounding the nanocavity by geometrically altering the bands in emission range and eliminating localized modes out of the emission range.
The epidermal growth factor receptor tyrosine kinase inhibitor ZD1839 selectively potentiates radiation response of human tumors in nude mice, with a marked improvement in therapeutic index. (2003)

ZD1839 significantly enhanced the antitumor action of RT against the test tumors without significant adverse effects, increasing the therapeutic selectively of ionizing radiation in these model systems. These results predict substantial benefits for this multimodality regimen of therapy in patients.
Structural design and molecular evolution of a cytokine receptor superfamily. (1990)

A family of cytokine receptors comprising molecules specific for a diverse group of hematopoietic factors and growth hormones has been principally defined by a striking homology of binding domains. This work proposes that the approximately 200-residue binding segment of the canonical cytokine receptor is composed of two discrete folding domains that share a significant sequence and structural resemblance. Analogous motifs are found in tandem approximately 100-amino acid domains in the extracellular segments of a receptor family formed by the interferon-alpha/beta and -gamma receptors and tissue factor, a membrane tether for a coagulation protease. Domains from the receptor supergroup reveal clear evolutionary links to fibronectin type III structures, approximately 90-amino acid modules that are typically found in cell surface molecules with adhesive functions. Predictive structural analysis of the shared receptor and fibronectin domains locates seven beta-strands in conserved regions of the chain; these strands are modeled to fold into antiparallel beta-sandwiches with a topology that is similar to immunoglobulin constant domains. These findings have strong implications for understanding the evolutionary emergence of an important class of regulatory molecules from primitive adhesive modules. In addition, the resulting double-barrel design of the receptors and the spatial clustering of conserved residues suggest a likely binding site for cytokine ligands.
Nondestructive nanostraw intracellular sampling for longitudinal cell monitoring (2017)

Here, we report a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 d through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with >95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual contents within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activity such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to understand dynamic cell behavior, including processes such as induced pluripotency and differentiation.
Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles (2011)

Most of the position weight matrix (PWM) based bioinformatics methods developed to predict transcription factor binding sites (TFBS) assume each nucleotide in the sequence motif contributes independently to the interaction between protein and DNA sequence, usually producing high false positive predictions. The increasing availability of TF enrichment profiles from recent ChIP-Seq methodology facilitates the investigation of dependent structure and accurate prediction of TFBSs. We develop a novel Tree-based PWM (TPWM) approach to accurately model the interaction between TF and its binding site. The whole tree-structured PWM could be considered as a mixture of different conditional-PWMs. We propose a discriminative approach, called TPD (TPWM based Discriminative Approach), to construct the TPWM from the ChIP-Seq data with a pre-existing PWM. To achieve the maximum discriminative power between the positive and negative datasets, the cutoff value is determined based on the Matthew Correlation Coefficient (MCC). The resulting TPWMs are evaluated with respect to accuracy on extensive synthetic datasets. We then apply our TPWM discriminative approach on several real ChIP-Seq datasets to refine the current TFBS models stored in the TRANSFAC database. Experiments on both the simulated and real ChIP-Seq data show that the proposed method starting from existing PWM has consistently better performance than existing tools in detecting the TFBSs. The improved accuracy is the result of modelling the complete dependent structure of the motifs and better prediction of true positive rate. The findings could lead to better understanding of the mechanisms of TF-DNA interactions.
Planning hydraulically fractured horizontal completions (1989)

This work discusses how candidates for horizontal wells are selected based on reservoir characteristics, cementing considerations and stimulation requirements. Several tests are available to determine when and where a well will have the best chance of being a success.
Sumoylation of Oct4 Enhances Its Stability, DNA Binding, and Transactivation (2007)

Transcription factor Oct4 is a master regulator affecting the fate of pluripotent stem cells and germ cell precursors. Oct4 expression is tightly regulated, and small changes in expression level can have dramatic effects on differentiation or oncogenesis. Post-translational modifications including phosphorylation and ubiquitination have been reported to regulate Oct4 transcriptional activity. Here we show that Oct4 is a target for small ubiquitin-related modifier (SUMO)-1 modification in vivo and in vitro. Sumoylation of Oct4 occurs at a single lysine, Lys(118), located at the end of the amino-terminal transactivation domain and next to the Pit1-Oct-Unc86 (POU) DNA binding domain. SUMO-1 and Oct4 colocalize at several promoter sequences in vivo, and a fraction of Oct4 molecules colocalized with SUMO-1 in nuclear aggregates. Sumoylation of Oct4 led to significantly increased Oct4 stability and increased DNA binding. In addition, SUMO-1 cotransfection led to augmented Oct4 transactivation potential that was reduced when the Oct4 sumoylation target site was mutated. Therefore, sumoylation of Oct4 results in increased stability, DNA binding, and transactivation and provides an important mechanism to regulate Oct4 activity.
Antitumor activity of degraded products of lentinan: its correlation with molecular weight. (1976)

Lentinan, an antitumor polysaccharide from Lentinus edodes, was degraded to seven fractions by treatment with formic acid. The low molecular-weight fractions (I and II) showed no antitumor activity against sarcoma-180 solid-type tumor and the absorption maximum of Congo Red did not shift in their presence in 0.1M sodium hydroxide. The medium molecular-weight fraction III, which required the increase of doses (5 or 10 mg/kg) for inhibition of tumor growth, caused a little shift. On the other hand, the absorption maximum of Congo Red shifted largely by the presence of high molecular-weight fractions (IV approximately VII) which showed the inhibition ratio of over 95% in a dose of 1 mg/kg. Participation of molecular weight in the antitumor activity of polysaccharides which contain (1 leads to 3)-beta-D-glucan main chain was discussed.
Project GROPEHaptic displays for scientific visualization (1990)

We began in 1967 a project to develop a haptic+display for 6-D force fields of interacting protein molecules. We approached it in four stages: a 2-D system, a 3-D system tested with a simple task, a 6-D system tested with a simple task, and a full 6-D molecular docking system, our initial goal. This paper summarizes the entire project---the four systems, the evaluation experiments, the results, and our observations. The molecular docking system results are new.Our principal conclusions are:&amp;bull; Haptic display as an augmentation to visual display can improve perception and understanding both of force fields and of world models populated with impenetrable objects.&amp;bull; Whereas man-machine systems can outperform computer-only systems by orders of magnitude on some problems, haptic-augmented interactive systems seem to give about a two-fold performance improvement over purely graphical interactive systems. Better technology may give somewhat more, but a ten-fold improvement does not seem to be in the cards.&amp;bull; Chemists using GROPE-III can readily reproduce the true docking positions for drugs whose docking is known (but not to them) and can find very good docks for drugs whose true docks are unknown. The present tool promises to yield new chemistry research results; it is being actively used by research chemists.&amp;bull; The most valuable result from using GROPE-III for drug docking is probably the radically improved situation awareness that serious users report. Chemists say they have a new understanding of the details of the receptor site and its force fields, and of why a particular drug docks well or poorly.&amp;bull; We see various scientific/education applications for haptic displays but believe entertainment, not scientific visualization, will drive and pace the technology.&amp;bull; The hardware-software system technology we have used is barely adequate, and our experience sets priorities for future development.&amp;bull; Some unexpected perceptual phenomena were observed. All of these worked for us, not against us.
Parity Fluctuations between Coulomb Blockaded Superconducting Islands (1995)

We find that if two superconducting islands of different number parity are linked by a tunnel junction, the unpaired electron in the odd island has a tendency to tunnel into the even island. This process leads to fluctuations in time of the number parity of each island, giving rise to a random telegraph noise spectrum with a characteristic frequency that has an unusual temperature dependence. This new phenomenon should be observable in a Cooper-pair pump and similar single-electron tunneling devices.
Tunable-focus lens for adaptive eyeglasses (2017)

We demonstrate the implementation of a compact tunable-focus liquid lens suitable for adaptive eyeglass application. The lens has an aperture diameter of 32 mm, optical power range of 5.6 diopter, and electrical power consumption less than 20 mW. The lens inclusive of its piezoelectric actuation mechanism is 8.4 mm thick and weighs 14.4 gm. The measured lens RMS wavefront aberration error was between 0.73 µm and 0.956 µm.