gebhart/patrepeval huggingface dataset:
N-myc Downstream Regulated Gene 1 (NDRG1) Is Fused to (2009)

A step toward the molecular classification of prostate cancer was the discovery of recurrent erythroblast transformation– specific rearrangements, most commonly fusing the androgen-regulated TMPRSS2 promoter to ERG .T heTMPRSS2-ERG fusion is observed in around 90% of tumors that overexpress the oncogene ERG. The goal of the current study was to complete the characterization of these ERG-overexpressing prostate cancers. Using fluorescence in situ hybridization and reverse transcription–polymerase chain reaction assays, we screened 101 prostate cancers, identifying 34 cases (34%) with the TMPRSS2-ERG fusion. Seven cases demonstrated ERG rearrangement by fluorescence in situ hybridization without the presence of TMPRSS2-ERG fusion messenger RNA transcripts. Screening for known 5′ partners, we determined that three cases harbored the SLC45A3-ERG fusion. To discover novel 5′ partners in these ERG-overexpressing and ERG-rearranged cases, we used paired-end RNA sequencing. We first confirmed the utility of this approach by identifying the TMPRSS2-ERG fusion in a known positive prostate cancer case and then discovered a novel fusion involving the androgen-inducible tumor suppressor, NDRG1 (N-myc downstream regulated gene 1), and ERG in two cases. Unlike TMPRSS2-ERG and SCL45A3-ERG fusions, the NDRG1-ERG fusion is predicted to encode a chimeric protein. Like TMPRSS2, SCL45A3 and NDRG1 are inducible not only by androgen but also by estrogen. This study demonstrates that most ERG-overexpressing prostate cancers harbor hormonally regulated TMPRSS2-ERG, SLC45A3-ERG ,o rNDRG1-ERG fusions. Broader implications of this study support the use of RNA sequencing to discover novel cancer translocations.
Rheological effects of drag-reducing polymers improve cerebral blood flow and oxygenation after traumatic brain injury in rats (2016)

Cerebral ischemia has been clearly demonstrated after traumatic brain injury (TBI); however, neuroprotective therapies have not focused on improvement of the cerebral microcirculation. Blood soluble drag-reducing polymers (DRP), prepared from high molecular weight polyethylene oxide, target impaired microvascular perfusion by altering the rheological properties of blood and, until our recent reports, has not been applied to the brain. We hypothesized that DRP improve cerebral microcirculation and oxygenation after TBI. DRP were studied in healthy and traumatized rat brains and compared to saline controls. Using in-vivo two-photon laser scanning microscopy over the parietal cortex, we showed that after TBI, nanomolar concentrations of intravascular DRP significantly enhanced microvascular perfusion and tissue oxygenation in peri-contusional areas, preserved blood-brain barrier integrity and protected neurons. The mechanisms of DRP effects were attributable to reduction of the near-vessel wall cell-free layer which increased near-wall blood flow velocity, microcirculatory volume flow, and number of erythrocytes entering capillaries, thereby reducing capillary stasis and tissue hypoxia as reflected by a reduction in NADH. Our results indicate that early reduction in CBF after TBI is mainly due to ischemia; however, metabolic depression of contused tissue could be also involved.
Rheological and Shearing Conditions for the Preparation of Monodisperse Emulsions (1999)

Monodisperse emulsions can be obtained by shearing a crude polydisperse one. The aim of this paper is to discover the required conditions for droplet fragmentation and resulting monodispersity, independently of the chemical nature of the system. We particularly examine (i) the role of the initial emulsion viscoelasticity and (ii) the nature of the applied shear. Taking into account these features, we show a large variety of monodisperse materials that are easily producible in reasonable quantity.
Shape intrinsic fingerprints for free-form object matching (2003)

This paper presents matching and similarity evaluation methods between two NURBS surfaces, and their application to copyright protection of digital data representing solids or NURBS surfaces. Two methods are employed to match objects: the moment and the curvature methods. The moment method uses integral properties, i.e. the volume, the principal moments of inertia and directions, to find the rigid body transformation as well as the scaling factor. The curvature method is based on the Gaussian and the mean curvatures to establish correspondence between two objects. The matching algorithms are applied to problems of copyright protection. A suspect model is aligned to an original model through the matching methods so that similarity between two models can be assessed to determine if the suspect model contains part(s) of the original model, which may be stored in an independent repository. Three types of tests, the weak, intermediate and strong tests, are proposed for similarity assessment between two objects. The weak and intermediate tests are performed at node points obtained through shape intrinsic wireframing. The strong test relies on isolated umbilical points which can be used as fingerprints of an object for supporting an ownership claim to the original model. The three tests are organized in two decision algorithms such that they produce systematic and statistical measures for a similarity decision between two objects in a hierarchical manner. Based on the systematic and statistical evaluation of similarity, a decision can be reached whether the suspect model is an illegal copy of the original model.
Synthesis and Biological Evaluation of 10,11-Dihydrodictyostatin, a Potent Analogue of the Marine Anticancer Agent Dictyostatin (2007)

By employing a diverted total synthesis strategy with late-stage intermediates, 10,11-dihydrodictyostatin ( 5) was prepared and evaluated in vitro for growth inhibition against a range of human cancer cell lines, including the NCI/ADR Taxol-resistant cell line. This novel dictyostatin analogue was found to retain potent antimitotic activity, with a comparable profile to discodermolide and Taxol, functioning by microtubule stabilization and G2/M arrest. These SAR studies provide further insight into the interaction between dictyostatin ( 1) and its tubulin target.
Development of Amphiphylic Mimics of Insect Neuropeptides for Pest Control (1999)

Insect neuropeptides regulate virtually all aspects of insect life and are excellent candidates for development of new methods for pest control. However, they do not penetrate insect cuticle and are degraded by enzymes both in the digestive system and hemolymph. We have designed mimics of model neuropeptides by attachment of various lipidic moieties to the amino terminus of the bioactive core of the neuropeptides. These mimics have amphiphylic characteristics that allowed them to penetrate the hydrophobic insect cuticle. The mimics also induced prolonged physiological responses (up to 20 hours) and were resistant to peptidase attack. This knowledge has been used to develop a novel, species-specific approach to insect control.
<title>Automatic shape analysis and classification of mammographic calcifications</title> (1997)

The morphology and distribution of mammographic calcifications and the way these elements vary within a cluster are valuable in distinguishing between benign and malignant calcifications. The specific aims of this study were (a) the development of an automatic tool that differentiates between benign and malignant clustered calcifications based on their morphological properties and (b) the determination of the effects of image spatial resolution on the classification process. The long term aim of the project is to use this tool to categorize detected clusters into the various types described in the breast imaging reporting and data systems of the American College of Radiology and assist the radiologists in their diagnosis.
Performance of photonic switches using cascade-structured integrated optic devices (1989)

In a practical photonic switching system using integrated optic devices, crosstalk and control are more of a problem than optical loss. In this paper, performances of photonic gate-type matrix switch 1 and a time slot interchanger 2 using cascaded-structured integrated optic modulators and switches are analyzed. Both have shown improved signal-to-crosstalk ratios (SXR) and the possibility of using a common control voltage without tuning for the switching components. We also compare these two photonic systems with those using conventional components by considering other performance factors such as optical insertion loss, device count, switch capability, and possible switch size, etc.
Selective catalytic reduction of sulfur dioxide to elemental sulfur. Quarterly technical progress report No. 7, January--March 1994 (1994)

Elemental sulfur recovery from S0{sub 2}-containing gas stream is highly attractive as it produces a salable product and no waste to dispose of However, commercially available schemes are complex and involve multistage reactors, such as, most notably in the Resox (reduction of S0{sub 2} with coke) and Claus plant (reaction of S0{sub 2} with H{sub 2}S over catalyst). This project will investigate a cerium oxide catalyst for the single stage selective reduction of S0{sub 2} to elemental sulfur by a reductant, such as carbon monoxide. Cerium oxide has been identified in recent work at MIT as a superior catalyst for S0{sub 2} reduction by CO to elemental sulfur because its high activity and high selectivity to sulfur over COS over a wide temperature range (400--650{degree}C). The detailed kinetic and parametric studies of S0{sub 2} reduction planned in this work over various CeO{sub 2}-formulations will provide the necessary basis for development of a very simplified process, namely that of a single-stage elemental sulfur recovery scheme from variable concentration gas streams. The potential cost- and energy-efficiency benefits from this approach can not be overstated. A first apparent application is treatment of a regenerator off-gases in power plants using regenerative flue gas desulfurization.more » Such a simple catalytic converter may offer the long-sought ``Claus-alternative`` for coal-fired power plant applications.« less
A Novel Time-Varying Spectral Filtering Algorithm for Reconstruction of Motion Artifact Corrupted Heart Rate Signals During Intense Physical Activities Using a Wearable Photoplethysmogram Sensor (2015)

Accurate estimation of heart rates from photoplethysmogram (PPG) signals during intense physical activity is a very challenging problem. This is because strenuous and high intensity exercise can result in severe motion artifacts in PPG signals, making accurate heart rate (HR) estimation difficult. In this study we investigated a novel technique to accurately reconstruct motion-corrupted PPG signals and HR based on time-varying spectral analysis. The algorithm is called Spectral filter algorithm for Motion Artifacts and heart rate reconstruction (SpaMA). The idea is to calculate the power spectral density of both PPG and accelerometer signals for each time shift of a windowed data segment. By comparing time-varying spectra of PPG and accelerometer data, those frequency peaks resulting from motion artifacts can be distinguished from the PPG spectrum. The SpaMA approach was applied to three different datasets and four types of activities: (1) training datasets from the 2015 IEEE Signal Process. Cup Database recorded from 12 subjects while performing treadmill exercise from 1 km/h to 15 km/h; (2) test datasets from the 2015 IEEE Signal Process. Cup Database recorded from 11 subjects while performing forearm and upper arm exercise. (3) Chon Lab dataset including 10 min recordings from 10 subjects during treadmill exercise. The ECG signals from all three datasets provided the reference HRs which were used to determine the accuracy of our SpaMA algorithm. The performance of the SpaMA approach was calculated by computing the mean absolute error between the estimated HR from the PPG and the reference HR from the ECG. The average estimation errors using our method on the first, second and third datasets are 0.89, 1.93 and 1.38 beats/min respectively, while the overall error on all 33 subjects is 1.86 beats/min and the performance on only treadmill experiment datasets (22 subjects) is 1.11 beats/min. Moreover, it was found that dynamics of heart rate variability can be accurately captured using the algorithm where the mean Pearson's correlation coefficient between the power spectral densities of the reference and the reconstructed heart rate time series was found to be 0.98. These results show that the SpaMA method has a potential for PPG-based HR monitoring in wearable devices for fitness tracking and health monitoring during intense physical activities.
Improved dielectrics for multilayer ceramic capacitors (1985)

This article discusses a series of new dielectrics for use in monolithic ceramic capacitors. The series includes the popular commercial ranges of dielectrics at lower cost and with improved electrical properties compared with previous generations
Hybrid Power Management Program Continued (2002)

Hybrid Power Management (HPM) is the innovative integration of diverse, state-of-the-art power devices in an optimal configuration for space and terrestrial applications. The appropriate application and control of the various power devices significantly improves overall system performance and efficiency. The advanced power devices include ultracapacitors and photovoltaics. HPM has extremely wide potential with applications including power-generation, transportation, biotechnology, and space power systems. It may significantly alleviate global energy concerns, improve the environment, and stimulate the economy.
Isolation of a new herpesvirus from human CD4+ T cells. (1990)

A new human herpesvirus has been isolated from CD4+ T cells purified from peripheral blood mononuclear cells of a healthy individual (RK), following incubation of the cells under conditions promoting T-cell activation. The virus could not be recovered from nonactivated cells. Cultures of lymphocytes infected with the RK virus exhibited a cytopathic effect, and electron microscopic analyses revealed a characteristic herpesvirus structure. RK virus DNA did not hybridize with large probes derived from herpes simplex virus, Epstein-Barr virus, varicella-zoster virus, and human cytomegalovirus. The genetic relatedness of the RK virus to the recently identified T-lymphotropic human herpesvirus 6 (HHV-6) was investigated by restriction enzyme analyses using 21 different enzymes and by blot hybridization analyses using 11 probes derived from two strains of HHV-6 (Z29 and U1102). Whereas the two HHV-6 strains exhibited only limited restriction enzyme polymorphism, cleavage of the RK virus DNA yielded distinct patterns. Of the 11 HHV-6 DNA probes tested, only 6 cross-hybridized with DNA fragments derived from the RK virus. Taken together, the maximal homology amounted to 31 kilobases of the 75 kilobases tested. We conclude that the RK virus is distinct from previously characterized human herpesviruses. We propose to designate it as the prototype of a new herpesvirus, the seventh human herpesvirus identified to date.
Drug-induced inhibition of the peripheral-type benzodiazepine receptor expression and cell proliferation in human breast cancer cells. (2000)

The peripheral-type benzodiazepine receptor (PBR) expression and localization correlate with human breast cancer cell proliferation and aggressive phenotype expression. The standardized extract of Ginkgo biloba leaves (EGb 761) and isolated ginkgolide B (GKB) were shown to decrease PBR mRNA expression in adrenal cells. We examined the effect of EGb 761 and GKB on PBR expression and cell proliferation in human breast cancer cells. EGb 761 and GKB decreased in a time- and dose-dependent manner PBR expression and cell proliferation in the highly aggressive, rich in PBR, human breast cancer cell line MDA-231 whereas they did not affect the proliferation of the non-aggressive human breast cancer cell line MCF-7, which contains very low PBR levels. This effect was reversible and not due to the antioxidant properties of the compounds tested. Using a human cDNA expression array we determined that EGb 761 treatment altered, in addition to PBR, the expression of 36 gene products involved in various pathways regulating cell proliferation. These in vitro data were further validated in an in vivo model where EGb 761 and GKB significantly inhibited the nuclear PBR expression and growth of MDA-231 cell xenografts in nude mice. Taken together, these data suggest that the manipulation of PBR expression could be used to control tumor growth and that EGb 761 and GKB, under the conditions used, exert cytostatic properties.
Molecular genetic improvements of cyanobacteria to enhance the industrial potential of the microbe: A review (2016)

The rapid increase in worldwide population coupled with the increasing demand for fossil fuels has led to an increased urgency to develop sustainable sources of energy and chemicals from renewable resources. Using microorganisms to produce high-value chemicals and next-generation biofuels is one sustainable option and is the focus of much current research. Cyanobacteria are ideal platform organisms for chemical and biofuel production because they can be genetically engineered to produce a broad range of products directly from CO<sub>2</sub> , H<sub>2</sub> O, and sunlight, and require minimal nutrient inputs. The purpose of this review is to provide an overview on advances that have been or could be made to improve strains of cyanobacteria for industrial purposes. First, the benefits of using cyanobacteria as a platform for chemical and biofuel production are discussed. Next, an overview of cyanobacterial strain improvements by genetic engineering is provided. Finally, mutagenesis techniques to improve the industrial potential of cyanobacteria are described. Along with providing an overview on various areas of research that are currently being investigated to improve the industrial potential of cyanobacteria, this review aims to elucidate potential targets for future research involving cyanobacteria as an industrial microorganism. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1357-1371, 2016.
High-resolution fiber-optic low-frequency voltage sensor based on the electrostrictive effect (1993)

A minimum detectable voltage of 40 nV/ square root Hz at 1 Hz is demonstrated in a fiber-optic interferometric low-frequency voltage sensor. The device maintains good resolution below 1 Hz, providing a minimum detectable voltage of 55 nV/ square root Hz at 0.1 Hz and 129 nV/ square root Hz at 0.03 Hz. High resolution at low frequencies is attainable due to the nonlinear strain response of the electrostrictive transducer under an applied electric field, which upconverts low-frequency voltage signals as sidebands of a high-frequency carrier where 1/f noise is not dominant. The measured low-frequency data represent an improvement of >45 dB over previously reported results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A comparative study on content-based music genre classification (2003)

Content-based music genre classification is a fundamental component of music information retrieval systems and has been gaining importance and enjoying a growing amount of attention with the emergence of digital music on the Internet. Currently little work has been done on automatic music genre classification, and in addition, the reported classification accuracies are relatively low. This paper proposes a new feature extraction method for music genre classification, DWCHs. DWCHs stands for Daubechies Wavelet Coefficient Histograms. DWCHs capture the local and global information of music signals simultaneously by computing histograms on their Daubechies wavelet coefficients. Effectiveness of this new feature and of previously studied features are compared using various machine learning classification algorithms, including Support Vector Machines and Linear Discriminant Analysis. It is demonstrated that the use of DWCHs significantly improves the accuracy of music genre classification.
Two-mode fiber modal coupler (1984)

When a single-mode fiber is used at a wavelength below the cutoff wavelength, the fiber guides second-order modes, which travel at different phase velocities from the fundamental mode. Periodically stressing this two-mode fiber once per beat length can cause coherent coupling between the modes. Such a modal coupler has been developed and is described here. Coupling to one of the second-order modes has been achieved, leaving less than -40-dB residual power in the fundamental mode. Two couplers have been mounted on a single strand of fiber to construct a Mach-Zehnder interferometer with better than a 30-dB on/off ratio. The coupler is polarization sensitive and can be used as an in-line polarizer. A 36-dB extinction ratio between polarizations has been observed.
CO-Free Hydrogen Production by Membrane Reactor Equipped with CO Methanator (2008)

A novel membrane reactor system equipped with a CO methanator was proposed for the efficient production of CO-free hydrogen by a simple and compact reactor unit without any additional purification of hydrogen. It is expected that a trace amount of CO in the permeate can be removed through the methanation at the sacrifice of a minimum amount of hydrogen. The effectiveness of this system was experimentally examined for the steam reforming of methane in the membrane reactor using a thin Pd/Ag membrane with a few defects and a Ru/Al2O3 catalyst for methanation. It was demonstrated that a highly concentrated and practically CO-free hydrogen could be successfully obtained with attaining the high methane conversion beyond the limit imposed by equilibrium, and the amount of hydrogen consumed by the CO and CO2 methanations was much lowered; that is, it was less than ca. 1% of hydrogen permeated through the membrane. Furthermore, the catalytic performance for methanation at relatively high temperature was investigated using a packed bed type reactor with a simulative permeate, because the loss of hydrogen due to the methanations can be more reduced by a catalyst with the ability for CO selective methanation in the presence of CO2. The experimental result that the selectivity toward CO methanation strongly depended on the metal catalyst and the support suggested the possibility of further improvement of the proposed system.