gebhart/patrepeval huggingface dataset:
Indexing Strategies for Rapid Searches of Short Words in Genome Sequences (2007)

Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries.
The Adipose-derived Stem Cell: Looking Back and Looking Ahead (2010)

In 2002, researchers at UCLA published a manuscript in Molecular Biology of the Cell describing a novel adult stem cell population isolated from adipose tissue-the adipose-derived stem cell (ASC). Since that time, the ASC has gone on to be one of the most popular adult stem cell populations currently being used in the stem cell field. With multilineage mesodermal potential and possible ectodermal and endodermal potentials also, the ASC could conceivably be an alternate to pluripotent ES cells in both the lab and in the clinic. In this retrospective article, a historical perspective on the ASC is given together with exciting new applications for the stem cell being considered today.
Semi-supervised Question Retrieval with Gated Convolutions (2016)

Tao Lei, Hrishikesh Joshi, Regina Barzilay, Tommi Jaakkola, Kateryna Tymoshenko, Alessandro Moschitti, Lluís Màrquez. Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2016.
Density estimation-based information fusion for multiple motion computation (2003)

Vision tasks, such as motion analysis, object tracking, robot localization, and 3D modeling, often require the fusion of estimates coming from different sources. Most of the fusion algorithms, however, are not robust with respect to outliers and only consider one source models. Their performance deteriorates when initial assumptions are not valid (e.g., the presence of outliers in the data or data corresponding to multiple motions). The paper presents a statistical solution to the fusion problem based on variable-bandwidth kernel density estimation. The fusion estimate is represented by the mode of a density function that exploits the uncertainty of the estimates to be fused. We show that the fusion estimate is consistent and conservative. Since our construction is founded on density estimation, it handles naturally outliers and multiple source models. We test the density-based fusion for the task of multiple motion computation. Superior experimental results validate our theory.
Drop impact on chemically structured arrays (2005)

We describe recent investigations on the impact behaviour of liquid drops onto chemically structured surfaces. The surface patterns were prepared via photochemical attachment of polymer molecules with different hydrophilicities using self-assembled monolayers of benzophenone bearing silanes. Immobilization of the polymer monolayers was followed by an ablation process to generate a chemical surface pattern. Impact experiments on systems consisting of very hydrophobic poly(perfluoroalkylethyl)acrylate coatings and hydrophilic areas show that within certain limitations the water drop has a strong tendency to reach the hydrophilic spots, even for inclined substrates. Impact experiments of drops on arrays of hydrophilic spots on the background of a perfluorinated polymer show that the drops spontaneously self-centre on the lithographically generated pattern. The obtained results suggest that the process can be used to circumvent some of the current problems in micro-array fabrication.
High RF performance TSV silicon carrier for high frequency application (2008)

Three dimensional system-in-package (3D SiP) based on silicon carriers or interposer is a fast emerging technology that offers system design flexibility and integration of heterogeneous technologies. One of the key technologies enabler for silicon carrier is through silicon via (TSV). The development of 3D SiP will require the devices with different functionality operating at high frequency to be densely packed on the silicon substrate. However, silicon substrate is usually of low resistivity, when a high frequency signal is transmitted vertically through the substrate via, significant signal attenuation can occur that leads to poor RF performance. In this paper, a coaxial TSV structure in silicon carrier is presented for high frequency applications. The coaxial TSV is able to suppress undesirable substrate loss as well as provide good impedance matching. Electrical modeling of coaxial TSV structure was carried out to obtain the required geometries for impedance matching. Three different types of test vehicles were fabricated; Cu-plug TSV in both low (~10 Omega-cm) and high resistivity (~4000 Omega-cm) silicon substrate, and coaxial TSV in low resistivity silicon substrate. The S-parameters of the via structure of the test vehicles were measured from 100 MHz to 10 GHz. The measured results show that the coaxial TSV structure is able to suppress silicon substrate loss and provide good RF performance compared to Cu-plug TSV structure.
Processing of Apple Pomace for Bioactive Molecules (2008)

The growth of horticulture industries worldwide has generated huge quantities of fruit wastes (25%-40% of the total fruits processed). These residues are generally a good source of carbohydrates, especially cell wall polysaccharides and other functionally important bioactive molecules such as proteins, vitamins, minerals and natural antioxidants. "Apple pomace" is a left-over solid biomass with a high moisture content, obtained as a by-product during the processing of apple fruits for juice, cider or wine preparation. Owing to the high carbohydrate content, apple pomace is used as a substrate in a number of microbial processes for the production of organic acids, enzymes, single cell protein, ethanol, low alcoholic drinks and pigments. Recent research trends reveal that there is an increase in the utilization of apple pomace as a food processing residue for the extraction of value added products such as dietary fibre, protein, natural antioxidants, biopolymers, pigments and compounds with unique properties. However, the central dogma is still the stability, safety and economic feasibility of the process(s)/product(s) developed. This review is mainly focused on assessing recent research developments in extraction, isolation and characterization of bioactive molecules from apple pomace, along with their commercial utilization, in food fortification.
A CMOS serial link for fully duplexed data communication (1995)

This paper describes a CMOS serial link allowing fully duplexed 500 Mbaud serial data communication. The CMOS serial link is a robust and low-cost solution to high data rate requirements. A central charge pump PLL for generating multiphase clocks for oversampling is shared by several serial link channels. Fully duplexed serial data communication is realized in the bidirectional bridge by separating incoming data from the mixed signal on the cable end. The digital PLL accomplishes process-independent data recovery by using a low-ratio oversampling, a majority voting, and a parallel data recovery scheme. Mostly, digital approach could extend its bandwidth further with scaled CMOS technology. A single channel serial link and a charge pump PLL are integrated in a test chip using 1.2 /spl mu/m CMOS process technology. The test chip confirms upto 500 Mbaud unidirectional mode operation and 320 Mbaud fully duplexed mode operation with pseudo random data patterns.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Formation Mechanism of Porous Silicon Layer by Anodization in  HF  Solution (1980)

The mechanism of formation of porous silicon layer (PSL) has been studied according to the following experimental results. PSL is formed by the local dissolution of silicon which occurs only at the base of the pores. The concentration of the electrolyte in the pores of PSL is constant during anodization and the anodic reaction in the pores proceeds uniformly in the thickness direction. The dissolution of silicon in the pores is the results of the divalent and the tetravalent reactions of silicon with , without the disproportionation reaction. The insoluble surface porous film (SPF) exists at the surface of PSL and the silicic acid is formed in PSL. A model of forming PSL is proposed, with emphasis being placed on the anodic reaction and the local dissolution of silicon which is initiated by SPF and is promoted by the hindrance layers composed of the silicic acid.
The Anaerobic Microflora of the Human Body (1993)

An overview is presented of the kinds of anaerobic bacteria that inhibit the surfaces of the human body. The anaerobic floras of the skin, oral cavity, alimentary tract, and genitourinary tract are described. The activities of these organisms that impact on the human host and their interactions are discussed. Emphasis is placed on the protective roles of the floras of the various bodily surfaces in preventing infections. Identified mechanisms of protection on the skin and in the colon and the vagina are explained.
PIM Kinase Inhibitor AZD1208 for Treatment of MYC-Driven Prostate Cancer (2014)

PIM inhibition is a potential treatment for MYC-driven prostate cancers including CRPC, and its effectiveness may be enhanced by activators of the p53 pathway, such as radiation.
A NUCA substrate for flexible CMP cache sharing (2005)

We propose an organization for the on-chip memory system of a chip multiprocessor, in which 16 processors share a 16MB pool of 256 L2 cache banks. The L2 cache is organized as a non-uniform cache architecture (NUCA) array with a switched network embedded in it for high performance. We show that this organization can support the spectrum of degrees of sharing: unshared, in which each processor has a private portion of the cache, thus reducing hit latency, completely shared, in which every processor shares the entire cache, thus minimizing misses, and every point in between. We find the optimal degree of sharing for a number of cache bank mapping policies, and also evaluate a per-application cache partitioning strategy. We conclude that a static NUCA organization with sharing degrees of two or four work best across a suite of commercial and scientific parallel workloads. We also demonstrate that migratory, dynamic NUCA approaches improve performance significantly for a subset of the workloads at the cost of increased power consumption and complexity, especially as per-application cache partitioning strategies are applied.
Abstract #4431: Campath-1H activates multiple pathways and transcription factors (CREB, ATF-1, Egr1&2 and Stat3) upon binding to CD52 on B-cells (2009)

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

The mature form of CD52 is a 12 amino acid peptide linked to the membrane via a glycophosphatidylinositol (GPI) anchor. CD52 is highly expressed on human lymphocytes and is an effective target for therapeutic antibodies. Campath-1H is a humanized monoclonal antibody directed against CD52, currently approved for the treatment of B-cell chronic lymphocytic leukemia (B-CLL). While molecular effects of Campath-1H in the presence of a cross-linking anti-Fc antibody on T lymphocytes have been described, little is known about the molecular changes induced by Campath-1H binding to CD52 on normal or malignant B lymphocytes. We investigated the effects of Campath-1H on PBMC of B-CLL patients and human B lymphocyte cell lines, BL31 and Wien133, in the presence and absence of a cross-linking agent. Cross-linking Campath-1H on BL31 and Wien133 cells induced a transient calcium flux followed by a transient protein phosphorylation. The increase in phosphorylated proteins at 2.5 min correlated with the peak of the calcium flux, and returned to the basal level after 15 min. Using a multiplex suspension phosphoprotein array system, Akt, CREB, ERK1/2, IRS-1, Jnk, p38-MAPK, p70S6, p90RSK and STAT3 were determined to be activated upon cross-linking. No phophorylation was observed for Bcr/Abl, c-Jun, NF-\#954;B, and Src. We also profiled gene expression changes by gene chip. From which, we observed TNF-\#945;, EGR1 & 2, MIP1, FOS and HBEGF are upregulated, and we confirmed the secretion of TNF-\#945; from B cell lines after the treatment. These observations are the first evidence that cross-linking Campath-1H on B cells activates specific pathways, leading to the activation of early responsive genes and inducing target cells to produce cytokines.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 4431.
Development and Navigation of a Mobile Robot for Floating Production Storage and Offloading Ship Hull Inspection (2009)

This paper describes the current development status of a mobile robot designed to inspect the outer surface of large oil ship hulls and floating production storage and offloading platforms. These vessels require a detailed inspection program, using several nondestructive testing techniques. A robotic crawler designed to perform such inspections is presented here. Locomotion over the hull is provided through magnetic tracks, and the system is controlled by two networked PCs and a set of custom hardware devices to drive motors, video cameras, ultrasound, inertial platform, and other devices. Navigation algorithm uses an extended-Kalman-filter (EKF) sensor-fusion formulation, integrating odometry and inertial sensors. It was shown that the inertial navigation errors can be decreased by selecting appropriate <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> matrices in the EKF formulation.
A practical VEP-based brain-computer interface (2006)

This paper introduces the development of a practical brain-computer interface at Tsinghua University. The system uses frequency-coded steady-state visual evoked potentials to determine the gaze direction of the user. To ensure more universal applicability of the system, approaches for reducing user variation on system performance have been proposed. The information transfer rate (ITR) has been evaluated both in the laboratory and at the Rehabilitation Center of China, respectively. The system has been proved to be applicable to > 90% of people with a high ITR in living environments.
Powering of remote node locations using flywheel energy storage (2002)

The telephone industry has long used lead acid batteries for back-up power to provide uninterruptible service. As an alternative to this approach, SatCon Technology Corporation has developed a flywheel energy storage system (FESS) specifically designed as a "plug for plug" replacement for batteries in telecommunications remote powering applications such as vaults, huts and cabinets. This paper describes the principles and practices of flywheel technology. In particular, the paper presents the SatCon 2.0 kWHr telecommunication flywheel specifications and components including composite rim, magnetic bearings, bi-directional inverter and PM motor/generator. In addition, the paper discusses monitoring capability, installation considerations and safety features as well as capital and operating cost of an installed unit.
Beta 2-glycoprotein-1 (apolipoprotein H) excretion in chronic renal tubular disorders: comparison with other protein markers of tubular malfunction. (1991)

Urinary beta 2-glycoprotein-1 was measured in 60 patients with conditions recognised as causing renal tubular impairment and compared with established markers of early tubular malfunction. Increased beta 2-glycoprotein-1 excretion was found in 49 (82%) of the subjects; raised excretion of alpha 1-microglobulin, retinol-binding protein, and beta 2-microglobulin was found in 46 (77%), 45 (75%), and 31 (52%), respectively, and increased urinary N-acetyl-beta-D-glucosaminidase activity in 32 of 54 of the subjects (59%). The increase was particularly pronounced in those with proximal tubule malfunction, although considerable variation occurred. beta 2-glycoprotein-1 was shown to be stable in urine over the physiological pH range, and it is concluded that its measurement provides a means of detecting chronic malfunction of the renal tubules that is marginally more sensitive than assays of alpha 1-microglobulin or retinol-binding protein, and more reliable than assays of beta 2-microglobulin or N-acetyl-beta-D-glucosaminidase.
Digital Control of Automatic Gun Systems Incorporating an Intermittently Rotating Chamber (2007)

Lately, there exist growing demands to increase the firepower of mid-calibre automatic guns despite spatial limitations of armament. In this context, ammunitions of simple cylindrical shape are considered so advantageous that associated automatic guns are under development incorporating an intermittently rotating chamber mechanism. In this paper, relevant subsystems for such guns are to be described, and a digital controller to automate the entire system as well. Via dynamic simulations it proves to function well being able to drive the chamber at any constant speed up to 200spm, which is merely limited by the recoil performance. It is remarkable that the system synchronization idea in use is applicable to any other multi-actuator systems that should operate on the basis of event rather than time.
Osteoporosis Due to Cancer Treatment: Pathogenesis and Management (2000)

Many therapeutic regimens in cancer treatment carry the risk of causing or favoring the development of osteoporosis. Therapies in which hypogonadism may occur are most relevant in this respect. Prompt hormone replacement therapy is indicated in these patients. In patients in whom this is undesirable because of a hormone-dependent tumor, the risk of osteoporosis should be assessed by means of osteodensitometry, and prophylactic or therapeutic measures should be instituted if necessary. Early intervention improves outcome because osteoporosis therapy is most effective in preventing deterioration of bone mass. There remains much uncertainty in assessing the risk of combination chemotherapy with regard to the development of osteoporosis. Negative effects on the skeleton have, however, been demonstrated for individual drugs, such as methotrexate and ifosfamide. Negative effects of the tumor itself on bone metabolism may aggravate the degree of osteoporosis. Detailed data and long-term experience to assess the risk are urgently needed in this area and constitute an important research topic for the coming years and decades. This review discusses the most prevalent mechanisms of osteoporosis caused by cancer treatment and outlines therapeutic strategies for the prevention and treatment of therapy-induced bone loss.
Fate of dietary glutathione: disposition in the gastrointestinal tract (1990)

Studies were performed in rats that had been fasted 24 h, fed a glutathione (GSH)-free semisynthetic diet (AIN-76), and fed the same diet supplemented with GSH. The results from the fasted rats and those fed GSH-free diet showed that the duodenum and jejunum contained 0.2-0.5 mumol of GSH/gram wet wt of luminal contents. The GSH contents of biliary juice was sufficient to maintain this amount of GSH in the intestinal lumen. Other analyses showed that cell sloughing, bacterial GSH content, and GSH secretion by epithelial cells of the jejunum were not sufficient to account for this content. GSH concentrations following consumption of a GSH-supplemented diet (5-50 mg/g AIN-76) showed a rapid increase in all regions of the small intestine and indicated that removal occurred primarily in the jejunum. However, the combined activities of brush-border gamma-glutamyltransferase and GSH uptake systems were not sufficient to remove all of the ingested GSH. Results from in situ vascular perfusions of small intestine showed that the upper jejunum is a principal site of GSH absorption. Measurements of the GSH-to-glutathione disulfide (GSSG) ratio in the lumen after ingestion of GSSG (5 mg/g diet) indicated that the upper small intestine also has a mechanism for reducing GSSG to GSH. The results therefore indicate that GSH is present in the lumen of the small intestine of rat under most if not all conditions. Although the physiological importance of luminal GSH remains unclear, it could potentially be used to detoxify reactive electrophiles in the diet or be absorbed for intracellular detoxication reactions.
Protein Splicing Converts the Yeast TFP1 Gene Product to the 69-kdDSubunit of the Vacuolar H + -Adenosine Triphosphatase (1990)

The TFP1 gene of the yeast Saccharomyces cerevisiae encodes two proteins: the 69-kilodalton (kD) catalytic subunit of the vacuolar proton-translocating adenosine triphosphatase (H(+)-ATPase) and a 50-kD protein. The 69-kD subunit is encoded by the 5' and 3' thirds of the TFP1 coding region, whereas the 50-kD protein is encoded by the central third. Evidence is presented that both the 69-kD and 50-kD proteins are obtained from a single translation product that is cleaved to release the 50-kD protein and spliced to form the 69-kD subunit.
Enantiomeric cannabidiol derivatives: synthesis and binding to cannabinoid receptors (2005)

(-)-Cannabidiol (CBD) is a major, non psychotropic constituent of cannabis. It has been shown to cause numerous physiological effects of therapeutic importance. We have reported that CBD derivatives in both enantiomeric series are of pharmaceutical interest. Here we describe the syntheses of the major CBD metabolites, (-)-7-hydroxy-CBD and (-)-CBD-7-oic acid and their dimethylheptyl (DMH) homologs, as well as of the corresponding compounds in the enantiomeric (+)-CBD series. The starting materials were the respective CBD enantiomers and their DMH homologs. The binding of these compounds to the CB(1) and CB(2) cannabinoid receptors are compared. Surprisingly, contrary to the compounds in the (-) series, which do not bind to the receptors, most of the derivatives in the (+) series bind to the CB(1) receptor in the low nanomole range. Some of these compounds also bind weakly to the CB(2) receptor.
Photodynamic therapy of cancer: An update (2011)

Photodynamic therapy (PDT) is a clinically approved, minimally invasive therapeutic procedure that can exert a selective cytotoxic activity toward malignant cells. The procedure involves administration of a photosensitizing agent followed by irradiation at a wavelength corresponding to an absorbance band of the sensitizer. In the presence of oxygen, a series of events lead to direct tumor cell death, damage to the microvasculature, and induction of a local inflammatory reaction. Clinical studies revealed that PDT can be curative, particularly in early stage tumors. It can prolong survival in patients with inoperable cancers and significantly improve quality of life. Minimal normal tissue toxicity, negligible systemic effects, greatly reduced long-term morbidity, lack of intrinsic or acquired resistance mechanisms, and excellent cosmetic as well as organ function-sparing effects of this treatment make it a valuable therapeutic option for combination treatments. With a number of recent technological improvements, PDT has the potential to become integrated into the mainstream of cancer treatment.