gebhart/patrepeval huggingface dataset:
A rapid method for detecting the predominant Ashkenazi Jewish mutation in the Bloom's syndrome gene (1998)

Bloom's syndrome (BS) is a rare, autosomal recessive disease characterized by sun sensitivity, short stature, and predisposition to cancer. Although rare in the general population, BS is more common in the Ashkenazi Jewish population (German, 1993). The isolation of the gene for BS, known as BLM, has permitted the identification of mutations within the gene and the discovery that most BS individuals of Ashkenazi Jewish origin carry the identical 6-bp deletion/7-bp insertion at position 2,281 of BLM (blmAsh). We have developed a rapid method for detecting blmAsh based on restriction enzyme digestion of a PCR product containing the mutation. blmAsh creates a restriction site within the amplified fragment allowing distinction of normal and mutant DNAs. This method has been designed for use with genomic DNA or cDNA. Hum Mutat 11:175–178, 1998. © 1998 Wiley-Liss, Inc.
Automatic selection of task spaces for imitation learning (2009)

Previous work [1] shows that the movement representation in task spaces offers many advantages for learning object-related and goal-directed movement tasks through imitation. It allows to reduce the dimensionality of the data that is learned and simplifies the correspondence problem that results from different kinematic structures of teacher and robot. Further, the task space representation provides a first generalization, for example wrt. differing absolute positions, if bi-manual movements are represented in relation to each other. Although task spaces are widely used, even if they are not mentioned explicitly, they are mostly defined a priori. This work is a step towards an automatic selection of task spaces. Observed movements are mapped into a pool of possibly even conflicting task spaces and we present methods that analyze this task space pool in order to acquire task space descriptors that match the observation best. As statistical measures cannot explain importance for all kinds of movements, the presented selection scheme incorporates additional criteria such as an attention-based measure. Further, we introduce methods that make a significant step from purely statistically-driven task space selection towards model-based movement analysis using a simulation of a complex human model. Effort and discomfort of the human teacher is being analyzed and used as a hint for important task elements. All methods are validated with real-world data, gathered using color tracking with a stereo vision system and a VICON motion capturing system.
Carbonic Anhydrase Inhibitors: The First Selective, Membrane‐Impermeant Inhibitors Targeting the Tumor‐Associated Isozyme IX. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Fast and Accurate Multilevel Inversion of the Radon Transform (2000)

A number of imaging technologies reconstruct an image function from its Radon projection using the convolution backprojection method. The convolution is an O(N2 log N) algorithm, where the image consists of N X N pixels, while the backprojection is an O(N3 ) algorithm, thus constituting the major computational burden of the convolution backprojection method. An O(N2 log N) multilevel backprojection method is presented here. When implemented with a Fourier-domain postprocessing technique, also presented here, the resulting image quality is similar or superior to the image quality of the classical backprojection technique.
The ac Josephson relation and inhomogeneous temperature distributions in large Bi<sub>2</sub>Sr<sub>2</sub>CaCu<sub>2</sub>O<sub>8+δ</sub>mesas for THz emission (2013)

journal article
Motion compensated 4D PET-CT-MR image generation for respiratory synchronized multi-modal image display (2013)

Positron emission tomography (PET) image has been widely used for early detection of malignant lesion(s) and its treatment, because it can provide functional information. Since computed tomography (CT) and magnetic resonance (MR) images can provide high resolution anatomical information, their simultaneous display with PET image may improve the clinical value of PET-image-based applications. Meanwhile, temporal information regarding anatomical changes due to respiration may be important in the radiation therapy planning of a thoracic or abdominal region. To provide such important information, we propose a framework for motion compensated 4D PET-CT-MR image generation. To realize the framework, we present a MR-driven motion compensation algorithm for respiratory-gated 4D PET imaging. We then introduce a respiratory-synchronized multi-modal image generation method. We expect that the respiratory-synchronized multi-modal image display can be useful for clinicians to efficiently utilize the temporal information as well as the complementary spatial information in their applications.
Continuously tunable smectic A* liquid-crystal color filter (1990)

A new continuously tunable color filter, which uses smectic A(*) liquid-crystal half-wave plates, is described and experimentally demonstrated. Multiple-stage Lyot filters with broad tunability and high finesse can be constructed with this design. The transmission characteristics of a single-stage filter, which is continuously tuned over 115 nm of the visible spectrum, are presented. Experimental results are compared with computer simulations, and they show excellent agreement. The advantages of the smectic A(*) liquid-crystal tunable filter over existing filter structures include low switching voltages (+/-30 V), rapid tunability (10 MHz), potentially high transmission, wide field of view, and large aperture.
Plastid engineering in land plants: a conservative genome is open to change. (1994)

We have developed efficient transformation protocols to modify each of the 500-10000 plastid genome copies in a tobacco cell. The transforming DNA is introduced on the surface of microscopic tungsten particles by the biolistic process. Selection for transplastomes is by spectinomycin resistance based on expression of aminoglycoside-3-adenyltransferase from a chimeric aadA gene in the transforming DNA. Manipulations that are now feasible include replacement of endogenous plastid genes with DNA sequences modified in vitro, targeted gene disruption, and insertion of reporter genes into the plastid genome. Alternative methods for plastid genome manipulations may be developed utilizing an extrachromosomal element which was identified during the transformation studies. Introduction of foreign genes under control of plastid gene expression elements results in duplication of endogenous regulatory sequences. A sensitive somatic assay to detect deletions via such direct repeats confirmed that these sequence duplications do not result in significant genome instability. The ability to transform plastids will facilitate the study of plastid gene regulation, and the application of genetic engineering to crop improvement.
Mass Measurement Accuracy in Analyses of Highly Complex Mixtures Based Upon Multidimensional Recalibration (2006)

Mass spectrometry combined with a range of on-line separation techniques has become a powerful tool for characterization of complex mixtures, including protein digests in proteomics studies. Accurate mass measurements can be compromised due to variations that occur in the course of an on-line separation, e.g., due to excessive space charge in an ion trap, temperature changes, or other sources of instrument "drift". We have developed a multidimensional recalibration approach that utilizes existing information on the likely mixture composition, taking into account variable conditions of mass measurements, and that corrects the mass calibration for sets of individual peaks binned by, for example, the total ion count for the mass spectrum, the individual peak abundance, m/z value, and liquid chromatography separation time. The multidimensional recalibration approach uses a statistical matching of measured masses in such measurements, often exceeding 105, to a significant number of putative known species likely to be present in the mixture (i.e., having known accurate masses), to identify a subset of the detected species that serve as effective calibrants. The recalibration procedure involves optimization of the mass accuracy distribution (histogram), to provide a more confident distinction between true and false identifications. We report the mass accuracy improvement obtained for data acquired using a TOF and several FTICR mass spectrometers. We show that the multidimensional recalibration better compensates for systematic mass measurement errors and also significantly reduces the mass error spread: i.e., both the accuracy and precision of mass measurements are improved. The mass measurement improvement is found to be virtually independent of the initial instrument calibration, allowing, for example, less frequent calibration. We show that this recalibration can provide sub-ppm mass measurement accuracy for measurements of a complex fungal proteome tryptic digest and provide improved confidence or numbers of peptide identifications.
Spiro hypervalent iodine(III)-mediated radiofluorination of non-activated and hindered aromatics (2014)

3 Objectives Radiolabeling of non-activated aromatics is not easily achieved by nucleophilic aromatic fluorination. The goal of this study was to develop a one-step and regiospecific 18F-fluorination method for (hetero)aromatics bearing electron-rich and/or sterically hindered substituents under metal-free conditions using spiro hypervalent iodine(III)-based precursors. Methods Azeotropically dried [18F]Et4NF (3 mCi) was resolubilized in DMF (400 μL), followed by addition of the respective spiroiodine(III) precursor (2 mg). The reaction was carried out at 120 °C for 10 min. Fluorine incorporation and product identities were determined by radioTLC and HPLC (n≥3). Fifteen substrates with diverse chemical scaffolds (18F-building blocks and radiotracers) were successfully labeled and key compounds were isolated. Results Using 4-[18F]fluorobiphenyl as a testing platform, eleven iodine(III) auxiliaries were explored as precursors. A spiroiodine(III) precursor (stable solid) afforded the highest incorporation yield (85±3%). With this spiro auxiliary, various non-activated aromatics (15 examples) were labeled in high yields. Representative examples include 2-[18F]fluoro-1,3,5-triisopropylbenzene (56%), 4-bromo-1-[18F]fluoro-2-methoxybenzene (56%), 1-[18F]fluoro-6-methyl-3-nitrobenzene (32%), 3-[18F]fluoro N-acetylaniline (17%), 6-[18F]fluoroindoline (34%), and 6-[18F]fluorophenyl alanine (55%). 4-[18F]Fluorobenzyl azide, a useful reagent for click chemistry, was synthesized in one-step and isolated with 28±8% uncorrected radiochemical yield and specific activity >100 mCi/μmol relative to only 3 mCi of starting [18F]fluoride in 45 min. Conclusions Spiroiodine(III) based precursors offer a one-step and regiospecific methodology to radiolabel non-activated and sterically hindered aromatic compounds with [18F]fluoride. Fifteen substrates were efficiently radiolabeled including the building block 4-[18F]fluorobenzyl azide. Applications of this technology to prepare new radiopharmaceuticals will be presented.
CTRP6 is an endogenous complement regulator that can effectively treat induced arthritis (2015)

The complement system is important for the host defence against infection as well as for the development of inflammatory diseases. Here we show that C1q/TNF-related protein 6 (CTRP6; gene symbol C1qtnf6) expression is elevated in mouse rheumatoid arthritis (RA) models. C1qtnf6(-/-) mice are highly susceptible to induced arthritis due to enhanced complement activation, whereas C1qtnf6-transgenic mice are refractory. The Arthus reaction and the development of experimental autoimmune encephalomyelitis are also enhanced in C1qtnf6(-/-) mice and C1qtnf6(-/-) embryos are semi-lethal. We find that CTRP6 specifically suppresses the alternative pathway of the complement system by competing with factor B for C3(H2O) binding. Furthermore, treatment of arthritis-induced mice with intra-articular injection of recombinant human CTRP6 cures the arthritis. CTRP6 is expressed in human synoviocytes, and CTRP6 levels are increased in RA patients. These results indicate that CTRP6 is an endogenous complement regulator and could be used for the treatment of complement-mediated diseases.
Patterned magnetic recording media (2006)

Recent progresses on the development of the patterned magnetic recording media are presented. There has been discussing several issues for the commercialization of the patterned media so far. The fabrication process by using nano imprint lithography seems to be possible solution of the productivity challenge. Good results on the flyability are also reported for the discrete track recording media. A couple of advantages for increasing the recording density have been reported regarding the system aspect. The patterned media is expected to be commercialized after the success of the discrete track media as a high density magnetic recording media
Crocetinic acid inhibits hedgehog signaling to inhibit pancreatic cancer stem cells (2015)

Pancreatic cancer is the fourth leading cause of cancer deaths in the US and no significant treatment is currently available. Here, we describe the effect of crocetinic acid, which we purified from commercial saffron compound crocetin using high performance liquid chromatography. Crocetinic acid inhibits proliferation of pancreatic cancer cell lines in a dose- and time-dependent manner. In addition, it induced apoptosis. Moreover, the compound significantly inhibited epidermal growth factor receptor and Akt phosphorylation. Furthermore, crocetinic acid decreased the number and size of the pancospheres in a dose-dependent manner, and suppressed the expression of the marker protein DCLK-1 (Doublecortin Calcium/Calmodulin-Dependent Kinase-1) suggesting that crocetinic acid targets cancer stem cells (CSC). To understand the mechanism of CSC inhibition, the signaling pathways affected by purified crocetinic acid were dissected. Sonic hedgehog (Shh) upon binding to its cognate receptor patched, allows smoothened to accumulate and activate Gli transcription factor. Crocetinic acid inhibited the expression of both Shh and smoothened. Finally, these data were confirmed in vivo where the compound at a dose of 0.5 mg/Kg bw suppressed growth of tumor xenografts. Collectively, these data suggest that purified crocetinic acid inhibits pancreatic CSC, thereby inhibiting pancreatic tumorigenesis.
Cartilage Tissue Engineering: Current Limitations and Solutions (1999)

Articular cartilage repair remains one of the most intensely studied orthopaedic topics. To date the field of tissue engineering has ushered in new methodologies for the treatment of cartilage defects. The authors' 10-year experience using principles of tissue engineering applied to resurfacing of cartilage defects is reported. Which cell type to use, chondrocytes versus chondroprogenitor cells, and their inherent advantages and disadvantages are discussed. Chondrocytes initially were used as the preferred cell type but were shown to have long term disadvantages in models used by the authors. Mesenchymal stem cells can be used effectively to overcome the limitations experienced with the use of differentiated chondrocytes. The use of mesenchymal stem cells as platforms for retroviral transduction of genes useful in cartilage repair introduces the concept of gene modified tissue engineering. The fundamental conditions for promoting and conducting a viable cartilage repair tissue, regardless of which cell type is used, also were studied. Placement of a synthetic porous biodegradable polymer scaffold was found to be a requirement for achieving an organized repair capable of functionally resurfacing a cartilage defect. A new modular device for intraarticular fixation of various graft composites has been developed. This new cartilage repair device is composed of bioabsorbable polymers and is capable of being delivered by the arthroscope.
Joint code and decoder design for implementation-oriented (3, k)-regular LDPC codes (2001)

Gallager's low-density parity-check (LDPC) codes have recently received a lot of attention because of their excellent performance. The decoder hardware implementation is obviously one of the most crucial issues determining the extent of LDPC applications in the real world. The straightforward fully parallel decoder architecture usually incurs too high complexity for many practical purposes and should be transformed to a partly parallel realization. We propose a joint code and decoder design approach to construct a class of (3, k)-regular LDPC codes which exactly fit to a partly parallel decoder implementation. The partly parallel decoder architecture is suitable for efficient VLSI implementation and it has been shown that the jointly developed (3, k)-regular LDPC codes have very good performance.
Helicopter with stabilator detuned in antisymmetric vibration modes from main rotor wake excitation frequency (1981)

First Page
Automatic model-based service hosting environment migration (2008)

The proper operation of Service-Oriented Architecture (SOA) depends on underlying system services of operating systems, so efficient and effective migration of Service Hosting Environment is critical to cope with intrinsic-changed nature of SOA. However, due to the large amount of configuration items, complicated mapping and complex dependency relationship among system services, migrating into a new Service Hosting Environment satisfying the operation requirement of SOA becomes an error-prone and time-consuming task. The SCM project in IBM develops a novel approach to migrate Service Hosting Environment shaped in Unix-like systems. Firstly, this approach builds a set of configuration models to describe various system services. Then based on models, it presents knowledge based mapping to translate system service configurations between Service Hosting Environments. Finally, it designs a dependency hierarchy deducting algorithm to compute the dependency relationship among system services for migration traceability and error determination. A SCM prototype has performed well on largely reducing time, labor and errors in real migration cases.
Nitrogen fixation in the treatment of pulp and paper wastewaters (1999)

Pulp and paper wastewaters are generally low in the key nutrient, nitrogen. Nitrogen supplementation is often practised to ensure effective BOD removal. Maintaining consistently low effluent discharge concentrations of nitrogen from nitrogen supplemented biological treatment systems is very difficult. Matching nitrogen addition rates to load variations is effective, but requires accurate flow and organic load measurements. By manipulating treatment conditions to select for the growth of nitrogen fixing microorganisms, it is possible to achieve good BOD removals without the addition of nitrogen. As the organisms only fix the nitrogen required for growth, very low soluble nitrogen discharge concentrations are possible. This concept has been explored in the development of a new technology for the treatment of nitrogen deficient wastewaters.
Fast frequency hopping OFDM concept (2005)

A system concept, combining orthogonal frequency division multiplexing (OFDM) with fast frequency hopping (FFH), termed FFH/OFDM concept, is illustrated. Data symbols in the frequency domain are mapped to time domain samples by a unitary transformation based on a shuffled version of the well-known inverse discrete Fourier transform. The FFH/OFDM concept shows a promising performance.
A Novel HEPA Filter Encapsulation Process (2008)

Waste management engineers at Lawrence Livermore National Laboratory have developed an innovative process for the treatment of contaminated HEPA filters. The In Situ Stabilization and Filter Encapsulation (IS SAFE) Process provides several advantages over existing HEPA filter treatment processes. Treatment is accomplished by filling a spent HEPA filter with a low viscosity resin that cures to form a solid monolith. Once a solid monolith has been formed, the HEPA filter has been transformed in two ways: (1) worker hazards/risks associated with handling the filter are eliminated and (2) the in situ encapsulated filter meets LDR requirements and can be disposed of in a permitted landfill. A patent has been filed for this process. The IS SAFE process will be applicable to hazardous, mixed, and low level radioactively contaminated spent filters. Spent HEPA filters are prepared for processing by attaching vacuum fittings to the top and bottom openings of the filter. These fittings are used to attach the filter to a vacuum system comprised of a vacuum pump, vacuum gauge, resin reservoir and associated tubing and fittings. Resin is delivered to the filter in a controlled fashion. The total processing time for a 50-cubic feet per minute (cfm) filter is approximately 25 minutes. The resin filled HEPA filter is allowed to cure at ambient temperature and pressure for at least 24 hours. The final product is a solid monolith with less that 0.1 percent by volume of void space and 100 percent of the filter media coated with resin. Proof of concept studies have been completed using 50, 135, and 1000 cfm closed face HEPA filters. During these studies, we were able to develop and demonstrate a resin delivery process that yielded a final product that was suitable for in ground disposal. Additional adaptations of the process may be required for specific application, but the process equipment, supplies, and methodology have been fully established for contact handled, closed face, contaminated HEPA filters.
Lensfree 3D Tracking of Sperms at High-throughput (2012)

A lensfree holographic imaging platform which can track the 3D motion of >1,500 human sperms within an observation volume of 8-17 mm3 is developed to reveal the statistics of the rare (~4.4%) and mostly right-handed (~90%) helical trajectories.
Quantitative electrical impedance analysis of cartilage degradation (2004)

Degradation of articular cartilage involves several physicochemical changes in the extracellular matrix, such as loss of highly charged glycosaminoglycan (GAG) molecules and increased water content. A variety of physical and biochemical techniques are currently being investigated for detection of cartilage degeneration or the staging cartilage repair tissue following surgery. Radiographic and MRI imaging give an overall assessment of cartilage loss, but few methods are available to probe the loss of physical properties of the cartilage. Lyyra et al. [3] developed a probe that measures the mechanical indentation properties of cartilage in situ, as a means of assessing cartilage stiffness. We have shown electrical impedance to be a sensitive indicator of biochemical composition and tissue integrity [5] using a minimally invasive, hand-held surface impedance device. Tissue electrical impedance is directly dependent on electrolyte content of a given tissue and is particularly appropriate to cartilage due to its high water content. Since impedance measurements are made using high frequency, they can be used to gather data on the state of a joint cartilage surface very quickly. The impedance probe described below uses multiple electrodes which may be reconfigured in such a way as to probe different depths into the tissue in order to assess surface fibrillation. In the studies presented here, we measured the electrical impedance of the articulating surface of intact joints to gauge (1) enzymatic degradation in vitro bovine articular cartilage, (2) OA degradation in human patellae, and (3) canine model graft repair tissue, by comparing impedance measurements with biomechanical measurements, biochemical analyses, and histology.