gebhart/patrepeval huggingface dataset:
Modeling the molecular consequences of unbalanced translocations in cancer: Lessons from acute lymphoblastic leukemia (2009)

Chromosomal rearrangements are recurrent findings in human cancer and result in aberrant restructuring of the genome. The majority of known fusion genes are the consequence of reciprocal (balanced) translocations. However, most translocations described in human cancer are unbalanced, suggesting that other cancer genes remain to be identified. Historically, it was assumed that these unbalanced rearrangements affected gene function through the loss or gain of chromosomal material. However, emerging data supports direct disruption of genes located at or close to the unbalanced translocation breakpoints. New approaches are required for the identification of those gene loci underlying unbalanced translocations in cancer, as traditional methods have had limited success. This review focuses on one such strategy, using traditional and innovative molecular technologies to characterize breakpoint heterogeneity within a series of acute lymphoblastic leukemia (ALL) patients with dicentric chromosomes. This approach has shown that in ALL, specific gene loci can be targeted by heterogeneous translocation breakpoints involving multiple partner chromosomes. Carcinomas have a high proportion of unbalanced rearrangements and relatively few significant genes have been identified. The application of the same strategy to their analysis will lead to the discovery of novel cancer genes and improve our understanding of the genetic basis of tumorigenesis.
Fibromyalgia patients show an abnormal dopamine response to pain (2007)

Abstract Fibromyalgia is characterized by chronic widespread pain and bodily tenderness and is often accompanied by affective disturbances. Accumulating evidence indicates that fibromyalgia may involve a dysfunction of modulatory systems in the brain. While brain dopamine is best known for its role in pleasure, motivation and motor control, recent evidence suggests that it is also involved in pain modulation. Because dopamine is implicated in both pain modulation and affective processing, we hypothesized that fibromyalgia may involve a disturbance of dopaminergic neurotransmission. Fibromyalgia patients and matched healthy control subjects were subjected to deep muscle pain produced by injection of hypertonic saline into the anterior tibialis muscle. In order to determine the endogenous release of dopamine in response to painful stimulation, we used positron emission tomography to examine binding of [ 11 C]‐raclopride (D2/D3 ligand) in the brain during injection of painful hypertonic saline and nonpainful normal saline. Fibromyalgia patients experienced the hypertonic saline as more painful than healthy control subjects. Control subjects released dopamine in the basal ganglia during the painful stimulation, whereas fibromyalgia patients did not. In control subjects, the amount of dopamine release correlated with the amount of perceived pain but in fibromyalgia patients no such correlation was observed. These findings provide the first direct evidence that fibromyalgia patients have an abnormal dopamine response to pain. The disrupted dopaminergic reactivity in fibromyalgia patients could be a critical factor underlying the widespread pain and discomfort in fibromyalgia and suggests that the therapeutic effects of dopaminergic treatments for this intractable disorder should be explored.
Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals (2014)

Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human ALU repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched in comparison to linear controls. By scoring the presence of reverse complementary sequences in human introns, we predicted and experimentally validated circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyperediting events. Knockdown of the double-strand RNA-editing enzyme ADAR1 significantly and specifically upregulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA-RNA interactions of introns form larger structures that promote circularization of embedded exons, whereas ADAR1 antagonizes circRNA expression by melting stems within these interactions.
Improved Syntheses and Characterization of the Isomers of 3-Methyl-1-Phenylphospholene 1-Oxide (1978)

Abstract Isomerically pure 3-methyl-1-phenyl-2-phospholene 1-oxide and 3-methyl-1-phenyl-3-phospholene 1-oxide were prepared and characterized by 1H (60 and 270 MHz), 31P and 13C nmr, IR, Laser Raman, and mass spectrometry. 1,4-Cycloaddition of isoprene and phenylphosphonous dichloride, after hydrolysis of the addition product, yielded a mixture of the above 2-isomer and small amounts of 3-isomer from which pure 2-isomer was separated by fractional crystallization. The analog reaction with phenylphosphonous dibromide gave isomerically pure 3-isomer. An improved and shortened work-up procedure for the phospholene oxides was used resulting in higher yields.
Method for controlling the shift invariance of optical correlators (1999)

Holographic correlators can implement many correlations in parallel. For most systems shift invariance limits the number of correlation templates that can be stored in one correlator. This is because the output plane must be divided among the individual templates in the system. When the system is completely shift invariant, the correlation peak from one correlator can shift into an area that has been reserved for a different template; in this case a shifted version of one object might be mistaken for a well-centered version of a different object. We describe a technique for controlling the shift invariance of a correlator system by moving the holographic material away from the Fourier plane.
Single event effects in PDSOI 4 M SRAM fabricated in UNIBOND (2003)

Heavy ion and proton single event upsets of 4 M SOI SRAM with a hardened delay element in each memory cell were evaluated. These 4 M SRAM were fabricated in UNIBOND substrates using a radiation hardened partially depleted silicon-on-insulator CMOS technology. Limiting heavy ion upset cross-section of 1.2/spl times/10/sup -10/ cm/sup 2//bit has been achieved. Limiting proton upset cross-section of 1.1/spl times/10/sup -17/ cm/sup 2//bit has also been obtained.
Allergen mimotopes for 3‐dimensional epitope search and induction of antibodies inhibiting human IgE (2000)

There is no definite information available on the structural characteristics of IgE binding epitopes on allergenic molecules, although it is widely accepted that most of them are conformational. In the current study we aimed to characterize the IgE epitope of Bet v 1, the major birch pollen allergen, by the application of phage display peptide libraries. We purified IgE specific for Bet v 1 from allergic patients' sera to select mimotopes representing artificial IgE epitopes by biopanning of phage libraries. By linear alignment, it was not possible to attribute mimotope sequences to the primary structure of Bet v 1. We developed a computer-aided, 3-dimensional coarse-grained epitope search. The 3-dimensional search, followed by statistical analysis, revealed an exposed area on the Bet v 1 molecule (located between residues 9-22 and 104-123) as the IgE binding structure. The IgE epitope was located at a 30 A distance from a previously described IgG epitope and the respective mimotope, designated Bet mim E. Such mimotopes could potentially be used for the induction of IgG capable of interfering with the IgE/allergen interaction. To test this hypothesis, we immunized BALB/c mice with the phage-displayed Bet mim E. Immunizations resulted in the induction of Bet v 1-specific IgG, which was able to block the IgE binding to Bet v 1 in vitro. Based on these observations, we propose that immunotherapy with IgE mimotopes generated by biopannings result in formation of blocking IgG. We conclude that mimotope immunotherapy may represent a new and promising concept for treatment of type I allergic disease.
RideBuddies &#x2014; Multi agent system for ride sharing/carpooling (2014)

Carpooling or ride-sharing is the sharing of car journeys so that more than one person travels in a car. Carpooling reduces each person's travel costs such as fuel costs, tolls, and the stress of driving. This research focuses on implementing a ride-sharing solution in Sri Lanka using a multiagent system through the communication, negotiation and coordination of agents.
Development of a Novel BAFF Responsive Cell Line Suitable for Detecting Bioactive BAFF and Neutralizing Antibodies against BAFF-Pathway Inhibiting Therapeutics (2014)

BAFF has a critical role in B-cell survival, maturation and function, which makes its pathway a prime therapeutic target for various autoimmune diseases, such as systemic lupus erythematosus (SLE), rheumatoid arthritis and Sjögren's syndrome. A cell-based assay that measures the functional activity of BAFF is required for many high throughput purposes, such as lead target screening and BAFF quantification. We report here the development of a sensitive BAFF responsive cell line via stable transfection of the BAFFR-TNFR1 hybrid receptor into monkey kidney epithelial COS-1 cells. The cellular response to BAFF can be detected by measuring the secretion of IL-8. This BAFF bioassay is not only reproducible and sensitive, but also responsive to a wide concentration range of BAFF stimulation in sera from various species. This cell line is useful in the development of sensitive bioassays to measure the levels of bioactive BAFF, inhibition of BAFF and neutralizing antibodies against any BAFF pathway-mediated therapeutic proteins.
Characteristic image quality of a third generation dual‐source MDCT scanner: Noise, resolution, and detectability (2015)

Image quality increased with increasing dose and decreasing phantom size. The CT system exhibited nonlinear noise and resolution properties, especially at very low-doses, large phantom sizes, and for low-contrast objects. Objective image quality metrics generally increased with increasing dose and ADMIRE strength, and with decreasing phantom size. The ADMIRE algorithm could offer comparable image quality at reduced doses or improved image quality at the same dose. The use of tube current modulation resulted in more consistent image quality with changing phantom size.
UV‐curable acrylic resins for production of glass laminates (1995)

Abstract Glass laminates have been readily obtained by photocuring at ambient temperature of an acrylic adhesive consisting either of a liquid resin or a solid thermoplastic polymer. The light‐induced polymerization process was followed by real‐time infrared spectroscopy. Close to 100% conversion was reached within a few seconds of exposure, by taking as the photoinitiator an α‐hydroxy alkylphenone or an aryl phosphine oxide. A liquid formulation containing an aliphatic polyurethane–acrylate oligomer, acrylic acid, and butyl acrylate gives the best performance in terms of reactivity, adhesion, impact resistance, and transparency. The impact resistance was further increased by introducing a polycarbonate core between the two glass plates. The solid thermoplastic polymer was obtained either by casting from a solution containing an aliphatic polyurethane, an acrylate oligomer, and the photoinitiator or by mixing these compounds in the molten state and further extrusion. The glass assembly was heated above the softening temperature (80°C) under a 1 MPa pressure and cured by a 1 min exposure to UV radiation to give a strongly adhesive laminate showing good transparency and long term weatherability. © 1995 John Wiley & Sons, Inc.
Capillary Flow in Containers of Polygonal Section (2001)

An improved understanding of the large-length-scale capillary flows arising in a low-gravity environment is critical to that engineering community concerned with the design and analysis of spacecraft fluids management systems. Because a significant portion of liquid behavior in spacecraft is capillary dominated, it is natural to consider designs that best exploit the spontaneous character of such flows. In the present work a recently verified asymptotic analysis is extended to approximate spontaneous capillary flows in a large class of cylindrical containers of irregular polygonal section experiencing a step reduction in gravitational acceleration. Drop tower tests are conducted using partially filled irregular triangular containers for comparison with the theoretical predictions. The degree to which the experimental data agree with the theory is a testament to the robustness of the basic analytical assumption of predominantly parallel flow. As a result, the closed-form analytical expressions presented serve as simple, accurate tools for predicting bulk flow characteristics essential to practical low-g system design and analysis
Genetically encoded sensors of protein hydrodynamics and molecular proximity (2015)

The specialized light organ of the ponyfish supports the growth of the bioluminescent symbiont Photobacterium leiognathi. The bioluminescence of P. leiognathi is generated within a heteromeric protein complex composed of the bacterial luciferase and a 20-kDa lumazine binding protein (LUMP), which serves as a Förster resonance energy transfer (FRET) acceptor protein, emitting a cyan-colored fluorescence with an unusually long excited state lifetime of 13.6 ns. The long fluorescence lifetime and small mass of LUMP are exploited for the design of highly optimized encoded sensors for quantitative fluorescence anisotropy (FA) measurements of protein hydrodynamics. In particular, large differences in the FA values of the free and target-bound states of LUMP fusions appended with capture sequences of up to 20 kDa are used in quantitative FA imaging and analysis of target proteins. For example, a fusion protein composed of LUMP and a 5-kDa G protein binding domain is used as an FA sensor to quantify the binding of the GTP-bound cell division control protein 42 homolog (Cdc42) (21 kDa) in solution and within Escherichia coli. Additionally, the long fluorescence lifetime and the surface-bound fluorescent cofactor 6,7-dimethyl-8- (1'-dimethyl-ribityl) lumazine in LUMP are utilized in the design of highly optimized FRET probes that use Venus as an acceptor probe. The efficiency of FRET in a zero-length LUMP-Venus fusion is 62% compared to ∼ 31% in a related CFP-Venus fusion. The improved FRET efficiency obtained by using LUMP as a donor probe is used in the design of a FRET-optimized genetically encoded LUMP-Venus substrate for thrombin.
Photoionisation spectroscopy of traps in AlGaN/GaN high electron mobility transistors grown by molecular beam epitaxy (2003)

Photoionisation spectroscopy has been carried out in bias-stressed AlGaN/GaN high electron mobility transistors grown by MBE in order to probe the nature of the deep trapping centres responsible for stress-induced current collapse in these devices. The results indicate that a GaN buffer layer trap previously associated with current collapse in devices grown by MOCVD is responsible for induced collapse in MBE-grown structures.
THE ELIZABETHAN PERIOD: POETRY AND PROSE: (2) The Earlier Stuart Age and the Commonwealth (1939)

Journal Article THE ELIZABETHAN PERIOD: POETRY AND PROSE: (2) The Earlier Stuart Age and the Commonwealth Get access L. C. MARTIN L. C. MARTIN Search for other works by this author on: Oxford Academic Google Scholar The Year's Work in English Studies, Volume XVIII, Issue 1, 1939, Pages 174–186, https://doi.org/10.1093/ywes/XVIII.1.174 Published: 01 January 1939
In Vivo Matrigel Migration and Angiogenesis Assay (2008)

The search for rapid and reproducible in vivo angiogenesis and antiangiogenesis assays is an area of intense interest. These types of assays are extremely useful in testing putative drugs and biological agents and for the comparison and enhancement of in vitro tests. The Matrigel plug assay is one such assay and has proved to be a relatively quick and easy method to evaluate both angiogenic and antiangiogenic compounds in vivo. Initial indications of the levels of activity of strong angiogenic or antiangiogenic compounds can be visually assessed even as the plugs come out of the mouse because there are color differences in the plugs compared to the controls. Further quantitation is then needed to determine levels of angiogenic/antiangiogenic activity, and this can be performed using a variety of methods. This chapter presents an overview of the basic methods used to set up both angiogenic and antiangiogenic assays, discusses factors influencing variability, and discusses the methods for quantitating the plugs obtained. The Matrigel plug assay provides another useful tool in angiogenesis research.
Open source apis for processing the XML result of web services (2017)

The aim of this system is to use open source APIs to invoke and process the results of the Web services and to apply confidentiality and integration to the result of the Web services. In this system Web Services are requested using URL (Uniform Resource Locator) query to the WWW instead of SOAP message. When invoking the web services using JAX-RPC (Java Api for Xml-Based Remote Procedure Call) with SOAP request, the result returned may not be received properly due to de-serialization problem of complex XML data sets. Therefore it is required to invoke such services by submitting the query as URL query and received the results as XML data set. This XML data set may be hampered by man-in-middle attack during transfer. Hence this system uses open source APIs for providing XML signature and XML encryption. At the receiver after decryption and integrity check, the required node from XML data set is extracted and presented to the user. This article is focused on usage of open source APIs (Application program interface) for invoking web services as Restful Web services, applying XML signature and XML encryption, parsing the XML result after reverse process at receiver side and extracting the required nodes according to the user given condition. The problem of de-serialization in receiving huge XML result is resolved in the proposed system.
Learning temporal sequences using dual‐weight neurons (2001)

Abstract This paper considers the use of neural networks (NN's) in learning temporal sequence recognition and reproduction for which the sequence degree is unknown. This approach uses the output ambiguity to train the network without the need to assume or construct a separate model for the input sequence degree. First we introduce a primitive network called the DNN, comprising a plurality of dual‐weight (DN) neurons. Each neuron is linked to other neurons by a long‐term excitatory weight and a short‐term inhibitory weight. Fast learning is made possible by employing a two‐pass training rule to encode the temporal distance between two arbitrary pattern occurrences. The resulting DNN is then extended into a more generalized model, namely the DNN2. By incorporating the two‐pass rule and a self‐organizing algorithm, the DNN2 can achieve autonomous temporal sequence recognition and reproduction. Using training efficiency and hardware complexity criteria, the DNN networks are also contrasted with the work of Wang and Yuwono (1995). Key words: neural networkstemporal sequencesself‐organizingspeech recognition Notes Correspondence addressee
EXTRACELLULAR GLYCOLIPIDS OF RHODOTORULA SPECIES: THE ISOLATION AND SYNTHESIS OF 3-<scp>D</scp>-HYDROXYPALMITIC AND 3-<scp>D</scp>-HYDROXYSTEARIC ACIDS (1964)

Several species of the red yeast Rhodotorula produce extracellular glycolipids which consist of a mixture of mannitol and pentitol esters of 3-D-hydroxypalmitic and 3-D-hydroxystearic acids. One molecule of the long chain acid is attached to each polyol molecule and most of the remaining hydroxyl groups including the one on the fatty acid are acetylated.
Anti-Aβ Drug Screening Platform Using Human iPS Cell-Derived Neurons for the Treatment of Alzheimer's Disease (2011)

These results indicate that the hiPS cell-derived neuronal cells express functional β- and γ-secretases involved in Aβ production; however, anti-Aβ drug screening using these hiPS cell-derived neuronal cells requires sufficient neuronal differentiation.
Holography And Four-Wave Mixing To See Through The Skin. (1985)

A few schemes will be described in which ultra short pulses are used to see through highly scattering specimens, as typified by biological objects. The information thus obtainable should be similar to X-ray pictures and reveal details about structure in the inside of the object by fleeting shadows on the exit skin. The schemes to be analysed are: The fast Kerr gate followed by photographic film, a holographic approach using high resolution film (the few experiments reported in this paper refer exclusively to this scheme) and various schemes involving non linear effects including four wave mixing. A few remarks will be made about peculiarities resulting from the shape of the wavefronts involved in ultra short pulse imaging and a few very preliminary experimental observations will be reported.
Occurrence and sequence of a DnaJ protein in plant (<i>Allium porrum</i>) epidermal cells (1993)

Antibodies raised against a purified fraction from microsomal membranes of leek epidermal cells were used to screen a lambda zap expression library from epidermal cells of leak plants. A near full-length clone was isolated. This cDNA contains an open reading-frame of 1,191 bp coding for a DnaJ protein (leek DNAJ 1 or LDJ1). Leek DnaJ1 represents the second protein of this type described in a pluricellular organism, the first being that sequenced from human cells.
Efficient Use of Domain Decomposition and Local Grid Refinement in Reservoir Simulation (1990)

ABSTRACT In order to get desired accuracy in reservoir simulation, one must refine the grid in certain regions, for example, the regions around wells. When this is done in conventional simulators, unnecessary refinement occurs in some regions. This problem is avoided by the use of "Local Grid Refinement" (LGR) techniques, but the resulting matrix is large and of irregular sparsity. In this paper we address several practical aspects of some methods of LGR, including the use of hybrid grid, and then present three highly efficient methods of solving resulting problems with some Domain Decomposition (DD) techniques. In the first method, a relaxation in the unknowns is performed. In the second one, we use overlapping boundaries between the subdomains. In the last one, a coarse grid solution is obtained first and it provides the boundary conditions for the fine grid solution. The LGR and DD methods developed in this work were implemented and tested in a three-dimensional, three-phase, black-oil model. The results are presented in this paper for three examples. It is also shown that the DD technique with overlapping boundaries is extremely efficient for solving problems containing one or more LGR regions. The method proposed in this paper can easily take advantage of parallel processors. Also, it is easy to implement the proposed techniques in existing simulators. The LGR and DD techniques discussed in this paper improve the accuracy of reservoir simulation around wells and in other regions of high activity. Using these techniques, one not only obtains the correct well pressure, but also the correct saturation near the well. A consequence of this is that WOR and GOR are predicted accurately without well pseudofunctions.