gebhart/patrepeval huggingface dataset:
Pathomechanism and therapeutic strategy of Fukuyama congenital muscular dystrophy and related disorders (2009)

Hypoglycosylation and reduced laminin-binding activity of alpha-dystroglycan are common characteristics of dystroglycanopathy, which is a group of congenital and limb-girdle muscular dystrophies. We previously identified the genes for Fukuyama congenital muscular dystrophy (FCMD) and muscle-eye-brain disease (MEB). FCMD, caused by a mutation in the fukutin gene, is a severe form of dystroglycanopathy. Knock-in mice carrying the founder retrotransposal insertion exhibited hypoglycosylated alpha-dystroglycan; however, no signs of muscular dystrophy were observed. More sensitive methods detected minor levels of intact alpha-dystroglycan, and solid-phase assays determined laminin binding levels to be approximately 50% of normal. In contrast, intact alpha-dystroglycan is undetectable in the dystrophic Large mouse, and laminin-binding activity is markedly reduced. These data indicate that a small amount of intact alpha-dystroglycan is sufficient to maintain muscle cell integrity in knock-in mice, suggesting that the treatment of dystroglycanopathies might not require the full recovery of glycosylation. Transfer of fukutin into knock-in mice restored glycosylation of alpha-dystroglycan. Transfer of LARGE produced laminin-binding forms of alpha-dystroglycan in both knock-in mice and the POMGnT1 mutant mouse. These data suggest that even partial restoration of alpha-dystroglycan glycosylation and laminin-binding activity by replacing or augmenting glycosylation-related genes might effectively deter dystroglycanopathy progression and thus provide therapeutic benefits.
Identification of new breast cancer candidate genes associated with stromal invasion. (2009)

Abstract Abstract #4036 Background: We recently reported our results of a study identifying a number of DNA copy number changes that differentiated low grade ductal carcinoma in situ (DCIS) lesions with and without associated stromal invasion. We now describe a series of validation experiments that support the role of four genes in early breast cancer progression, most of which were not previously implicated in mammary neoplasia.&#x2028; Materials and Methods: DNA was extracted from microdissected paraffin sections of formalin fixed low grade DCIS lesions with an invasive component (n=25), as well as morphologically similar DCIS lesions without associated invasion within at least 5 years (n=20). The DNA was used for comparative PCR, with GAPDH as the reference gene. Specific primers were designed for fourteen candiate genes. Amplicon sizes ranged from 80 to 90 base pairs. Using log2 ratio cutoffs of +1.0 and -0.5, respectively, the frequency of copy number gains and losses was determined for each candidate gene. Additional validation studies employed genomic DNA samples from an independent cohort of 35 microdissected DCIS lesions with (n=17) and without (n=18) an associated invasive component.&#x2028; Results: Our previous whole genome profiling study using high density BAC arrays revealed that DNA copy number changes on 1q, 3p, 5q, 6p, 9p, 10q, 11q, 12q, 16p, 16q, 18q, 20q, and 22q may occur at different rates in low grade DCIS lesions with and without associated stromal invasion. From the differentially amplified or deleted chromosomal sites, thus far we have selected fourteen candidate genes for validation by comparative PCR, utilizing aliquots of the same DNA samples that had previously been used for array CGH analysis. Four genes were confirmed to have differential copy number changes. NCOR2 (on 12q24.31), DYNLRB2 (on 16q23.2), CELSR1 and UPK3A (both on 22q13.31) were more frequently amplified in DCIS lesions that had no invasive component. Moreover, NCOR2 and DYNLRB2 showed more frequent copy number losses in DCIS lesions that had progressed to invasive carcinoma. For NCOR2, these observations held true in an independent cohort of microdissected low grade DCIS cases. The other ten candidate genes revealed significant frequencies of copy number changes that were not differentially distributed, however. TEME9, CALN1, and CENTA1 were amplified in 30-40% of all cases. IRF8, THAP7, and FIGNL1 were deleted in 20-50% of all cases. FBXO31, CDH13, IKZF1, and MAPK9 revealed both gains and losses in &gt;20% of all cases.&#x2028; Discussion: Our validation experiments have provided additional evidence for the role of several novel genes in early breast cancer progression. Four of the candidate genes we assayed so far may function as invasion suppressor genes. Ten additional genes showed significant copy number changes but did not discriminate DCIS lesions with and without the propensity to invade the stroma. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4036.
Reversible Size Modification of Iron and Gallium Molecular Wheels: A Ga<sub>10</sub> “Gallic Wheel” and Large Ga<sub>18</sub> and Fe<sub>18</sub> Wheels (2006)

Wheelin' and dealin': The M10 molecular wheels [M10(OMe)20(O2CR)10] (M=Ga, R=Me; M=Fe, R=Ph) were modified to M18 wheels in a nontemplate synthesis upon incorporation of a diolate ligand (see space-filling model of [Ga18(pd)12(pdH)12(O2CMe)6(NO3)6]6+; Ga yellow, O red, N blue, C gray; pdH2=1,3-propanediol). Remarkably, dissolution in MeOH converts both M18 wheels back into the M10 wheels.
3-Mercaptopropionic Acid: A New Tool in the Synthesis of Symmetrical Diaryl Sulfides from Unactivated Aryl Iodides as Substitute for Anhydrous Sodium Sulfide (1989)

A series of symmetrical diaryl sulfides has been prepared by the coppercatalyzed reaction of 3-mercaptopropionic acid with unactivated aryl iodides. The yields are comparable with those obtained using anhydrous sodium sulfide under optimized reaction conditions.
DISEÑO DE UN MODULO DE CONTROL HALF-DUPLEX UTILIZANDO LA RED ELÉCTRICA COMO MEDIO FÍSICO DE TRANSMISIÓN (2008)

The electric net has been considered lately like a quite attractive alternative for the transmission of data, its use in this sense allows the saving of havi...
Quantification of the Brückner test for strabismus. (1995)

It is estimated that this technique can be automated to detect the presence of 2 degrees to 3 degrees of ocular misalignment based on the difference in brightness of the bright pupil images between the two eyes.
Electronic control of H+ current in a bioprotonic device with Gramicidin A and Alamethicin (2016)

In biological systems, intercellular communication is mediated by membrane proteins and ion channels that regulate traffic of ions and small molecules across cell membranes. A bioelectronic device with ion channels that control ionic flow across a supported lipid bilayer (SLB) should therefore be ideal for interfacing with biological systems. Here, we demonstrate a biotic-abiotic bioprotonic device with Pd contacts that regulates proton (H<sup>+</sup>) flow across an SLB incorporating the ion channels Gramicidin A (gA) and Alamethicin (ALM). We model the device characteristics using the Goldman-Hodgkin-Katz (GHK) solution to the Nernst-Planck equation for transport across the membrane. We derive the permeability for an SLB integrating gA and ALM and demonstrate pH control as a function of applied voltage and membrane permeability. This work opens the door to integrating more complex H<sup>+</sup> channels at the Pd contact interface to produce responsive biotic-abiotic devices with increased functionality.
Mechanistic Insights into Free Chlorine and Reactive Oxygen Species Production on Irradiation of Semiconducting Silver Chloride Particles (2014)

Silver halide based plasmonic absorbers are excellent photocatalysts under visible light irradiation. In this work we have investigated the kinetics and mechanism of generation of free chlorine and reactive oxygen species (ROS), both of which may play a role in organic degradation, on irradiation of AgCl(s). Our work shows that generation of free chlorine occurs via oxidation of Cl– by photogenerated holes in the valence band. Photogenerated electrons in the conduction band reduce Ag+ to form Ag0 atoms which coalesce and aggregate to form silver nanoparticles (AgNPs). Superoxide and its more stable disproportionation product hydrogen peroxide (H2O2) are also presumably formed as a result of the reduction of dioxygen by photogenerated electrons; however, H2O2 was not detected, possibly as a result of its reaction with free chlorine and AgNPs. Confirmation that this reaction in all likelihood occurred was provided by quantification of the formation of singlet oxygen (1O2), a product of this reaction. On the basis of our experimental observations, we have developed a kinetic model that adequately describes the generation of free chlorine, ROS, and AgNPs on irradiation of AgCl(s).
[Construction of LACK gene recombinant plasmid and detection of its expression in eukaryotic cell]. (2004)

The LACK gene from Leishmania, an analogue of the receptor of activated protein kinase C, was discovered recently. In this study, the LACK gene of Leishmania donovani was obtained from the recombinant plasmid T-LACK by PCR. The gene was cloned into eukaryotic expressed plasmid pcDNA3.1(+) to construct recombinant plasmid. This recombinant plasmid then was transfected into the eukaryotic cell COS-7, and the expression of LACK gene in eukaryotic cell was detected by RT-PCR and immunofluorescent staining. Both RT-PCR and immunofluorescent staining of recombinant plasmid transfected COS-7 showed positive reaction, thus indicating that the recombinant plasmid pcDNA3-LACK can express LACK protein in euka ryotic cell COS-7.
An overview of Double-Gate MOSFETs (2004)

The Double-Gate (DG) Fully Depleted (FD) SOI MOSFET, and its many implementations, is the leading device candidate for Silicon nano-scale CMOS. Their main characteristics, as compared to the single gate bulk MOSTET, are less S/D capacitance, larger saturated current drive, smaller short channel effects (DIBL), scalability to L=10 nm, near ideal subthreshold slopes (S), and the possibility of electrically adjustable threshold voltages.
Effect of Chlorsulfuron, a Potent Inhibitor of Acetohydroxyacid Synthase, on Metabolism of Claviceps purpurea (1988)

Chlorsulfuron (CS) is a potent sulfonylurea herbicide inhibiting specifically acetohydroxyacid synthase which catalyzes the first step in the biosynthesis of branched-chain amino acids in plant cells, bacteria and yeast. The peptide portion of some ergot alkaloids contain inter alia branchedchain amino acids. The influence of CS on growth and alkaloid formation in Claviceps was studied. In an ergotoxine strain growth is inhibited by chlorsulfuron in the range of 10-100 μᴍ. Under CS influence ergosine is accumulated besides ergotoxines. Growth inhibition caused by CS could be reversed by addition of ʟ-valine ( ~ 35 mᴍ), but neither by leucine nor isoleucine. Ergosine did not occur under these conditions. Acetohydroxyacid synthase (AHAS) from Claviceps purpurea was partially purified. AHAS preparations are not inhibited even by high concentrations of chlorsulfuron.
Design of an ASP Pilot for the Mangala Field: Laboratory Evaluations and Simulation Studies (2008)

Abstract Mangala is the largest discovered oil field in the Barmer Basin of Rajasthan, India having a STOIIP of over 1 billion barrels in multiple stacked fluvial clastic reservoirs. It contains medium gravity (20-28°API), waxy, viscous crude (9-17 cp) in high permeability (1-25 Darcy) clean sandstone reservoirs. Initial development plans for the field are based on waterflooding, with at least the initial volumes of water heated to minimize any issues with wax dropout in the reservoir. Owing to the relatively high oil viscosity and adverse mobility displacement for waterflooding, the desirability of implementing an appropriate EOR process was identified shortly after the field discovery. Screening studies identified aqueous-based chemical flooding processes as the most favorable for Mangala. Detailed laboratory studies have now identified the potential of alkaline-surfactant-polymer (ASP) processes in significantly improving the sweep and displacement efficiency. The laboratory studies involved screening and optimization of the ASP slug formulation based on IFT measurements, adsorption measurements, polymer rheological and thermal stability studies; followed by a series of linear and radial corefloods. Experiments indicate the ASP process is the most effective chemical EOR process for Mangala, with improvement in recovery efficiency above the waterflood recovery of over 30% STOIIP. Chemical EOR simulations with STARSTM have been used extensively to understand the process mechanisms via matching of the coreflood experiments. Simulation parameters tuned to the laboratory data were used to evaluate the process performance under field conditions. A closely spaced five-spot pilot with 100m well spacing has been designed to evaluate the process. The pilot consists of four injectors, the central producer, three saturation monitoring wells and two post-pilot core holes. An ASP pilot will be implemented in the field shortly after startup of the waterflood.
2-D array transducers for medical ultrasound at Duke University: 1996 (2002)

l 1/2 -D and 2-D arrays offer a myriad of new imaging modalities and benefits when compared to the linear array. However, with added benefits come many problems and challenges. The increase in transducer channels needed in a l 1/2 -D and 2-D array can be reduced using a sparse periodic or sparse random array. The complexity of the fabrication is overcome using a multi-layer flexible connector designed and fabricated using microelectronic techniques. The low SNR of 1 1/2 -D and 2-D arrays can be increased with the application of multi-layer ceramic elements to optimize the SNR given a specific transmit and receive configuration. We are also looking at PZT/polymer composites for SNR improvement as well as better acoustic matching to tissue. In addition, opto-electronic transmitters allow for the reductions in size and increase in flexibility of the transducer cable because of the use of fiber optics.
Dosimetric, mechanical, and geometric verification of conformal dynamic arc treatment (2003)

A conformal dynamic arc (CD-arc) technique has been implemented at the S. Giovanni Calibita-Fatebenefratelli Hospital Radiotherapy Center. This technique is performed by rotational beams and a dynamic multileaf collimator (DMLC): during the treatment delivery the gantry rotates and the field shape, formed by the DMLC changes continuously. The aim of this study was to perform dosimetric, mechanical, and geometric verification to ensure that the dose calculated by a commercial treatment planning system and administered to the patient was correct, before and during the clinical use of this technique. Absolute dose values, at the isocenter and at other points placed in dose heterogeneity zone, have been verified with an ionization chamber in a solid homogeneous phantom. In uniform dose regions measured dose values resulted in agreements with the calculated doses within 2%. Isodose distributions have also been determined by radiographic films and compared with those predicted by the planning system. Distance to agreement between calculated and measured isodoses in dose gradient zone was within 2 mm. In conclusion, our results demonstrated the feasibility and the accuracy of the CD-arc technique for achieving highly conformal dose distributions. Up till now 20 patients have been treated with CD-arc therapy.
Ambition is not what it used to be (2008)

Ambition seems to me a frightening notion. It conjures up images of sharp suits and hair gel; sales targets and management-speak. Ambition, I think, is a gene. If you do not possess it, forget it. Content yourself with comfy slippers and leave The Apprentice to others.
Modelling and Diagnostics of Low Pressure Plasma Discharges (2002)

The presented thesis deals with various aspects of models for low pressure discharges. As well the theoretical background of hydrodynamic plasma models as the comparison of calculated data with experimental results are discussed. In the first part of this work hydrodynamic conservation equations are derived from the Boltzmann equation. Main focus is the application to low pressure plasmas. Different model systems for electrons and ions are presented. The question in which case simplified models can be applied, is treated as well as numerical aspects and algorithms for obtaining a solution are discussed. In a second part hydrodynamic models were used for performing one-dimensional simulations. The sensitivity of the model in dependence of input parameters like momentum exchange frequencies was analysed. As well different model systems were compared qualitatively in order to get an estimate for the error introduced by using simple and numerical more stable model systems. In the third part hydrodynamic models were applied to simulate different kinds of low pressure discharges. Main focus were inductively driven plasmas like they are used in semiconductor fabrication as high density plasma source. Calculated data for this kind of discharge were compared with experimental values obtained from Langmuir probe measurements. Theory and experiment show very good agreement. In a final part the scaling laws and geometry dependence derived from hydrodynamic models were used to assemble a set of general reactor design rules. Examples were presented, how reactor performance can be optimised by careful choice of geometry parameters. Also general dependencies on external parameters like discharge pressure were discussed.
Fast vocabulary-independent audio search using path-based graph indexing (2005)

Classical audio retrieval techniques consist in transcribing audio documents using a large vocabulary speech recognition system and indexing the resulting transcripts. However, queries that are not part of the recognizer’s vocabulary or have a large probability of getting misrecognized can significantly impair the performance of the retrieval system. Instead, we propose a fast vocabulary independent audio search approach that operates on phonetic lattices and is suitable for any query. However, indexing phonetic lattices so that any arbitrary phone sequence query can be processed efficiently is a challenge, as the choice of the indexing unit is unclear. We propose an inverted index structure on lattices that uses paths as indexing features. The approach is inspired by a general graph indexing method that defines an automatic procedure to select a small number of paths as indexing features, keeping the index size small while allowing fast retrieval of the lattices matching a given query. The effectiveness of the proposed approach is illustrated on broadcast news and Switchboard databases.
Stable segmentation of 2D curves (1998)

Institute of Perception, Action and Behaviour
Modified Method of Characteristics for Simulating Microscale Energy Transport (2004)

This paper presents a new numerical scheme for simulating multidimensional transient and steady-state microscale energy transport. The new method is based on the method of characteristics that follows heat carriers along their pathline. Unlike traditional methods, it uses a fixed computational grid and follows the heat carriers backward in time. The method 1) is accurate, 2) is unconditionally stable, 3) can deal with complex geometries without a large increase in computational cost, and 4) can be used for solving coupled equations using other numerical schemes. First, the numerical scheme is described. Then, simulations for transient and steady-state phonon transport in dielectric thin films are discussed. Numerical results are compared with analytical and reported numerical solutions and good agreement is obtained.
Using quantitative models for setting retail prices (2000)

Products that have a short selling season face high uncertainty in demand. Retailers who sell such products therefore find the task of pricing and inventory challenging. Many retailers consider making these decisions as an art form and do not use quantitative models that are developed by researchers. Describes how retailers typically make pricing and inventory decisions and also reviews quantitative models that have been developed by researchers to improve on one or more of these decisions. A classification of these models is developed and how they can assist the retailer is explained. A simple explanation of two mathematical tools, Bayesian updating of information and dynamic programming, which are commonly mentioned in the literature are also given.
A sorting classification of parallel rendering (2008)

We describe a classification scheme that we believe provides a more structured framework for reasoning about parallel rendering. The scheme is based on where the sort from object coordinates to screen coordinates occurs, which we believe is fundamental whenever both geometry processing and rasterization are performed in parallel. This classification scheme supports the analysis of computational and communication costs, and encompasses the bulk of current and proposed highly parallel renderers - both hardware and software. We begin by reviewing the standard feed-forward rendering pipeline, showing how different ways of parallelizing it lead to three classes of rendering algorithms. Next, we consider each of these classes in detail, analyzing their aggregate processing and communication costs, possible variations, and constraints they may impose on rendering applications. Finally, we use these analyses to compare the classes and identify when each is likely to be preferable. >
The transcriptional regulation of the Colony-Stimulating Factor 1 Receptor (csf1r) gene during hematopoiesis (2007)

The colony-stimulating-factor 1 receptor (CSF-1 R) is a tyrosine kinase receptor that is absolutely required for macrophage differentiation and thus occupies a central role in hematopoiesis. Mice deficient for the csf1r gene show multiple defects in macrophage development, reproduction and tissue remodeling. Moreover, deregulation of this gene is a hallmark of many tumors. This includes repression of expression in acute myeloid leukemia and aberrant activation in certain solid tumors, such as breast cancer. Expression of this gene therefore needs to be tightly controlled. This review summarizes experiments providing a detailed picture of how transcription of csf1r gene expression is regulated. Aside from the direct relevance to hematopoiesis, studies of csf1r transcriptional regulation provide a model for understanding the molecular mechanisms that control mammalian cell fate.
Use of single cell gel electrophoresis (comet assay) modifications for analysis of DNA damage. (1999)

Single cell gel electrophoresis (SCGE) or comet assay is a rapid and sensitive fluorescent microscopic method which allows measurement of DNA strand breaks in individual cells. Modifications of SCGE conditions permitted to detect different types of DNA damage. In order to characterize DNA damage induced by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and hydrogen peroxide (H2O2) in Chinese hamster V79 cells, two approaches were used: (1) two pH values of unwinding and electrophoresis solutions (pH > or = 13.0 and pH = 12.1) to specify the type of DNA lesions [the alkali-labile sites and true DNA single-strand breaks (ssb)] and (2) DNA glycosylases [endonuclease III (EndoIII) and formamidopyrimidine-DNA glycosylase (FaPy)] or DNA inhibitors [hydroxyurea (HU) + 1-(beta-D-arabinofuranosyl)cytosine (AraC)] to characterize the types of DNA damage. Our results showed that the lesions induced by H2O2 represented mainly the true DNA ssb, while MNNG formed predominantly alkali-labile sites, which were converted to DNA ssb under strong alkaline conditions (pH > or = 13.0). The effects of DNA repair enzymes and DNA inhibitors were more significant under lower pH (pH = 12.1) of unwinding and electrophoresis solution. Both, DNA glycosylases and DNA inhibitors increased the level of DNA ssb.