gebhart/patrepeval huggingface dataset:
The Disease-associated r(GGGGCC) Repeat from the C9orf72 Gene Forms Tract Length-dependent Uni- and Multimolecular RNA G-quadruplex Structures (2013)

Certain DNA and RNA sequences can form G-quadruplexes, which can affect promoter activity, genetic instability, RNA splicing, translation, and neurite mRNA localization. Amyotrophic lateral sclerosis and frontotemporal dementia were recently shown to be caused by expansion of a (GGGGCC)n·(GGCCCC)n repeat in the C9orf72 gene. Mutant r(GGGGCC)n-containing transcripts aggregate in nuclear foci possibly sequestering repeat-binding proteins, suggesting a toxic RNA pathogenesis. We demonstrate that the r(GGGGCC)n RNA but not the C-rich r(GGCCCC)n RNA forms extremely stable uni- and multimolecular parallel G-quadruplex structures (up to 95 °C). Multimolecular G-quadruplex formation is influenced by repeat number and RNA concentration. MBNL1, a splicing factor that is sequestered in myotonic dystrophy patients by binding to expanded r(CUG)n repeat hairpins, does not bind the C9orf72 repeats, but the splicing factor ASF/SF2 can bind the r(GGGGCC)n repeat. Because multimolecular G-quadruplexes are enhanced by repeat length, RNA-RNA interactions facilitated by G-quadruplex formation at expanded repeats might influence transcript aggregation and foci formation in amyotrophic lateral sclerosis-frontotemporal dementia cells. Tract length-dependent G-quadruplex formation by the C9orf72 RNA should be considered when assessing the role of this repeat in C9orf72 gene activity, protein binding, transcript foci formation, and translation of the C9orf72 product, including the noncanonical repeat-associated non-ATG translation (RAN translation) into pathologic dipeptide repeats, as well as any oligonucleotide repeat-based therapy.
Sugar Sulfonates and Their Behavior (1961)

SUMMARY New crystalline bisulfite addition products of mannose and galactose were prepared, namely α‐hydroxy‐galactose sulfonate, and α‐hydroxy‐mannose sulfonate, and their properties studied. In addition, the rates of dissociation of these sulfonates were studied, and further evidence is presented to show that these products have an open‐chain configuration. The evidence obtained supports the theory put forward previously by one of the authors, namely, that sulfur dioxide and sulfates interact only with the open‐chain aldehyde configuration of the sugars when the cyclic forms of the sugars open during their mutarotation. A maltose sulfonate was prepared in which only half of the molecule was capable of interaction with sulfites. This addition product failed to crystallize. It is probable that the same mechanism is of importance in interpreting the browning phenomena during the Maillard reaction.
Object-oriented real time systems modeling and verification (2002)

An object-oriented real-time systems conceptual modeling approach is described. In this approach, each object is specified by an object type, consisting of supertypes (inheritance), component types (aggregation), attributes, operations, static constraints and timed temporal constraints. An object type specification defines a theory of a type of objects. In particular, the static constraints define the valid states of the objects, the operations define the valid state transitions, each consisting of a set of execution rules. Each execution rule consists of a precondition and a postcondition. The timed temporal constraints define the permissible sequences of state transitions. Atomic and composite object state diagrams (AOSDs and COSDs) are then constructed from a formal specification for verification of the satisfiability of the timed temporal constraints.
Migrating legacy systems towards object-oriented platforms (1997)

Presents an approach to migrate legacy systems to object-oriented platforms. The process consists of six sequential phases and encompasses reverse engineering and re-engineering activities. The aim of the reverse engineering phases is to decompose programs into components implementing user interface management and components implementing application domain objects. The identification of objects is centred around a persistent data store and exploits object-oriented design metrics. Wrapping techniques are the core of the re-engineering activities. They make new systems able to exploit existing resources, thus allowing an incremental and selective translation of the identified objects
Calculation of Resistances to Ground (1936)

Formulas for practical use in the calculation of the resistances from grounding conductors of variou forms to the earth are given in this paper and their use illustrated by examples. The accuracy of the formulas varies considerably, as discussed in the paper, but is sufficiently good that the methods should be helpful to those whose work involves problems of grounding.
Antenna radiation pattern measurement using time-to-frequency transformation (TFT) techniques (1973)

A method of inferring microwave antenna radiation patterns over wide bandwidths from a series of subnanosecond pulse measurements is described. Monochromatic patterns can be inferred from the time-domain measurements with simple apparatus. Results are presented which show that the method is inherently insensitive to errors caused by reflections from the environment.
Characterization of a glycine N‐methyltransferase gene knockout mouse model for hepatocellular carcinoma: Implications of the gender disparity in liver cancer susceptibility (2008)

Hepatocellular carcinoma (HCC) is the fifth common cancer in the world and it mainly occurs in men. Glycine N-methyltransferase (GNMT) participates in one-carbon metabolism and affects DNA methylation by regulating the ratio of S-adenosylmethionine to S-adenosylhomocystine. Previously, we described that the expression of GNMT was diminished in human HCC. Here, we showed that 50% (3/6) male and 100% (7/7) female Gnmt-/- mice developed HCC, and their mean ages of HCC development were 17 and 16.5 months, respectively. In addition, 42.9% (3/7) of female Gnmt-/- mice had hemangioma. Wnt reporter assay demonstrated that Gnmt is a negative regulator for canonical Wnt signaling pathway. Beta-catenin, cyclin D1 and c-Myc, genes related to Wnt pathway, were upregulated in the liver tissues from both 11 weeks and HCC stage of Gnmt-/- mice. Furthermore, global DNA hypomethylation and aberrant expression of DNA methyltransferases 1 and 3b were found in the early and late stages of HCC development. Hierarchical cluster analysis of 6,023 transcripts from microarray data found that gene expression patterns of HCC tumors from male and female Gnmt-/- mice were distinctively different. Real-time PCR confirmed that Gadd45a, Pak1, Mapk3 and Dsup3 genes of mitogen-activated protein kinase (MAPK) pathway were activated in Gnmt-/- mice, especially in the female mice. Therefore, GNMT is a tumor suppressor gene for liver cancer, and it is associated with gender disparity in liver cancer susceptibility.
Calibration between a central catadioptric camera and a laser range finder for robotic applications (2006)

This paper presents several methods for estimating the relative position of a central catadioptric camera (including perspective cameras) and a laser range finder in order to obtain depth information in the panoramic image. The problem is analysed from a robotic perspective and according to the available information (visible or invisible laser beam, partial calibration, drift of laser data,...). The feasibility of the calibration is also discussed. The feature extraction process and real data are presented
Measuring cough severity: Perspectives from the literature and from patients with chronic cough (2009)

Results suggest that patients describe cough severity in terms of frequency, intensity, and disruptiveness, indicating these 3 domains should be addressed when evaluating cough severity and outcomes of treatment.
Inherently reactive polyHIPE material from dicyclopentadiene (2010)

A simple formulation of a stable high internal phase emulsion of dicyclopentadiene which is cured by using properly selected ring opening metathesis polymerization initiators yields highly porous monolithic materials with paramount mechanical properties and the possibility of easy functionalisation.
Steht sächsischen Schulen ein Qualitätsverlust bevor? Ein Überblick internationaler Studien zur Lehrqualität von Seiteneinsteigern (2017)

Der derzeitige Mangel an voll ausgebildeten Lehrkräften führte dazu, dass aktuell knapp zwei Drittel der neuen Stellen an sächsischen Grundschulen mit Seitenein-steigern besetzt wurden. Gleichzeitig sind die Anforderungen an das Lehrpersonal durch die Zunahme von Schülern mit Migrationshintergrund und sonderpädagogi-schem Bedarf deutlich gestiegen. Dies wirft die Frage auf, ob Seiteneinsteiger ohne eine pädagogische Vollausbildung diesen Herausforderungen gewachsen sind. In diesem Beitrag fassen wir Forschungsergebnisse aus der Literatur zu Lehrqualifikation und Schulerfolg zusammen. In der Mehrzahl der vergleichenden Studien zeigt es sich, dass Schüler von Seiteneinsteigern im Durchschnitt schlechter abschneiden als Schüler von traditionell ausgebildeten Lehrern. Zurückzuführen sind die Leistungsunterschiede vornehmlich auf die fehlende Lehrerfahrung von Seiteneinsteigern zum Berufseinstieg. Nach zwei bis drei Jahren Berufstätigkeit sind hingegen kaum noch Unterschiede zu vermerken.
Dural sealants for the management of cerebrospinal fluid leakage after intradural surgery: current status and future perspectives (2019)

<b>Introduction</b>: Cerebrospinal fluid leakage is a complication after intradural surgery and is associated with severe secondary complications like compromised wound healing and meningitis. Dural sealants are meant to augment the primary dural closure in order to achieve a watertight closure. <b>Areas covered</b>: This review summarizes the efficacy of currently available dural sealants. Potential future improvements and biomaterials are discussed. <b>Expert opinion</b>: The use of a dural sealant seems to be the logical method to prevent CSF leakage. However, based on the efficacy of currently available dural sealants according to systematic reviews and <i>in vitro</i> studies, a significant effective dural sealant seems is still lacking. A new dural sealant has to be thoroughly assessed before clinical application in <i>in vitro</i>, in vivo and clinical trials. A new research area within sealant development might be the introduction of dural sealants with both antimicrobial and analgesic properties.
Engineering of leucine-responsive regulatory protein improves spiramycin and bitespiramycin biosynthesis (2019)

SSP_Lrp in S. spiramyceticus was a negative regulator involved in the SP and BT biosynthesis. The deletion of SSP_Lrp putative L-Leu binding domain was advantageous for production of BT and SP, especially their III components.
Reliability characteristics of IrMn dual synthetic spin valves (2000)

Dual synthetic spin valves using IrMn as the antiferromagnetic layer have been fabricated with areal densities from 10 to 36 Gbit/in/sup 2/. Tests for the environmental corrosion resistance, thermal stability, and ESD damage thresholds show these devices are reliable and viable as high density spin valve designs.
Chromosome Studies in Human Leukemia. II. Chronic Granulocytic Leukemia (1961)

Chromosome studies in 10 patients with chronic granulocytic leukemia are reported. The patients examined varied from asymptomatic untreated cases to extensively treated cases of several years' duration in terminal myeloblastic crisis. In 9 of the 10 patients, a similar chromosome abnormality was found. One of the four smallest acrocentric chromosomes in the leukemic cells was markedly reduced in size, apparently due to the loss of approximately half of its longer arm. With the exception of this finding, no frequent or regular abnormality in either chromosome number or structure was observed. The findings demonstrate a specific, consistent chromosome change associated with a particular human neoplasm and suggest that it is the chromosome change which confers on the leukocytes their neoplastic character. Such an association has not yet been demonstrated in any other human tumor.
ANALYZING GENERAL-PURPOSE COMPUTING PERFORMANCE ON GPU (2015)

Analyzing General-Purpose Computing Performance on GPU Graphic Processing Unit (GPU) has become one of the most important components in modern computer systems. GPUs have evolved from a single -purpose graphic rendering hardware to a powerful processor that is capable of handling many different kinds of computing tasks. However, GPUs don’t perform well on every application, and it takes a lot of design effort to get good performance on a GPU. This thesis aims to investigate the relative performance of a GPU vs. CPU. Design effort is held minimum for both CPU implementations and GPU implementations. Matrix multiplication, Advance Encryption Standard (AES) and 32-bit Cyclic Redundancy Check (CRC32) are implemented on both a CPU and GPU. Input data size is varied to test the performance of the CPU and the GPU. The GPU generally has better performance than the CPU for matrix multiplication and AES because of the applications' good instruction and data parallelism. CRC has very poor parallelism, so the CPU performs better. For very small data inputs, the CPU generally outperformed the GPU because of GPU memory transfer overhead.
<title>Applications of a fast continuous wavelet transform</title> (1997)

A fast, continuous, wavelet transform, justified by appealing to Shannon's sampling theorem in frequency space, has been developed for use with continuous mother wavelets and sampled data sets. The method differs from the usual discrete-wavelet approach and from the standard treatment of the continuous-wavelet transform in that, here, the wavelet is sampled in the frequency domain. Since Shannon's sampling theorem lets us view the Fourier transform of the data set as representing the continuous function in frequency space, the continuous nature of the functions is kept up to the point of sampling the scale-translation lattice, so the scale-translation grid used to represent the wavelet transform is independent of the time-domain sampling of the signal under analysis. Although more computationally costly and not represented by an orthogonal basis, the inherent flexibility and shift invariance of the frequency-space wavelets are advantageous for certain applications. The method has been applied to forensic audio reconstruction, speaker recognition/identification, and the detection of micromotions of heavy vehicles associated with ballistocardiac impulses originating from occupants' heart beats. Audio reconstruction is aided by selection of desired regions in the 2D representation of the magnitude of the transformed signals. The inverse transform is applied to ridges and selected regions to reconstruct areas of interest, unencumbered by noise interference lying outside these regions. To separate micromotions imparted to a mass- spring system by an occupant's beating heart from gross mechanical motions due to wind and traffic vibrations, a continuous frequency-space wavelet, modeled on the frequency content of a canonical ballistocardiogram, was used to analyze time series taken from geophone measurements of vehicle micromotions. By using a family of mother wavelets, such as a set of Gaussian derivatives of various orders, different features may be extracted from voice data. For example, analysis of the 'blobs' in a low-order, Gaussian- derivative wavelet transform extracts the glottal-closing rate, while the ridges of a high-order wavelet transform give good indication of the formant frequencies and allow automatic word and phrase segmentation.
Virtual Screening in Drug Discovery - A Computational Perspective (2007)

Virtual screening emerged as an important tool in our quest to access novel drug like compounds. There are a wide range of comparable and contrasting methodological protocols available in screening databases for the lead compounds. The number of methods and software packages which employ the target and ligand based virtual screening are increasing at a rapid pace. However, the general understanding on the applicability and limitations of these methodologies is not emerging as fast as the developments of various methods. Therefore, it is extremely important to compare and contrast various protocols with practical examples to gauge the strength and applicability of various methods. The review provides a comprehensive appraisal on several of the available virtual screening methods to-date. Recent developments of the docking and similarity based methods have been discussed besides the descriptor selection and pharmacophore based searching. The review touches upon the application of statistical, graph theory based methods machine learning tools in virtual screening and combinatorial library design. Finally, several case studies are undertaken where the virtual screening technology has been applied successfully. A critical analysis of these case studies provides a good platform to estimate the applicability of various virtual screening methods in the new lead identification and optimization.
Potential field power spectrum inversion for scaling geology (1995)

We propose a method for inverting the power spectrum of gravity and magnetic data. The method is demonstrated on aeromagnetic and borewell data from the German Continental Deep Drilling Project (KTB). Density and susceptibility distributions in the Earth's crust exhibit scaling behavior with power spectra proportional to ƒ −β , where f is the wavenumber and β is the scaling exponent of the source distribution. We model the sources of the potential field by a random function with scaling properties, defined on a half‐space with its top at a specified depth beneath the observation plane. Comparing the theoretical power spectrum for this model with the power spectrum of the measured data, we obtain the best values for the depth to source and the scaling exponent as a global minimum of the misfit function. Despite the simplicity of the model, it offers a new understanding of the factors influencing the shape of the potential field power spectrum. In particular, the low wavenumber part of the power spectrum can be dominated by the scaling properties of the source distribution and not by the depth to some kind of basement. The scaling exponent of the field varies with the type of surface geology. The question of whether the scaling exponent can actually be used to identify different types of geology gives an interesting new aspect to power spectrum inversion.
Human tumor cells synthesize and secrete alpha‐2‐macroglobulin <i>in vitro</i> (1986)

In previous studies we showed that human sarcoma and melanoma cell lines synthesize and secrete into culture medium a glycoprotein, migrating in urea sodium dodecyl sulfate-polyacrylamide gel electrophoresis at Mr 140,000. It is not detected in cultures of the corresponding normal cells. Conditioned medium of the melanoma cell line HMB-2, producing among the cell lines tested the largest amounts of this glycoprotein, has now been used as a source for purification of the protein. NH2-terminal amino-acid sequence determination of the purified glycoprotein showed that it is identical to human alpha 2-macroglobulin (alpha 2M). Rabbit antibodies raised against the glycoprotein specifically reacted in immunoblotting and immunodiffusion tests with alpha 2M present in human plasma. Likewise, these antibodies immunoprecipitated from the conditioned media of 35S-methionine-labelled melanoma and osteosarcoma cell lines the protein which had a molecular weight corresponding to alpha 2M. alpha 2M was also synthesized and secreted by 2 strains of fetal lung fibroblasts but not by fetal skin fibroblasts or adult skin fibroblasts autologous to the osteosarcoma cell line.
Ferrite plating on porous silica microspheres for ultrasonic contrast agents (1994)

Porous silica microspheres, 1-3 /spl mu/m in diameter, were coated with Fe/sub 3/O/sub 4/ by "reactor method" ferrite plating. The polycrystalline Fe/sub 3/O/sub 4/ coating was synthesized from an aqueous solution (pH=7.3) of FeCl/sub 2/ at 60-70/spl deg/C, using oxidizing solution of NaNO/sub 2/ mixed with CH/sub 3/COONH/sub 4/ (pH buffer). The magnetite capsulated silica microspheres can be potentially used for contrast agents for clinical ultrasonography, especially for blood flowmetry; the air trapped in the silica pores enhances the ultrasound echogenicity. The contrast agents are controllable by magnetic fields, and their virtual density can be adjusted to that of ambient fluid by changing the thickness of the Fe/sub 3/O/sub 4/ coating.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of Sucrose Fatty Acid Esters on Transdermal Permeation of Lidocaine and Ketoprofen (2005)

The effect of sucrose fatty acid esters on transdermal permeation of lidocaine (LC) and ketoprofen was examined. A drug solution was applied to excised hairless mouse skin pretreated with a sugar ester solution to examine the direct effects of the sugar esters on skin permeability. LC was applied with a pH 6 buffer solution (98.8% ionized), pH 10 buffer solution (99.2% unionized), or propylene glycol, while KP was applied with a pH 6 buffer solution (99.1% ionized), pH 2 buffer solution (98.9% unionized), or propylene glycol. Pretreatment with J-1216 (sucrose laurate, HLB = 16) or J-1205 (sucrose laurate, HLB = 5) significantly increased the permeation of LC from the pH 6 solution and KP from propylene glycol, respectively. The permeability coefficients of the ionized and unionized LC and KP were calculated from the permeability data. The ionized LC and KP permeated even through skin not pretreated with sugar esters, although the permeability coefficients were 24 times and 38 times less than those of the unionized LC and KP, respectively. J-1216 pretreatment increased the permeability of ionized LC from aqueous vehicle 2.7 fold. In the next series of experiments, we formulated 1.5% of J-1205 and J-1216 in various vehicles to examine their effect on the permeation of LC applied on the excised hairless mouse skin with no pretreatment. The results coincided with the results of the pretreatment experiment, and the effect of J-1205 in propylene glycol was more remarkable than that observed in the pretreatment study. When these sugar esters were dissolved in propylene glycol at 1.5%, J-1205 increased significantly the KP permeation rate as well as LC permeation rate, suggesting that the combination of J-1205 and propylene glycol would be a potent vehicle for transdermal formulations.
Global DNA hypomethylation in breast carcinoma (1999)

The current shows that DNA hypomethylation is increased in breast carcinomas, playing a potentially important role in tumor development. These findings also suggest that DNA methylation status may be a biologic marker with prognostic significance in this group of neoplasms.