gebhart/patrepeval huggingface dataset:
The frequency of a novel <i>KANK1</i> and <i>NTRK3</i> translocation and BRAF<sup>V600E</sup> mutation in patients diagnosed with metanephric adenoma utilizing molecular mechanisms. (2017)

1537 Background: Renal metanephric adenoma (MA) is a very rare benign renal tumor, which is frequently misclassified when microscopic features alone are applied. Despite the classification of adenoma as a benign tumor, it is difficult to differentiate from other renal carcinomas such as malignant papillary renal cell carcinomas and in children it can be mistaken with Wilms tumor. The correct classification of a renal tumor is critical for diagnostic, prognostic, and therapeutic purposes. Despite the advancements in cancer genomics, there is limited data available regarding the genetic alterations critical to the metanephric adenoma development. Recent data suggest that 90% of MA have BRAF V600E mutations; the genetics of the remaining 10 % are unclear. Methods: This study was conducted on 13 FFPE specimens from patients who were diagnosed with renal metanephric adenoma. H&E stained slides from all cases were reviewed by study pathologist, and representative tissue blocks were further selected for BRAF V600E sequencing and fluorescent in situ hybridization was adapted to detect chromosomal rearrangement between KANK1 on chromosome 9 (9p24.3) and NTRK3 on chromosome 15 (15q25.3). Results: In this study, we identified a novel chromosomal translocation t(9;15)(p24;q24) between KANK1 and NTRK3, and provided new insights into molecular mechanisms which might identify a subset of metanephric adenomas. Such findings imply that recurrent cytogenetic aberrations may be of prognostic significance as well. Interestingly, our data suggested mutual exclusivity of BRAF V600E and t(9;15) aberrations. Conclusions: Molecular and cytogenetic analyses have allowed us to elucidate a genetic aberration, which may be specific to metanephric adenoma. Aberrant expression of the KANK1-NTRK3 gene fusion may be one mechanism by which functionally relevant genes are altered in the development of metanephric adenoma, and thus mark a subgroup of metanephric adenomas with particular clinicopathological features. Also, our study adds KANK1 and NTRK3 to the list of candidate genes that may play a role in the 10% of renal metanephric adenomas that lack a BRAF V600E mutation.
Complex of the herpes simplex virus type 1 origin binding protein UL9 with DNA as a platform for the design of a new type of antiviral drugs (2013)

The herpes simplex virus type 1 origin-binding protein, OBP, is a DNA helicase encoded by the UL9 gene. The protein binds in a sequence-specific manner to the viral origins of replication, two OriS sites and one OriL site. In order to search for efficient inhibitors of the OBP activity, we have obtained a recombinant origin-binding protein expressed in Escherichia coli cells. The UL9 gene has been amplified by PCR and inserted into a modified plasmid pET14 between NdeI and KpnI sites. The recombinant protein binds to Box I and Box II sequences and possesses helicase and ATPase activities. In the presence of ATP and viral protein ICP8 (single-strand DNA-binding protein), the initiator protein induces unwinding of the minimal OriS duplex (≈80 bp). The protein also binds to a single-stranded DNA (OriS*) containing a stable Box I-Box III hairpin and an unstable AT-rich hairpin at the 3'-end. In the present work, new minor groove binding ligands have been synthesized which are capable to inhibit the development of virus-induced cytopathic effect in cultured Vero cells. Studies on binding of these compounds to DNA and synthetic oligonucleotides have been performed by fluorescence methods, gel mobility shift analysis and footprinting assays. Footprinting studies have revealed that Pt-bis-netropsin and related molecules exhibit preferences for binding to the AT-spacer in OriS. The drugs stabilize structure of the AT-rich region and inhibit the fluctuation opening of AT-base pairs which is a prerequisite to unwinding of DNA by OBP. Kinetics of ATP-dependent unwinding of OriS in the presence and absence of netropsin derivatives have been studied by measuring the efficiency of Forster resonance energy transfer (FRET) between fluorophores attached to 5'- and 3'- ends of an oligonucleotide in the minimal OriS duplex. The results are consistent with the suggestion that OBP is the DNA Holiday junction (HJ) binding helicase. The protein induces conformation changes (bending and partial melting) of OriS duplexes and stimulates HJ formation in the absence of ATP. The antiviral activity of bis-netropsins is coupled with their ability to inhibit the fluctuation opening of АТ base pairs in the А + Т cluster and their capacity to stabilize the structure of the АТ-rich hairpin in the single-stranded oligonucleotide corresponding to the upper chain in the minimal duplex OriS. The antiviral activities of bis-netropsins in cell culture and their therapeutic effects on HSV1-infected laboratory animals have been studied.
Superprism phenomenon based on holographic polymer dispersed liquid crystal films (2006)

The polarization-dependent superprism phenomenon was demonstrated using holographic polymer-dispersed liquid crystal (HPDLC) films. The HPDLC film is designed and fabricated using three coplanar beams. The fabricated HPDLC film contained two-dimensional ordered nano-sized LC domains (∼150nm in diameter) embedded in a polymer matrix; its periodicity was estimated to be ∼350nm. The dispersion of white light from this HPDLC superprism was ∼50°, and the deflection of light output from it was consistent with the theoretical value obtained by the plane wave expansion method.
Turing-like mechanism in a stochastic reaction-diffusion model recreates three dimensional vascular patterning of plant stems (2019)

Vascular tissue in plants provides a resource distribution network for water and nutrients that exhibits remarkable diversity in patterning among different species. In many succulent plants, the vascular network includes longitudinally-oriented supplemental vascular bundles (SVBs) in the central core of the succulent stems and roots in addition to the more typical zone of vascular tissue development (vascular cambium) in a cylinder at the periphery of the succulent organ. Plant SVBs evolved in over 38 plant families often in tandem with evolutionary increases in stem and root parenchyma storage tissue, so it is of interest to understand the evolutionary-developmental processes responsible for their recurrent evolution and patterning. Previous mathematical models have successfully recreated the two-dimensional vascular patterns in stem and root cross sections, but such models have yet to recreate three-dimensional vascular patterning. Here, a stochastic reaction-diffusion model of plant vascular bundle patterning is developed in an effort to highlight a potential mechanism of three dimensional patterning-Turing pattern formation coupled with longitudinal efflux of a regulatory molecule. A relatively simple model of four or five molecules recreated empirical SVB patterns and many other common vascular arrangements. SVBs failed to develop below a threshold width of parenchymatous tissues, suggesting a mechanism of evolutionary character loss due to changes in the spatial context in which development takes place. Altered diffusion rates of the modeled activator and substrate molecules affected the number and size of the simulated SVBs. This work provides a first mathematical model employing a stochastic Turing-type mechanism that recreates three dimensional vascular patterns seen in plant stems. The model offers predictions that can be tested using molecular-genetic approaches. Evolutionary-developmental ramifications concerning evolution of diffusion rates, organ size and geometry are discussed.
Structure-Determining Step in the Hierarchical Assembly of Peptoid Nanosheets (2014)

Organic two-dimensional nanomaterials are of growing importance, yet few general synthetic methods exist to produce them in high yields and to precisely functionalize them. We previously developed an efficient hierarchical supramolecular assembly route to peptoid bilayer nanosheets, where the organization of biomimetic polymer sequences is catalyzed by an air-water interface. Here we determine at which stages of assembly the nanoscale and atomic-scale order appear. We used X-ray scattering, grazing incidence X-ray scattering at the air-water interface, electron diffraction, and a recently developed computational coarse-grained peptoid model to probe the molecular ordering at various stages of assembly. We found that lateral packing and organization of the chains occurs during the formation of a peptoid monolayer, prior to its collapse into a bilayer. Identifying the structure-determining step enables strategies to influence nanosheet order, to predict and optimize production yields, and to further engineer this class of material. More generally, our results provide a guide for using fluid interfaces to catalytically assemble 2D nanomaterials.
Tichy's response to R. W. Schwanke and G. E. Kaiser's “Smarter Recompilation” (1988)

Schwanke and Kaiser's extension of smart recompilation is an intriguing idea. Their mechanism aims at delaying recompilation work by permitting “harmless” compilation inconsistencies to remain after changes. Full consistency can be reestablished at a later time, after the change has been tested in a subpart of the system. If the change was inadequate, then no needless compilation work was performed. This strategy is used frequently in practice, by exploiting loopholes in system generation tools. Schwanke and Kaiser's mechanism is novel in that it makes this practice safe. The compiler is aware of the inconsistencies, and will not overlook dangerous ones. Furthermore, it can help reestablish full consistency once a change is deemed acceptable. Smarter recompilation defines a harmless inconsistency as follows. If a declaration is changed, this action is treated as introducing a new version of the declaration. The coexistence of both the old and new versions in the same configuration is a harmless inconsistency as long as the uses of the two versions do not conflict. The system must be separable into two partitions, one that uses the old version and the other the new one, such that the interface between the two depends on neither. Since the inconsistent declarations do not cross the interface, the two partitions may even communicate with each other. Of course, inconsistencies not captured by the type system cannot be treated in this way. Schwanke and Kaiser's note leaves a few minor questions unanswered. For instance, a new or changed declaration might cause a redeclaration or overloading error that can only be detected by recompilation. Is this potential problem left undetected until full consistency is desired, or is it checked immediately? If a declaration is deleted that is still in use, is the deletion treated as an error or as a delayed deletion that will take effect after the last use disappears? If the old and new versions of a procedure operate on the same data structure, is it always desirable to let both versions coexist, or can the programmer indicate that the old version should be eliminated before the next program execution? Perhaps a future paper about an implementation will clarify these points. Smarter recompilation also opens the door for more powerful programming tools. For example, since the mechanism maintains cross-reference information, a tool like Masterscope [1] could be built relatively easily. The tool would have the advantage that cross-reference information is immediately available once a module has been compiled. Only little additional data would be needed to classify the uses of symbols. The information could also be exploited by a Maintainer's Assistant. This program helps with reestablishing consistency after changes by suggesting corrections of the affected program parts. For example, it could attempt to make call sites of changed procedures consistent with their headers, update operations on changed record fields, or perform some simple program transformations in response to data structure changes.
Using the CAN protocol and reconfigurable computing technology for Web-based smart house automation (2001)

Abstract: This paper presents the hardware implementation of a multiplatform control system for house automation using FPGAs. Such a system belongs to a domain usually named domotics or smart house systems. The approach combines hardware and software technologies. The system is controlled through the Internet and the home devices being connected use the CAN control protocol. Users can remotely control their houses using a web browser (Client). Locally, instructions received from the Client are translated by the Server, which distributes the commands to the domestic appliances. The implemented system has the following characteristics, which distinguish it from existing approaches: (i) the client interface is automatically updated; (ii) a standard communication protocol (CAN) is used in the hardware implementation, providing reliability and error control; (iii) new appliances are easily inserted in the system; (iv) system security is provided by user authentication; (v) user rights can be set up by an administration interface.
Stark Spectroscopy of Photosynthetic Systems (2006)

SummaryThe effects of applied electric fields on the absorption or emission spectrum of a molecule is known as Stark Spectroscopy. This method probes the movement of charge associated with optical excitation, and is thus sensitive to features which are important for chromophore systems that carry out charge separation, such as photosynthetic systems. This chapter updates a review written about 2 years ago which also described electric field effects on reaction dynamics, notably electron transfer reactions (Boxer, 1993). Several recent extensions of the method such as higher order Stark Spectroscopy and vibrational Stark Spectroscopy are discussed along with examples. Experimental methods and methods of analyzing spectra are discussed in great detail, along with a discussion of experimental and conceptual issues which complicate the analysis of Stark spectra.
Teacher education and drama: possibilities, promise, potential. (2015)

Contemporary discussions about curricula, whether for schools or for higher education, come with demands for change to cope with uncertainty, unpredictability, and 21st century challenge. Core notions however of curriculum as structure for providing access to knowledge (Young, 2014), or a set of teaching and learning prescriptions (Scott, 2014) are hard to shift, yet questions of what knowledge and how is it formed are ones which should be critical for teacher education, where, as a site of higher education, decisions about that knowledge are contested (Barnett, 2015). The prospective teacher continues to negotiate tensions between knowledge of content and of curriculum, pedagogical knowledge and generic teaching skill, knowing as process and knowing in performative terms, and between shaping a role as teacher and as educator for the 21st century. This paper makes a case for the potential that an arts oriented course, specifically drama, holds for helping student teachers to conceptualise their own learning experiences within a teacher education curriculum, to better understand the facilitation of learning experiences within school and classroom curricula, and to begin to shape their teacher identity.
Influence of the refractive index-mismatch at the boundaries measured in fluorescenceenhanced frequency-domain photon migration imaging (2002)

Over the past decade, developments towards near-infrared (NIR) optical tomography involve the recovery of interior optical maps from boundary measurements using the first principles of light propagation models. The refractive-index mismatch parameter in the boundary condition of the light propagation model, namely the diffusion equation, can significantly impact model prediction of measurements and therefore image recovery. In this contribution, the influence of refractive-index mismatch parameter between predictions and referenced measurements of fluorescence-enhanced frequency-domain photon migration (FDPM) are established; its greater influence on emission over excitation predictions are demonstrated, and the methods to accurately determine refractive index mismatch parameter from basic principles are reviewed.
Mitigating Receiver's Buffer Blocking by Delay Aware Packet Scheduling in Multipath Data Transfer (2013)

Reliable in order multipath data transfer under asymmetric heterogeneous network conditions has known problems related to receiver's buffer blocking, caused by out of order packet arrival. Several mitigation techniques have been proposed to address this issue mostly by using various packet retransmission schemes, load-balancing and bandwidth-estimation based mechanisms. In comparison to the existing reactive techniques for buffer block mitigation, we propose a novel and yet simpler to implement, delay aware packet scheduling scheme for multipath data transfer over asymmetric network paths, that proactively minimizes the blocking inside receiver's buffer. Our initial simulation results show that, in comparison to the default round robin packet scheduler, by using our proposed delay aware packet scheduling scheme, we can significantly improve overall performance while notably minimizing the receiver's buffer usage, which is also beneficial for multi-homed hand-held mobile devices with limited buffering capacity, which, due to their multi-homing and heterogeneous wireless network features (i.e. availability of 3G and Wi-Fi) are also one of the most common use cases for multi-path transport.
Tumour necrosis factor-alpha synthesis by cerebrospinal-fluid-derived T cell clones from patients with multiple sclerosis. (1992)

T-cell clones derived from the CSF (cerebrospinal fluid) of MS (multiple sclerosis) patients have been analysed for the production of interferon-gamma (IFN-gamma), tumour necrosis factor-alpha (TNF-alpha), interleukin-2 (IL-2) and interleukin-4 (IL-4). Each CSF-T clone (both CD4+ and CD8+) produced substantial amounts of IFN-gamma and especially TNF-alpha compared with autologous peripheral T clones and liver-infiltrating T clones from patients with chronic active hepatitis. The large quantities of TNF produced by CSF-T cell clones suggest an important role for this cytokine in MS immunopathogenesis.
Synthesis and characterization of acryloyloxy guar gum (2010)

Abstract Guar gum is a galactomannan commonly used as a viscosity modifier in the food, pharmaceutical, and cosmetics industry. The aim of this study was to synthesize acryloyloxy guar gum via a Schotten‐Bauman reaction in aqueous media. The reaction products were characterized using FTIR, C 13 ‐NMR, wide angle X‐ray diffraction techniques to ascertain the effect of acrylation on the structure of guar gum. The acrylation of guar gum was found to be limited to the primary hydroxyl groups on the guar gum molecule. The maximum degree of substitution (DS) was found to be 0.56, which was observed after 3 h of reaction. Since the reaction was carried out in an aqueous medium after 3 h of reaction the DS of the derivatised guar gum was found to decrease, because of hydrolysis of the formed ester linkages. The ester content and intrinsic viscosity of the derivatised guar gums were also evaluated. Thermal analysis showed that a higher DS resulted in products with lower thermal stability and there was no evidence of reaction via the acrylate groups on heating. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Pyrimidine derivatives and related compounds. 15. Synthesis and analgetic and antiinflammatory activities of 1,3-substituted 5-amino-6-methyluracil derivatives (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrimidine derivatives and related compounds. 15. Synthesis and analgetic and antiinflammatory activities of 1,3-substituted 5-amino-6-methyluracil derivativesShigeo Senda, Kosaku Hirota, and Kazuo BannoCite this: J. Med. Chem. 1972, 15, 5, 471–476Publication Date (Print):May 1, 1972Publication History Published online1 May 2002Published inissue 1 May 1972https://pubs.acs.org/doi/10.1021/jm00275a008https://doi.org/10.1021/jm00275a008research-articleACS PublicationsRequest reuse permissionsArticle Views243Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Eosinophilic ascites with marked peripheral eosinophilia (2014)

Eosinophilic disease of the gastrointestinal tract is rare and is characterized by the presence of gastrointestinal symptoms in association with eosinophilic infiltration of any part of the gastrointestinal tract. Clinical presentation of eosinophilic gastroenteritis (EGE) varies not only by the part of the gastrointestinal tract involved but also with the depth of eosinophilic infiltration of the gut wall. We describe the case of a 41-year-old woman with a history of atopy who presented with severe abdominal pain and diarrhoea. Investigations showed large-volume eosinophil-rich ascites and a markedly elevated peripheral blood eosinophil count and immunoglobulin E level. Bone marrow aspirate, trephine biopsy and T-cell studies showed no evidence of underlying haematological malignancy. Vasculitic disease and parasitic infection were systematically excluded. Colonic and upper gastrointestinal biopsies confirmed a diagnosis of EGE with eosinophilic ascites. The patient was treated with systemic corticosteroids and dietary allergen elimination with dramatic therapeutic response. The diagnostic and therapeutic challenges associated with EGE in its various forms are discussed.
Molecular Characterization of Organic Electronic Films (2010)

Organic electronics have emerged as a viable competitor to amorphous silicon for the active layer in low-cost electronics. The critical performance of organic electronic materials is closely related to their morphology and molecular packing. Unlike their inorganic counterparts, polymers combine complex repeat unit structure and crystalline disorder. This combination prevents any single technique from being able to uniquely solve the packing arrangement of the molecules. Here, a general methodology for combining multiple, complementary techniques that provide accurate unit cell dimensions and molecular orientation is described. The combination of measurements results in a nearly complete picture of the organic film morphology.
A simple approach to interrater agreement. (1976)

We have described a simple method for computing a measure of interrater agreement or reliability. This method depends on an experimental design that uses a consensus rating as well as individual ratings. The computations required are counting and percentages; the overall agreement index uses a simple weighting average.