gebhart/patrepeval huggingface dataset:
Expression and Function of the Ror‐Family Receptor Tyrosine Kinases During Development: Lessons from Genetic Analyses of Nematodes, Mice, and Humans (2003)

Receptor tyrosine kinases (RTKs) play crucial roles in various developmental processes. Ror-family RTKs are characterized by the intracellular tyrosine kinase domains, highly related to those of the Trk-family RTKs, and by the extracellular Frizzled-like cysteine-rich domains (CRDs) and Kringle domains. Rors are evolutionally conserved among Caenorhabditis elegans, Aplysia, Drosophila melanogaster, Xenopus, mice, and humans. In D. melanogaster and mammals, pairs of structurally related Rors are found, while a single Ror protein is identified in C. elegans or Aplysia. In Aplysia and D. melanogaster, Rors are expressed exclusively in developing nervous systems. On the other hand, rather widespread expression of Rors was observed in C. elegans and mammals. Mutations in Ror of C. elegans cause inappropriate axon outgrowth as well as defects in cell migration and asymmetric cell division. It has also been reported that the nematode Ror possesses kinase-dependent and kinase-independent functions. Mouse Rors, Ror1, and Ror2, are expressed mainly in migrating neural crest cells and mesenchymal cells, and Ror2-deficient mice exhibit skeletal abnormalities and ventricular septal defects in the heart. Although Ror1-deficient mice exhibit no apparent skeletal or cardiac abnormalities, Ror1/Ror2 double mutant mice show markedly enhanced skeletal and cardiac abnormalities compared with Ror2 mutant mice, indicating genetic interaction of Ror1 and Ror2. In humans, mutations within Ror2 have been found in two genetic skeletal disorders, recessive Robinow syndrome and dominant Brachydactyly type B (BDB), further emphasizing critical functions of Ror2 during developmental morphogenesis. In this article, we also discuss the signaling machinery mediated by Ror-family RTKs with a particular emphasis on our recent structure-function analyses of Ror-family RTKs.
Clinical Trials with Exogenous Interferon: Summary of a Meeting (1979)

Journal Article Clinical Trials with Exogenous Interferon: Summary of a Meeting Get access June K. Dunnick, June K. Dunnick National Institute of Allergy and Infectious Diseases National Institutes of Health, Bethesda, Maryland Please address requests for reprints to Dr. June K. Dunnick, Development and Applications Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Westwood Building, Room 750, Bethesda, Maryland 20014. Search for other works by this author on: Oxford Academic PubMed Google Scholar George J. Galasso George J. Galasso National Institute of Allergy and Infectious Diseases National Institutes of Health, Bethesda, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 139, Issue 1, January 1979, Pages 109–123, https://doi.org/10.1093/infdis/139.1.109 Published: 01 January 1979
Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution (2016)

UV-induced DNA lesions are important contributors to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. Genome-wide profiling of repair activity in UV irradiated cells has revealed significant variations in repair kinetics across the genome, not only among large chromatin domains, but also at individual transcription factor binding sites. Here we report that there is also a striking but predictable variation in initial UV damage levels across a eukaryotic genome. We used a new high-throughput sequencing method, known as CPD-seq, to precisely map UV-induced cyclobutane pyrimidine dimers (CPDs) at single-nucleotide resolution throughout the yeast genome. This analysis revealed that individual nucleosomes significantly alter CPD formation, protecting nucleosomal DNA with an inward rotational setting, even though such DNA is, on average, more intrinsically prone to form CPD lesions. CPD formation is also inhibited by DNA-bound transcription factors, in effect shielding important DNA elements from UV damage. Analysis of CPD repair revealed that initial differences in CPD damage formation often persist, even at later repair time points. Furthermore, our high-resolution data demonstrate, to our knowledge for the first time, that CPD repair is significantly less efficient at translational positions near the dyad of strongly positioned nucleosomes in the yeast genome. These findings define the global roles of nucleosomes and transcription factors in both UV damage formation and repair, and have important implications for our understanding of UV-induced mutagenesis in human cancers.
Accurate modeling of optical system aberrations applied to the design of a stationary Fourier transform spectroradiometer (2005)

Stationary Fourier transform spectrometry is a well-known concept to build reliable field or embedded spectroradiometers, especially for the mid- and far- infrared. However, the quality of the interference pattern imaged on the focal plane array is crucial to obtain a good spectrum by Fourier transform. We describe here an accurate modeling of the interferometer behavior that takes into account the instrument aberrations and field of view in order to quantitatively predict, at each wavelength and for a spatially extended uniform incoherent source, the real interferogram defects, namely, fringe distortion, fringe blurring and illumination non-uniformity. To investigate these effects, we first derive the properties of the elementary interferograms built by each source point. For this purpose, we use ray-tracing to extract optical path and vignetting information with the help of a commercial optical design software package, and we reconstruct from them the two wavefronts that hit the detector using general numerical methods with the help of standard computing tools. The whole interferogram being formed by the incoherent superposition of all elementary interferograms, we next, compute the relevant quantities by appropriate numerical quadratures. We illustrate this method with two potential layouts of a Fourier transform spectrometer that we are currently designing for accurate radiometric measurements in the 2.9μm-9.6μm range with a spectral resolution better than 8cm<sup>-1</sup> on a 4.5°x0.6° field of view.
Critical role of spatial resolution in dynamic contrast‐enhanced breast MRI (2001)

The spatial resolution of three-dimensional (3D) gradient-echo T1-weighted images, from 40 women with 25 malignant and 23 benign lesions, was purposely degraded to determine the role of spatial resolution in recording, analysis, and diagnosis of dynamic contrast-enhanced breast MRI. Images were recorded and analyzed at pixel resolution according to the 3TP method (Degani et al., Nat Med 1997;3:780-782). Reduction in spatial resolution degraded the appearance of foci with fast wash-in and fast washout dynamics. This resulted in an increase in false-negative diagnoses. The sensitivity for differentiating between malignant and benign lesions, using threshold criteria defined by the 3TP analysis, of 76% decreased to 60% and 24% for a 2- and 4-fold reduction in spatial resolution, respectively, without affecting significantly the high specificity (96-100%). In order to minimize false-negative diagnoses of contrast-enhanced breast MRI and maintain high specificity, it is essential to record and analyze the dynamic behavior at high spatial resolution. J. Magn. Reson. Imaging 2001;13:862-867.
An analysis of the frequency characteristics of corona discharge at low pressure (1991)

Abstract : Corona discharge is becoming more of a concern now that the space program is looking at higher power and voltage requirements for future missions. Improved detection methods for studying corona discharge will increase the knowledge base of how this phenomenon occurs, what effects it has on power systems, and how it is affected by outside influences. A better understanding of corona discharge will enable designers to improve on the space applications of insulation and dielectrics, and develop proper detection techniques. A test system was designed and constructed to measure the frequency spectrum of corona discharge current in low pressure. Various test samples in different arrangements were energized by ac voltage until corona discharge occurred. This same test was repeated at different pressures. The results indicate that the frequency spectrum of the discharge current changes with a change in pressure. At low pressures, the discharge frequency spectrum is concentrated in a narrow band with a peak at 17 kHz. As the pressure is increased, the spectral width increases to include components across a much broader band. Other tests were performed to correlate the frequency spectrum data to the shape of the discharge pulse and the physical appearance of the glow discharge. (Author)
Recent progress in studies of infantile hemangioma (2010)

A hallmark of infantile hemangioma, the most common tumor of infancy, is its dramatic growth after birth, by diffuse proliferation of immature endothelial cells, followed by spontaneous regression. The growth and involution of infantile hemangioma is quite different from other vascular anomalies, which do not regress and can occur at any time during life. Some hemangioma lesions can be extremely disfiguring and destructive to normal tissue and may even be life-threatening. Unfortunately, existing therapeutic approaches have limited success and significant adverse effects of some treatment modalities limit their use. Better understanding of the pathogenesis of hemangioma will enable the development of better therapeutic strategies. Here, we review recent studies and new hypotheses on the pathogenesis of the tumor. Detailed mechanisms of activated vascular endothelial growth factor signaling in tumor cells, identification of their origin and characterization of multipotent stem cells that can give rise to infantile hemangioma are shedding new light on this intriguing vascular tumor.
REVIEW: Sea of Gray: The Around-the- World Odyssey of the Confederate Raider Shenandoah (2007)

Review of the non-fiction book "Sea of Gray: The Around-the-World Odyssey of the Confederate Raider Shenandoah," by Tom Chaffin.
Divergent Proteome Patterns of Egg Albumen from Domestic Chicken, Duck, Goose, Turkey, Quail and Pigeon (2017)

To uncover a diversity of genetic and biological unknowns, a comprehensive and comparative proteomic analysis is performed on egg albumen of domestic chicken, duck, goose, turkey, quail, and pigeon with tandem mass tags quantification technology. In this study, a total of 148, 138, 150, 162, 183, and 179 proteins are identified in egg albumen of the above six species, respectively. Venn plots, PCA, and cluster analysis all reveal the highest similarity of protein composition between duck and goose (≈75%). Additionally, the six species have 52 proteins detected in common in the egg albumen. As revealed by GO and pathway analyses, the plausible functions of these highly conserved proteins are to provide a secure environment and prevent the early death of embryonic cells. Species-specific proteins such as haptoglobin in pigeon, serpin-like protein HMSD in duck, and ovodefensin in chicken are also screened and are likely associated with species-dependent biological processes. Furthermore, Enzyme Code analysis indicated egg albumen have abundant enzyme activity, with hydrolases accounting for more than half of the total enzymes. This study is the first to provide the proteome profiles of egg albumen for the major poultry species, which will be instructive for the understanding of species-specific biological problems with egg albumen.
Parametric spectro-temporal analyzer (PASTA) for real-time optical spectrum observation (2013)

Real-time optical spectrum analysis is an essential tool in observing ultrafast phenomena, such as the dynamic monitoring of spectrum evolution. However, conventional method such as optical spectrum analyzers disperse the spectrum in space and allocate it in time sequence by mechanical rotation of a grating, so are incapable of operating at high speed. A more recent method all-optically stretches the spectrum in time domain, but is limited by the allowable input condition. In view of these constraints, here we present a real-time spectrum analyzer called parametric spectro-temporal analyzer (PASTA), which is based on the time-lens focusing mechanism. It achieves a frame rate as high as 100 MHz and accommodates various input conditions. As a proof of concept and also for the first time, we verify its applications in observing the dynamic spectrum of a Fourier domain mode-locked laser, and the spectrum evolution of a laser cavity during its stabilizing process.
The NAC Transcription Factors NST1 and NST2 of<i>Arabidopsis</i>Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscence (2005)

In plants, secondary wall thickenings play important roles in various biological processes, although the factors regulating these processes remain to be characterized. We show that expression of chimeric repressors derived from NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST2 in Arabidopsis thaliana resulted in an anther dehiscence defect due to loss of secondary wall thickening in anther endothecium. Plants with double, but not single, T-DNA-tagged lines for NST1 and NST2 had the same anther-indehiscent phenotype as transgenic plants that expressed the individual chimeric repressors, indicating that NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls. The activity of the NST2 promoter was particularly strong in anther tissue, while that of the NST1 promoter was detected in various tissues in which lignified secondary walls develop. Ectopic expression of NST1 or NST2 induced ectopic thickening of secondary walls in various aboveground tissues. Epidermal cells with ectopic thickening of secondary walls had structural features similar to those of tracheary elements. However, among genes involved in the differentiation of tracheary elements, only those related to secondary wall synthesis were clearly upregulated. None of the genes involved in programmed cell death were similarly affected. Our results suggest NAC transcription factors as possible regulators of secondary wall thickening in various tissues.
Massively Parallel Interrogation of Aptamer Sequence, Structure and Function (2008)

The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.
A 3-level e-Business Registry Meta Model (2008)

Business partners willing to do business electronically with each other must reach an agreement (1) on the economic level, (2) on the inter-organizational process choreography, and (3) on the services implementing the choreography. In order to search for a potential business partner, one will first look for a partner who offers a required service on the economic level and who supports a complementary role in a choreography, before binding to its IT services. In as much, a registry for inter-organizational systems should cover all three levels and maintain the dependencies between them. In this paper we set up on well accepted approaches on the different levels, i.e. (1) the e <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> value ontology, (2) the UN/CEFACT modeling methodology (UMM), and (3) the business process execution language (BPEL). We specify a registry meta model on top of ebRIM registering the artifacts on the different levels and defining their inter-dependencies.
Enhanced Strain‐Dependent Electrical Resistance of Polyurethane Composites with Embedded Oxidized Multiwalled Carbon Nanotube Networks (2013)

The effect of different chemical oxidation of multiwalled carbon nanotubes with H 2 O 2 , HNO 3 , and KMnO 4 on the change of electrical resistance of polyurethane composites with embedded oxidized nanotube networks subjected to elongation and bending has been studied. The testing has shown about twenty‐fold increase in the electrical resistance for the composite prepared from KMnO 4 oxidized nanotubes in comparison to the composites prepared from the pristine and other oxidized nanotubes. The evaluated sensitivity of KMnO 4 treated composite in terms of the gauge factor increases with strain to nearly 175 at the strain 11%. This is a substantial increase, which ranks the composite prepared from KMnO 4 oxidized nanotubes among materials as strain gauges with the highest electromechanical sensitivity. The observed differences in electromechanical properties of the composites are discussed on basis of their structure which is examined by the measurements of Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy, and scanning electron microscope. The possible practical use of the composites is demonstrated by monitoring of elbow joint flexion during two different physical exercises.
Pseudo-Boolean Solving by incremental translation to SAT (2011)

We revisit pseudo-Boolean Solving via compilation to SAT. We provide an algorithm for solving pseudo-Boolean problems through an incremental translation to SAT that works with any incremental SAT solver as a backend. Experimental evaluation shows that our incremental algorithm solves industrial problems that previous SAT-based approaches do not. We also show that SAT-based algorithms for solving pseudo-Boolean problems should be a part of any portfolio solver.
[Differential diagnosis of non-epithelial rectal neoplasms]. (1995)

Experience in the treatment of 118 patients with nonepithelial new growths of the rectum has been accumulated at the Scientific Research Institute of Proctology in the period from 1970 to 1991. They accounted for 1.5% of all benign and malignant tumors of this organ. Leiomyoma was diagnosed in 44, leiomyosarcoma in 18, lipoma in 30, fibroma in 17, neurinoma in 7 and rhabdomyoma in 2 of these patients. A differential diagnosis was made between benign and malignant tumors, as well as with other nonepithelial new growth of the rectum. On the basis of the clinical picture and the results of digital and instrumental (radiological, endoscopic, and ultrasonic) examination of the rectum the correct preoperative diagnosis may be established with certain probability. This influences directly the choice of the volume of the operative intervention in various types of nonepithelial rectal tumors. Morphological verification of the tumor is the principal method of examination in establishing the differential diagnosis in the preoperative and postoperative periods.
Simple causal minimizations for temporal persistence and projection (1987)

Formalizing temporal persistence and solving the temporal projection problem within traditional non-monotonic logics is shown possible through two different approaches, neither of which respecial minimization techniques. $$$z~ ~ potential causes is shown to yield a type of temporal persistence that is useful for the temporal projection problem, although it differs significantly from the ordinary conception of temporal persistence. A conception of determined causes is then developed whose minimization does yield the results preferred by ordinary temporal persistence. Finally, previous approaches to formalizing temporal persistence using chronological minimizations are shown inadequate for certain classes of scenarios, which causal minimizations formalize correctly. 1.
Essential Oil Constituents of The Rhizomes of Two Types of <i>Curcuma longa</i> of Bangladesh (1970)

Essential oil from the rhizomes of two types of Curcuma longa, yellow and red originated in Bangladesh was analyzed by GC-MS. 54 compounds have been identified from the yellow type of which the major compounds are ar-tumerone (27.78%), tumerone (17.16%), culone (13.82%), 2-carene (4.78%), zingiberene (4.37%) and β-sesquiphellandrene (5.57%). The red type contained 39 compounds with carvacrol (21.14%), citral (13.91%), methyleugenol (7.31%), geraniol (6.99%), menthol (5.11%) and caryophyllene oxide (4.14%) as major constituents. Key words: Curcuma longa, GC-MS, Ar-tumerone, Carvacrol, Tumerone, Citral. DOI: 10.3329/bjsir.v43i2.970 Bangladesh J. Sci. Ind. Res. 43(2), 259-266, 2008
Mechanical behavior of polymer microlayers (1999)

Abstract The mechanical behavior of polycarbonate (PC) coextruded as microlayers with a brittle polymer, either poly(styrene‐ co ‐acrylonitrile) (SAN) or poly(methyl methacrylate) (PMMA), was examined. Adhesion between layers was measured with the T‐peel method. The much higher interfacial toughness of PC/PMMA microlayers compared to PC/SAN was attributed to partial miscibility. Comparison of the microdeformation behavior of 32‐layer PC/SAN and PC/PMMA microlayers revealed that very good adhesion between PC and PMMA constrained yielding of the PC. This was seen in the tensile stress‐strain curves as a broader stress drop at the yield point and a lower fracture strain. Decreasing the layer thickness by increasing the number of layers enhanced the ductility of both PC/SAN and PC/PMMA microlayers. A PC/PMMA microlayer with 4096 layers and a composition of 80% PC achieved the ballistic performance of polycarbonate.
Multi-Agent based Control and Protection of Power Distributed System - Protection Scheme with Simplified Information Utilization - (2006)

On the premise of future improvement of information infrastructures, we proposed a multi-agent based protection scheme for distribution systems with high penetration of distributed generators (DGs). In the proposed protection scheme, various relays designed as relay agents cooperate to locate and isolate fault zone. Binary state signal, e.g. current direction, magnitude, etc. is determined autonomously just by sensing a sudden change of the current at the relay. Each relay simultaneously utilizes binary state signals provided by the other relays at breakers involved to the same zone for detecting a fault location. By using PSCAD/EMTDC, the proposed protection scheme is tested with a distribution system which has loop structure and is divided into several protection zones. Extensive simulation studies show that the proposed protection scheme can be adopted for various conditions of distribution structure and DGs operation, and may contribute to a selective and quick disconnection of faulted zone with less coordination between relays
Uncloaking the invisible killer and developing an antidote to SARS-CoV-2 (2020)

It’s something so many in global healthcare expected, even prepared for, yet the sheer scale and complexity of the COVID-19 pandemic has left us awestruck. Lives have been lost, economies have suffered, countries have locked down but, as yet, no cure has been found. We need to find an antidote and we need to do so quickly. One solution may lie in ultra-personalized genetic medicine — in this case, medicine that can be quickly designed to specifically target SARS-CoV-2, the novel virus that causes COVID.