gebhart/patrepeval huggingface dataset:
SAM 1.1 and JOSH 4.4: two RFLPs within the human DCC gene (1992)

Journal Article SAM 1.1 and JOSH 4.4: two RFLPs within the human DCC gene Get access J.W. Simons, J.W. Simons The Johns Hopkins Oncology Center424 N.Bond Street, Baltimore, MD 21231, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J.D. Oliner, J.D. Oliner The Johns Hopkins Oncology Center424 N.Bond Street, Baltimore, MD 21231, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar K.R. Cho, K.R. Cho The Johns Hopkins Oncology Center424 N.Bond Street, Baltimore, MD 21231, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar K.W. Kinzler, K.W. Kinzler The Johns Hopkins Oncology Center424 N.Bond Street, Baltimore, MD 21231, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar B. Vogelstein B. Vogelstein * The Johns Hopkins Oncology Center424 N.Bond Street, Baltimore, MD 21231, USA *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 1, Issue 5, August 1992, Page 352, https://doi.org/10.1093/hmg/1.5.352 Published: 01 August 1992
Renal organoid modeling of tuberous sclerosis complex reveals lesion features arise from diverse developmental processes (2022)

Tuberous sclerosis complex (TSC) is a multisystem tumor-forming disorder caused by loss of TSC1 or TSC2. Renal manifestations predominately include cysts and angiomyolipomas. Despite a well-described monogenic etiology, the cellular pathogenesis remains elusive. We report a genetically engineered human renal organoid model that recapitulates pleiotropic features of TSC kidney disease in vitro and upon orthotopic xenotransplantation. Time course single-cell RNA sequencing demonstrates that loss of TSC1 or TSC2 affects multiple developmental processes in the renal epithelial, stromal, and glial compartments. First, TSC1 or TSC2 ablation induces transitional upregulation of stromal-associated genes. Second, epithelial cells in the TSC1<sup>-/-</sup> and TSC2<sup>-/-</sup> organoids exhibit a rapamycin-insensitive epithelial-to-mesenchymal transition. Third, a melanocytic population forms exclusively in TSC1<sup>-/-</sup> and TSC2<sup>-/-</sup> organoids, branching from MITF<sup>+</sup> Schwann cell precursors. Together, these results illustrate the pleiotropic developmental consequences of biallelic inactivation of TSC1 or TSC2 and offer insight into TSC kidney lesion pathogenesis.
Balloon Aortic Valvuloplasty under Temporary Mechanical Circulatory Support as a Bridge to Aortic Valve Replacement in a Patient with Hemodynamic Failure Secondary to Critical Aortic Valve Stenosis (2012)

Aortic valve replacement in the setting of critical aortic valve stenosis with cardiogenic shock is associated with high mortality, yet surgery is the only definitive treatment. We present the case of a patient with critical aortic valve stenosis and cardiogenic shock who received a short period of percutaneous mechanical support and balloon aortic valvuloplasty that resulted in rapid clinical improvement. The patient then underwent uneventful aortic valve replacement. We believe that temporary mechanical circulatory support coupled with balloon aortic valvuloplasty helped to restore hemodynamic stability before surgery, leading to a better outcome.
A Comprehensive Review of Secondary Carbon Bio-Carriers for Application in Metallurgical Processes: Utilization of Torrefied Biomass in Steel Production (2022)

This review aims to show the significance of the use of secondary carbon bio-carriers for iron and steel production. The term ‘secondary carbon bio-carriers’ in this review paper refers to biomass, torrefied biomass, biochar, charcoal, or biocoke. The main focus is on torrefied biomass, which can act as a carbon source for partial or complete replacement of fossil fuel in various metallurgical processes. The material requirements for the use of secondary carbon bio-carriers in different metallurgical processes are systematized, and pathways for the use of secondary carbon bio-carriers in four main routes of steel production are described; namely, blast furnace/basic oxygen furnace (BF/BOF), melting of scrap in electric arc furnace (scrap/EAF), direct reduced iron/electric arc furnace (DRI/EAF), and smelting reduction/basic oxygen furnace (SR/BOF). In addition, there is also a focus on the use of secondary carbon bio-carriers in a submerged arc furnace (SAF) for ferroalloy production. The issue of using secondary carbon bio-carriers is specific and individual, depending on the chosen process. However, the most promising ways to use secondary carbon bio-carriers are determined in scrap/EAF, DRI/EAF, SR/BOF, and SAF. Finally, the main priority of future research is the establishment of optimal parameters, material quantities, and qualities for using secondary carbon bio-carriers in metallurgical processes.
End stopping and length tuning in psychophysical spatial filters (1997)

Psychophysical spatial filters or channels are usually modeled after simple-cell receptive fields, although many cortical cells are end stopped and length tuned. Using psychophysical masking, we demonstrate an analog to receptive field end stopping and length tuning in psychophysical spatial filters tuned to a wide range of spatial frequencies. Specifically, masking is maximal when the mask is approximately 5-6 arcmin longer than the target but is reduced when the mask exceeds this length, consistent with the properties of end-stopped cells. The strength and the extent of psychophysical end stopping appear to be determined by filter's spatial-frequency tuning, but length tuning varies with target length. The latter implies that spatial filters tuned to the same spatial frequency could have different length tuning and that there is no fixed length-to-width ratio of the filter size. Phase effects suggest linear length summation but nonlinear psychophysical end stopping which suggest that both first- and second-order visual processing is involved in end-stopped spatial filters.
A Guide to In Silico Drug Design (2022)

The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as <i>in silico</i> structure prediction, refinement, modelling and target validation, that are commonly used in this area.
Interaction of Escherichia coli RNA polymerase with promoters of several coliphage and plasmid DNAs. (1979)

The interaction of Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) with restriction fragments obtained from various E. coli related DNAs was studied in vitro. The DNAs investigated included several coliphage genomes (T5, lambda, T7, fd) and plasmid DNAs (pML 21, pSC101). By using the nitrocellulose filter binding of the enzyme-DNA complexes, fragment-specific relative rates of complex formation as well as complex stabilities were determined. Promoter-specific relative rates of polymerase binding were derived from fragment-specific rates by taking into account the number of major binding sites for RNA polymerase within several DNAs. Estimates of the stability of complexes formed between some major binding sites and the enzyme were obtained by studying the rate of complex decay. Both characteristics--rate of complex formation and rate of decay--varied widely and independently of each other. The promoters reacting most efficiently with E. coli RNA polymerase were found in the early region of coliphage T5 whereas some promoters in pML 21, or for example, the lambda promoter PI, belong to signals binding the enzyme most slowly. Based on the second-order rate constant determined for the interaction of E. coli RNA polymerase with promoters of phage fd, the fastest promoters characterized so far reacted with rates in the order of 10(8) M-1s-1. The hierarchy of promoters established here is of interest from the viewpoint that promoter strength correlates with the rate of polymerase binding. Among the promoters studied here this rate spans a range of 2 orders of magnitude.
Computational Imaging VI (2004)

vii Conference Committee ix Stationary features and cat detection (Keynote PresentationViewgraphs) [6814-21] D. Geman, Johns Hopkins Univ. (USA); F. Fleuret, INRIA Rocquencourt (France) KEYNOTE PRESENTATION 6814 02 Fast acquisition and reconstruction in imaging enabled by sampling theory (Invited Paper) [6814-01] Y. Bresler, Univ. of Illinois at Urbana-Champaign (USA) IMAGE RECONSTRUCTION I 6814 03 Regularized estimation of Stokes images from polarimetric measurements [6814-02] J. R. Valenzuela, J. A. Fessler, Univ. of Michigan (USA) 6814 04 Non-homogeneous ICD optimization for targeted reconstruction of volumetric CT [6814-03] Z. Yu, Purdue Univ. (USA); J.-B. Thibault, GE Healthcare Technologies (USA); C. A. Bouman, Purdue Univ. (USA); K. D. Sauer, Univ. of Notre Dame (USA); J. Hsieh, GE Healthcare Technologies (USA) GEOMETRY-BASED TECHNIQUES IN IMAGE ANALYSIS 6814 07 MCMC curve sampling and geometric conditional simulation [6814-06] A. Fan, J. W. Fisher III, Massachusetts Institute of Technology (USA); J. Kane, Shell EP A. S. Willsky, Massachusetts Institute of Technology (USA) 6814 08 Mixing geometric and radiometric features for change classification [6814-07] A. Fournier, X. Descombes, J. Zerubia, INRIA (France) 6814 09 3D object recognition using fully intrinsic skeletal graphs [6814-08] D. Aouada, H. Krim, North Carolina State Univ. (USA) 6814 0A Content based image retrieval for matching images of improvised explosive devices in which snake initialization is viewed as an inverse problem [6814-09] S. T. Acton, A. D. Gilliam, B. Li, Univ. of Virginia (USA); A. Rossi, Platinum Solutions (USA) SEGMENTATION 6814 0B Segmentation of digital microscopy data for the analysis of defect structures in materials using nonlinear diffusions [6814-10] L. M. Huffman, Purdue Univ. (USA); J. Simmons, Air Force Research Lab. (USA); I. Pollak, Purdue Univ. (USA)
Supplementary Figures 1 - 8 from Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer (2023)

&lt;p&gt;PDF file - 1020K, Supplementary Figure S1. A cassette event in MAPT gene. Supplementary Figure S2. Validation of the cell model of SRSF1 down-regulation. Supplementary Figure S3. Validation of differential alternative splicing events from the top 20 genes selected by the ExonPointer algorithm using microarray data from the Oryzon platform. Supplementary Figure S4. Validation of differential alternative splicing events in a set of genes selected by the ExonPointer algorithm using microarray data from the GeneSplice platform. Supplementary Figure S5. Ingenuity pathway network related to "Cell Morphology, Developmental Disorder and Hereditary Disorder" and derived from the analysis of differential alternative splicing events after SRSF1 down-regulation. Supplementary Figure S6 Ingenuity pathway network with annotations: "Cell Cycle, Cellular Assembly and Organization and Cellular Movement" and derived from the analysis of differential alternative splicing events after SRSF1 down-regulation. Supplementary Figure S7. Ingenuity pathway network with annotations: "Organismal Development, Cancer, Cell Death and Survival" and derived from the analysis of differential alternative splicing events after SRSF1 down-regulation. Supplementary Figure S8. Growth effect of PRRC2C splice variants in HCC827, H2087 and HCC95 cell growth.&lt;/p&gt;
Dynamic Simulator for a PEM Fuel Cell System With a PWM DC/DC Converter (2008)

Polymer electrolyte membrane (PEM) fuel cells typically have low voltage, high current, terminal characteristics that cannot accommodate common electric loads like electric motors or power utility grids. Thus, a dc/dc converter is required to boost the output voltage of these power systems. Furthermore, the terminal characteristics are dependent on loads and operating conditions of the fuel cell system. The continuously changing power demand of an electric load requires dynamically replenishing the air and fuel, by properly maintaining humidity in the cell and efficiently rejecting the heat produced. These factors present important challenges for the design of reliable and durable power systems. We present new dynamic models for a fuel cell system and a pulsewidth modulation dc/dc converter with associated controls and integration. The model for the system consists of three subsystems that include an PEM fuel cell stack, an air supply, and a thermal system. Four different controllers were designed to control the air, the coolant, and the output voltage of the converter, and to optimize the power flow between the fuel cell and the output capacitor. The integrated model with its controls was tested using a real-time simulator that reduced computational time and facilitated the analysis of the interactions between loads and the fuel cell components and also allowed the optimization of a power control strategy. The responses of a static and dynamic load show that the power controls proposed can coordinate two energy sources, resulting in improved dynamics and efficiency.
Antenna-Mediated Near Field Spectroscopic Imaging: Extension to the Time and Frequency Domains (2013)

Scattering scanning near field microscopy is capable of measuring the response of a material to incident infrared light with a resolution determined by the tip radius of the antenna. We present new methods and results here, in which broad band and ultrafast sources are used to extend this technique into the time and frequency domains.
Substrates with Patterned Extracellular Matrix and Subcellular Stiffness Gradients Reveal Local Biomechanical Responses (2013)

A substrate fabrication process is developed to pattern both the extracellular matrix (ECM) and rigidity at sub-cellular spatial resolution. When growing cells on these substrates, it is found that cells respond locally in their cytoskeleton assembly. The presented method allows unique insight into the biological interpretation of mechanical signals, whereas photolithography-based fabrication is amenable to integration with complex microfabricated substructures.
FEM-based method to determine mechanical stress evolution during process flow in microelectronics. Application to stress-voiding (2004)

Mechanical stress is a major concern in microelectronics: the reliability of VLSI interconnects is mainly controlled by the stress levels. The increasing complexity of processes and the shrinking of feature sizes make it necessary to use quantitative modelling in order to optimise process parameters and device geometries. We had developed a method based on the use of some finite element analysis (FEA) tools, to quantitatively determine the stress evolution along the process flow. This method allows us to simulate material deposition, etching and thermal ramping steps. It was used to monitor the stress level in two metallic levels interconnected by a via during the fabrication. Our numerical results were analysed regarding the so-called stress-voiding phenomenon: these results allow us to point out the critical interface to focus on. All the obtained results are in good agreement with experimental observations. This method can be used to determine the evolution of the most probable void position as the geometry varies and then to optimise both the geometry and the process to minimize stress-induced voiding.
Deposition of Copper Particles and Films by the Displacement of Two Immiscible Supercritical Phases and Subsequent Reaction (2009)

Copper (Cu) particles and films were produced by forming Cu(II) compound (Cu(hfac)2·H2O) films on substrates using a displacement from two immiscible supercritical phases (DISP) technique followed by reducing the copper(II) compound films in hydrogen at 200 °C. Various surfaces including native oxide of silicon (SiOx), titanium nitride (TiN), tungsten (W), and low-k dielectric materials such as Coral, JSR5109, and Silox were used as substrates. The nucleation and growth behavior of the Cu DISP process was evaluated over a range of reduction times (from 5 to 60 min) and copper(II) compound concentrations (0.5−3 wt %). At short reduction periods (5−15 min) or low Cu(II) compound concentrations (∼ 0.5 wt %), Cu particles ranging from 60 to 95 nm in diameter were produced. In contrast, at long reduction periods (45−60 min) and high concentrations (∼3 wt %), continuous Cu films with 220−450 nm in thickness were deposited on the substrates. A morphology transition from particle to film was observed at medium reduction period (∼30 min) or medium concentration range (∼1 wt %). High affinity of TiN to Cu nucleation and film formation leads to more dense and smooth films than Cu films deposited under similar conditions on SiOx. However, nucleation of Cu DISP is not very sensitive to the surface conditions of the substrates compared with Cu CVD (chemical vapor deposition). Chemical composition analysis of the Cu film on TiN and SiOx by X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS) revealed that highly pure Cu films were obtained from Cu DISP.
Photocatalytic water disinfection on oxide semiconductors: Part 1 – basic concepts of TiO2photocatalysis (2011)

Water disinfection (removal of microbial agents) using sunlight is an emerging technology, which has the capacity to address the global shortage of drinking water. Therefore, intensive investigations in many laboratories aim to develop photocatalyst for water disinfection. The research is focused on titanium dioxide (TiO2), which is the most promising candidate for high performance photocatalyst able to address the commercial requirements. The present work (Part 1) considers the effect of defect disorder on semiconducting and photocatalytic properties of TiO2 (rutile) in water disinfection using solar energy. It is shown that photocatalytic properties of TiO2 in water are closely related to the light induced reactivity of TiO2 with water leading to the formation of active species, such as OH*, H2O2 and , which have the capacity to oxidise microorganisms. It is also shown that the ability of TiO2 to form the active radicals is closely associated with the presence of point defects in the TiO2 lattice and the related semiconducting properties. Therefore, photocatalytic properties of TiO2 may be modified in a controlled manner by changes in its defect disorder. Consequently, defect chemistry may be used as the framework in the development of TiO2 with controlled properties that are desired for solar water disinfection. The following work (Part 2) considers the structure of bacteria and their reactivity/photoreactivity with TiO2 in aqueous environments. Both Part 1 and 2 bring together the concepts of TiO2 photocatalysis and the concepts of microbiology in order to derive the theoretical models that are needed for the development of high performance photocatalysts for solar water disinfection.
Peniophora lycii phytase is stabile and degrades phytate and solubilises minerals in vitro during simulation of gastrointestinal digestion in the pig (2007)

Stability of P. lycii phytase during gastric digestion was not found to be critical for phytate hydrolysis. Furthermore, original phytate solubility was not an absolute requirement for phytate degradation; phytate solubility seemed to be in a steady state, allowing insoluble phytate to solubilise as soluble phytate was degraded. This is new and interesting knowledge that adds to the current understanding of phytate-phytase interaction. Copyright © 2007 Society of Chemical Industry.
Intramolekulare Diels-Alder-Reaktion vom Typ 2: Synthese und Chemie von Brückenkopf-Alkenen (2001)

Anti-Bredt-Alkene, bicyclische Moleküle mit einer Brückenkopf-Doppelbindung, galten lange als chemische Kuriosität. Mit der intramolekularen Diels-Alder-Reaktion vom Typ 2 gelangt man in einem Reaktionsschritt zu dieser faszinierenden Klasse von Molekülen, und man erhielt so zahlreiche anti-Bredt-Alkene für Strukturuntersuchungen und chemische Studien. Kristallstrukturanalysen zeigten das Ausmaß der mit der Brückenkopf-Doppelbindung einhergehenden Deformationen auf, und die Messung von Reaktionsgeschwindigkeiten ermöglichte quantitative Aussagen zu kinetischen Konsequenzen der Verzerrungen. In neuerer Zeit wurden die intramolekulare Diels-Alder-Reaktion vom Typ 2 und die dabei entstehenden anti-Bredt-Alkene auch in der präparativen Organischen Chemie eingesetzt. Die aus der Art der Verknüpfungen in der Vorstufe resultierenden Einschränkungen bewirken im Cycloadditionsschritt eine starke regio- und stereochemische Präferenz mit dem Ergebnis einer stereoselektiven Synthese hochsubstituierter Sechsringe. Die Reaktion ermöglicht aber auch in einem Schritt eine einfache Synthese von Sieben- und Achtringen aus acyclischen Vorstufen. In letzter Zeit hat sich außerdem ihre Nützlichkeit bei der Totalsynthese komplexer Naturstoffe verwiesen.
‘Dry bases’: carbon dioxide capture using alkaline dry water (2014)

An alkaline form of ‘dry water’—a ‘dry base’—is prepared by the high-speed mixing of aqueous solutions of metal carbonates or organic amines with hydrophobic silica nanoparticles.
Immunization of a wild koala population with a recombinant Chlamydia pecorum Major Outer Membrane Protein (MOMP) or Polymorphic Membrane Protein (PMP) based vaccine: New insights into immune response, protection and clearance (2017)

We assessed the effects of two different single-dose anti-Chlamydia pecorum (C. pecorum) vaccines (containing either Major Outer Membrane Protein (3MOMP) or Polymorphic Membrane Protein (Pmp) as antigens) on the immune response of a group of wild koalas. Both vaccines elicited a systemic humoral response as seen by the production of anti-chlamydial IgG antibodies in more than 90% of vaccinated koalas. A mucosal immune response was also observed, with an increase in Chlamydia-specific mucosal IgG and/or IgA antibodies in some koalas post-vaccination. Both vaccines elicited a cell-mediated immune response as measured by the production of the cytokines IFN-γ and IL-17 post-vaccination. To determine the level of protection provided by the vaccines under natural conditions we assessed C. pecorum infection loads and chlamydial disease status of all vaccinated koalas pre- and post-vaccination, compared to a non-vaccinated cohort from the same habitat. The MOMP vaccinated koalas that were infected on the day of vaccination showed significant clearance of their infection at 6 months post-vaccination. In contrast, the number of new infections in the PMP vaccine was similar to the control group, with some koalas progressing to disease. Genotyping of the ompA gene from the C. pecorum strains infecting the vaccinated animals, identified genetic variants of ompA-F genotype and a new genotype ompA-O. We found that those animals that were the least well protected became infected with strains of C. pecorum not covered by the vaccine. In conclusion, a single dose vaccine formulated with either recombinant PmpG or MOMP can elicit both cell-mediated and humoral (systemic and mucosal) immune responses, with the MOMP vaccine showing clearance of infection in all infected koalas. Although the capability of our vaccines to stimulate an adaptive response and be protective needs to be fully evaluated, this work illustrates the necessity to combine epitopes most relevant to a large panel of variable strains with an efficient adjuvant.