gebhart/patrepeval huggingface dataset:
Implementation of a prostate cancer‐specific targeted sequencing panel for credentialing of patient‐derived cell lines and genomic characterization of patient samples (2022)

We evaluated a prostate cancer-specific targeted NGS panel to detect common and clinically relevant alterations (including ETS family gene fusions) in prostate cancer. The panel detected driver mutations in a diverse set of clinical samples of prostate cancer, including fresh-frozen tumors, cell-free DNA, CTCs, and cell lines. Targeted sequencing of patient-derived cell lines highlights the challenge of deriving cell lines from primary prostate cancers and the importance of genomic characterization to credential candidate cell lines. Our study supports that a prostate cancer-specific targeted sequencing panel provides an efficient, clinically feasible approach to identify genetic alterations across a spectrum of prostate cancer samples and cell lines.
Highly Stereoselective Intramolecular Hydroamination/Cyclization of Conjugated Aminodienes Catalyzed by Organolanthanoids. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
An exclusion map for Von Recklinghausen neurofibromatosis. (1987)

By using all the genetic linkage data available between Von Recklinghausen neurofibromatosis (VRNF) and various loci on the autosomes, a graphical display of all the non-excluded areas is presented. The probability of VRNF being on any of the 22 autosomes is also shown. The exclusion map presented is for 90 markers that have been localised relatively accurately. Data are also presented for a further 24 markers that have not yet been adequately localised. This exclusion map shows that most of the genome has been excluded as a likely location of any locus responsible for this disorder in the majority of families. Chromosomes 5, 10, 17, and 18 remain largely unexcluded. Concentration on these parts of the genome should help in the identification of the site of the VRNF gene.
Chemo‐Enzymatic Total Synthesis of Some Conduritols, Carbasugars and (+)‐Fortamine (1997)

This chapter contains sections titled: Introduction Results Substrates and Enantioselective Enzymatic Hydrolysis The Synthesis of Some Advanced Intermediates Synthesis of Conduritols Synthesis of Carba-Sugars Synthesis of (+)-Fortamine (78) References
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8 (2003)

The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of TT1542 are present in a wide range of organisms. The TT1542 homologs in eukaryotes, PIG-L in mammals, and GPI12 in yeast and protozoa, have N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI) de-N-acetylase activity. Although most of the homologs in prokaryotes are hypothetical and have no known function, Rv1082 and Rv1170 from Mycobacterium tuberculosis are enzymes involved in the mycothiol detoxification pathway. Here we report the crystal structure of the TT1542 protein at 2.0 A resolution, which represents the first structure for this superfamily of proteins. The structure of the TT1542 monomer consists of a twisted beta-sheet composed of six parallel beta-strands and one antiparallel beta-strand (with the strand order 3-2-1-4-5-7-6) sandwiched between six alpha-helices. The N-terminal five beta-strands and four alpha-helices form an incomplete Rossmann fold-like structure. The structure shares some similarity to the sugar-processing enzymes with Rossmann fold-like domains, especially those of the GPGTF (glycogen phosphorylase/glycosyl transferase) superfamily, and also to the NAD(P)-binding Rossmann fold domains. TT1542 is a homohexamer in the crystal and in solution, the six monomers forming a cylindrical structure. Putative active sites are suggested by the structure and conserved amino acid residues.
Electromagnetic Properties of Checkerboard-like Metallic Structures at Terahertz Frequencies (2017)

京都大学
NADH‐Dependent Halogenases Are More Likely To Be Involved in Halometaolite Biosynthesis Than Haloperoxidases (1997)

NADH instead of hydroged peroxide is required by two newly identified, substrate-specific and regioselective halogenases. Both were isolated from a pyrrolnitrin-producing Pseudomonas fluorescens strain. One enzyme catalyzes the chlorination of L-tryptophan to 7-chloro-L-tryptophan (1).
Non-Premixed Burner-Attached Jet Flames in Crossflow Pulsed at Resonance Frequency (2017)

The flame behavior, flow patterns, and thermochemical structures of a combusting propane gas jet in crossflow excited acoustically at resonance frequency were studied in a wind tunnel. The jet and crossflow Reynolds numbers were 1530 and 1399, respectively. The jet-to-crossflow momentum flux ratio was 0.192. The flame behavior was found to be closely related to the shear-layer vortical flow structures in the near-tube region. Six characteristic flame modes were observed in the domain of jet pulsation intensity . In flame modes 1 and 2 , the shear-layer vortices were dominant. In flame modes 3–6 , the flames were dominated by a puffing bent jet. Vortical structures increased in size with increasing . Temperature and combustion product measurements showed significant improvements in mixing and combustion, as well as a reduction of combustion-induced pollutants at the near-tube region of the flame. However, pulsing the jet flame in crossflow at pulsation intensities greater than 0.9 led to a significant increase in the maximum values of carbon monoxide and nitric oxide concentrations at the middle- to far-tube flame regions. Therefore, strongly pulsing a jet flame in crossflow may not necessarily lead to an improved combustion.
ARBlocks: A projective augmented reality platform for educational activities (2012)

This demonstration will allow visitors to use different applications builded for the ARBlocks, a dynamic blocks platform based on projective augmented reality and tangible user interfaces aiming early childhood educational activities. Those applications, along with the platform itself, were designed to be useful tools for educators to teach general subjects for children, such as mathematical and language skills, as well as develop important abilities, like motor coordination and collaboration.
Control of surface oxide formation in plasma-enhanced quasiatomic layer etching of tantalum nitride (2020)

Surface oxide formation inhibiting the etch of a tantalum nitride (TaN) film was controlled through step pressure modulation and H2 addition in a Cl2/Ar based plasma-assisted cyclic etch process. Sources contributing to the oxidation of the film included the mask materials, specifically the silicon-containing antireflective coating, as measured by optical emission spectroscopy. Surface analysis of etched films by secondary ion mass spectroscopy showed the presence of a modified surface layer ∼2 nm thick with localized oxygen concentrations 0.02 and 0.003 that of the control sample (without and with H2 addition, respectively). Reduced Ta–O bonding observed via x-ray photoelectron spectroscopy as a result of H2 addition was found to enhance etch rate uniformity of both blanket and patterned films. Minimization of redeposited oxidized TaN on the mask sidewalls of patterned samples was achieved using this etch process and by controlling the lithographic stack composition.
Network Architectures for 4G: Cost Considerations [Wireless Broadband Access] (2007)

As 3G wireless networks evolve toward 4G, various wireless network technology organizations are considering a major redesign of the network architecture. We present a perspective on such a redesign motivated primarily by cost considerations. We examine some tenets for the design of 4G wireless network architectures that are aimed at improving costs in various aspects of the network. One tenet is the maximization of economies of scale by partitioning the functionality among network elements in a way that maximizes the potential domain of applicability of the network elements. Another is reduction of the number of distinct types of network elements needed by flattening the levels of hierarchy in the execution of various functions. We explain our reasoning by illustrating a way of redesigning the current 3GPP network architecture based on these tenets.
Dynamic modeling of a single-switch power factor correction circuit (2002)

A PWM switch large signal model for a flyback converter having arbitrary transformer polarity is presented. This model will preserve the input-output property regardless of the transformer polarity. A small signal model for a novel one-stage, switched-mode power factor correction (PFC) converter is also presented in this paper. The model is obtained by applying the small signal perturbation technique to the circuit equations derived from the state-space averaging method. It is shown that this converter exhibits the characteristics of a second order low-pass system for the output-to-input transfer function, and that of a combined second order low-pass and band-pass system for the output-to-control transfer function. The validity of the derived mathematical model was verified by the given experimental results.
Wireless Remote Monitoring of Toxic Gases in Shipbuilding (2014)

Large-scale wireless sensor networks have not achieved market impact, so far. Nevertheless, this technology may be applied successfully to small-scale niche markets. Shipyards are hazardous working environments with many potential risks to worker safety. Toxic gases generated in soldering processes in enclosed spaces (e.g., cargo holds) are one such risk. The dynamic environment of a ship under construction makes it very difficult to plan gas detection fixed infrastructures connected to external monitoring stations via wired links. While portable devices with gas level indicators exist, they require workers to monitor measurements, often in situations where they are focused on other tasks for relatively long periods. In this work, we present a wireless multihop remote gas monitoring system for shipyard environments that has been tested in a real ship under construction. Using this system, we validate IEEE 802.15.4/Zigbee wireless networks as a suitable technology to connect gas detectors to control stations outside the ships. These networks have the added benefit that they reconfigure themselves dynamically in case of network failure or redeployment, for example when a relay is moved to a new location. Performance measurements include round trip time (which determines the alert response time for safety teams) and link quality indicator and packet error rate (which determine communication robustness).
High efficiency small molecule tandem photovoltaic devices (2023)

A high efficiency small molecule tandem solar cell is disclosed. The tandem cell may include a first subcell comprising a first photoactive region and a second subcell comprising a second photoactive region. The first and second photoactive regions are designed to minimize spectral overlap and maximize photocurrent. The device may further include an interconnecting layer, disposed between the first subcell and the second subcell, that is at least substantially transparent.
Model-based control of a high-temperature crystal growth process (2008)

This paper describes a modeling and control approach for the thermal aspects of a high-temperature semiconductor crystal growth process. From a thermal perspective, each crystal growth cycle is composed of three distinct phases, heat up, growth, and cool down, each with specific control challenges and objectives. This paper focuses on the heat up and growth phases. A simulation model is first developed based on the induction furnace geometry and known material properties. This model is calibrated using the experimental process data by minimizing the weighted error between the predicted and actual temperature measurements. The two critical temperatures for the process are the temperature of the source material and the temperature of the crystal seed. For the heat up phase, the input profile is generated to rapidly ramp up the source and crystal temperature while avoiding damaging temperature spikes. In the crystal growth phase, the objective is to maintain the source temperature above sublimation while keeping the crystal temperature sufficiently low to allow condensation. These temperatures cannot be directly measured. Instead, an observer-based controller achieves the temperature control objective. Simulation results with FEM-in-the-loop validation are presented.
Optically-athermalized construction optical design for the IMACS short camera (2003)

The optical performance of a large, optically fast, all-refracting spectrograph camera is extremely sensitive to potential temperature changes which might occur during an extended signle observation, over the duration of an observing run, and/or on seasonal time scales. A small temprature change, even at the level of a few degrees C, will lead to changs in the rerfractive indices of the glasses and the coupling medium, changes in the lens-element geometries and in the dimensions of the lens cell. These effects combine in a design-specific manner to cause potential changes of focus and magnification within the camera as well as inherent loss of image quality. We have used an optical design technique originally developed for the Smithsonian Astrophysical Observatory's BINOSPEC instrument in order to produce a construction optical design for the Carnegie IMACS Short camera. This design combines the above-mentioned temperature-dependent parameter variations in such a way that their net effect upon focus and magnification is passively reduced to negligible residuals, without the use of high-expansion plastics, "negative-c.t.e." mechanisms or active control within the lens cell. Simultaneously, the design is optimized for best inherent image quality at any temperature within the designated operating range. The optically-athermalized IMACS Short camera is under construction. We present its quantitative optical design together with our assessment of its expected performance over a (T = -4.0 to +20.0) C temperature range.
Topology Optimization for Photonic Crystal Waveguide Intersection with Wide and Flat Bandwidths in Ultra-Fast All-Optical Switch (PC-SMZ) (2006)

Numerical and experimental studies on the photonic crystal waveguide intersection based on the topology optimization design method are reported and the effectiveness is shown by achieving high transmission spectra with low crosstalk for the straightforward beam-propagation line.
Emergence and evolution of TP53 mutations are key features of disease progression in myelodysplastic patients with lower-risk del(5q) treated with lenalidomide (2017)

et la diffusion de documents scientifiques de niveau recherche, publis ou non, manant des tablissements d'enseignement et de recherche franais ou trangers, des laboratoires publics ou privs.
Language Model is all You Need: Natural Language Understanding as Question Answering (2021)

Different flavors of transfer learning have shown tremendous impact in advancing research and applications of machine learning. In this work we study the use of a certain family of transfer learning, where the target domain is mapped to the source domain. Specifically we map Natural Language Understanding (NLU) problems to Question Answering (QA) problems and we show that in low data regimes this approach offers significant improvements compared to other approaches to NLU. Moreover, we show that these gains could be increased through sequential transfer learning across NLU problems from different domains. We show that our approach could reduce the amount of required data for the same performance by up to a factor of 10.
Interactions of urate transporter URAT1 in human kidney with uricosuric drugs (2010)

Comparing these IC(50) values with intratubular concentrations of unbound drugs in humans, it is thought that URAT1 is a target molecule of uricosuric drugs, including 6-hydroxybenzbromarone, probenecid, indomethacin and salicylate, to inhibit urate reabsorption in vivo. In addition, a cell line that stably expressing URAT1 could be a useful tool for the development of uricosuric drugs.
Machine learning algorithm for autonomous control of walking robot (2018)

This work presents our development of autonomous walking robot control using machine learning algorithm. We have investigated sensor driven walking robot movement to develop supervised learning based control algorithm using neural network methods. We used robots hardware data such as pressure sensor data for accurate neural network (NN) classification. The analyzed result shows that ~25-30 numbers of hidden neurons will perform the best result in terms of mean square error (mse), error-gradient, learning time and regression for small scale data analysis. The analyzed results are useful for next generation FPGA based artificial intelligence (AI) chip development for robot movement control.
Transgenic mice expressing human Bcl-2 in their neurons are resistant to 6-hydroxydopamine and 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine neurotoxicity (1998)

The protooncogene bcl-2 inhibits neuronal apoptosis during normal brain development as well as that induced by cytotoxic drugs or growth factor deprivation. We have previously demonstrated that neurons of mice deficient in Bcl-2 are more susceptible to neurotoxins and that the dopamine (DA) level in the striatum after systemic 1-methyl-4-phenyl-1,2,3,6 tetrahydropyridine (MPTP) administration was significantly lower than in wild-type mice. In the present study we have used transgenic mice overexpressing human Bcl-2 under the control of neuron-specific enolase promoter (NSE-hbcl-2) to test the effects of the neurotoxins 6-hydroxydopamine (6-OHDA) and MPTP on neuronal survival in these mice. Primary cultures of neocortical neurons from normal and transgenic mice were exposed to these dopaminergic neurotoxins. Addition of 6-OHDA resulted in cell death of essentially all neurons from normal mice. In contrast, in cultures generated from heterozygous NSE-hbcl-2 transgenic mice, only 69% of the cells died while those generated from homozygous transgenic mice were highly resistant and exhibited only 34% cell death. A similar effect was observed with neurons treated with MPP+. Moreover, while the striatal dopamine level after MPTP injections was reduced by 32% in the wild type, the concentration remained unchanged in the NSE-hbcl-2 heterozygous mice. In contrast levels of glutathione-related enzymes were unchanged. In conclusion, overexpression of Bcl-2 in the neurons provided protection, in a dose-dependent manner, against neurotoxins known to selectively damage dopaminergic neurons. This study provides ideas for inhibition of neuronal cell death in neurodegenerative diseases and for the development of efficient neuroprotective gene therapy.
Supplementary Figures from Discovery of a Novel ERK Inhibitor with Activity in Models of Acquired Resistance to BRAF and MEK Inhibitors (2023)

&lt;p&gt;Supplementary Figures - PDF file 1385K, File contains Supplementary figures of resistant cell lines, proliferation assay of a panel of cell lines, TdF binding assay transcriptional out and kinome selectivity&lt;/p&gt;
The Initial Clinical Presentation of Spinocerebellar Ataxias Type 1, 2, 3, and 6 (P6.393) (2016)

Objective: To characterize the initial clinical presentation of spinocerebellar ataxias (SCA) type 1, 2, 3, and 6. Background: The SCAs are a group of genetically and clinically diverse neurodegenerative diseases and the understanding of initial clinical presentation of each SCA type will help pinpoint the clinical diagnosis. Methods: The Clinical Research Consortium for Spinocerebellar Ataxias (CRC-SCA) enrolled 317 participants with SCA 1, 2, 3 and 6 from 12 medical centers in the United States. The initial presentation to ataxia specialist was recorded, including age of onset of any gait, speech, vision, and hand abnormalities. Since the majority of patients had gait abnormality as the first symptom, we divided SCA patients into two groups: gait onset group or non-gait onset group. We compared the number of pathological CAG repeats and the age of disease onset between the gait onset group and the non-gait onset group using t-test or the Wilcoxon Mann-Whitney test. Results: The majority of SCA patients had gait problems initially and the percentage of these patients was similar across different types of SCAs (92.3[percnt] in SCA1, 87.0[percnt] in SCA2, 87.5[percnt] in SCA3, and 83.8[percnt] in SCA6, p= 0.59). The pathological CAG repeat expansions were similar between gait onset group and non-gait onset group in all four types of SCA patients. In addition, the disease onset for non-gait group in SCA2 patients was 9 years earlier than their counterpart (non-gait onset group 28.2 ± 14.8 years old vs. gait onset 37.2 ± 11.4 years old, p= 0.039). We did not observe any differences in disease onset between gait onset group and non-gait onset group in SCA1, 3, and 6. Conclusions: Gait abnormality is the most common initial presentation of SCAs. Interestingly, SCA2 patients with non-gait onset tend to have a younger disease onset, which might represent a subtype of SCA2.
Role of the autonomic nervous system in the genesis of first and second degree atrio-ventricular nodal block (1986)

Thirty-four patients with a prolonged A-H interval (group I) and 26 with A-V nodal Wenckebach block (group II) were studied in the basal state and after autonomic blockade (propranolol 0.2 mg kg-1 and atropine 0.04 mg kg-1 in order to assess the role of autonomic system in A-V nodal conduction disturbances. In group I, the A-H intervals did not change significantly after autonomic blockade, whereas pacing cycle length for Wenckebach block, effective and functional refractory periods of the A-V node decreased significantly (P less than 0.05). In the 22 patients with organic heart disease these variables did not change significantly after autonomic blockade, whereas in the 12 without underlying heart disease, they decreased in all cases (P less than 0.001). In the former, the variables of intrinsic A-V nodal conduction were normal in only 9% of patients, whereas in the latter they were normal in 66%. Also in group II, the intrinsic A-H intervals were normal in only 6% of patients with cardiac disease but were normal in 63% without underlying heart disease. These data suggest that in the patients with first and second degree A-V nodal block and organic heart disease, the conduction disturbance is predominantly related to intrinsic involvement of A-V node, whereas in the subjects without underlying heart disease the A-V nodal blocks appear mainly related to autonomic alterations.
Characterization of MHC class I restricted cytotoxic T cell responses to tax in HTLV-1 infected patients with neurologic disease. (1993)

To understand the nature of the cytotoxic T cell response generated in human T lymphotropic virus type 1 (HTLV-1)-infected patients with HTLV-1-associated myelopathy/tropical spastic paraparesis, we cloned CTL from the peripheral blood and cerebrospinal fluid from patients with neurologic diseases and demonstrated the presence of HLA-A2, A3, and B14 restricted responses to the HTLV-1 p40x (tax) protein. We identified the minimal amino acid residues within the epitopes required for binding and recognition by HLA-A2- and B14-restricted CTL, identified the critical residues within the peptide sequence defining the HLA-A2-restricted response, and demonstrated that CTL can lyse T cells infected with HTLV-1. This study shows that the CTL response to HTLV-1 tax in patients with neurologic diseases is heterogenous in nature and is not confined to patients of a single HLA haplotype or to a specific region of the tax protein.