gebhart/patrepeval huggingface dataset:
Enzymatic Resolution of 2-Oxazolidinone Esters (1985)

Journal Article Enzymatic Resolution of 2-Oxazolidinone Esters Get access Shigeki Hamaguchi, Shigeki Hamaguchi Biochemical Research Laboratories, Kanegafuchi Chemical Industry Co., Ltd., Takasago, Hyogo 676, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiroshi Yamamura, Hiroshi Yamamura Biochemical Research Laboratories, Kanegafuchi Chemical Industry Co., Ltd., Takasago, Hyogo 676, Japan Search for other works by this author on: Oxford Academic Google Scholar Junzo Hasegawa, Junzo Hasegawa Biochemical Research Laboratories, Kanegafuchi Chemical Industry Co., Ltd., Takasago, Hyogo 676, Japan Search for other works by this author on: Oxford Academic Google Scholar Kiyoshi Watanabe Kiyoshi Watanabe Biochemical Research Laboratories, Kanegafuchi Chemical Industry Co., Ltd., Takasago, Hyogo 676, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 49, Issue 5, 1 May 1985, Pages 1509–1511, https://doi.org/10.1080/00021369.1985.10866929 Published: 01 May 1985 Article history Received: 26 July 1984 Published: 01 May 1985
An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images (2001)

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-A resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.
Compact fiber-based multi-photon endoscope working at 1700 nm (2018)

We present the design, implementation and performance analysis of a compact multi-photon endoscope based on a piezo electric scanning tube. A miniature objective lens with a long working distance and a high numerical aperture (≈ 0.5) is designed to provide a diffraction limited spot size. Furthermore, a 1700 <i>nm</i> wavelength femtosecond fiber laser is used as an excitation source to overcome the scattering of biological tissues and reduce water absorption. Therefore, the novel optical system along with the unique wavelength allows us to increase the imaging depth. We demonstrate that the endoscope is capable of performing third and second harmonic generation (THG/SHG) and three-photon excitation fluorescence (3PEF) imaging over a large field of view (> 400 <i>μm</i>) with high lateral resolution (2.2 <i>μm</i>). The compact and lightweight probe design makes it suitable for minimally-invasive in-vivo imaging as a potential alternative to surgical biopsies.
HAMR Thermal Reliability via Inverse Electromagnetic Design (2014)

Heat-Assisted Magnetic Recording (HAMR) has promise to allow for data writing in hard disks of beyond 1 Tb/in2 areal density, by temporarily heating the area of a single datum to its Curie temperature while simultaneously applying a magnetic field from a conventional electromagnet. However, the metallic optical antenna or near-field transducer (NFT) used to apply the nano-scale heating to the media may self-heat by several hundreds of degrees. With the NFT reaching such extreme temperatures, demonstrations of HAMR technology observe write-head lifetimes that are orders of magnitude less than that required for commercial product. Hence, thermal reliability of the NFT is of upmost importance. In this paper, we first derive fundamental limits on the self-heating of the NFT to drive design choices for low temperature operation. Next, we employ Inverse Electromagnetic Design software, which provides deterministic gradient-based optimization of electromagnetic structures with thousands of degrees of freedom using the adjoint method. The Inverse Design software solves for unintuitive solutions to Maxwells equations, and we present computationally generated structures for HAMR write-heads that offer a 40 percent or 170 C reduction in NFT self-heating compared to typical industry designs.
RhoA/Rho-kinase activation promotes lung fibrosis in an animal model of systemic sclerosis (2016)

Our findings confirm HOCl-induced pulmonary inflammation and fibrosis in mice, and provide further evidence for a key role of RhoA/ROCK pathway in several pathological processes of experimental SSc. Fasudil could be a promising therapeutic approach for the treatment of SSc.
Visual odometry for the Autonomous City Explorer (2009)

The goal of the autonomous city explorer (ACE) is to navigate autonomously, efficiently and safely in an unpredictable and unstructured urban environment. To achieve this aim, an accurate localization is one of the preconditions. Due to the characteristics of our navigation environment, an elaborated visual odometry system is proposed to estimate the current position and orientation of the ACE platform. The existing algorithms of optical flow computation are experimentally evaluated and compared. The method based on pyramidal Lucas-Kanade algorithm with high-speed performance is selected. Based on the optical flow in 2D images, the camera ego-motion is estimated using image Jacobian matrix and least squares method. The kinematic model is set up to map the camera ego-motion to the robot motion. To eliminate systematic errors, a novel system calibration approach is proposed. Finally the odometry system is evaluated in experiments.
Pharmacologic Activation of p53 by Small-Molecule MDM2 Antagonists (2011)

Restoring p53 activity by inhibiting the interaction between p53 and MDM2 represents an attractive approach for cancer therapy. To this end, a number of small-molecule p53-MDM2 binding inhibitors have been developed during the past several years. Nutlin-3 is a potent and selective small-molecule MDM2 antagonist that has shown considerable promise in pre-clinical studies. This review will highlight recent advances in the development of small-molecule MDM2 antagonists as potential cancer therapeutics, with special emphasis on Nutlin-3.
SAT-Based Methods for Sequential Hardware Equivalence Verification without Synchronization (2003)

The BDD- and SAT-based model checking and verification methods normally require an initial state. Here we are concerned with sequential hardware verification, where an initial state must be one of the reset states. In practice, a reset state is not always given by the designer, and computing a reset state of a circuit is a hard problem. In this paper we propose a method allowing usage of SAT-based verification methods without a need for a user-given or a computed initial state. The idea is to employ a binary encoding of 3-valued modeling of circuits, and use the undefined state X as a reset state.
Hair Cortisol Analysis: A Promising Biomarker of HPA Activation in Older Adults: Figure 1. (2015)

Prolonged stress is a potentially harmful and often undetected risk factor for chronic illness in older adults. Cortisol, one indicator of the body's hormonal responses to stress, is regulated by the hypothalamic-pituitary-adrenal (HPA) axis and is commonly measured in saliva, urine, or blood samples. Cortisol possesses a diurnal pattern and thus collection timing is critical. Hair cortisol is a proxy measure to the total retrospective activity of the HPA axis over the preceding months, much like hemoglobin A1c is a proxy measure of glucose control over the past 3 months. The aim of this review is to examine a novel biomarker, hair cortisol, as a practical measure of long-term retrospective cortisol activity associated with chronic stress in older adults. Hair cortisol analysis advances the science of aging by better characterizing chronic stress as a risk factor for chronic illness progression and as a biomarker of the effectiveness of stress reduction interventions.
Demonstration of a Very Inexpensive, Turbidimetric, Real-Time, RT-LAMP Detection Platform Using Shrimp Laem-Singh Virus (LSNV) as a Model (2014)

Rapid and accurate detection of pathogens under field laboratory conditions is necessary for effective control of veterinary pathogens. Here we describe a prototype, portable, pathogen detection device developed for single tube, real-time, reverse transcription, loop-mediated isothermal amplification (RT-LAMP) using Laem-Singh virus (LSNV) as a model. LSNV is an RNA virus and a component cause of growth retardation in black tiger shrimp. We chose its RNA-dependent RNA polymerase (RdRp) gene as the target for our tests. The basis for detection was measurement of turbidity arising from formation of a white, insoluble magnesium pyrophosphate precipitate byproduct upon amplification of the RdRp target sequence from 100 ng template RNA extracted from shrimp. The measurement device consisted of a heating block to maintain constant temperature in the RT-LAMP reaction for 8 Eppindorf sample tubes, a light-emitting diode (LED) light source providing red light emission at 650 nm wavelength to pass through sample tubes, a light dependent resistance (LDR) photo-detector and a software program to report turbidity events and could potentially be marketed for under US$3000. The device was connected to a computer to display real-time results in a variety of formats. The optimized protocol for LSNV detection consisted of incubation of the sample tubes at 65 °C for 1 h during which turbidity was continuously measured, and quantitative results could be obtained by reaction time measurement. The sensitivity of detection was comparable to that of conventional nested RT-PCR and there was no cross reaction with other common shrimp viruses. The device was used for quantitative measurement of relative copy numbers of LSNV RdRp in 8 shrimp tissues and they were found to be highest in the gills followed in order by the lymphoid organ and hemolymph (p ≤ 0.05). This platform can be easily adapted for detection of other pathogens under field laboratory settings.
Formation of ordered assemblies from deposited gold clusters (2002)

A novel technique for producing intense, parallel beams of mass-selected nanocrystals from a magnetron cluster source has been used to study the low-energy impact of size-selected gold nanocrystals, 2.0-8 nm diameter, on 2 nm thick carbon films. The measurements of the sizes using transmission electron microscopy show that it is possible to deposit, intact, nanocrystals with a very narrow size range (ΔD(FWHM)/D = 0.06) as long as the impact energy is below 40 eV. The subsequent surface motion of the nanocrystals after impact (with the substrate) results in cluster-cluster collisions, which for large clusters (>4 nm) produces aggregations but for small clusters (<3.5 nm) results in complete fusion and reformation into larger aggregated clusters with approximate spherical symmetry. However, when the energy is reduced to 10 eV, clusters of a size of around 5 nm form some localized ordered arrays rather than random aggregates. This implies that the clusters forming these arrays can undergo local spatial rearrangement during their formation in order to reduce the total energy. The clear absence of sintering other than that expected from random impact collisions requires either a repulsive cluster-cluster interaction or surface passivation of the particles. These issues are discussed in this article.
Z-contrast-Microscopy and Density-Functional-Theory Determination of the Atomic Structure of the Fe/AlGaAs Interface and its Impact on Spin Transport (2006)

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005
Optimization of casting stoppers (2003)

The development of a new type of stopper rod, Argorod, makes it possible to improve the steel quality during continuous casting. The main results that have been obtained concern the tightness of the joint : the new Argorod system, of second generation, has a better tightness, the assembling operation is simplified and more reliable; the optimization of the system for argon introduction: sized tube, more accurate adjustment of the couple argon flow rate / back pressure ; the accurate control of steel throughput: choice of the nozzle shape factor “material strength / stopper rod weight”: weight saving for the same or for a higher transverse strength.
Quadratically Constrained Attitude Control via Semidefinite Programming (2004)

We consider the attitude control problem augmented with an arbitrary number of nonconvex quadratic constraints. By utilizing the implicit magnitude constraint of the state vector (i.e., quaternion), we are able to reduce this problem to a convex quadratically constrained quadratic program or a semidefinite program. This result leads to an efficient solution strategy for general quadratically constrained attitude control problems. An example demonstrates the proposed methodology.
Two Novel Iron(II) Materials Based on Dianionic N<sub>4</sub>O<sub>2</sub>Schiff Bases:  Structural Properties and Spin-Crossover Characteristics in the Series [Fe(3-X,5-NO<sub>2</sub>-sal-N(1,4,7,10)] (X = H, 3-MeO, 3-EtO) (2005)

Two spin-crossover (SCO) complexes [Fe(II)(3-MeO,5-NO2-sal-N(1,4,7,10)] (1) and [Fe(II)(3-EtO,5-NO2-sal-N(1,4,7,10)] (2) have been prepared and studied (3-MeO,5-NO2-sal-N(1,4,7,10) and 3-EtO,5-NO2-sal-N(1,4,7,10) are deprotonated 2-[12-(hydroxy-3-methoxy-5-nitrophenyl)-2,5,8,11-tetraazadodeca-1,11-dien-1-yl]-2-methoxy-4-nitrophenol and 2-[12-(hydroxy-3-ethoxy-5-nitrophenyl)-2,5,8,11-tetraazadodeca-1,11-dien-1-yl]-2-ethoxy-4-nitrophenol, respectively). The X-ray diffraction analysis of complex 1 (C22H26N6O8Fe) evidenced the same Pbnb orthorhombic system at 160 K (high-spin (HS) state) and 100 K (low-spin (LS) state). At 160 K, a = 8.4810(9) A, b = 14.7704(14) A, c = 18.769(2) A, V = 2351.2(4) A3, and Z = 4. At 100 K, a = 8.5317(8) A, b = 14.4674(15) A, c = 18.814(2) A, and V = 2322.2(4) A3. Complex 2 (C28H38N6O9Fe) crystallizes in the P1 triclinic system. At 160 K (HS state), a = 10.265(4) A, b = 10.861(4) A, c = 14.181(5) A, alpha = 84.18(4) degrees, beta = 70.53(5) degrees, gamma = 88.95(5) degrees, V = 1482.6(10) A3, and Z = 2. The iron(II) coordination sphere is distorted octahedral in 1 and 2 with a cis-alpha arrangement of the N4O2 donor set of the hexadentate ligand. The molecules are connected into 1D infinite chains through hydrogen contacts involving the secondary amine functions and O(nitro) atoms of the ligands in adjacent molecules. Investigation of their magnetic properties and Mossbauer spectra has revealed very different SCO behaviors: complex 1 exhibits a cooperative SCO without residual LS or HS fraction; complex 2 shows a LS <--> HS SCO involving approximately 5% of the Fe(II) ions in the 30-150 K range. The phenomenological cooperative interaction parameter J = 138 K evaluated from the area of the hysteresis loop indicates a cooperative effect weaker in 1 than in [Fe(II)(5NO2-sal-N(1,4,7,10))]. The theoretical approach to the SCO in 2 indicates a HS ground state and a LS first excited level 53 K above: the thermal dependence of the system occurs through population of vibrational states. Comparison of the structural and electronic properties of the ferrous SCO materials with parent N4O2 ligands shows that the properties of SCO are closely related to intermolecular interactions and crystal packing.
Discriminant Analysis Using Multigene Expression Profiles in Classification of Breast Cancer. (2007)

Abstract- Microarrays provide a promising tool for the diagnosis of cancers on a molecular level. However, due to the large dimensions and the intrinsic variations of such data, feature selection that reduces the data to a small number of “informative genes” is important before any discriminant analysis based on such data. Many marginal statistical measures have been applied to gene expression data despite the fact that gene-gene interactions are not negligible. In this paper, we propose a gene selection procedure, the multigene profile association score (MPAS) method, based on backward screenings using multigene association information that captures interactions. As a result, not only genes with marginal significance are detected, but also those contain information on interactions that are only detectable when being evaluated together with other genes.
Efficient and robust approximate nearest neighbor search using Hierarchical Navigable Small World graphs (2016)

We present a new approach for the approximate K-nearest neighbor search based on navigable small world graphs with controllable hierarchy (Hierarchical NSW, HNSW). The proposed solution is fully graph-based, without any need for additional search structures, which are typically used at the coarse search stage of the most proximity graph techniques. Hierarchical NSW incrementally builds a multi-layer structure consisting from hierarchical set of proximity graphs (layers) for nested subsets of the stored elements. The maximum layer in which an element is present is selected randomly with an exponentially decaying probability distribution. This allows producing graphs similar to the previously studied Navigable Small World (NSW) structures while additionally having the links separated by their characteristic distance scales. Starting search from the upper layer together with utilizing the scale separation boosts the performance compared to NSW and allows a logarithmic complexity scaling. Additional employment of a heuristic for selecting proximity graph neighbors significantly increases performance at high recall and in case of highly clustered data. Performance evaluation has demonstrated that the proposed general metric space search index is able to strongly outperform previous opensource state-of-the-art vector-only approaches. Similarity of the algorithm to the skip list structure allows straightforward balanced distributed implementation.
Interferometric polarization mode dispersion measurements with femtosecond sensitivity (1997)

The standard interferometric measurement technique for polarization mode dispersion (PMD) measures the cross correlation of the electromagnetic field at the output of the fiber or optical device under test when a broadband light source is used. The sensitivity (smallest measurable PMD delay) of this technique is limited by the coherence time of the light source. In this contribution, we critically analyze extensions of the interferometric technique to lower values and present a new extension which provides a sensitivity of a few femtoseconds.
Delayed oxidative degradation of polyunsaturated diacyl phospholipids in the presence of plasmalogen phospholipids <i>in vitro</i> (1997)

The oxidative degradation of plasmalogen (alkenylacyl) phospholipids was analysed in the absence and the presence of polyunsaturated ester phospholipids by 1H-NMR and by chemical determination. Brain lysoplasmenylethanolamine (lyso-P-PE), brain P-PE and erythrocyte P-PE, containing an increasing number of intrachain double bonds at sn2, were oxidized with 2,2'-azobis-(2-amidinopropane hydrochloride) (AAPH; 2 or 10 mM) in Triton X-100 micelles (detergent/phospholipid 1:5, mol/mol). The formation of two peroxyl radicals was accompanied by the degradation of approx. one molecule of brain lyso-P-PE. On oxidation of brain P-PE or erythrocyte P-PE (320 nmol) with 2 mM AAPH, the (alpha-vinyl) methine 1H signal of the enol ether decreased more rapidly than the methine proton peak of intrachain double bonds. The rate of enol ether degradation increased in the order: erythrocyte P-PE>brain P-PE>brain lyso-P-PE. The disappearance of the polyunsaturated ester phospholipids 1-palmitoyl-2-arachidonoyl phosphatidylcholine (16:0/20:4-PC) and 1-palmitoyl-2-linoleoyl phosphatidylcholine (16:0/18:2-PC) (100 nmol), as induced by 10 mM AAPH, was nearly completely inhibited by the plasmalogens (25 nmol) in the first 30 and 60 min of incubation respectively, and was delayed at later time points. Plasmalogens and vitamin E (4-25 nmol) mitigated the decreases in 16:0/[3H]20:4-PC (100 nmol) induced by 2 mM AAPH in a similar manner. The initial rate of degradation of intrachain double bonds of 16:0/20:4-PC and 16:0/18:2-PC (320 nmol; 2 mM AAPH) was decreased by 59% and 81% respectively in the presence of 80 nmol of brain lyso-P-PE. In conclusion, plasmalogens markedly delay the oxidative degradation of intrachain double bonds under in vitro conditions. Interactions of enol ether double bonds with initiating peroxyl radicals as well as with products generated by prior oxidation of polyunsaturated fatty acids are proposed to be responsible for this capacity of plasmalogens. Furthermore, the products of enol ether oxidation apparently do not propagate the oxidation of polyunsaturated fatty acids.
Hair Follicle Epidermal Stem Cells Define a Niche for Tactile Sensation (2018)

Abstract The heterogeneity and compartmentalization of stem cells is a common principle in many epithelia, and is known to function in epithelial maintenance, but its other physiological roles remain elusive. Here we show transcriptional and anatomical contributions of compartmentalized epidermal stem cells (EpSCs) in tactile sensory unit formation in the hair follicle (HF). EpSCs in the follicle upper-bulge, where mechanosensory lanceolate complexes (LCs) innervate, express a unique set of extracellular matrix (ECM) and neurogenesis-related genes. These EpSCs deposit an ECM protein EGFL6 into the collar matrix, a novel ECM that tightly ensheathes LCs. EGFL6 is required for the proper patterning, touch responses, and αv integrin-enrichment of LCs. By maintaining a quiescent original EpSC niche, the old bulge, EpSCs provide anatomically stable HF-LC interfaces, irrespective of the stage of follicle regeneration cycle. Thus, compartmentalized EpSCs provide a niche linking the HF and the nervous system throughout the hair cycle.