gebhart/patrepeval huggingface dataset:
FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways (2018)

Prediction of functional potential of bacteria can only be ascertained by the accurate annotation of its metabolic pathways. Homology based methods decipher metabolic gene content but ignore the fact that homologs of same protein can function in different pathways. Therefore, mere presence of all constituent genes in an organism is not sufficient to indicate a pathway. Contextual occurrence of genes belonging to a pathway on the bacterial genome can hence be exploited for an accurate estimation of functional potential of a bacterium. In this communication, we present a novel annotation resource to accurately identify pathway presence by using gene context. Our tool FLIM-MAP (Functionally Important Modules in bacterial Metabolic Pathways) predicts biologically relevant functional units called 'GCMs' (Gene Context based Modules) from a given metabolic reaction network. We benchmark the accuracy of our tool on amino acids and carbohydrate metabolism pathways.
A novel caged Cookson‐type reagent toward a practical vitamin D derivatization method for mass spectrometric analyses (2019)

DAP-PA was stable enough for mid- to long-term storage in solution. This advantage shall contribute to the detection and quantification of VD in clinical laboratories, and as such to the broader use of clinical mass spectrometry.
FlexLION: A Reconfigurable All-to-All Optical Interconnect Fabric with Bandwidth Steering (2019)

We demonstrate an all-to-all interconnect fabric with bandwidth steering by wavelength routing, wavelength add/drop filtering and spatial switching. We report a proof-of-concept experiment and demonstrate scalability up to 32 ports with aggregated bandwidth of 51.2 Tb/s under worst-case crosstalk. © 2019 The Author(s)
2‐Mercaptoimidazoles, a New Class of Potent CCR2 Antagonists. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
X'tal cube detector composed of a stack of scintillator plates segmented by laser processing (2012)

We have developed a 3-dimasional (3D) position sensitive radiation detector named "X'tal cube". The X'tal cube is composed of a scintillation crystal block and multipixel photon counters (MPPCs). No reflector is inserted in the crystal block. It is segmented 3 dimensionally into small cubes (3D segmentation) by only optical discontinuity and scintillation light from a segment is detected by all MPPCs which are coupled on all six surfaces of the crystal block. We have already succeeded to make the 3D segmentation inside of a monolithic scintillator block by laser processing technique instead of arranging small cubic scintillator elements into a 3D array as a general way. We obtained the result that utilizing the laser processing technique not only eliminates the difficulty of fabrication with the small scintillator elements but also improves detector performance. As a new trial, we fabricated the crystal block by stacking the scintillator plates which are segmented 2 dimensionally by the laser processing technique (2D segmentation). Plates are also easy to handle compared to the small scintillator elements and for the laser processing, 2D segmentation is much simpler than the 3D segmentation. In this study, we evaluated performance of the X'tal cube with the scintillator plates (Plate-XC) to confirm its feasibility. Performance was measured by irradiating 662 keY gamma-rays. Used scintillator were LYSO plates of 2.0 mm in thick. They had 2D segmentation by laser to make 2.0 mm × 2.0 mm × 2.0 mm segments. Between the plates was chosen as air gap. We coupled a 4 × 4 array of the MPPC to six surfaces of the crystal block. Results showed sufficient performance in crystal identification performance and energy resolution. As a further investigation to understand character of the Plate-XC, scintillation light distribution in the crystal block was also measured. Results indicate that light spread from outer segments is influenced by the segment boundary conditions, air gap or laser processed gap, while the spread from the center segment does not seem to get the influence. In energy performance, around 10% energy resolution was obtained for the outer segments as well as for the center segment.
An Advanced 12Cr Steel Rotor Applicable to Elevated Steam Temperature 593°C (1987)

The upper limit of steam temperature which 12Cr steel rotors can withstand has been considered to be 566°C, but the recent projects on the advanced steam turbine of large capacity demand to raise it. The key factor in upgrading the creep rupture strength of the existing 12Cr steel rotors is to adjust “Equivalent Molybdenum Content” to the optimum, which is 1.5 percent in case no tungsten is contained. A HP-IP rotor, of 11 tons in final machined weight, for EPDC’s Wakamatsu high-temperature turbine to be operated with 593/593°C steam, has been manufactured with the chemical composition of C 0.14, Si 0.08, Mn 0.51, P 0.013, S 0.001, Ni 0.60, Cr 10.23, Mo 1.48, V 0.17, Nb 0.056, N 0.045, and Al 0.002 percent, respectively, through ESR process, Its creep rupture strength after heat treatment is 122 MPa for 593°C and 105 hr. The paper reports the concept of this material and the actual achievement in Wakamatsu rotor forging, referring to the working condition expected on the rotors for 1000 MW-class advanced steam turbine.
Coherent beam combining and optical space-time division multiple access (2010)

We have developed an approach to multiple-access lasercom that adopts the commercial paradigm of sharing the most expensive terminal resources among all users. Space-time division multiple access (STDMA), analogous to an optical space-time switch, hops the transmit beam and receive direction among multiple users and exchanges data while the beam dwells on a user. A key enabler of STDMA is electronic beam steering using liquid crystal optical phased arrays, which provides fast, precise, and agile beam re-pointing. We have built the first optical STDMA terminal, combining beam hopping between remote terminals with coherent combining of both transmit and receive apertures, which is an effective means for increasing antenna gain in systems for which large aperture components are impractical. Coherent beam combining provided the expected increase in antenna gain, and the terminal was found to re-point the beam among users quickly and precisely enough to suffer only minor throughput degradation. Communications test were performed using 10 Gb/s Ethernet for a single-aperture configuration. Performance is presented as a function of angle scan speed and STDMA dwell time per remote terminal. The results suggest that STDMA is a viable technology for supporting multiple-access space-based laser communication.
Improved Accelerometer‐Based Rate Adaptive Pacing by Means of Second‐Generation Signal Processing (1996)

Accelerometer-based rate adaptive pacing has gained widespread clinical use. Limitations exist for the distinction between walking upstairs and downstairs. It was the aim of this study to evaluate a new signal processing algorithm for more physiological rate adaptation. A custom-made pacemaker incorporating an accelerometer was randomly fixed to the left or right chest of 16 pacemaker patients (7 females, age: 64 +/- 11 years), 18 elderly study participants (6 females, age: 62 +/- 11 years), and 15 students (7 females age: 23 +/- 2 years). Study participants walked on level ground, upstairs and downstairs at five different step rates (72, 84, 96, 108, and 120 steps/min) controlled by an acoustic quartz metronome. The accelerometer signals, recorded on a portable data recorder, were analyzed with respect to frequency content, peak average of the mean acceleration, and morphology characteristics of the acceleration signal above and below zero baseline. By calculating the quotient of the signal's duration above and below zero baseline, a reliable discrimination between walking upstairs and downstairs was possible. A correction of the Leaky integrator signal by the new quotient yielded a more adequate rate adaptation to walking up and downstairs to represent at the patient's daily life activities. A more physiological rate adaptation can be achieved when using not only the accelerometer signal's amplitude, but applying additionally the morphology criterium of the acceleration signal's content in the positive and negative direction.
Management of Severe Recurrent Focal Segmental Glomerulosclerosis Through Circulating Soluble Urokinase Receptor Modification (2013)

Circulating soluble urokinase receptor (suPAR) was recently identified as one of the causes responsible for native and recurrent focal segmental glomerulosclerosis (FSGS) through overactivation of podocyte β(3) integrin. Here, we discuss the management of a patient with very high suPAR serum levels and FSGS recurrence. The suPAR reduction using plasmapheresis and immunoadsorption allowed for lowering of suPAR and reduced podocyte β(3) integrin activation and proteinuria. The patient is successfully weaned to bimonthly suPAR removal treatments with improved renal parameters. In summary, we provide an approach for the successful management of severe recurrent FSGS using available therapies with biomarker guidance.
Identification of a Novel Orally Bioavailable Phosphodiesterase 10A (PDE10A) Inhibitor with Efficacy in Animal Models of Schizophrenia. (2014)

We report the continuation of a focused medicinal chemistry program aimed to further optimize a series of imidazo[1,2-a]pyrazines as a novel class of potent and selective phosphodiesterase 10A (PDE10A) inhibitors. In vitro and in vivo pharmacokinetic and pharmacodynamic evaluation allowed the selection of compound 25a for its assessment in preclinical models of psychosis. The evolution of our medicinal chemistry program, structure-activity relationship (SAR) analysis, as well as a detailed pharmacological profile for optimized lead 25a are described.
Total Synthesis of Cryptophycins. Revision of the Structures of Cryptophycins A and C (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal Synthesis of Cryptophycins. Revision of the Structures of Cryptophycins A and CRussell A. Barrow, Thomas Hemscheidt, Jian Liang, Seunguk Paik, Richard E. Moore, and Marcus A. TiusCite this: J. Am. Chem. Soc. 1995, 117, 9, 2479–2490Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ja00114a011https://doi.org/10.1021/ja00114a011research-articleACS PublicationsRequest reuse permissionsArticle Views3859Altmetric-Citations153LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
<title>Computerized lung nodule detection: comparison of performance for low-dose and standard-dose helical CT scans</title> (2001)

The vast amount of image data acquired during a computed tomography (CT) scan makes lung nodule detection a burdensome task. Moreover, the growing acceptance of low-dose CT for lung cancer screening promises to further impact radiologists' workloads. Therefore, we have developed a computerized method to automatically analyze structures within a CT scan and identify those structures that represent lung nodules. Gray-level thresholding is performed to segment the lungs in each section to produce a segmented lung volume, which is then iteratively thresholded. At each iteration, remaining voxels are grouped into contiguous three-dimensional structures. Structures that satisfy a volume criterion then become nodule candidates. The set of nodule candidates is subjected to feature analysis. To distinguish candidates representing nodule and non-nodule structures, a rule-based approach is combined with an automated classifier. This method was applied to 43 standard-dose (diagnostic) CT scans and 13 low-dose CT scans. The method achieved an overall detection sensitivity of 71% with 1.5 false-positive detections per section on the standard-dose database and 71% sensitivity with 1.2 false-positive detections per section on the low-dose database. This automated method demonstrates promising performance in its ability to accurately detect lung nodules in standard-dose and low-dose CT images.
3D multislab, multishot acquisition for fast, whole‐brain MR elastography with high signal‐to‐noise efficiency (2013)

The acquisition presented allows for the capture of whole-brain MRE displacement data in a short scan time, and may be used to generate local mechanical property estimates of neuroanatomical features throughout the brain.
Polyimides containing carbonyl and ether connecting groups (1987)

Abstract Geveral new polyimides were prepared from the reaction of four aromatic dianhydrides with four new diamines containing carbonyl and ether connecting groups between the aromatic rings. The diamines were prepared from the reaction of 4‐aminophenol with activated aromatic difluoro compounds in the presence of potassium carbonate. Several of these polyimides were shown to be semicrystalline as evidenced by wide angle x‐ray diffraction and differential scanning calorimetry. Glass transition temperatures ranged between 192 and 247°C and crystalline melt temperatures were observed between 350 and 442°C. The polyimide from the reaction of 3,3′,4,4′‐benzophenonetetracarboxylic acid dianhydride and 1,3‐bis(4‐aminophenoxy‐4′‐benzoyl)benzene provided a semicrystalline solvent resistant transparent film with high tensile properties and compression molded compact tension specimens with high fracture toughness.
Divided-Pulse Amplification of Ultrashort Pulses (2006)

We demonstrate an approach to avoid nonlinear effects in the amplification. The initial pulse is divided into a sequence of lower-energy identical pulses. The low-intensity pulses are amplified and recombined to create a final pulse.</b> Article not available.
Fiber-optic current sensor with self-compensation of source wavelength changes (2016)

We demonstrate a method for self-compensation of scale factor changes of an interferometric fiber-optic current sensor caused by source wavelength shifts, e.g., due to changes in source temperature or drive current. An adequately tailored fiber-optic retarder in the optical circuit introduces wavelength-dependent mixing of the orthogonal polarization modes of the sensor. The resulting change in scale factor balances the variation of the Faraday effect with wavelength. The wavelength dependence of the sensor is suppressed by more than an order of magnitude to <0.2% over wavelength spans of at least 10 nm around 1305 nm. The retarder is designed as an athermal device for operation between -40°C and 80°C.
Sequence comparison of porcine respiratory coronavirus isolates reveals heterogeneity in the S, 3, and 3-1 genes (1995)

Four new porcine respiratory coronavirus (PRCV) isolates were genetically characterized. Subgenomic mRNA patterns and the nucleotide sequences of the 5' ends of the S genes, the open reading frame (ORF) 3/3a genes, and the ORF 3-1/3b genes of these PRCV isolates were determined and compared with those of other PRCV and transmissible gastroenteritis virus (TGEV) isolates. The S, ORF 3/3a, and ORF 3-1/3b genes are under intense study because of their possible roles in determining tissue tropism and virulence. Northern (RNA) blot analysis of subgenomic mRNAs revealed that mRNA 2, which encodes for the S gene, of the PRCV isolates migrated faster than the mRNA 2 of TGEV. The PRCV isolates AR310 and LEPP produced eight subgenomic mRNA species, the same number as produced by the virulent Miller strain of TGEV. However, the PRCV isolates IA1894 and ISU-1 produced only seven subgenomic mRNA species. All four of the PRCV isolates were found to have a large in-frame deletion in the 5' end of the S gene; however, the size and location of the deletion varied. Analysis of the ORF 3/3a gene nucleotide sequences from the four PRCV isolates also showed a high degree of variability in this area. The ORF 3 gene of the PRCV isolates AR310 and LEPP was preceded by a CTAAAC leader RNA-binding site, and the ORF 3 gene was predicted to yield a protein of 72 amino acids, the same size as that of the virulent Miller strain of TGEV. The PRCV isolates AR310 and LEPP are the first PRCV isolates found to have an intact ORF 3 gene. The ORF 3a gene of the PRCV isolate IA1894 was preceded by a CTAAAC leader RNA-binding site and was predicted to yield a truncated protein of 54 amino acids due to a 23-nucleotide deletion. The CTAAAC leader RNA-binding site and ATG start codon of ORF 3 gene of the PRCV isolate ISU-1 were removed because of a 168-nucleotide deletion. Analysis of the ORF 3-1/3b gene nucleotide sequences from the four PRCV nucleotides isolates also showed variability.
Specificities of antibodies to acetylcholine receptors in sera from myasthenia gravis patients measured by monoclonal antibodies. (1982)

The pattern of antibody specificities in sera from patients with myasthenia gravis (MG) was determined by the ability of monoclonal antibodies against defined determinants on the acetylcholine receptor molecule to inhibit binding of the serum antibodies to receptor from human muscle. We found that MG patients produce fundamentally the same pattern of specificities as that produced by animals immunized with receptor purified from fish electric organs or mammalian muscle. Most of the antibodies are directed at the "main immunogenic region' which is located on the extracellular surface of the alpha subunit and is distinct from the acetylcholine binding site. Regions on the beta and gamma subunits near the main immunogenic region are also significantly immunogenic. In one patient the proportions of antibodies to various regions are constant over time despite changes in total antibody amount and clinical state. Between patients there is no obvious correlation between antibody specificities and clinical state. These data suggest that the autoimmune response in MG is stimulated by human receptor rather than a crossreacting (e.g., viral) antigen and that in both MG and experimental autoimmune MG the pattern of specificities produced is determined by the inherently immunogenic structural features of the receptor molecule. They also suggest that the wide differences in clinical state sometimes observed between patients with the same total concentration of antireceptor antibody are due primarily to differences in endogenous factors which affect the safety factor for neuromuscular transmission rather than to the presence of especially pathogenic antireceptor specificities.
Amorphous alloys as soft magnetic materials (1975)

The preparation, structure, and mechanical properties of amorphous metallic alloys are briefly reviewed, and the magnetic properties, especially the low‐field properties of engineering interest, are described. The materials reported are ribbons about 1.5 mm by 35 μm in cross‐section, made under the trade name Metglas alloys by Allied Chemical Corp. These alloys have low coercive fields and very square hysteresis loops; the effective magnetization in low fields is greatly increased by the application of a tensile stress. When held under stress, amorphous ribbons have magnetic properties comparable to the best available crystalline materials. Some of the improvement due to stress can be made permanent by annealing under stress. Possible applications of these alloys are discussed.
Efficient navigation using slow feature gradients (2017)

A model of hierarchical Slow Feature Analysis (SFA) enables a mobile robot to learn a spatial representation of its environment directly from images captured during a random walk. After the unsupervised learning phase a subset of the resulting representations are orientation invariant and code for the position of the robot. Hence, they change monotonically over space even though the variation of the sensory signals received from the environment might change drastically e.g. during rotation on the spot. Furthermore, the property of spatial smoothness allows us to infer a navigation direction by taking the difference between the measurement at the current location and a measurement at a target location. In our work we investigated the use of slow feature representations, learned for a specific environment, for the purpose of navigation. We present a straightforward method for navigation using gradient descent on the difference between two points specified in slow feature space. Due to its slowness objective, the resulting slow feature representations implicitly encode information about static obstacles, allowing a mobile robot to efficiently circumnavigate them by simply following the steepest gradient in slow feature space.
Fluorene-based Two-Photon Fluorescent Probes for Specific Biomolecule Labeling and Oligopeptide Conjugation (2008)

Two-photon absorbing amine-reactive fluorenyl-based probes were synthesized for biomolecule labeling and oligopeptide conjugation. Conventional and two-photon fluorescence microscopy imaging of H1299 and HeLa cells, incubated with novel efficient two-photon absorbing fluorescent probes, is demonstrated. © 2008 Optical Society of America.
Development of Pyrene Photosensitizers for Cationic Photopolymerizations (2002)

This article describes the preparation of monomeric and oligomeric derivatives of pyrene and their use as electron-transfer photosensitizers for onium-salt-induced cationic photopolymerizations. The synthetic methods that were employed involved simple, straightforward, and high-yield routes to these derivatives. Using Fourier transform real-time infrared spectroscopy, the photoinduced polymerizations of several model epoxide monomers and a vinyl ether monomer were examined in the presence and absence of the photosensitizers. It was observed that in all cases the pyrene derivatives markedly accelerated the rates of the UV-irradiation-induced photopolymerizations. Use of the pyrene derivatives also provided sensitivity to visible light so that photopolymerizations could be carried out in a short time by exposure to direct sunlight. The pyrene compounds investigated in this study are potentially attractive photosensitizers that may find use in many practical photocuring applications.