gebhart/patrepeval huggingface dataset:
A Firefly Bioluminescence ATP Assay Method for Rapid Detection and Enumeration of Brewery Microorganisms (1976)

A rapid, sensitive firefly bioluminescence ATP assay using a liquid scintillation counter for measurement of assay light output is described. The use of partially purified luciferase and synthetic D-luciferin in this assay permits the detection of as little as 10−16 moles ATP and as few as 10 yeast cells. The assay light output is directly proportional to the quantity of ATP from at least 10 to 104 fmol and is on scale throughout this range. The method developed for detection and enumeration of viable microorganisms, which requires only a few minutes per sample, involves extraction of the cellular ATP with DMSO at room temperature and estimation of the ATP by the bioluminescence assay—for dilute suspensions, prior concentration and isolation of the cells by membrane filtration is necessary. The ATP contents of a selection of yeast and bacteria determined using this technique are reported. A linear relation between quantity of ATP and number of yeast cells is demonstrated, and the changes in intracellular yeast ATP pools during fermentation of wort by ale and lager yeast are presented. A number of other possible applications of this ATP assay in brewing research, development, and microbiological quality control are evaluated and/or discussed.
Atom images and diffraction patterns of high Tc superconductors photographed by Ca-L2,3 shell loss electrons (2022)

Using Ca L2,3 (350 eV, 346 eV) shell loss electrons, images and diffraction patterns of high Tc superconductors containing single, double and triple Ca atomic columns were recorded with 6eV energy window using 200 kV field emission electrons and drift free goniometer. The images which were recorded with 60 seconds exposures had heavy quantum noise. Using image processing in real space and Fourier space, images of Ca-atoms were revealed. Characteristics of the nature of electron diffraction patterns are discussed.
A Strategy for Sample Retrieval and Possible Onboard Biosafety Controls: Perspectives (2015)

会議情報: 国際アストロバイオロジーワークショップ2013（第6回日本アストロバイオロジーネットワーク年次研究会）（2013年11月28日-30日. 宇宙航空研究開発機構宇宙科学研究所（JAXA)（ISAS)）, 相模原市, 神奈川県
Data-driven Improved Sampling in PET (2017)

Positron Emission Tomography (PET) scanners are usually designed with the goal to obtain the best compromise between sensitivity, resolution, field-of-view size, and cost. Therefore, it is difficult to improve the resolution of a PET scanner with hardware modifications, without affecting some of the other important parameters. Iterative image reconstruction methods such as the ordered subsets expectation maximization (OSEM) algorithm are able to obtain some resolution recovery by using a realistic system response matrix that includes all the relevant physical effects. Nevertheless, this resolution recovery is often limited by reduced sampling in the projection space, determined by the geometry of the detector. The goal of this work is to improve the resolution beyond the detector size limit by increasing the sampling with data-driven interpolated data. A maximum-likelihood estimation of the counts in each virtual sub-line-of-response (subLOR) is obtained after a complete image reconstruction, conserving the statistics of the initial data set. The new estimation is used for the next complete reconstruction. The method typically requires two or three of these full reconstructions (superiterations). We have evaluated it with simulations and real acquisitions for the Argus and Super Argus preclinical PET scanners manufactured by SMI, considering different types of increased sampling. Quantitative measurements of recovery and resolution evolution against noise per iteration for the standard OSEM and successive superiterations show promising results. The procedure is able to reduce significantly the impact of depth-of-interaction in large crystals, and to improve the spatial resolution. The proposed method is quite general and it can be applied to other scanners and configurations.
Modeling, Simulation and Monitoring of Electrical Contacts Temperature in Railway Electric Traction (2021)

The paper presents a mathematical modeling approach to determine the permanent regime temperature of an electric contact found in the supply system of the railway electric traction. Mathematical modeling is a basic procedure in the preliminary determination of parameters of interest in various fields of scientific analysis. The numerical modeling method used for determining the electric contact temperature represents the base for developing a finite-element thermal model. The simulation of the electric contact was verified by an experimental infrared investigation of an electric contact realized on a realistic laboratory setup. The results interpretation reveals a good synchronization between the calculated, simulated and measured temperatures.
Spatial perception in binaural reproduction with sparse head-related transfer function measurement grids (2017)

Growing interest in virtual reality has led to greater demand for immersive virtual audio systems. High fidelity spatial audio requires individualized head related transfer functions (HRTFs). Individualized HRTFs are, however, typically unavailable as they require specialized equipment and a large number of measurements. This motivates the development of a simpler more accessible HRTF estimation process. Previous work has demonstrated that spherical-harmonics (SH) can be used to reconstruct the HRTF from a smaller number of sample points, but this method has two known types of error: spatial aliasing and truncation error. Aliasing refer to loss of ability to represent high frequencies. Truncation error refer to the fact the SH representation will be order-limited which further limits spatial resolution. In this paper, the effect of sparse measurement grids on the reproduced binaural signal is studied by analyzing both types of errors. The expected effect of these errors on the perceived location, externalization and source width, is studied using a theoretical model and an experimental investigation. Preliminary results indicate relatively large effects of SH order on sound localization and smaller effects due to aliasing errors.
Dynamic performance and control of a static VAr generator using cascade multilevel inverters (2002)

A cascade multilevel inverter is proposed for static VAr compensation/generation applications. The new cascade M-level inverter consists of (M-1)/2 single-phase full bridges in which each bridge has its own separate DC source. This inverter can generate an almost sinusoidal waveform voltage with only one time switching per cycle. It can eliminate the need for transformers in multipulse inverters. A prototype static VAr generator (SVG) system using an 11-level cascade inverter (21-level line-to-line voltage waveform) has been built. The output voltage waveform is equivalent to that of a 60-pulse inverter. This paper focuses on the dynamic performance of the cascade inverter based SVG system. Control schemes are proposed to achieve a fast response which is impossible for a conventional static VAr compensator (SVC). Analytical, simulation and experimental results show the superiority of the proposed SVG system.
The future of proteasome inhibitors in relapsed/refractory multiple myeloma. (2011)

The ubiquitin-proteasome pathway was first validated as a target for cancer therapy with the demonstration of the activity of the boronic acid proteasome inhibitor (PI) bortezomib (Velcade) against relapsed and relapsed/refractory multiple myeloma. Another generation of PIs is now entering the clinical arena; this includes intravenous agents such as carfilzomib, CEP-18770, and marizomib, and oral drugs such as MLN9708 and ONX 0912. These novel agents will likely first be used for patients with disease that has either relapsed or been refractory to prior therapy (including bortezomib-based regimens) because of their ability to overcome drug resistance, or will be used in patients who are intolerant of, or are not candidates for bortezomib. Preclinical studies also suggest that PIs may act synergistically with other conventional and novel agents, or even with one another in rationally designed combination regimens. In addition, other inhibitors that selectively target only the immunoproteasome and not the constitutive proteasome, as well as agents that bind to noncatalytic proteasome subunits, are emerging as potential drug candidates. Taken together, it seems likely that we have only begun to appreciate the full potential of inhibition of the proteasome. This article extrapolates our current knowledge into an algorithm for the future use of these inhibitors against multiple myeloma.
Regulation of glycosylphosphatidylinositol-anchored proteins and GPI-phospholipase D in a c-Myc transgenic mouse model of hepatocellular carcinoma and human HCC (2016)

Abstract Recent research implicated glycosylphosphatidylinositol-anchored proteins (GPI-AP) and GPI-specific phospholipase D (GPI-PLD) in the pathogenesis of fatty liver disease and hepatocellular carcinoma (HCC). Given that c-Myc is frequently amplified in HCC, we investigated their regulation in a c-Myc transgenic disease model of liver cancer and HCC patient samples. Whole genome scans defined 54 significantly regulated genes coding for GPI-AP of which 29 and 14 were repressed in expression in transgenic tumors and steatotic human hepatocyte cultures, respectively, to influence lipid-mediated signal transduction, extracellular matrix and immunity pathways. Analysis of gene specific promoter revealed &gt;95% to carry c-Myc binding sites thus establishing a link between c-Myc activity and transcriptional response. Alike, serum GPI-PLD activity was increased 4-fold in transgenic mice; however its tissue activity was reduced by 70%. The associated repression of the serine/threonine phosphatase 2A (PP2A), i.e. a key player of c-Myc proteolysis, indicates co-ordinate responses aimed at impairing tissue GPI-PLD anti-proliferative activities. Translational research identified &gt;4-fold increased GPI-PLD serum protein expression though enzyme activities were repressed by 60% in NASH and HCC patients. Taken collectively, c-Myc influences GPI-AP signaling transcriptionally and posttranslational and represses GPI-AP anti-proliferative signaling in tumors. The findings broaden the perspective of molecular targeted therapies and disease monitoring.
Selection for Delayed Intravenous Alteplase Treatment Based on a Prognostic Score (2013)

Selection of patients between 4·5 and 6 h based on simple clinical measures failed to deliver a population in whom the alteplase effect would be safe and effective.
Distributed multirobot localization (2002)

In this paper, we present a new approach to the problem of simultaneously localizing a group of mobile robots capable of sensing one another. Each of the robots collects sensor data regarding its own motion and shares this information with the rest of the team during the update cycles. A single estimator, in the form of a Kalman filter, processes the available positioning information from all the members of the team and produces a pose estimate for every one of them. The equations for this centralized estimator can be written in a decentralized form, therefore allowing this single Kalman filter to be decomposed into a number of smaller communicating filters. Each of these filters processes the sensor data collected by its host robot. Exchange of information between the individual filters is necessary only when two robots detect each other and measure their relative pose. The resulting decentralized estimation schema, which we call collective localization, constitutes a unique means for fusing measurements collected from a variety of sensors with minimal communication and processing requirements. The distributed localization algorithm is applied to a group of three robots and the improvement in localization accuracy is presented. Finally, a comparison to the equivalent decentralized information filter is provided.
Emerging GII.4 norovirus variants affect children with diarrhea in Palermo, Italy in 2006 (2008)

Although the genetic/antigenic heterogeneity of human noroviruses (NoVs) is impressive, a few genogroup II strains of genotype 4 (GII.4) are dominant worldwide. GII.4 NoVs evolve rapidly and in the last 15 years six epidemic variants have been identified. In 2005-2006, surveillance of sporadic viral gastroenteritis in children in Palermo, Italy, resulted in the detection of NoV strains in 20.9% of the patients admitted to hospital. By restriction fragment length polymorphism (RFLP) and sequence analysis of region A in the RNA-dependent RNA-polymerase (RdRp) gene, 59 NoV strains were successfully characterized. Eighty-one percent of the strains were characterized as GII.4, 14% as GIIb/Hilversum and 5% as GI.1. Phylogenetic analysis of region A and of the ORF1/ORF2 overlapping region of the GII.4 strains recovered in Palermo in the years 2002-2006 revealed the sequential emergence of four variants, GII.4 2002, 2004, 2006a, and 2006b. The variant GII.4 2006a was detected in June and July, 2006, while the variant 2006b first appeared in August, 2006, becoming predominant thereafter. Based on these findings, the dynamics of replacement and circulation of the GII.4 NoV variants in Italy in 2005-2006 appear to have matched the temporal pattern observed in Europe during the same period.
Is iterative reconstruction an alternative to filtered backprojection in routine processing of dopamine transporter SPECT studies? (2005)

Iterative reconstruction of (123)I-FP-CIT SPECT studies for the assessment of DAT is feasible in routine clinical practice. A close correlation between FBP and OSEM data suggested that the latter also allow reliable quantification of DAT binding. Because of a better separation between the caudate and the putamen in the visual evaluation, as suggested by phantom and patient studies, OSEM may even be considered the preferable approach.
Illustration of the Stages of Idiopathic Macular Holes by Laser Biomicroscopy (1996)

Background: The determination of the developmental stage of macular holes is difficult to assess clinically. This may be the reason for the conflicting reports on the risk of vision loss in patients with macular holes and on the value of prophylactic surgery. We have developed a new method, laser biomicroscopy, which provides visualization and photographic record of vitreoretinal structures at the macula. Objective: To test the applicability of this method to the identification of macular holes stages. Methods: Laser biomicroscopy and slit-lamp biomicroscopy were used to examine 18 patients with macular holes, identify the lesions, and classify them according to the various stages of development of idiopathic macular holes as proposed by Gass. Results: Reflections considered to originate from the hyaloid membrane were observed more frequently by laser biomicroscopy than by conventional slit-lamp biomicroscopy. Two fellow eyes were diagnosed by laser biomicroscopy as having stage 1 lesions while slit-lamp biomicroscopy failed to yield a clear diagnosis. In four eyes with stage 3 holes the vitreoretinal separation was apparent only on laser biomicroscopy. Four cases were selected to illustrate the laser biomicroscopic findings in the different stages of macular hole development. Conclusions: The ease of visualization of the macular lesions with laser biomicroscopy may facilitate the evaluation of the early stages of macular holes and reduce the incidence of misdiagnosis. Furthermore, photographs obtained by laser biomicroscopy may be a useful tool in studies of early stages of macular holes.
Electrolyte engineering for effective seawater splitting based on manganese iron chromium layered triple hydroxides as novel bifunctional electrocatalysts (2023)

The use of anionic inhibitor, especially carbonate, provide a much-needed anionic protective layer at anode surface, selectively restricting chlorides but allowing hydroxides thereby favouring OER over CER during direct seawater electrolysis.
Comprehensive, open‐source resource usage measurement and analysis for HPC systems (2014)

SUMMARY The important role high‐performance computing (HPC) resources play in science and engineering research, coupled with its high cost (capital, power and manpower), short life and oversubscription, requires us to optimize its usage – an outcome that is only possible if adequate analytical data are collected and used to drive systems management at different granularities – job, application, user and system. This paper presents a method for comprehensive job, application and system‐level resource use measurement, and analysis and its implementation. The steps in the method are system‐wide collection of comprehensive resource use and performance statistics at the job and node levels in a uniform format across all resources, mapping and storage of the resultant job‐wise data to a relational database, which enables further implementation and transformation of the data to the formats required by specific statistical and analytical algorithms. Analyses can be carried out at different levels of granularity: job, user, application or system‐wide. Measurements are based on a new lightweight job‐centric measurement tool ‘TACC_Stats’, which gathers a comprehensive set of resource use metrics on all compute nodes and data logged by the system scheduler. The data mapping and analysis tools are an extension of the XDMoD project. The method is illustrated with analyses of resource use for the Texas Advanced Computing Center's Lonestar4, Ranger and Stampede supercomputers and the HPC cluster at the Center for Computational Research. The illustrations are focused on resource use at the system, job and application levels and reveal many interesting insights into system usage patterns and also anomalous behavior due to failure/misuse. The method can be applied to any system that runs the TACC_Stats measurement tool and a tool to extract job execution environment data from the system scheduler. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Unambiguous Analysis of Woman Breast Shape for Plastic Surgery Outcome Evaluation (2006)

This paper reports a multidisciplinary research between computer science and plastic and reconstructive surgery. In particular, a new method is proposed to unambiguously define a geometric partitioning of a large thoracic area including the breast mound. The new technique uses only well-defined anatomical points, defined and selected by surgeons. A simple sequence of geometric operations is performed to partition the breast surface into four anatomic subunits, according to clinically derived breast meridian and equator lines. Using this breast shape partition, useful measurement can be extrapolated on 3D model data set. Our method has been validated on a number of breast 3D models acquired by means of a commercial scanner on real clinical cases collected by Istituto Nazionale dei Tumori in Milan (INT).
Supplementary Figure S4 from EGFR Inhibition by Cetuximab Modulates Hypoxia and IFN Response Genes in Head and Neck Squamous Cell Carcinoma (2023)

&lt;p&gt;(A-C) Clinical Proteomic Tumor Analysis Consortium head and neck squamous cell carcinoma cohort. The gene expressions were compared for pathways enriched in: (A) Immune vs Hypoxia. Red: enriched in Immune, Blue: enriched in Hypoxia. (B) Immune vs Mixture. Red: enriched in Immune, Blue: enriched in Mixture. (C) Hypoxia vs Mixture. Red: enriched in Hypoxia, Blue: enriched in Mixture. Indicated are the top 10 most differentially expressed pathways in Cancer Hallmarks gene sets. NES: Normalized Enrichment Score&lt;/p&gt;
Identification of metabolic fluxes in hepatic cells from transient 13C‐labeling experiments: Part I. Experimental observations (2007)

An experimental set-up for acquiring metabolite and transient (13)C-labeling data in mammalian cells is presented. An efficient sampling procedure was established for hepatic cells cultured in six-well plates as a monolayer attached to collagen, which allowed simultaneous quenching of metabolism and extraction of the intracellular intermediates of interest. Extracellular concentrations of glucose, amino acids, lactate, pyruvate, and urea were determined by GC-MS procedures and were used for estimation of metabolic uptake and excretion rates. Sensitive LC-MS and GC-MS methods were used to quantify the intracellular intermediates of tricarboxylic acid cycle, glycolysis, and pentose phosphate pathway and for the determination of isotopomer fractions of the respective metabolites. Mass isotopomer fractions were determined in a transient (13)C-labeling experiment using (13)C-labeled glucose as substrate. The absolute amounts of intracellular metabolites were obtained from a non-labeled experiment carried out in exactly the same way as the (13)C-labeling experiment, except that the media contained naturally labeled glucose only. Estimation of intracellular metabolic fluxes from the presented data is addressed in part II of this contribution.
Toxoplasma gondii and Cytomegalovirus: Mixed Infection by a Parasite and a Virus (1968)

Human fibroblasts infected in vitro with cytomegalovirus are relatively resistant to infection by Toxoplasma gondii during the first 4 days of virus infection. After 5 days, however, the cytomegalovirus-infected cells become susceptible to the parasites. The toxoplasmas replicate in paracentral rosettes surrounded by host cell mitochondria. This growth configuration differs from that seen in human fibroblasts infected in vitro with toxoplasma only but resembles the pattern seen in doubly infected cells found in human necropsy tissue.
Electro-optic terahertz transceiver (2000)

The authors demonstrate the operation of an electro-optic terahertz transceiver based on the reciprocal behaviour of optical rectification and an electro-optic effect in a nonlinear optical crystal. With optical excitation and sampling of an ultrafast laser, the electro-optic terahertz transceiver alternately transmits pulsed electromagnetic radiation (optical rectification) and receives the return signal (electro-optic effect) from the same crystal.
First-principles calculations of the vibrational spectra of one-dimensionalC60polymers (2006)

The vibrational properties of several ${\mathrm{C}}_{60}$ dimers belonging to the Stone-Wales rearrangement sequence [described by E. Osawa and K. Honda, Full. Sci. Technol. 4, 939 (1996)], along with a trimer and a tetramer isomer are investigated by tight-binding and density functional calculations. The IR absorption bands found by Onoe, Nakayama, Aono and Hara [Appl. Phys. Lett. 82, 595 (2003)] in the spectra of electron-beam irradiated ${\mathrm{C}}_{60}$ films are explained and attributed mainly to surface vibrations located in the waist region of the considered polymers. The features of the Raman spectra are also discussed and related to experimental spectra of photopolymerized ${\mathrm{C}}_{60}$.