gebhart/patrepeval huggingface dataset:
Fast Acquisition for Quantitative MRI Maps: Sparse Recovery from Non-Linear Measurements (2016)

This work addresses the problem of estimating proton density and T1 maps from two partially sampled K-space scans such that the total acquisition time remains approximately the same as a single scan. Existing multi-parametric non-linear curve fitting techniques require a large number (8 or more) of echoes to estimate the maps - resulting in prolonged (clinically infeasible) acquisition times. Our simulation results show that our method yields very accurate and robust results from only two partially sampled scans (total scan time being the same as a single echo MRI). We model PD and T1 maps to be sparse in some transform domain. The PD map is recovered via standard Compressed Sensing based recovery technique. Estimating the T1 map requires solving an analysis prior sparse recovery problem from non-linear measurements, since the relationship between T1 values and intensity values / K-space samples is not linear. For the first time in this work, we propose an algorithm for analysis prior sparse recovery for non-linear measurements. We have compared our approach with the only existing technique based on matrix factorization from non-linear measurements, our method yields considerably superior results.
Data Analytics Approach for Understanding the Relationship Between the Thermal and Energy Performance in Ferronickel Large Industrial Rotary Kilns (2021)

Abstract The ferronickel production process closely resembles that of cement and steel. Published studies typically take the developments of the latter and adapt them to ferronickel. However, few open publications allow for a proper understanding of the calcination and reduction of lateritic nickel minerals. This research analyzes the operation of a rotary kiln calciner of 135 m length, a diameter of 6 m, and a mass flow rate between 170 and 180 t/h of partially dry mineral. The calciner uses coal as a reducing agent and natural gas as a thermal energy source. Principal component analysis (PCA) was used in a large industrial dataset to determine the variables with a greater influence on the process performance. Also, k-means clustering is used to locate operation points favorable to calcined mineral production. Results show that the most relevant variables are mineral and gas temperatures and the mass flow rates of air, mineral, natural gas, and coal.
Here Come the States III (2016)

Approximately a century ago, the US Congress was debating product standards for traded commodities. In Historical Review of the US Grades and Standards for Grain, Hoffman and Hill noted that: “Congress finally took action in 1906 … ten more years went by before any legislation adopting uniform standards was passed”. They added that, “In place of research, trade practices and public hearings were used to identify acceptable grades”. Is history repeating itself in the current US debate on climate change? Is it possible that federal law on greenhouse gas (GHG) emissions will be driven by state and local governments as well as private sector activity…
Supplementary Table 3 from N-myc–Mediated Translation Control Is a Therapeutic Vulnerability in Medulloblastoma (2023)

&lt;p&gt;Translation efficiency in Rapalink-1 and Rapamycin treated samples&lt;/p&gt;
IMPROVING SPECTRAL SYNTHESIS PERFORMANCE BY UP TO 5 ORDERS OF MAGNITUDE WITH THE DISCRETE INTEGRAL TRANSFORM APPROACH (2021)

The increasing number and size of large Line-By-Line (LBL)-databases, routinely exceeding hundreds of millions of lines, calls for spectral synthesis algorithms that can process these large number of lines efficiently. In the special case where the lineshape is identical for every line in the database, the spectrum can be rapidly synthesized by the convolution of a stick-spectrum and the constant lineshape. We propose an integral transform that extends this procedure to databases with unique lineshapes for each line, by generalizing the stick spectrum to a 3D “lineshape distribution function”, which is a function of line position and Gaussian- $\\&amp;$ Lorentzian width axes. \n\nA fast discrete version of the integral transform based on the Fast Fourier Transform (FFT) is formulated for which the computation time scales with $c_1N_i + c_2N_\\nu\\log{N_\\nu}$ (where $N_i$ is the number of lines, $N_\\nu$ the number of spectral points, and $c_1$ and $c_2$ are small constants), which is much more efficient than the traditional $N_i \\times N_\\nu$ scaling. Furthermore, since the lineshape calculation is no longer a performance bottleneck, lineshapes such as exact Voigt profiles without cutoff can be computed with arbitrary precision. Our procedure can be implemented in existing spectral codes, providing a new level of accuracy and performance for high temperature, high resolution spectroscopy. \n\nThe procedure was benchmarked against traditional methods within the open source package RADIS: A benchmark HITEMP CO$_2$ spectrum consisting of 1.8M lines and 200k spectral points took 3.1s, an improvement of $\\sim300\\times$. The new procedure has since been implemented as the default synthesis method for RADIS. The method's calculations can be easily divided up and are ideally suited for parallel computation. An experimental GPU procedure, also implemented in RADIS, was used to synthesize a CDSD-4000 CO$_2$ spectrum of 200M lines and 300k spectral points, which took only 150 ms per spectrum regardless of temperature (after an initialization of $\\sim$5 s), or $4\\cdot10^{14}$ lines$\\times$spectral points/s -- an improvement of 5 orders of magnitude compared to the state-of-the-art -- with no appreciable loss in accuracy.
When to initiate hiv therapy: a control theoretic approach (2003)

This paper shows an application of control theory to human immunodeficiency virus (HIV)/AIDS models. Minimum singular value decomposition is applied to HIV/AIDS models to measure the extent to which the different stages in the progression of HIV/AIDS disease are controllable and, consequently, when best to initiate therapy such that the general objectives of therapy are satisfied. Simulations will be used to demonstrate the effect of treatment at various stages. Comparisons will be made between mono-class and combination therapies and between when therapy is initiated at the acute infection, asymptomatic and the advanced stages.
The Handbook of Photonics (2018)

Reflecting changes in the field in the ten years since the publication of the first edition, The Handbook of Photonics, Second Edition explores recent advances that have affected this technology. In this new, updated second edition editor Mool Gupta is joined by John Ballato, strengthening the handbook with their combined knowledge and the continued contributions of world-class researchers.New in the Second Edition:Information on optical fiber technology and the economic impact of photonicsCoverage of emerging technologies in nanotechnologySections on optical amplifiers, and polymeric optical materialsThe book covers photonics materials, devices, and systems, respectively. An introductory chapter, new to this edition, provides an overview of photonics technology, innovation, and economic development. Resting firmly on the foundation set by the first edition, this new edition continues to serve as a source for introductory material and a collection of published data for research and training in this field, making it the reference of first resort.
Dynamic Preamble-Resource Partitioning for Critical MTC in Massive MIMO Systems (2021)

Preamble resources are scarce and precious in random access (RA), which need to be efficiently utilized to support critical machine-type communication (MTC) with stringent access requirements. In this article, we study a grant-free RA scenario for critical MTC in the context of massive multiple-input–multiple-output (MIMO). To enhance the access reliability of delay-sensitive devices within a predefined latency budget, two dynamic preamble-resource partitioning (DPP) schemes are proposed. Particularly, by leveraging massive MIMO, we first analytically investigate the feasibility of DPP in the considered RA scenario and demonstrate its performance superiority to the conventional scheme. Based on the analytical results, we then propose a greedy DPP scheme that performs locally optimal preamble-resource partitioning in each RA slot. To find the globally optimal DPP solution, we further propose a reinforcement learning (RL)-based scheme by modeling the considered RA scenario as a Markov decision process. Simulation results show the practicality and effectiveness of the proposed DPP schemes. In particular, to achieve a target access failure rate of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1\times 10^{-2}$ </tex-math></inline-formula> , the proposed RL-based scheme is able to enhance the RA traffic load by 42% and improve the preamble resource utilization by over 25% compared to the conventional baseline scheme.
Myeloid Arginase 1 Insufficiency Exacerbates Amyloid-β Associated Neurodegenerative Pathways and Glial Signatures in a Mouse Model of Alzheimer’s Disease: A Targeted Transcriptome Analysis (2021)

Brain myeloid cells, include infiltrating macrophages and resident microglia, play an essential role in responding to and inducing neurodegenerative diseases, such as Alzheimer's disease (AD). Genome-wide association studies (GWAS) implicate many AD casual and risk genes enriched in brain myeloid cells. Coordinated arginine metabolism through arginase 1 (<i>Arg1</i>) is critical for brain myeloid cells to perform biological functions, whereas dysregulated arginine metabolism disrupts them. Altered arginine metabolism is proposed as a new biomarker pathway for AD. We previously reported <i>Arg1</i> deficiency in myeloid biased cells using lysozyme M (LysM) promoter-driven deletion worsened amyloidosis-related neuropathology and behavioral impairment. However, it remains unclear how <i>Arg1</i> deficiency in these cells impacts the whole brain to promote amyloidosis. Herein, we aim to determine how <i>Arg1</i> deficiency driven by LysM restriction during amyloidosis affects fundamental neurodegenerative pathways at the transcriptome level. By applying several bioinformatic tools and analyses, we found that amyloid-β (Aβ) stimulated transcriptomic signatures in autophagy-related pathways and myeloid cells' inflammatory response. At the same time, myeloid <i>Arg1</i> deficiency during amyloidosis promoted gene signatures of lipid metabolism, myelination, and migration of myeloid cells. Focusing on Aβ associated glial transcriptomic signatures, we found myeloid <i>Arg1</i> deficiency up-regulated glial gene transcripts that positively correlated with Aβ plaque burden. We also observed that Aβ preferentially activated disease-associated microglial signatures to increase phagocytic response, whereas myeloid <i>Arg1</i> deficiency selectively promoted homeostatic microglial signature that is non-phagocytic. These transcriptomic findings suggest a critical role for proper <i>Arg1</i> function during normal and pathological challenges associated with amyloidosis. Furthermore, understanding pathways that govern <i>Arg1</i> metabolism may provide new therapeutic opportunities to rebalance immune function and improve microglia/macrophage fitness.
Multidimensional encoding of brain connectomes (2017)

The ability to map brain networks in living individuals is fundamental in efforts to chart the relation between human behavior, health and disease. Advances in network neuroscience may benefit from developing new frameworks for mapping brain connectomes. We present a framework to encode structural brain connectomes and diffusion-weighted magnetic resonance (dMRI) data using multidimensional arrays. The framework integrates the relation between connectome nodes, edges, white matter fascicles and diffusion data. We demonstrate the utility of the framework for in vivo white matter mapping and anatomical computing by evaluating 1,490 connectomes, thirteen tractography methods, and three data sets. The framework dramatically reduces storage requirements for connectome evaluation methods, with up to 40x compression factors. Evaluation of multiple, diverse datasets demonstrates the importance of spatial resolution in dMRI. We measured large increases in connectome resolution as function of data spatial resolution (up to 52%). Moreover, we demonstrate that the framework allows performing anatomical manipulations on white matter tracts for statistical inference and to study the white matter geometrical organization. Finally, we provide open-source software implementing the method and data to reproduce the results.
Coupling of Phenols to 2-Chlorotrityl Resins under Non-basic Conditions (1999)

A new procedure for the coupling of phenols to 2-chlorotrityl resins has been developed using polymer bound 2-pyridyl ether derivative 1 as tritylation agent. The method allows the immobilisation of phenols under non-basic conditions and is particularly suited for base sensitive phenolic compounds. Scope and limitation of this new coupling method have been investigated.
Reevaluation of Alcohol Synthesis and Tolerance in Brewer's Yeast (1985)

Ethanol tolerance in Saccharomyces yeasts is still not well understood. Recent developments in the measurement of ethanol tolerance, as well as studies dealing with mechanisms of ethanol toxicity and the role of “wort” lipid components on the cell membrane, have been substantial. Research on production of up to 16% (v/v) concentrations of alcohol from high gravity worts has also led to reevaluation of the factors influencing tolerance in Saccharomyces uvarum. The industrial ramifications of such findings may be significant, because many of the factors influencing tolerance can be environmentally manipulated or altered by changes to the wort.
The structures of oligosaccharides excreted by sheep with swainsonine toxicosis. (1988)

Eleven oligosaccharides were purified form the urine of sheep with swainsonine toxicosis induced by the feeding of Astragalus lentiginosus. Oligosaccharides were extracted by charcoal adsorption, chromatographed on Bio-Gel P-2, and partially fractionated by preparative-layer chromatography. Separation into individual compounds was completed by semi-preparative high pressure liquid chromatography. Structures were determined by a combination of high pressure liquid chromatography and exo- and endo- glycosidase action, methanolysis followed by gas-liquid chromatography, methylation analysis, and high resolution nuclear magnetic resonance spectroscopy. Two homologous series of oligosaccharides were identified: (a) alpha-D-Manp-(1----6)-beta-D-Manp-(1----4)-D-GlcpNAc, alpha-D-Manp(1----3)-[alpha-D-Manp-(1----6)]-beta-D-Manp+ ++-(1----4)-D-GlcpNAc, alpha-D-Manp-(1----2)-alpha-D-Manp(1----3)-[alpha-D-Manp+ ++-(1----6)]-beta-D-Manp-(1----4)-D-GlcpNAc, and alpha-D-Manp-(1----2)-alpha-D-Manp-(1----2)-alpha-D-Manp+ ++-(1----3)-[alpha- D-Manp-(1----6)]-beta-D-Manp-(1----4)-D-GlcpNAc (minor series); (b) alpha-D-Manp-(1----6)-beta-D-Manp-(1----4)-beta-D-GlcpNAc- (1----4)-D-GlcpNAc, alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-beta-D-Manp -(1----4)-beta-D-GlcpNAc-(1----4)-D-GlcpNAc, alpha-D-Manp(1----3)-alpha-D-Manp-(1----6)-beta-D-Manp -(1----4)-beta-D-GlcpNAc- (1----4)-D-GlcpNAc, alpha-D-Manp-(1----6)-alpha-D-Manp-(1----6)-beta-D-Manp++ +-(1----4)-beta-D-GlcpNAc - (1----4)-D-GlcpNAc, alpha-D-Manp-(1----3)-alpha-D-Manp-(1----6)-[alpha-D-Manp -(1----3)]-beta-D- Manp-(1----4)-beta-D-GlcpNAc-(1----4)-D-GlcpNAc, alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-alpha-D-Man p-(1----6)-beta-D- Manp-(1----4)-beta-D-GlcpNAc-(1----4)-D-GlcpNAc, and alpha-D-Manp-(1----3)-[alpha-D-Manp-(1----6)]-alpha-D-Man p-(1----6)- [alpha-D-Manp-(1----3)]-beta-D-Manp-(1----4)-beta-D-GlcpNAc- (1----4)-D- GlcpNAc (major series).
Refinement of the crystal structure of (1-ethyl-2,3,4,5-tetramethylcyclopentadienyl)[ 2,4-bis(trifluoromethyl)pentadienyl]ruthenium(II), C18H22F6Ru, at 150 Κ (2002)

Article Refinement of the crystal structure of (1-ethyl-2,3,4,5-tetramethylcyclopentadienyl)[ 2,4-bis(trifluoromethyl)pentadienyl]ruthenium(II), C18H22F6Ru, at 150 Κ was published on December 1, 2002 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 217, issue 1).
WfBench: Automated Generation of Scientific Workflow Benchmarks (2022)

The prevalence of scientific workflows with high computational demands calls for their execution on various distributed computing platforms, including large-scale leadership-class high-performance computing (HPC) clusters. To handle the deployment, monitoring, and optimization of workflow executions, many workflow systems have been developed over the past decade. There is a need for workflow benchmarks that can be used to evaluate the performance of workflow systems on current and future software stacks and hardware platforms.We present a generator of realistic workflow benchmark specifications that can be translated into benchmark code to be executed with current workflow systems. Our approach generates workflow tasks with arbitrary performance characteristics (CPU, memory, and I/O usage) and with realistic task dependency structures based on those seen in production workflows. We present experimental results that show that our approach generates benchmarks that are representative of production workflows, and conduct a case study to demonstrate the use and usefulness of our generated benchmarks to evaluate the performance of workflow systems under different configuration scenarios.
Eccentricity Estimator for Wide-Angle Fovea Vision Sensor (2008)

This paper proposes a method for estimating eccentricity that corresponds to an incident angle to a fovea sensor. The proposed method uses Fourier-Mellin Invariant descriptor to estimate rotation, scale, and translation, by taking both geometrical distortion and non-uniform resolution of a space-variant image from the fovea sensor into account. The following 2 points are focused in this paper. One is to use multi-resolution images by Discrete Wavelet Transform for reducing noise caused by foveation properly. Another is to use a variable window function (although the window function is generally used for reducing DFT leakage caused by both ends of a signal) for changing an effective field of view (FOV) in order not to sacrifice high accuracy. The simulation compares the root mean square (RMS) of the foveation noise between uniform and non-uniform resolutions, when a resolution level and a FOV level are changed, respectively. The result shows the proposed method is suitable for the wide-angle space-variant image by the fovea sensor, and, moreover, it does not sacrifice high accuracy in the central FOV. Another simulation result examines a reliable resolution level.
The basic-helix–loop–helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors (1998)

We report that MOP3 is a general dimerization partner for a subset of the basic-helix-loop-helix (bHLH)-PER-ARNT-SIM (PAS) superfamily of transcriptional regulators. We demonstrated that MOP3 interacts with MOP4, CLOCK, hypoxia-inducible factor 1alpha (HIF1alpha), and HIF2alpha. A DNA selection protocol revealed that the MOP3-MOP4 heterodimer bound a CACGTGA-containing DNA element. Transient transfection experiments demonstrated that the MOP3-MOP4 and MOP3-CLOCK complexes bound this element in COS-1 cells and drove transcription from a linked luciferase reporter gene. We also deduced the high-affinity DNA binding sites for MOP3-HIF1alpha complex (TACGTGA) and used transient transfection experiments to demonstrate that the MOP3-HIF1alpha and MOP3-HIF2alpha heterodimers bound this element, drove transcription, and responded to cellular hypoxia. Finally, we found that MOP3 mRNA expression overlaps in a number of tissues with each of its four potential partner molecules in vivo.
A Quantum Mechanical Study of the Thermal Conduction Across a ZrB2-SiC Interface as a Function of Temperature and Strain (2011)

Atomistic analyses of thermal conduction across ZrB2/SiC based nanocomposite interface are performed using first principles density functional theory (DFT) with plane-wave basis sets. The changes in the thermal properties of nanocomposites have been analyzed under the effect of straining and temperature and compared for their phononic and electronic dependence.
Designing a fast, on-line backup system for a log-structured file system (1996)

this paper, we explain the features of the Spiralog file system that helped achieve this goal and outline the design of the major backup functions, namely volume save, volume restore, file restore, and incremental management. We then present some performance results arrived at using Spiralog version 1.1. The paper concludes with a discussion of other design approaches and areas for future work.
Antifungal mechanism of Streptomyces ma. FS‐4 on fusarium wilt of banana (2020)

These results may indicate the prevention and control of banana wilt, which is of great significance to the healthy development of banana industry system.
Identifying named entities in biomedical text based on stacked generalization (2008)

Biomedical named entity recognition is a basic technique in the biomedical knowledge discovery and its performance has direct effects on further discovery and processing in biomedical texts. In this paper, we present stacked generalization strategy for biomedical named entity recognition including homogeneous classifier ensembles and heterogeneous classifier ensembles based on stacked generalization. Evaluations show that stacked generalization strategy can take advantage of more useful evidences, and make use of compensation and relativity among different classifiers to learn the correlation between individual classifiers predictions and the correct prediction to improve the performances of the system. This method breaks through the limitation of single classifier and achieves promising performances.
Anaphylaxis and cardiovascular disease: therapeutic dilemmas (2015)

Cardiovascular disease (CVD) increases the risk of severe or fatal anaphylaxis, and some medications for CVD treatment can exacerbate anaphylaxis. The aim of this article is to review the effect of anaphylaxis on the heart, the potential impact of medications for CVD on anaphylaxis and anaphylaxis treatment, and the cardiovascular effects of epinephrine. The therapeutic dilemmas arising from these issues are also discussed and management strategies proposed. PubMed searches were performed for the years 1990-2014 inclusive, using terms such as angiotensin-converting enzyme (ACE) inhibitors, adrenaline, allergic myocardial infarction, anaphylaxis, angiotensin-receptor blockers (ARBs), beta-adrenergic blockers, epinephrine, and Kounis syndrome. Literature analysis indicated that: cardiac mast cells are key constituents of atherosclerotic plaques; mast cell mediators play an important role in acute coronary syndrome (ACS); patients with CVD are at increased risk of developing severe or fatal anaphylaxis; and medications for CVD treatment, including beta-adrenergic blockers and ACE inhibitors, potentially exacerbate anaphylaxis or make it more difficult to treat. Epinephrine increases myocardial contractility, decreases the duration of systole relative to diastole, and enhances coronary blood flow. Its transient adverse effects include pallor, tremor, anxiety, and palpitations. Serious adverse effects (including ventricular arrhythmias and hypertension) are rare, and are significantly more likely after intravenous injection than after intramuscular injection. Epinephrine is life-saving in anaphylaxis; second-line medications (including antihistamines and glucocorticoids) are not. In CVD patients (especially those with ACS), the decision to administer epinephrine for anaphylaxis can be difficult, and its benefits and potential harms need to be carefully considered. Concerns about potential adverse effects need to be weighed against concerns about possible death from untreated anaphylaxis, but there is no absolute contraindication to epinephrine injection in anaphylaxis.