gebhart/patrepeval huggingface dataset:
Spatially Evolving Turbulent Boundary-Layer Flow over a Wall-Mounted Cube (2021)

Turbulent flow over a wall-mounted cube presents an important canonical problem with applications in circuit design, urban building design, or aerodynamics. Flow over a cube placed in a fully developed turbulent channel flow has long been the preferred problem of investigation for researchers. However, a more relevant practical scenario is flow over a cube placed in a spatially evolving turbulent boundary layer (SETBL). In this work, wall-resolved large-eddy simulations of flow over a wall-mounted cube placed in an SETBL on a flat plate are performed at a Reynolds number of 19,600 based on the mean velocity and the inlet boundary-layer thickness. The incompressible Navier–Stokes equations are solved using a second-order finite-volume approach with a dynamic -equation eddy-viscosity model. At this Reynolds number, the key nondimensional parameter governing this problem is the ratio of cube height to boundary-layer thickness, . This paper investigates the dependence of the turbulence wake characteristics on . Specifically, this paper analyzes the vortical structures and the separation and reattachment lengths. It is further examined how the turbulent kinetic energy budget varies with . It is found that the size of the horseshoe vortex roughly scales with the size of the cube, and that the decay of turbulent kinetic energy per unit area over streamwise distance in the near wake exhibits a power-law behavior.
Active soft matter (2011)

M. E. Cates and F. C. MacKintosh, Soft Matter, 2011, 7, 3050 DOI: 10.1039/C1SM90014E
Information Systems (1999)

This qualitative study examines what users expect or perceive about a computerized student management information system (SMIS) and how these perceptions influence effective use. The research was conducted in a suburban southeast Texas school district with more than 30,000 students that had implemented an SMIS in the last four years. The study of this SMIS investigated the relationships between design, use, and effects in developing a model for understanding strategies for effective implementation and use. The article concludes with a discussion of the development and implications of the model.
Activity-Based Protein Profiling Delivers Selective Drug Candidate ABX-1431, a Monoacylglycerol Lipase Inhibitor, To Control Lipid Metabolism in Neurological Disorders (2018)

Monoacylglycerol lipase (MGLL or MAGL) is a critical point of regulation of both endocannabinoid and eicosanoid signaling pathways in the brain, thereby providing novel therapeutic opportunities for neurological and neurodegenerative diseases. In this issue Cisar et al. disclose the discovery, optimization, and initial preclinical profiling of ABX-1431, a covalent, irreversible MGLL inhibitor. Activity-based protein profiling was key to the discovery of ABX-1431. ABX-1431 is a first-in-class experimental drug that was well-tolerated and safe in phase 1 clinical studies. Data from an exploratory phase 1b study indicate that it has the potential to treat symptoms of adult patients with syndrome of Gilles de la Tourette. ABX-1431 is currently entering clinical phase 2 studies for this neurological disorder as well as for other indications, such as neuromyeltis optica and multiple sclerosis.
DAPI (4',6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites (1992)

The interaction of DAPI and propidium with RNA (polyA.polyU) and corresponding DNA (polydA.polydT) sequences has been compared by spectroscopic, kinetic, viscometric, Tm, and molecular modeling methods. Spectral changes of propidium are similar on binding to the AT and AU sequences but are significantly different for binding of DAPI. Spectral changes for DAPI with the DNA sequence are consistent with the expected groove-binding mode. All spectral changes for complexes of propidium with RNA and DNA and for DAPI with RNA, however, are consistent with an intercalation binding mode. When complexed with RNA, for example, DAPI aromatic protons signals shift significantly upfield, and the DAPI UV-visible spectrum shows significantly larger changes than when complexed with DNA. Slopes of log kd (dissociation rate constants) versus-log [Na+] plots are similar for complexes of propidium with RNA and DNA and for the DAPI-RNA complex and are in the range expected for an intercalation complex. The slope for the DAPI-DNA complex, however, is much larger and is in the range expected for a groove-binding complex. Association kinetics results also support an intercalation binding mode for the DAPI-RNA complex. The viscosity of polyA.polyU solutions increases significantly on addition of both propidium and DAPI, again in agreement with an intercalation binding mode for both molecules with RNA. Molecular modeling studies completely support the experimental findings and indicate that DAPI forms a very favorable intercalation complex with RNA. DAPI also forms a very stable complex in the minor groove of AT sequences of DNA, but the stabilizing interactions are considerably reduced in the wide, shallow minor groove of RNA. Modeling studies,thus,indicate that DAPI interaction energetics are more favorable for minor-groove binding in AT sequences but are more favorable for interaction in RNA.
Combining frontend-based memory with MFCC features for Bandwidth Extension of narrowband speech (2009)

In this paper, we continue our previous work on improving Bandwidth Extension (BWE) of narrowband speech. We have shown that including memory into the parametrization frontend (through delta features) results in higher highband certainty irrespective of feature type, with MFCCs exhibiting higher correlation, in general, between both bands, reaching twice that using LSFs. By incorporating memory into the frontend of a conventional LP-based BWE system, we were able to translate the higher correlation due to memory into BWE performance improvement. Using high-resolution inverse DCT, we also achieved high quality speech reconstruction from MFCCs, thus enabling MFCC-based BWE with improved performance compared to conventional static LP-based BWE. We continue this work by incorporating the superior correlation properties of frontend memory into our MFCC-based BWE system. Log-Spectral Distortion as well as the more perceptually-correlated Itakura-based measures show that incorporating memory into our MFCC-based BWE system results in BWE performance superior to that of our dynamic LP-based BWE system.
Accessibility and Morphology of Cellulose Fibres Treated with Sodium Hydroxide (2014)

Cellulose fibres were treated with sodium hydroxide (NaOH) to improve the accessibility of chemical reagents and the roughness of fibre surface at low temperatures. The accessibility, supermolecular structure, morphology, and physical properties of fibres were investigated using solid-state cross polarisation/magic angle spinning 13C nuclear magnetic resonance (CP/MAS 13C NMR), wide-angle X-ray diffraction (WAXD), and scanning electron microscopy (SEM). The results showed that in low temperature (-16 °C), the iodine sorption value of cellulose fibres is 145.2 mg. The shift from the C6 signal of the molecular structure to the amorphous area indicated a decrease in the crystallinity of the material from 66% to 8%, and the transformation from cellulose I to II occurred. The SEM revealed fold shapes in the fibre surface, which increased the fibre surface area.
Optimal filtering for denial of service mitigation (2003)

An optimal approach to mitigation of denial of service flooding attacks is presented. The objective is to protect the server while minimizing the effect of the mitigation. The approach relies on routers filtering enough packets so that the server is not overwhelmed while ensuring that as little filtering as possible is performed. The optimal solution is to filter packets at routers through which the "attack packets" are passing. The identification of which router is forwarding the packets is carried out by routers filtering packets at time varying ratios. Then the correlation between the arrival of packets at the server and the router filtering ratios provides an indication of which routers are forwarding the attack packets. Once sufficient confidence in the identification is achieved, the routers that forward more attack packets will filter more packets than routers that forward less attack packets.
Acetic, lactic and citric acids and pH inhibition of Listeria monocytogenes Scott A and the effect on intracellular pH. (1993)

The effects of acetic, lactic and citric acids and pH on the growth and intracellular pH (pHin) of Listeria monocytogenes Scott A were documented and compared for total acid concentrations ranging from 50 mmol ml-1 to 250 mmol ml-1 for acetic and lactic acids and from 25 mmol ml-1 to 100 mmol ml-1 for citric acid. Initial pH values ranged from 4.7 to 6.0. Although the growth rate of L. monocytogenes Scott A was slower when incubated at 25 degrees C than at 37 degrees C, the relative acid and pH inhibition was identical at both temperatures. As the initial pH values decreased and/or the total acid concentrations increased, the growth rates of L. monocytogenes Scott A decreased. Compared at equal initial pH values and on an equimolar total acid basis, the relative inhibition effect was generally acetic > lactic > citric. When based on initial undissociated acid concentrations, the inhibition effect was citric > lactic > acetic. The effect of differing acid and pH environments on pHin was determined. At equimolar total acid concentrations, the pHin of the cell was changed the least by citric acid and the most by acetic acid. Growth rates were influenced by the pHin and the acid used to adjust the system.
The Fibronectin–ILT3 Interaction Functions as a Stromal Checkpoint that Suppresses Myeloid Cells (2021)

Suppressive myeloid cells inhibit antitumor immunity by preventing T-cell responses. Immunoglobulin-like transcript 3 (ILT3; also known as LILRB4) is highly expressed on tumor-associated myeloid cells and promotes their suppressive phenotype. However, the ligand that engages ILT3 within the tumor microenvironment and renders tumor-associated myeloid cells suppressive is unknown. Using a screening approach, we identified fibronectin as a functional ligand for ILT3. The interaction of fibronectin with ILT3 polarized myeloid cells toward a suppressive state, and these effects were reversed with an ILT3-specific antibody that blocked the interaction of ILT3 with fibronectin. Furthermore, <i>ex vivo</i> treatment of human tumor explants with anti-ILT3 reprogrammed tumor-associated myeloid cells toward a stimulatory phenotype. Thus, the ILT3-fibronectin interaction represents a "stromal checkpoint" through which the extracellular matrix actively suppresses myeloid cells. By blocking this interaction, tumor-associated myeloid cells may acquire a stimulatory phenotype, potentially resulting in increased antitumor T-cell responses.
You are a mathematician: a wise and witty introduction to the joy of numbers (1998)

From basic arithmetic to algebraic equations, from the purely practical to the abstract, this is a guide to the potential of maths. Patterns emerge from the simplest grouping of numbers. The many secrets hidden inside triangles are revealed, as are the origins of a host of mathematical theories and principles, from Aristotle to Euclid and Galileo. On a journey from the Ancient Greeks to quantum theory, Wells shares anecdotes from history, such as how 18th-century European military commanders calculated how many cannonballs their enemies had stacked up next to their cannons. Offering a comprehensive look at the myriad aspects of mathematics - whether as a household helper or a tool of science - this book covers a wide range of topics and applications.
Combinatorial <i>Gli</i> gene function in floor plate and neuronal inductions by Sonic hedgehog (1998)

ABSTRACT Within the developing vertebrate nervous system, it is not known how progenitor cells interpret the positional information provided by inducing signals or how the domains in which distinct groups of neural cells differentiate are defined. Gli proteins may be involved in these processes. In the frog neural plate, we have previously shown that the zinc finger transcription factor Gli1 is expressed in midline cells and mediates the effects of Shh inducing floor plate differentiation. In contrast, Gli2 and Gli3 are expressed throughout the neural plate except for the midline. Here, it is shown that Gli3 and Shh repress each other whereas Gli2, like Gli1, is a target of Shh signaling. However, only Gli1 can induce the differentiation of floor plate cells. In addition, Gli2 and Gli3 repress the ectopic induction of floor plate cells by Gli1 in co-injection assays and inhibit endogenous floor plate differentiation. The definition of the floor plate domain, therefore, appears to be defined by the antagonizing activities of Gli2 and Gli3 on Gli1 function. Because both Gli1 and Gli2 are induced by Shh, these results establish a regulatory feedback loop triggered by Shh that restricts floor plate cells to the midline. We have also previously shown that the Gli genes induce neuronal differentiation and here it is shown that there is specificity to the types of neurons the Gli proteins induce. Only Gli1 induces Nkx2.1/TTF-1+ ventral forebrain neurons. Moreover, Gli2 and Gli3 inhibit their differentiation. In contrast, the differentiation of spinal motor neurons can be induced by the two ventrally expressed Gli genes, Gli1 and Gli2, suggesting that Gli2 directly mediates induction of motor neurons by Shh. In addition, Gli3 inhibits motor neuron differentiation by Gli2. Thus, combinatorial Gli function may pattern the neural tube, integrating positional information and cell type differentiation.
Bulked Segregant Analysis Using the GoldenGate Assay to Locate the <i>Rpp3</i> Locus that Confers Resistance to Soybean Rust in Soybean (2009)

ABSTRACT Few resistance loci to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd., have been genetically mapped and linked to molecular markers that can be used for marker assisted selection. New technologies are available for single nucleotide polymorphism (SNP) genotyping that can be used to rapidly map traits controlled by single loci such as resistance to SBR. Our objective was to demonstrate that the high‐throughput SNP genotyping method known as the GoldenGate assay can be used to perform bulked segregant analysis (BSA) to find candidate regions to facilitate efficient mapping of a dominant resistant locus to SBR designated Rpp3 We used a 1536 SNP GoldenGate assay to perform BSA followed by simple sequence repeat (SSR) mapping in an F 2 population segregating for SBR resistance conditioned by Rpp3 A 13‐cM region on linkage group C2 was the only candidate region identified with BSA. Subsequent F 2 mapping placed Rpp3 between SSR markers BARC_Satt460 and BARC_Sat_263 on linkage group C2 which is the same region identified by BSA. These results suggest that the GoldenGate assay was successful at implementing BSA, making it a powerful tool to quickly map qualitative traits since the GoldenGate assay is capable of screening 1536 SNPs on 192 DNA samples in three days.
Selective Genetic Overlap Between Amyotrophic Lateral Sclerosis and Diseases of the Frontotemporal Dementia Spectrum (2018)

This study found novel genetic overlap between ALS and diseases of the FTD spectrum, that the MAPT H1 haplotype confers risk for ALS, and identified the mitophagy-associated, proapoptotic protein BNIP1 as an ALS risk gene. Together, these findings suggest that sporadic ALS may represent a selectively pleiotropic, polygenic disorder.
Utilizing the activation mechanism of serine proteases to engineer hepatocyte growth factor into a Met antagonist (2007)

Hepatocyte growth factor (HGF), the ligand for the receptor tyrosine kinase Met, is secreted as single chain pro-HGF that lacks signaling activity. Pro-HGF acquires functional competence upon cleavage between R494 and V495, generating a disulfide-linked alpha/beta-heterodimer, where the beta-chain of HGF (HGF beta) has a serine protease fold that lacks enzymatic activity. We show that, like serine proteases, insertion of the newly formed N terminus in the beta-chain is critical for activity, here by allosterically stabilizing interactions with Met. The HGF beta crystal structure shows that V495 inserts into the "activation pocket" near the Met binding site where the positively charged N terminus forms a salt bridge with the negatively charged D672, and the V495 side chain has hydrophobic interactions with main- and side-chain residues. Full-length two-chain HGF mutants designed to interrupt these interactions (D672N, V495G, V495A, G498I, and G498V) displayed <10% activity in Met receptor phosphorylation, cell migration, and proliferation assays. Impaired signaling of full-length mutants correlated with >50-fold decreases in Met binding of the low-affinity HGF beta domain alone bearing the same mutations and further correlated with impaired N-terminal insertion. Because high-affinity binding resides in the HGF alpha-chain, full-length mutants maintained normal Met binding and efficiently inhibited HGF-mediated Met activation. Conversion of HGF from agonist to antagonist was achieved by as little as removal of two methyl groups (V495A) or a single charge (D672N). Thus, although serine proteases and HGF have quite distinct functions in proteolysis and Met signal transduction, respectively, they share a similar activation mechanism.
Ultralinear small-angle phase modulator (2002)

A DC electric field applied to a quartz plate resonator causes changes in the elastic constants which can lead to a change in the frequency of the resonator. This effect, known as the polarizing effect, has been shown to be extremely linear. A method for measuring the polarizing effect in high-Q SC-cut 5-MHz quartz resonators for small AC electric fields is introduced. This polarizing effect was used to make an ultralinear small angel phase modulator with low added phase noise. The second harmonic distortion was measured to be less than -17 dB relative to the fundamental in three different units, even though the modulation frequency was more than 20 times larger than the half-bandwidth of the resonators. The measurement techniques to verify this performance are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Field proven high speed micro optical density profiler sampling 1000 times per second with 10/sup -6/ precision (2003)

A miniature fiber-optical point sea-refractometer with industrial prototype status has been developed for use in high-speed profiling applications. It can be used for a quick, precise survey of the density field of the ocean by directly measuring the index of refraction. Field data evaluation studies have shown that index of refraction profiles provide an extremely good representation of the actual density distribution. Significant correlation anomalies between CTD (current-temperature-density) derived density data and densities determined from index of refraction measurements have been observed. These differences can serve as parameters for a much more detailed description of bodies of water.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Classification Algorithm for High-dimensional Data (2015)

With the advent of high-dimensional stored big data and streaming data, suddenly machine learning on a very large scale has become a critical need. Such machine learning should be extremely fast, should scale up easily with volume and dimension, should be able to learn from streaming data, should automatically perform dimension reduction for high-dimensional data, and should be deployable on hardware. Neural networks are well positioned to address these challenges of large scale machine learning. In this paper, we present a method that can effectively handle large scale, high-dimensional data. It is an online method that can be used for both streaming and large volumes of stored big data. It primarily uses Kohonen nets, although only a few selected neurons (nodes) from multiple Kohonen nets are actually retained in the end; we discard all Kohonen nets after training. We use Kohonen nets both for dimensionality reduction through feature selection and for building an ensemble of classifiers using single Kohonen neurons. The method is meant to exploit massive parallelism and should be easily deployable on hardware that implements Kohonen nets. Some initial computational results are presented.
Leveraging Gas-Phase Fragmentation Pathways for Improved Identification and Selective Detection of Targets Modified by Covalent Probes (2016)

The recent approval of covalent inhibitors for multiple clinical indications has reignited enthusiasm for this class of drugs. As interest in covalent drugs has increased, so too has the need for analytical platforms that can leverage their mechanism-of-action to characterize modified protein targets. Here we describe novel gas phase dissociation pathways which yield predictable fragment ions during MS/MS of inhibitor-modified peptides. We find that these dissociation pathways are common to numerous cysteine-directed probes as well as the covalent drugs, Ibrutinib and Neratinib. We leverage the predictable nature of these fragment ions to improve the confidence of peptide sequence assignment in proteomic analyses and explore their potential use in selective mass spectrometry-based assays.
Constraint-based specification of hybrid position-impedance-force tasks (2014)

This work aims to extend the application field of the constraint-based control framework called iTaSC (instantaneous task specification using constraints) toward tasks where physical interaction between the robot and the environment, or a human, is contemplated. iTaSC, in its original formulation, allows for a systematic derivation of control schemes from task descriptions; tasks are defined as constraints enforced on outputs (e.g. distances, angles), and the iTaSC control takes care to fulfil such constraints by computing desired velocities to be commanded to the robot(s) joints. This approach, being based on a velocity resolution scheme, principally addresses tasks where positioning is the main issue. However, tasks that involve contacts with the environment or with the user, either desired or accidental, can be considered as well, taking advantage of impedance control, when position is controlled, or with force control. This paper describes the implementation of force tasks, and, by the combination of conflicting force and position tasks, impedance control, within the iTaSC formalism. This result is achieved by taking advantage of an approximate physical modelling of the robotic system and the environment. The proposed control scheme is tested by means of experiments where constraints on forces and/or positions described in cylindrical coordinates are imposed on a Kuka LWR arm.