gebhart/patrepeval huggingface dataset:
An efficient adaptive Cross-Layer interaction mechanism for TCP traffic over heterogeneous networks (2008)

We present an effective end-to-end mechanism of interaction between link layer and TCP over wired/wireless network. The motivation for adopting this method is to overcome both sources of error, namely; channel errors and congestion errors. This mechanism is adaptive in nature where channel encoding parameters (i.e. coding rate) will vary based on the deterioration level in the channel conditions. It is worth to note that whatever TCP flavor is implemented at the end systems, the proposed algorithm will not impose any change to it. NS2 is used to simulate the heterogeneous networks and implement the proposed adaptive method. Extensive simulation experiments have been conducted to evaluate the performance of the proposed approach and examine against fixed FEC approach. The simulation results have proven the ability of the proposed scheme to track the changes in the wireless channel and provide the necessary level of redundancy for FEC coding. Hence, it optimally uses the available resources and at the same time it achieves the maximum possible throughput.
Making of an &amp;#x2018;all reason&amp;#x2019; electric Vehicle (2013)

Mahindra Reva (Earlier Reva Electric Car Company) has been pioneering the development of electric vehicles in India. The `decade long' experience of putting over 4500 Reva cars on the road in 24 different countries has given Reva a unique `insider view' into the changing context of mobility around the world. The evolving new mobility context uniquely places electric vehicles to signify disruptive changes in the automotive DNA. This also necessitates taking a fresh look at the philosophies of designing new generation electric vehicles. The very reason for Electric vehicles to exist goes beyond the well articulated environmental advantages. These include making changes in every aspect, starting with the very way mobility is perceived to the way solutions are designed, manufactured and used. At Mahindra Reva, practice of these philosophies has been distilled into simple articulations of the 5Cs. This paper presents the implementation of these philosophies in a new electric car developed for `all reasons'. The car is named e2O (E-To-Oh) and will be referred to as such in the rest of the paper.
WE‐A‐134‐07: RapidTrack: A Versatile Tool for Template‐Based Target Tracking During Radiotherapy (2013)

Purpose: To investigate the accuracy that can be obtained by using various template‐based methods to track target motion from radiographic projections during radiation therapy dose delivery. Methods: We have developed a non‐clinical software suite (RapidTrack) in two parts to accomplish template‐based tracking. RapidTrack‐Planning is an application used to generate templates from plan CT. These templates are oriented to correspond with the imaging angle of the online images to which they will be matched. Templates may be derived from the actual voxel values of the plan CT (using MIP or tomosynthesis) or may be generated from the plan contours without reference to the voxel values. The RapidTrack‐Lung application performs the actual matching with online projections using a cross‐correlation method. The match locations can be used to derive a 3D position of the target. Quality of the match is measured using a peak‐to‐sidelobe ratio (PSR) metric, which reduces the incidence of false detection. Results: The RapidTrack suite was shown to be quite versatile for tracking of radiotherapy targets. The generated templates are not dependent on any particular shape or structure of target; hence they are applicable to a variety of fiducial shapes as well as to fiducial‐less scenarios. RapidTrack was used on intra‐fraction images of seeds in pancreas; quality of the match was visually illustrated by overlaying the planning contour on the image at the match location. PSR of the match was consistently over 2.2 at all angles. Tracking of embolization coils in lung produced similar results. Breathing motion of a lung tumor was successfully tracked using a markerless algorithm based on synthetic contour template. Conclusion: The template‐based algorithm demonstrated shows promise for tracking radiotherapy targets during treatment, both in fiducial and fiducial‐less scenarios. The PSR metric is an effective means of measuring the quality of tracking. Varian Medical Systems
Artificial Intelligence to Accelerate the Discovery of N<sub>2</sub> Electroreduction Catalysts (2019)

The development of catalysts for the electrochemical N2 reduction reaction (NRR) with a low limiting potential and high Faradaic efficiency is highly desirable but remains challenging. Here, to achieve acceleration, we develop and report a slab graph convolutional neural network (SGCNN), an accurate and flexible machine learning (ML) model that is suited for probing surface reactions in catalysis. With a self-accumulated database of 3040 surface calculations at the density-functional-theory (DFT) level, SGCNN predicted the binding energies, ranging over 8 eV, of five key adsorbates (H, N2, N2H, NH, NH2) related to NRR performance with a mean absolute error (MAE) of only 0.23 eV. SGCNN only requires the low-level inputs of elemental properties available in the periodic table of elements and connectivity information of constituent atoms; thus, accelerations can be realized. Via a combined process of SGCNN-driven predictions and DFT verifications, four novel catalysts in the L12 crystal space, including V3Ir(111), Tc3Hf(111), V3Ni(111), and Tc3Ta(111), are proposed as stable candidates that likely exhibit both a lower limiting potential and higher Faradaic efficiency in the NRR, relative to the reference Mo(110). The ML work combined with a statistical data analysis reveals that catalytic surfaces with an average d-orbital occupation between 4 and 6 could lower the limiting potential and potentially overcome the scaling relation in the NRR.
Mesenchymal stromal cell-derived extracellular vesicles promote myeloid-biased multipotent hematopoietic progenitor expansion via Toll-like receptor engagement (2017)

PAGE 24612: There were several errors in the original figure legend to Fig. 4. The figure legend should be replaced with the following. FIGURE 4. MSC-derived EVs activate NF-κB and Notch signaling to promote HSPC differentiation. A, diagrammatic representation of the lentiviral vector design used to generate the NF-κB enhancer-luciferase reporter cell line. Stably transduced and sorted SIM-A9 microglial cells were used for EV exposure followed by luciferase assay. The SIM-A9-NF-κB-Luc cells were exposed with MSC EVs and incubated for 48 h followed by luciferase assay. Non-treated SIM-A9-NF-κB-Luc and LPS-treated SIM-A9-NF-κB-Luc cells were used as negative and positive controls, respectively. Luciferase activity was measured as relative fluorescence units (RFU). Data represent n = 4 independent experiments; error bars depict S.D. All p values have been calculated using two-tailed Student’s t test. B, quantitative mRNA expression of NF-κB and Notch-1 signaling and downstream targets involved in cell proliferation in MSC EV-exposed HSPCs. Data represent n = 3 independent experiments; error bars are S.D. C, we next tested a candidate panel of canonical TLR4 responsive cytokines for both transcriptional activation and secretion, either after EV or S100 exposure. Transcriptional analysis of EV-exposed HSPCs reveals an up-regulation of several known TLR4-responsive cytokine genes (IL6, TNFa, Stat1, and EGFR) in WT but not MyD88−/− HSPCs. Data represent n = 3 independent experiments; error bars are S.D. D, TLR4 signaling was specifically inhibited in WT MSC-EV-exposed HSPCs using TAK-242. Transcriptional analysis of EV-exposed HSPCs with and without TLR4 inhibitor showed down-regulation of the same TLR-responsive genes described above. Data represent n = 2 independent experiments; error bars represent S.D. E, cytokines released by HSPCs after 48 h co-culture, with MSC EVs compared with S100, were measured using a Luminex assay, whereby error bars are S.D. and p values are an indication of the variance across three technical replicates in this screening panel.
PhoB Activates Escherichia coli O157:H7 Virulence Factors in Response to Inorganic Phosphate Limitation (2014)

Enterohemorrhagic Escherichia coli (EHEC), an emerging food- and water-borne hazard, is highly pathogenic to humans. In the environment, EHEC must survive phosphate (Pi) limitation. The response to such Pi starvation is an induction of the Pho regulon including the Pst system that senses Pi variation. The interplay between the virulence of EHEC, Pho-Pst system and environmental Pi remains unknown. To understand the effects of Pi deprivation on the molecular mechanisms involved in EHEC survival and virulence under Pho regulon control, we undertook transcriptome profiling of the EDL933 wild-type strain grown under high Pi and low Pi conditions and its isogenic ΔphoB mutant grown in low Pi conditions. The differentially expressed genes included 1067 Pi-dependent genes and 603 PhoB-dependent genes. Of these 131 genes were both Pi and PhoB-dependent. Differentially expressed genes that were selected included those involved in Pi homeostasis, cellular metabolism, acid stress, oxidative stress and RpoS-dependent stress responses. Differentially expressed virulence systems included the locus of enterocyte effacement (LEE) encoding the type-3 secretion system (T3SS) and its effectors, as well as BP-933W prophage encoded Shiga toxin 2 genes. Moreover, PhoB directly regulated LEE and stx2 gene expression through binding to specific Pho boxes. However, in Pi-rich medium, constitutive activation of the Pho regulon decreased LEE gene expression and reduced adherence to HeLa cells. Together, these findings reveal that EHEC has evolved a sophisticated response to Pi limitation involving multiple biochemical strategies that contribute to its ability to respond to variations in environmental Pi and to coordinating the virulence response.
Current Status of Liquid-cell Transmission Electron Microscopy (2019)

Even though, nanoscale materials of various shapes and compositions have been synthesized in the liquid, their underlying growth and transformation mechanisms are not well understood due to a lack of analytical methods. The advent of liquid cell for transmission electron microscope (TEM) enables the direct imaging of chemical reactions that occur in liquids with nanometer resolution of the electron microscope (EM). Here, the technical development of liquid cell TEM equipment and their applications to the study of nanomaterials analysis in liquid are discussed. Also new findings discovered through liquid cell TEM studies such as nucleation & growth, coalescence process and transformation are discussed.
Hydrotreatment of pyrolytic lignins to aromatics and phenolics using heterogeneous catalysts (2019)

The pyrolysis of lignocellulosic biomass generates a liquid product, known as pyrolysis oil, that can be further processed into biofuels and value-added chemicals. During pyrolysis, cellulose and hemicelulose fractions are converted into a range of water-soluble sugar derivatives, for which several valorisation strategies exist. On the other hand, lignin is broken down into so-called pyrolytic lignin, a water-insoluble complex mixture of aromatic oligomers that requires different upgrading strategies than the sugar rich fraction. Here, we report an experimental study on the valorisation of pyrolytic lignin via catalytic hydrotreatment in the absence of an external solvent. A variety of carbon-supported noble-metal heterogeneous catalysts were tested (Ru/C, Pd/C, Pt/C and Rh/C), as well as conventional hydrotreatment catalysts (sulphided NiMo/Al2O3 and CoMo/Al2O3) to obtain valuable low molecular weight aromatic and phenolic compounds. Overall, depolymerized liquids were obtained with organic yields of up to 63 wt%. Pd/C was shown to be the best catalyst, yielding 59 wt% of monomers based on the organic product (i.e. 33 wt% based on pyrolytic lignin intake). While noble metal catalysts favored higher monomer yields, though with some over-reduction of aromatic rings to saturated hydrocarbons, sulphided catalysts were more efficient in deoxygenation and aromatization reactions, but yielded less monomers. The hydrocracking efficiency was shown to be strongly dependent on the reaction temperature. Based on the experimental data, a global reaction network is proposed. The high monomer yields reveal the potential of catalytic hydrotreatment for the upgrading of pyrolytic lignin into valuable phenolics and aromatics.
Longitudinal and lateral dispersion in packed beds: Effect of column length and particle size distribution (1985)

Abstract Longitudinal and lateral dispersion coefficients were measured at various axial positions in a packed bed in the Peclet number range from 10 2 to 10 4 . Three different types of packings were used: uniform size particles, a narrow size distribution, and a wide size distribution. For the case of uniform particles the longitudinal dispersivities were found to be strong functions of position in the bed unless the dispersion length satisfies a constraint dependent on the value of the Peclet number. Generally, the larger the Peclet number, the larger the required length for constant axial dispersivities to be achieved. For the case of the wide size distribution, longitudinal dispersivities were larger than in the uniform particle case, and they required a longer dispersion length to achieve a constant value. This suggests a characteristic length for dispersion larger than the mean hydraulic radius. The lateral dispersivities were found to be insensitive to the distribution of particle sizes or location in the bed.
Filters and calibration sources for the soft x-ray spectrometer (SXS) instrument on ASTRO-H (2010)

The SXS instrument is the Soft X-ray micro-calorimeter Spectrometer planned for the Japanese ASTRO-H satellite, scheduled to be launched in 2014. In this paper, the trade off and modelling for the X-ray absorption and optical blocking filters will be described. The X-ray absorption filter will optimize the efficiency for high spectral resolution observations for bright sources at higher energies (notably around the Fe-K line at 6.4 KeV), given the characteristics of the instrument while the optical blocking filter allows X-ray observations of optically bright sources. For this mission a novel type of on-off-switchable X-ray calibration source, using light sensitive photo-cathodes, is being developed, which will be used for gain calibration and contamination monitoring. These sources will be used by both the SXS and SXI (Soft X-ray Imager) instruments and have the capability to be pulsed at millisecond intervals. Details of these sources will also be discussed.
Model-Based Data Generation for Support Vector Machine Stroke Classification (2021)

This paper presents a new and efficient method to generate a dataset for brain stroke classification. Exploiting the Born approximation, it derives scattering parameters at antennas locations in a 3-D scenario through a linear integral operator. This technique allows to create a large amount of data in a short time, if compared with the full-wave simulations or measurements. Then, the support vector machine is used to create the classifier model, based on training set data with a supervised method and to classify the test set. The dataset is composed by 9 classes, differentiated for presence, typology and position of the stroke. The algorithm is able to classify the test set with a high accuracy.
P4‐225: SYNTHETIC β‐AMYLOID DIMER IN ANTI‐PARALLEL CONFORMATION INDUCES <i>IN VIVO</i> SYNAPTIC PLASTICITY DEFICITS (2014)

Soluble Aβ dimers are considered to play a critical role in Alzheimer's disease. Despite many efforts to investigate Aβ dimers via isolation or chemical synthesis, structural understanding of the dimeric conformation is unclear. As the smallest oligomeric species, Aβ dimers, directly extracted from the cerebral cortex of AD patients, are found to impair synaptic plasticity and memory in rodents. Accordingly, substantial efforts have been devoted to understanding the pathophysiological function of Aβ dimers by chemical approaches. The synthesis of a disulfide-linked Aβ (1-40S26C) dimer enabled generation of anti-dimer monoclonal antibodies to neutralize synaptic plasticity. As Aβ monomers are essential for brain function, selectively targeting pathogenic dimers is a considerable therapeutic and diagnostic approach for AD. Although covalently linked Aβ dimers have given freedom from concerns of unstable oligomerization throughout biological studies, conformational relativity of full-length Aβ dimers to AD pathogenesis in vivo is yet to be discovered. Here we explore the pathologically favored dimeric conformation using synthetic parallel and anti-parallel Aβ (1-40) dimers with flexible linkers to facilitate dimerization. We synthesized Aβ dimers in parallel and anti-parallel conformations by modified stepwise Fmoc solid-phase peptide synthesis protocols. To investigate if our dimer models facilitate interactions between linked Aβ monomer strands, we performed simulations of molecular dynamics. We assessed amyloidogenic properties of the synthetic Aβ dimers in a time-dependent manner using thioflavin-T assay, electrophoresis and transmission electron microscopy. At last, we induced AD-like behaviors in ICR mice by direct infusion of Aβ peptides into the intracerebroventricular region and performed Y-maze / passive avoidance tests. Of the two constructs, the anti-parallel dimer showed substantial development of oligomers and fibrils. When administered by intracerebroventricular injection, the anti-parallel dimer induced hippocampus-dependent learning and memory deficits in normal mice, similar to the monomer with doubled concentration. Our data place the anti-parallel conformation as the neurotoxic and amyloidogenic structure of Aβ dimers.
Treatment timing and the effects of rhythm control strategy in patients with atrial fibrillation: nationwide cohort study (2021)

Early initiation of rhythm control treatment was associated with a lower risk of adverse cardiovascular outcomes than rate control treatment in patients with recently diagnosed atrial fibrillation. This association was not found in patients who had had atrial fibrillation for more than one year.
Generalized feedforward filters with complex poles (2003)

The authors propose an extension to an existing structure, the gamma filter, replacing the real pole on the tap-to-tap transfer function with a pair of complex conjugate poles and a zero. The new structure is, like the gamma filter, an IIR filter with restricted feedback whose stability is trivial to check. While the gamma filter decouples the memory depth from the filter order for low-pass signals, the proposed structure decouples the memory depth and the central frequency from the filter order for band-pass signals. The learning equations of the model parameters are presented and shown to introduce an additive O(p) complexity to the backpropagation algorithm, where p is the filter order. The error surface for a linear filter is investigated in a system identification context, and the presence of local minima is confirmed. The performance of the proposed model was found to be better than that of the time-delay neural net in a nonlinear system identification context.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On capacity of a class of acoustic channels (2014)

We use a per-path Rician fading model to analyze the capacity of acoustic channels, and provide experimental data to confirm the practicality of simulation results. Three power allocation policies are considered: water-filling, uniform power allocation across selected, channel-favored frequencies (“on-off” carriers in an OFDM system), and uniform power allocation across all carriers irrespective of the channel (“all-on”). The impact of channel estimation errors and feedback delay is taken into account. The three policies are found to differ little in terms of the achievable rate, and to suffer similar loss from imperfect channel knowledge at the receiver (about 1 bps/Hz loss from 4 bps/Hz at 20 dB for the experimental channel). Unlike water-filling and on-off power allocation, which are additionally sensitive to outdated channel feedback, all-on uniform power allocation does not require feedback and is simple to implement, thus emerging as a justified practical solution.
Externally-driven H-mode studies in CCT (1996)

Test particle radial flux surface excursions are reduced during the H-mode. Particle transport is reduced by a factor of 10 in the H-mode, but energy confinement increases are small. In the H-mode the evolution of poloidally resolved turbulent statistics are not explained by published theory. Turbulent momentum transport leads to a concentration of poloidal momentum within the transport barrier, and compressibility leads to poloidal shock-like phenomena. The electron distribution functions may be modified by this shock, leading to kinetic instabilities. A physics-based understanding of the H-mode must therefore include toroidal effects combined with an adequate treatment of particle orbits, plasma compressibility and associated kinetic effects, and at least a two-species model of turbulent transport. The results suggest that rapid poloidal core-plasma rotation could form core transport barriers without reliance on fluid shear or reversed magnetic shear effects.
Synthesis and application of <scp>L</scp>-<i>N</i>-Boc-<i>N</i>-methyl-β-hydroxyvaline in the preparation of a depsipeptide (2005)

Enantiopure (&gt;99% ee) L-N-tert-butyloxycarbonyl-N-methyl-β-hydroxyvaline (2) was synthesized in six steps and 43% overall yield from D-serine methyl ester (5). Methyl (4S)-N-(9-phenylfluoren-9-yl)-oxazolidine-4-carboxylate (7) was prepared in two steps and 73% yield by N-phenylfluorenation of 5 followed by cyclization of N-(PhF)amino alcohol 6 with formaldehyde and catalytic p-toluenesulfonic acid (PhF = 9-phenylfluoren-9-yl). The addition of MeLi to oxazolidine carboxylate 7 produced the tertiary alcohol 8 in 91% yield. Oxazolidines 8 equilibrated with oxazolidine 9 under acidic conditions. Reduction of pure 8 or the mixture of oxazolidines 8 and 9 with NaCNBH 3 and hydrochloric acid in anhydrous dioxane afforded N-methyl amino diol 11 in 86%92% yields. Attempts to selectively oxidize N-(PhF)amino diol 11 were unsuccessful; however, hydrogenation of 11 in the presence of di-tert-butyl dicarbonate gave the corresponding N-(Boc)amino diol 12 in 82% yield. Selective oxidation of diol 12 was performed using a cocktail containing TEMPO free radical, NaClO 2 , and NaOCl to give L-N-Boc-N-methyl-β-hydroxyvaline (2) in 87% yield. Coupling of β-hydroxyvaline 2 and (S)-2-hydroxy-3-methylbutanoate (15) was accomplished by using the methodology of Mitsunobu to provide depsipeptide Boc-(S)-HOMeVal-(R)-Hmb (4) for use as a building block in the synthesis of the cyclic antifungal depsipeptide aureobasidin B.Key words: N-methylated amino acid, serine, depsipeptide, aureobasidin.