gebhart/patrepeval huggingface dataset:
A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation (2019)

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Bacterial populations that colonize a host can play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based on assessment of whether serial samples represent a single population or distinct colonization events. With the use of whole genome sequencing to determine genetic distance between isolates, a common solution to estimate acquisition and clearance rates has been to assume a fixed genetic distance threshold below which isolates are considered to represent the same strain. However, this approach is often inadequate to account for the diversity of the underlying within-host evolving population, the time intervals between consecutive measurements, and the uncertainty in the estimated acquisition and clearance rates. Here, we present a fully Bayesian model that provides probabilities of whether two strains should be considered the same, allowing us to determine bacterial clearance and acquisition from genomes sampled over time. Our method explicitly models the within-host variation using population genetic simulation, and the inference is done using a combination of Approximate Bayesian Computation (ABC) and Markov Chain Monte Carlo (MCMC). We validate the method with multiple carefully conducted simulations and demonstrate its use in practice by analyzing a collection of methicillin resistant Staphylococcus aureus (MRSA) isolates from a large recently completed longitudinal clinical study. An R-code implementation of the method is freely available at: https://github.com/mjarvenpaa/bacterial-colonization-model.
Deposition of Gallium Nitride Epilayers by OMVPE (1998)

Abstract : Gallium nitride films have been deposited on sapphire substrates by organometallic vapor phase epitaxy and their structural quality assessed by Transmission Electron Microscopy and high resolution x-ray diffraction. The dominant type of threading dislocation was determined to be pure edge with Burgers vector 1/3 . Dislocations are arranged into arrays corresponding to low angle twist grain boundaries with typical in-basal-plane misorientations of about 1 degree. The granular structure of the GaN film originates at the nucleation growth phase within low temperature GaN buffer. A new figure of merit for structural quality of nitride films (phi scan value) was proposed in order to track the amount of twist. New defects characteristic of GaN and AlGaN films have been observed and reported for the first time. These are nano-pipes or nano-tubes, empty cylinders with diameters of approximately 10 nanometers propagating along the c-axis. Nano-tubes penetrate the entire film thickness and terminate in the facetted surface crater. Their density correlates with oxygen and silicon concentration in the film and can exceed 10(exp5)/cm2 in AlGaN.
Flash memory solid state disks (2010)

Flash memory is increasingly being used as a storage medium for mobile devices such as mobile phones, PMPs, and UMPCs because of low power consumption, fast random access, and high shock & vibration resistance. In this talk, first I will explain the basics and current trends of NAND flash memory, the type of flash memory used for storage applications. Second, I will introduce the concept of a flash memory solid state disk (SSD) that provides an interface identical to that of hard disk drive (HDD) out of flash memory. Third, I will explain the motivations, design, implementation, and performance evaluation of the Hydra solid state disk that our research group has developed. Finally, I will conclude with future research directions on flash memory in general and solid state disks in particular.
Tribological properties of oleic acid-modified graphene as lubricant oil additives (2011)

Liquid phase exfoliated graphene sheets were modified by oleic acid and dispersed in lubricant oils as additives. The tribological behaviours of graphene-contained oils were investigated using a four-ball tribometer. The lubricant with optimized graphene concentrations of 0.02–0.06 wt% showed enhanced friction and anti-wear performance, with friction coefficient and wear scar diameter reduced by 17% and 14%, respectively.
Extensive homology between the subunits of the phytohemagglutinin mitogenic proteins derived from Phaseolus vulgaris. (1975)

The phytohemagglutinin mitogenic proteins derived from Phaseolus vulgaris comprise a class of five glycoproteins that are isomeric tetramers composed of varying proportions of two different subunits (L and R). Within the native tetramer, the L subunit is a potent leukoagglutinin and mitogen that lacks hemagglutinating properties, whereas the R subunit is a potent hemagglutinin with little or no mitogenic activity. The subunits have been isolated in homogeneous form by isoelectric focusing in 8 M urea. Previous work has shown that they have equal molecular weights and differ in amino-acid sequence from residues 1-7, but are identical in positions 8-24 [(1973) J. Exp. Med. 138, 939-951]. We now report amino-acid composition studies which reveal striking similarities between the subunits. Both lack methionine and cysteine. The twelfth residue in each subunit is a glycosylated asparagine, with the identical carbohydrate composition in each. The last three residues of the subunits, as determined by carboxypeptidase A digestion, are identical. Tryptic peptide mapping of the succinylated phytohemagglutinin subunits reveals a high degree of similarity. We conclude that the substantial difference in biological properties among the tetrameric phytohemagglutinin mitogens is a result of relatively restricted differences in the primary structure of their constituent subunits.
Molecular dynamics simulations of pentacene thin films: The effect of surface on polymorph selection (2010)

Molecular dynamics simulations were performed for multi-layer pentacene thin films using a simple model surface. Two pentacene polymorphs, low-temperature (LT) and high-temperature (HT), were compared by examining their stability on a substrate and under free surface conditions. It was found that the LT polymorph was destabilised by the presence of substrate and free surface effects, which transformed the HT-polymorph over the course of our simulations. Suppression of the molecular fluctuations along the long molecular axis by these surface effects was suggested as the source of this destabilisation.
Wavelet Scattering on the Pitch Spiral (2016)

We present a new representation of harmonic sounds that linearizes the dynamics of pitch and spectral envelope, while remaining stable to deformations in the time-frequency plane. It is an instance of the scattering transform, a generic operator which cascades wavelet convolutions and modulus nonlinearities. It is derived from the pitch spiral, in that convolutions are successively performed in time, log-frequency, and octave index. We give a closed-form approximation of spiral scattering coefficients for a nonstationary generalization of the harmonic source-filter model.
Crowd analytics via one shot learning and agent based inference (2016)

For the purposes of inferring social behavior in crowded conditions, three concepts have been explored: 1) the GE Sherlock system which makes use of computer vision algorithms for the purposes of the opportunistic capture of various of social cues, 2) a one shot learning paradigm where behaviors can be identified based on as few as a single example and 3) an agent based approach to inference where generative models become the basis for social behavior recognition. The Sherlock system makes use of tracking, facial analysis, gaze estimation and upper body motion analysis. The one-shot learning paradigm makes use of semantically meaningful affects as descriptors. The agent based inference methods allows for the incorporation of cognitive models as a basis for inference.
Flexible strength-improved and crack-resistant biocomposites based on plasticised wheat gluten reinforced with a flax-fibre-weave Part A Applied science and manufacturing (2017)

This paper presents strength-improved and crack-resistant wheat gluten biocomposites, using flax-fibre-weaves as reinforcement. The composites were produced by dip-coating of the weave into a wheat gluten/glycerol (WGG) solution, or by compression moulding. The most extensive coverage and wetting of the flax yarns occurred during the compression moulding, and the adhesion between the fibres and the matrix increased with increasing glycerol content. The compression-moulded sheets were, at a comparable flax content, stiffer than those produced by dipping, whereas their strength was similar and their extensibility slightly lower. Tensile tests on notched samples showed that the flax yarn improved the crack-resistant properties significantly; the maximum stress increased from 2 to 29MPa using a content of 19wt.% flax fibres. A clear advantage of this novel mechanically flexible biocomposite is that it can be shaped plastically under ambient conditions, while at the same time providing in-plane stiffness, strength and crack-resistance.
Transcatheter aortic valve implantation compared with surgical aortic valve replacement in patients with anaemia (2017)

These results suggest that TAVI is not superior to SAVR in patients with anaemia.
INTERGENERATIONAL CONTRACTION OF THE CTG REPEATS IN 2 FAMILIES WITH MYOTONIC DYSTROPHY TYPE 1 (2009)

Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by the expansion of an unstable CTG trinucleotide repeat at chromosome region 19q13.3.1 The number of CTG repeats is unstable in the abnormal range and usually increases in size in successive generations, in association with anticipation.2,3 A decrease in the CTG repeat size during transmission from parents to child can also occur in about 6.4% of transmissions, most frequently during paternal transmissions (10%).4 In the French-Canadian DM1 population, intergenerational contractions occur in about 7.4% of transmissions, all in cases of paternal transmission. We report here 2 French-Canadian DM1 families with paternal transmission, both originating from the Saguenay-Lac St-Jean, in which all affected children display CTG contractions. Although it was already reported that intergenerational contractions could be observed in several sibs in a same family, it was not noted whether this occurred in all affected sibs.4 Overall, these observations support the existence of a paternal factor that prevents CTG expansion.

### Case reports.

The pedigree of the 2 families and Southern blot analysis are shown in the figure.





Figure Family tree and Southern blot

Pedigree of family (A, B). (C, D) Southern blot analysis. The DNA (3–5 μg) was …
Synthesis of mono‐dispersed spherical silica particles containing covalently bonded chromophores (2005)

Organic-inorganic ultraviolet (UV) active hybrid materials have been prepared by a sol-gel process from benzophenone derivatives and tetraethylorthosilicate. The silica particles are spherical in shape and have a narrow size distribution which remains unchanged up to organic chromophore concentrations of 0.2 mmol g(-1). At higher concentrations the spheres become less regular and fuse. A dependence of the material absorption properties on the particle size (at the same organic chromophore concentration) and on the concentration of surface grafted chromophores was noted. The most effective UV filter materials were found in a combination of silica incorporated chromophores and surface grafted chromophores at an overall low chromophore concentration. A comparison of the photostability of chromophores at standardized UV irradiation revealed an increase in stability for silica incorporated and surface immobilized benzophenone compared to benzophenone in a homogeneous solution.
Cross-layer congestion and contention control for wireless ad hoc networks (2008)

We consider joint congestion and contention control for multihop wireless ad hoc networks, where the goal is to find optimal end-to-end source rates at the transport layer and per-link persistence probabilities at the medium access control (MAC) layer to maximize the aggregate source utility. The primal formulation of this problem is non-convex and non-separable. Under certain conditions, by applying appropriate transformations and introducing new variables, we obtain a decoupled and dual-decomposable convex formulation. For general non-logarithmic concave utilities, we develop a novel dual-based distributed algorithm using the subgradient method. In this algorithm, sources at the transport layer adjust their log rates to maximize their net benefits, while links at the MAC layer select transmission probabilities proportional to their conceived contribution to the system reward. The two layers are connected and coordinated by link prices. Our solutions enjoy the benefits of cross-layer optimization while maintaining the simplicity and modularity of the traditional layered architecture.
Organically modified silica nanoparticles as drug delivery vehicles in photodynamic therapy (2011)

To investigate the effect of hydrophobicity, charge and size of photosensitizers (PS) on their encapsulation efficiency in organically modified silica nanoparticles (ORMOSIL), a series of alkyl ether analogs of 2-(1′-hexyloxyethyl)-2-devinyl pyropheophorbide-a (HPPH) containing varied number of carbon units, HPPH with anionic and cationic functionalities, and HPPH analogs with molecular weight ranging from ~630 to 6000 Daltons were synthesized. Our preliminary results suggest that these factors play a significant role in encapsulation of the photosensitizers and their release from ORMOSIL nanoparticles. The synthesis and characterization of PS-encapsulated ORMOSIL and a comparative study on the effect of PS size, lipophilicity and charge on encapsulation efficiency, photophysical characteristics and release kinetics are discussed.
End-to-End Deep ROI Image Compression (2020)

In this paper, we present the effectiveness of image compression based on a convolutional auto encoder (CAE) with region of interest (ROI) for quality control. We propose a method that adapts image quality for prioritized parts and non-prioritized parts for CAE-based compression. The proposed method uses annotation information for the distortion weights of the MS-SSIM-based loss function. We show experimental results using a road damage image dataset that is used to check damaged parts and an image dataset with segmentation data (ADE20K). The experimental results reveals that the proposed weighted loss function with CAE-based compression from F. Mentzer et al. learns some characteristics and preferred bit allocations of the prioritized parts by end-to-end training. In the case of using road damage image dataset, our method reduces bpp by 31% compared to the original method while meeting quality requirements that an average weighted MS-SSIM for the road damaged parts be larger than 0.97 and an average weighted MS-SSIM for the other parts be larger than 0.95.
On the Performance of k-ary n-cube Interconnection Networks (1986)

The performance of k-ary n-cube interconnection networks is analyzed under the assumption of constant wire bisection. It is shown that low-dimensional k-ary n-cube networks (e.g., tori) have lower latency and higher hot-spot throughput than high-dimensional networks (e.g., binary n-cubes) with the same bisection width.
Conformation and membrane activity of an analogue of the peptaibol antibiotic trichogin GA IV with a lipophilic amino acid at the N-terminus (1998)

We have synthesized by solution-phase methods two analogues of the 11-residue lipopeptaibol antibiotic trichogin GA IV in which the N-terminal n-octanoyl group is replaced either by an N-acetylated 2-amino-2-methyl-l-undecanoic acid or by an N-acetylated α-aminoisobutyric acid. CD, FTIR absorption, and NMR analyses unequivocally show that the main structural features of trichogin GA IV are preserved in these analogues. Since only the peptide containing the lipophilic chain exhibits membrane-modifying properties, these results strongly support the view that moving the long acyl moiety from the Nα-blocking group to the side chain of the N-terminal extra-residue does not affect the conformational properties or the membrane activity of trichogin GA IV. © 1998 European Peptide Society and John Wiley & Sons, Ltd.
Atomic incremental garbage collection and recovery for a large stable heap (1993)

A stable heap is storage that is managed automatically using garbage collection, manipulated using atomic transactions, and accessed using a uniform storage model. These features enhance reliability and simplify programming by preventing errors due to explicit deallocation, by masking failures and concurrency using transactions, and by eliminating the distinction between accessing temporary storage and permanent storage. Stable heap management is useful for programming languages for reliable distributed computing, programming languages with persistent storage, and object-oriented database systems. Many applications that could benefit from a stable heap (e.g., computer-aided design, computer-aided software engineering, and office information systems) require large amounts of storage, timely responses for transactions, and high availability. We present garbage collection and recovery algorithms for a stable heap implementation that meet these goals and are appropriate for stock hardware. The collector is incremental: it does not attempt to collect the whole heap at once. The collector is also atomic: it is coordinated with the recovery system to prevent problems when it moves and modifies objects. The time for recovery is independent of heap size, even if a failure occurs during garbage collection.
Inhibition of growth and induction of apoptosis in human lung cancer cells by Br-oxph (2014)

The study was aimed at evaluating apoptotic potential of Br-oxph (4-bromoN,N-diethyl-5,5-dimethyl-2,5-dihydro-1,2-oxaphosphol-2-amine 2-oxide) in vitro. The dose response effect of Br-oxph (dose range 1-3 mg/ml, for 48 h) on SK-MES-1 cells viability was determined by means of WST-1 cell proliferation assay. The half maximal inhibitory concentration (??50) value was determined - 1.8 mg/ml. The ability of the compound tested to induce apoptosis was tested by ELISA to detect cellular DNA fragmentation. We provided a quantitative assessment of the apoptotic potential of Br-oxph in human lung carcinoma cells at concentrations corresponding to ??50 and 2???50 for 3 hours. Treatment with 2???50 significantly increased the amount of cytoplasmic DNA-fragments. Results obtained from the present study confirm that Br-oxph target the cancerous cells towards apoptosis.
Supplemental Figure 4 from SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells (2023)

&lt;p&gt;FaDu-mock and FaDu-SMAD4 cells were serum starved for 24 hours and then incubated with DMSO or JNK inhibitor (SP600125) for 24 hours. Cell lysates were analyzed by (A) western blot for SMAD4, total and phosphorylated JNK (T183/Y185), and GAPDH as a loading control. (B) AlamarBlue assay measuring cell viability with JNKi or DMSO treatment for 48 hours. (C) Matrigel colony growth assay with 5uM JNK inhibitor for 7 days. FaDu-mock and FaDu-SMAD4 cells were serum starved and then incubated with either DMSO or MEK inhibitor (U0126) for 24 hours. Cell lysates were analyzed by (D) western blot for SMAD4, total and phosphorylated MAPK (T202/Y204), and GAPDH as a loading control. (E) AlamarBlue assay measuring cell viability with MEKi or DMSO treatment for 48 hours. (F) Clonogenic survival in response to 5uM MEKi was examined by the Matrigel colony growth assay for 7 days.&lt;/p&gt;
Practical interference alignment and cancellation for MIMO underlay cognitive radio networks with multiple secondary users (2013)

In the underlay cognitive radio approach, secondary users (SUs) are allowed to transmit their messages as long as the negative impact on the performance of the primary user (PU) is below a certain threshold. We consider a MIMO underlay cognitive radio network with a single PU and multiple SUs. We propose a practical interference alignment and cancellation scheme that not only avoids interference at the PU, but also optimizes SUs' performance in terms of degrees of freedom. Given any SU, the interference from the other SUs is aligned, and the interference at the SU from the PU is cancelled in the spatial domain. We give the feasibility condition for achieving interference alignment and cancellation. Due to the NP-hardness of the problem, we resort to approximation algorithms. We also consider practical issues for implementation. The effectiveness of the proposed scheme is shown by simulation results.
ChemInform Abstract: Photochemical Conversion of Sulfonium Salts to Sulfides via a 1,3‐Sigmatropic Rearrangement. (1986)

Abstract Aus den Sulfoniumsalzen (I) entstehen bei der Photolyse in Acetonitril die Naphthyl‐methyl‐sul?de (II) und (III) neben den Acetamiden (IV).
Adaptive Response Enzyme AlkB Preferentially Repairs 1-Methylguanine and 3-Methylthymine Adducts in Double-Stranded DNA (2016)

The AlkB protein is a repair enzyme that uses an α-ketoglutarate/Fe(II)-dependent mechanism to repair alkyl DNA adducts. AlkB has been reported to repair highly susceptible substrates, such as 1-methyladenine and 3-methylcytosine, more efficiently in ss-DNA than in ds-DNA. Here, we tested the repair of weaker AlkB substrates 1-methylguanine and 3-methylthymine and found that AlkB prefers to repair them in ds-DNA. We also discovered that AlkB and its human homologues, ABH2 and ABH3, are able to repair the aforementioned adducts when the adduct is present in a mismatched base pair. These observations demonstrate the strong adaptability of AlkB toward repairing various adducts in different environments. (Chemical Equation Presented).
Numerical differentiation in magnetic field postprocessing (1996)

Postprocessing encompasses graphic display and numerical computation. The critical process in this work is numerical differentiation. Methods of numerical differentiation of approximate solutions may be divided into three groups: direct numerical differentiation, smoothing methods based on superconvergence properties, and methods that exploit properties the solution is known to possess though the numerical approximation does not. The choice of method is determined by the problem, as well as the use to which derivatives are put: graphical display, local field calculation, mesh refinement or a a posteriori error estimation. The paper compares current derivative extraction methods and reviews progress in this field, with particular attention to superconvergent patch recovery and methods based on Green's second identity. A new modification of the method based on Green's second identity is presented, to include inhomogeneous and discontinuous materials.
Centre for Green Chemistry, Monash University, Australia (2001)

Abstract The Centre for Green Chemistry is an Australian Research Council (ARC) Special Research Centre (SRC), located at Monash University in Melbourne, Australia. SRCs are funded by the Australian federal government, via the vehicle of the ARC, with the express goal of supporting excellent basic research and research training that has strong international links. The goal of the center is to provide a fundamental scientific base for future green chemical technology, identifying niche areas in the Australian context and beyond. Establishment of this SRC and its modus operandi are discussed.