gebhart/patrepeval huggingface dataset:
Dopant activation and ultralow resistance ohmic contacts to Si-ion-implanted GaN using pressurized rapid thermal annealing (2004)

Activation annealing of Si implants in metalorganic-chemical-vapor-deposition-grown GaN has been studied for use in ohmic contacts. Si was implanted in semi-insulating GaN at 100keV with doses from 5×1014to1.5×1016cm−2. Rapid thermal annealing at ∼1500°C with 100bar N2 overpressure was used for dopant activation, resulting in a minimum sheet resistance of 13.9Ω∕square for a dose of 7×1015cm−2. Secondary-ion-mass-spectroscopy measurements showed a post-activation broadening of the dopant concentration peak by 20nm (at half the maximum), while x-ray triple-axis ω–2θ scans indicated nearly complete implant damage recovery. Transfer-length-method measurements of the resistance of Ti∕Al∕Ni∕Au contacts to activated GaN:Si (5×1015cm−2 at 100keV) indicated contact resistances of 0.07 and 0.02Ωmm for as-deposited and subsequently annealed contacts, respectively.
A consistent explanation of the role of the SiN composition on the program/retention characteristics of MANOS and NROM like memories (2010)

In this work, we show that a detailed atomistic model of SiN defects provides a consistent explanation of the program/erase/retention characteristics of both NROM and MANOS charge-trap cells. Our analysis of devices with SiN layers of different stoichiometry is also consistent with original KFM measurements of trapped charge drift in SiN layers.
A Deep Neural Network Compression Pipeline: Pruning, Quantization, Huffman Encoding (2015)

Neural networks are both computationally intensive and memory intensive, making them difficult to deploy on embedded systems with limited hardware resources. To address this limitation, we introduce deep compression, a three stage pipeline: pruning, trained quantization and Huffman coding, that work together to reduce the storage requirement of neural networks by 35x to 49x without affecting their accuracy. Our method first prunes the network by learning only the important connections. Next, we quantize the weights to enforce weight sharing, finally, we apply Huffman coding. After the first two steps we retrain the network to fine tune the remaining connections and the quantized centroids. Pruning, reduces the number of connections by 9x to 13x; Quantization then reduces the number of bits that represent each connection from 32 to 5. On the ImageNet dataset, our method reduced the storage required by AlexNet by 35x, from 240MB to 6.9MB, without loss of accuracy. Our method reduced the size of VGG-16 by 49x from 552MB to 11.3MB, again with no loss of accuracy. This allows fitting the model into on-chip SRAM cache rather than off-chip DRAM memory. Our compression method also facilitates the use of complex neural networks in mobile applications where application size and download bandwidth are constrained. Benchmarked on CPU, GPU and mobile GPU, compressed network has 3x to 4x layerwise speedup and 3x to 7x better energy efficiency.
A Fixed-Point Theoretic Solution of the Hamilton-Jacobi Equation and Its Application to Nonlinear H&infin; Control (2009)

This paper proposes a novel approach to the Hamilton-Jacobi equation (HJE). Through a functional analytic formulation, a stabilizing solution of the HJE is derived from a fixed-point of a nonlinear mapping on a function space. A sufficient condition for the existence of such a fixed-point is derived quantitatively. For computing the fixed-point, a numerical method based on optimization techniques is introduced. Based on these results, the nonlinear H&infin; control problem is reconsidered. Simple numerical examples show that the resulting controllers have enough performance and computed solutions can approximate their analytical counterparts almost uniformly in the entire region under consideration.
Mg-rich precipitates in the p-type doping of InGaN-based laser diodes (2002)

Uniformly distributed precipitates have been observed by transmission electron microscopy in the p-type layers of laser structures. The precipitate density decreases with decreasing flow of biscyclopentadienyl-magnesium (Cp2Mg), and the hole concentration in the laser structure was higher for a lower precipitate density. The higher hole concentration reduces the threshold current density and improves the internal quantum efficiency of the laser because of the higher number of holes available for radiative recombination. The lasers with higher precipitate density also exhibit a higher resistance. The threshold voltage was reduced 30% from 20.8 V for lasers with a high precipitate density to 14.3 V for lasers with a lower precipitate density due to the lower resistance.
Strict Conservation yet Non-Essential Nature of Plasmid Gene bba40 in the Lyme Disease Spirochete Borrelia burgdorferi (2023)

The highly segmented genome of Borrelia burgdorferi, the tick-borne bacterium that causes Lyme disease, is composed of a linear chromosome and more than 20 co-existing endogenous plasmids. Many plasmid-borne genes are unique to B. burgdorferi and some have been shown to provide essential functions at discrete points of the infectious cycle between a tick vector and rodent host. In this study, we investigated the role of <i>bba40</i>, a highly conserved and differentially expressed gene on a ubiquitous linear plasmid of B. burgdorferi. In a prior genome-wide analysis, inactivation of <i>bba40</i> by transposon insertion was linked with a noninfectious phenotype in mice, suggesting that conservation of the gene in the Lyme disease spirochete reflected a critical function of the encoded protein. To address this hypothesis, we moved the <i>bba40::Tn</i> allele into a similar wild-type background and compared the phenotypes of isogenic wild-type, mutant and complemented strains <i>in vitro</i> and throughout the <i>in vivo</i> mouse/tick infectious cycle. In contrast to the previous study, we identified no defect in the ability of the <i>bba40</i> mutant to colonize the tick vector or murine host, or to be efficiently transmitted between them. We conclude that <i>bba40</i> joins a growing list of unique, highly conserved, yet fully dispensable plasmid-borne genes of the Lyme disease spirochete. We infer that the experimental infectious cycle, while including the tick vector and murine host, lacks key selective forces imposed during the natural enzootic cycle. <b>IMPORTANCE</b> The key finding of this study contradicts our premise that the ubiquitous presence and strict sequence conservation of a unique gene in the Lyme disease spirochete, Borrelia burgdorferi, reflect a critical role in either the murine host or tick vector in which these bacteria are maintained in nature. Instead, the outcome of this investigation illustrates the inadequate nature of the experimental infectious cycle currently employed in the laboratory to fully model the enzootic cycle of the Lyme disease spirochete. This study also highlights the importance of complementation for accurate interpretation of mutant phenotypes in genetic studies of Borrelia burgdorferi.
Demo Abstract: More Than Two Decades of IoT (2020)

While the popularity of the acronym IoT is fairly new, the concept certainly is not. In this demo, we will illustrate the use of remote communications (all the way back to POTS) for monitoring and managing what are now called IoT systems.
Effect of 70-nm silica particles on the toxicity of acetaminophen, tetracycline, trazodone, and 5-aminosalicylic acid in mice. (2011)

Exposure to nano-sized particles is increasing because they are used in a wide variety of industrial products, cosmetics, and pharmaceuticals. Some animal studies indicate that such nanomaterials may have some toxicity, but their synergistic actions on the adverse effects of drugs are not well understood. In this study, we investigated whether 70-nm silica particles (nSP70), which are widely used in cosmetics and drug delivery, affect the toxicity of a drug for inflammatory bowel disease (5-aminosalicylic acid), an antibiotic drug (tetracycline), an antidepressant drug (trazodone), and an antipyretic drug (acetaminophen) in mice. Co-administration of nSP70 with trazodone did not increase a biochemical marker of liver injury. In contrast, co-administration increased the hepatotoxicity of the other drugs. Co-administration of nSP70 and tetracycline was lethal. These findings indicate that evaluation of synergistic adverse effects is important for the application of nano-sized materials.
Immunobiology and host response. (2007)

Herpesviruses began to evolve prior to the development of acquired immunity (Arzul et al., 2002). It is therefore likely that evasion of innate immunity is an ancient function of alphaherpesviruses. Additional immune evasion functions have developed to adapt to the diverse repertoires of B- and T-cell immune receptors that characterize acquired immunity (Roizman and Pellet, ; Littman et al., 1999). Immune evasion is covered in detail elsewhere in this volume. The innate and acquired immune responses to HSV are relevant to preventative and therapeutic vaccines for HSV, HSV-induced immunopathology, and the use of modified HSV for gene or cancer therapy. While human studies are, of necessity, observational or ex vivo in nature and seldom access sites of neuronal latency, we review them in detail because of their medical relevance. The excellent tools available for murine studies, including exquisite control of the DNA sequence of HSV challenge strains, and of the phenotype and genotype of recipient animals, are yielding dramatic new insights as well. Reactivation of HSV from neuronal latency is less frequent in mice than in humans, limiting immunologic studies of this challenging phenomenon. Readers are referred to excellent reviews (Schmid and Rouse, ; Nash, ; Lopez et al., , Simmons et al., ; Kohl,1992) for models and materials that cannot be covered in detail.
Dynamic Scheduling for Federated Edge Learning with Streaming Data (2023)

In this work, we consider a Federated Edge Learning (FEEL) system where training data are randomly generated over time at a set of distributed edge devices with long-term energy constraints. Due to limited communication resources and latency requirements, only a subset of devices is scheduled for participating in the local training process in every iteration. We formulate a stochastic network optimization problem for designing a dynamic scheduling policy that maximizes the time-average data importance from scheduled user sets subject to energy consumption and latency constraints. Our proposed algorithm based on the Lyapunov optimization framework outperforms alternative methods without considering time-varying data importance, especially when the generation of training data shows strong temporal correlation.
Reproducibility of tract‐specific magnetization transfer and diffusion tensor imaging in the cervical spinal cord at 3 tesla (2009)

Damage to specific white matter tracts within the spinal cord can often result in the particular neurological syndromes that characterize myelopathies such as traumatic spinal cord injury. Noninvasive visualization of these tracts with imaging techniques that are sensitive to microstructural integrity is an important clinical goal. Diffusion tensor imaging (DTI)- and magnetization transfer (MT)-derived quantities have shown promise in assessing tissue health in the central nervous system. In this paper, we demonstrate that DTI of the cervical spinal cord can reliably discriminate sensory (dorsal) and motor (lateral) columns. From data derived from nine healthy volunteers, two raters quantified column-specific parallel (lambda(||)) and perpendicular (lambda(perpendicular)) diffusivity, fractional anisotropy (FA), mean diffusivity (MD), and MT-weighted signal intensity relative to cerebrospinal fluid (MTCSF) over two time-points separated by more than 1 week. Cross-sectional means and standard deviations of these measures in the lateral and dorsal columns were as follows: lambda(||): 2.13 +/- 0.14 and 2.14 +/- 0.11 microm(2)/ms; lambda(perpendicular): 0.67 +/- 0.16 and 0.61 +/- 0.09 microm(2)/ms; MD: 1.15 +/- 0.15 and 1.12 +/- 0.08 microm(2)/ms; FA: 0.68 +/- 0.06 and 0.68 +/- 0.05; MTCSF: 0.52 +/- 0.05 and 0.50 +/- 0.05. We examined the variability and interrater and test-retest reliability for each metric. These column-specific MR measurements are expected to enhance understanding of the intimate structure-function relationship in the cervical spinal cord and may be useful for the assessment of disease progression.
[Geriatry]. (2016)

n 2015, several studies about hypertension and TAVI emphasize the importance of individualizing treatment goals in very old or vulnerable patients. The anti-pneumococcal conjugate vaccine has demonstrated its effectiveness in community-acquired pneumonia and the arsenal against shingles is extended by a subunit vaccine. A clinical trial confirms the ineffectiveness of testosterone supplementation in arteriosclerotic disease but not its safety. Regarding dementia, a rigorous study shows that a multimodal approach can reduce the risk of cognitive decline. The value of imaging technologies using Tau protein radiotracers is confirmed for monitoring the evolution of Alzheimer's disease and the latest studies about anti-amyloid vaccines finally demonstrate encouraging results.
Inotuzumab ozogamicin as single agent in pediatric patients with relapsed and refractory acute lymphoblastic leukemia: results from a phase II trial (2022)

Inotuzumab Ozogamicin is a CD22-directed antibody conjugated to calicheamicin, approved in adults with relapsed or refractory (R/R) B cell acute lymphoblastic leukemia (BCP-ALL). Patients aged 1-18 years, with R/R CD22 + BCP-ALL were treated at the RP2D of 1.8 mg/m<sup>2</sup>. Using a single-stage design, with an overall response rate (ORR) ≤ 30% defined as not promissing and ORR > 55% as expected, 25 patients needed to be recruited to achieve 80% power at 0.05 significance level. Thirty-two patients were enrolled, 28 were treated, 27 were evaluable for response. The estimated ORR was 81.5% (95%CI: 61.9-93.7%), and 81.8% (18/22) of the responding subjects were minimal residual disease (MRD) negative. The study met its primary endpoint. Median follow up of survivors was 16 months (IQR: 14.49-20.07). One year Event Free Survival was 36.7% (95% CI: 22.2-60.4%), and Overall Survival was 55.1% (95% CI: 39.1-77.7%). Eighteen patients received consolidation (with HSCT and/or CAR T-cells therapy). Sinusoidal obstructive syndrome (SOS) occurred in seven patients. MRD negativity seemed correlated to calicheamicin sensitivity in vitro, but not to CD22 surface expression, saturation, or internalization. InO was effective in this population. The most relevant risk was the occurrence of SOS, particularly when InO treatment was followed by HSCT.
Comparison of Software Tools for microRNA Next Generation Sequencing Data Analysis (2016)

Next-generation sequencing (NGS) appears to be very promising to study miRNAs comprehensively, which can not only profile known miRNAs, but also predict novel miRNAs. There are an increasing number of software tools developed for microRNA NGS data analysis. Nevertheless, an overall comparison of these tools is still rare and how divergent these software tools are is still unknown, which confuses the researchers to select an optimal tool. In our study, we performed a comprehensive comparison of seven representative software tools based on real data in various aspects, including detected known miRNAs, miRNAs abundance, differential expression and predicted novel miRNAs. We presented the divergences and similarities of these tools and gave some basic evaluation of the tools’ performances. In addition, some extreme cases in miRNAkey were explored. The comparison of these tools suggests that the performances of these software tools are very diverse and the caution is necessary to take when choosing a software tool. The summarization of the tools’ features and comparison of their performances in our study will provide useful information for the researchers to promote their selection of an appropriate software tool.
Supplementary Data from ErbB3 Ablation Impairs PI3K/Akt-Dependent Mammary Tumorigenesis (2023)

&lt;p&gt;Supplementary Figures S1-S3; Supplementary Methods.&lt;/p&gt;
Conception et synthèse de dendrimères séquencés de type Janus : Etude de leur organisation supramoléculaire (2004)

Les dendrimeres sont des macromolecules hyperbranchees multifonctionnelles basees sur une architecture arborescente. En particulier, les materiaux dendritiques se sont reveles etre une source assez originale pour la conception de nouveaux types de produits mesomorphes. En effet, ces systemes presentent plusieurs avantages comme la possibilite de moduler la microsegregation par modification du coeur, des branches ou de la surface, permettant de fait le controle de l'organisation des mesophases et leur stabilite et donc ouvrant un nouveau champ d'investigation dans le domaine des cristaux liquides. Le but de ce travail de these a essentiellement consiste dans l'elaboration de nouveaux systemes dendritiques segmentes et dans l'etude de leurs proprietes physico-chimiques en fonction de la generation et de la nature chimique des blocs, en considerant plus particulierement les proprietes mesomorphes et de films minces de type Langmuir. Deux familles de nouveaux dendrimeres segmentes ont ete synthetisees selon la methode convergente et divergente - dendrimeres amphiphiles composes d'un bloc hydrophile et d'un bloc hydrophobe, et dendrimeres semifluores composes de blocs lipophobe et lipophile. Ces materiaux presentent des mesophases thermotropes dans lesquelles les dendrimeres s'auto-organisent en phases smectiques, colonnaires et/ou cubiques selon le type d'architecture chimique intrinseque de chaque compose. L'introduction du bloc fluore augmente beaucoup la stabilite thermique par rapport aux analogues amphiphiles. Les dendrimeres amphiphiles forment aussi des films minces homogenes de type Langmuir solides et liquides ce qui confirme leur nature de surfactant. En conclusion l'ingenierie moleculaire de dendrimeres en blocs permet d'obtenir des materiaux a proprietes mesomorphes bien controlees et egalement de conduire a des objets macromoleculaires presentant des proprietes lyotropes, contribuant ainsi a l'elaboration de bio-molecules modeles.
Successful Implementations of Integrated Asset Modeling (2017)

Abstract Oil and gas production systems are complex and usually consist of several production elements and corresponding models: (1) reservoirs modelled with reservoir simulators using geological and fluid data, (2) wells and surface production networks modelled with flow assurance applications, (3) surface processing facilities modelled in process simulators and (4) economic models. The traditional approach ("silo" approach) consists of modelling each part of the system independently from the others without considering upstream and/or downstream interactions. Integrated Asset Modelling (IAM) is a maturing solution incorporating effects of all the elements of an asset. This paper shows the benefits of successful IAM implementations in four highly complex and technically challenging assets around the globe. IAM aims to bring together all models of the value chain, from the reservoir to the point of sales. It enables us to perform numerous sensitivity analysis by changing any parameter across the value chain and investigate its influence on the entire system. The presentation concludes with guidelines and best practices for IAM implementation. It especially focuses on three very important issues faced when dealing with IAM: (1) software and model integration, (2) PVT consistency across the value chain and (3) optimization. Several case studies from the industry are used as illustration: diluent injection optimization for a heavy oil field in the North Sea, integration of reservoir and process models for a complex offshore multi-field asset in Indonesia, production allocation for an onshore multi-field asset in South America and API blending optimization for a multi-field asset in Middle East. The different case studies show that benefits of implementing an IAM approach can be significant and immediate: higher production, lower OPEX or better information for further CAPEX. In the current market situation, IAM approach is a cost-effective solution to optimize oil and gas production. By bringing together existing information and models from all parts of the production system, IAM breaks barriers between disciplines and enables an asset-scale overview that leads to more informed decision-making and ultimately higher profits for operators.
Over‐expression of heme oxygenase‐1 promotes oxidative mitochondrial damage in rat astroglia (2005)

Glial heme oxygenase-1 is over-expressed in the CNS of subjects with Alzheimer disease (AD), Parkinson disease (PD) and multiple sclerosis (MS). Up-regulation of HO-1 in rat astroglia has been shown to facilitate iron sequestration by the mitochondrial compartment. To determine whether HO-1 induction promotes mitochondrial oxidative stress, assays for 8-epiPGF(2alpha) (ELISA), protein carbonyls (ELISA) and 8-OHdG (HPLC-EC) were used to quantify oxidative damage to lipids, proteins, and nucleic acids, respectively, in mitochondrial fractions and whole-cell compartments derived from cultured rat astroglia engineered to over-express human (h) HO-1 by transient transfection. Cell viability was assessed by trypan blue exclusion and the MTT assay, and cell proliferation was determined by [3H] thymidine incorporation and total cell counts. In rat astrocytes, hHO-1 over-expression (x 3 days) resulted in significant oxidative damage to mitochondrial lipids, proteins, and nucleic acids, partial growth arrest, and increased cell death. These effects were attenuated by incubation with 1 microM tin mesoporphyrin, a competitive HO inhibitor, or the iron chelator, deferoxamine. Up-regulation of HO-1 engenders oxidative mitochondrial injury in cultured rat astroglia. Heme-derived ferrous iron and carbon monoxide (CO) may mediate the oxidative modification of mitochondrial lipids, proteins and nucleic acids in these cells. Glial HO-1 hyperactivity may contribute to cellular oxidative stress, pathological iron deposition, and bioenergetic failure characteristic of degenerating and inflamed neural tissues and may constitute a rational target for therapeutic intervention in these conditions.
Online reorganization in read optimized MMDBS (2011)

Query performance is a critical factor in modern business intelligence and data warehouse systems. An increasing number of companies uses detailed analyses for conducting daily business and supporting management decisions. Thus, several techniques have been developed for achieving near realtime response times - techniques which try to alleviate I/O bottlenecks while increasing the throughputs of available processing units, i.e. by keeping relevant data in compressed main-memory data structures and exploiting the read-only characteristics of analytical workloads.
DISCRETE VARIATIONAL OPTIMAL CONTROL (2016)

Abstract. This paper develops numerical methods for optimal control of mechanical systems in the Lagrangian setting. It extends the theory of discrete mechanics to enable the solutions of optimal control prob-lems through the discretization of variational principles. The key point is to solve the optimal control problem as a variational integrator of a specially constructed higher-dimensional system. The developed frame-work applies to systems on tangent bundles, Lie groups, underactuated and nonholonomic systems with symmetries, and can approximate ei-ther smooth or discontinuous control inputs. The resulting methods in-herit the preservation properties of variational integrators and result in numerically robust and easily implementable algorithms. Several the-oretical and a practical examples, e.g. the control of an underwater vehicle, will illustrate the application of the proposed approach. 1.