gebhart/patrepeval huggingface dataset:
The Combined Approach for Anomaly Detection Using Neural Networks and Clustering Techniques (2012)

Nowadays detection of new threats has become a necessity for secured communication to provide absolute data confidentiality, integrity and availability. Design and development of such an intrusion detection system in the communication world, should not only be new, accurate and fast but also effective in an environment encompassing the surrounding network. In this paper, a new approach is proposed for network anomaly detection by combining neural network and clustering algorithms. We propose modified Self Organizing Map algorithms which initially starts with null network and grows with the original data space as initial weight vector, updating neighbourhood rules and learning rate dynamically in order to overcome the fixed architecture and random weight vector assignment of simple SOM. New nodes are created using distance threshold parameter and their neighbourhood is identified using connection strength and its learning rule and the weight vector updation is carried out for neighbourhood nodes. The k-means clustering algorithm is employed for grouping similar nodes of Modified SOM into k clusters using similarity measures. Performance of the new approach is evaluated with standard bench mark dataset. The new approach is evaluated using performance metrics such as detection rate and false alarm rate. The result is compared with other individual neural network methods, which shows considerable increase in the detection rate and 2% false alarm rate.
On-chip synchronous communication between clock domains with quotient frequencies (2007)

Data transfer between arbitrary asynchronous clock domains is complicated, and practical solutions can be subject to synchronisation failure. But many practical systems use quotient frequencies and the direct conversion method (DCM) exploits this to achieve reliable data transfer without any handshaking. DCM minimises throughput, even between distant cores, is provably correct and has been assessed through transistor-level simulations.
Phase 1 study of the safety, pharmacokinetics, and antitumour activity of the <scp>BCL</scp>2 inhibitor navitoclax in combination with rituximab in patients with relapsed or refractory <scp>CD</scp>20<sup>+</sup> lymphoid malignancies (2015)

The oral BCL2 inhibitor navitoclax has moderate single-agent efficacy in chronic lymphocytic leukaemia (CLL) and minor activity in lymphoma in Phase 1 trials. Navitoclax synergizes with rituximab in preclinical models of B-cell lymphoid cancers. We report the safety, pharmacokinetics and clinical activity of this combination. Patients received navitoclax (200-325 mg) daily and four standard weekly doses of rituximab. Twenty-nine patients were enrolled across three dose-escalation cohorts and a safety expansion cohort (250 mg/d navitoclax). The combination was well tolerated. Common toxicities were mild diarrhoea (79%) and nausea (72%). Grade 4 thrombocytopenia occurred in 17% of patients (dose limiting at 325 mg/d). CD19(+) counts were severely reduced, while CD3(+) cells (~ 20%) and serum immunoglobulin M levels (~ 33%) were also reduced during the first year. The maximum tolerated dose for navitoclax in combination was 250 mg/d. Pharmacokinetic analyses revealed no apparent interactions between the drugs. The response rate in patients with follicular lymphoma was 9/12, including five complete responses. All five patients with CLL/small lymphocytic leukaemia achieved partial responses. One of nine patients with aggressive lymphoma responded. The addition of rituximab to navitoclax 250 mg/d is safe; the combination demonstrates higher response rates for low-grade lymphoid cancers than observed for either agent alone in previous Phase 1 trials.
Effect of Subchondral Drilling on the Microarchitecture of Subchondral Bone (2012)

The subchondral bone remains fragile after subchondral drilling for longer durations than previously expected. Further evaluations of structural subchondral bone parameters of patients undergoing marrow stimulation are warranted.
Durability Study of Geopolymer Paste Blended with Blast Furnace Slag (2014)

In this program consequence of incorporating blast furnace slag on mechanical properties and durability of resulting fly ash geopolymer paste sample was investigated. The program consisted immersion of geopolymer samples having percentage blast furnace slag ranging from 10 to 20 of fly ash in a 10% magnesium sulfate solution up to a period of 15 weeks and evaluation of its resistance in terms visual appearance, change in weight and compressive strength at regular interval. Addition of blast furnace slag considerably improved mechanical properties and durability of geopolymers paste.
Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS (2013)

Variovorax paradoxus is a ubiquitous betaproteobacterium involved in plant growth promotion, the degradation of xenobiotics, and quorum-quenching activity. The genome of V. paradoxus strain EPS consists of a single circular chromosome of 6,550,056 bp, with a 66.48% G+C content.
New mud system gets field trial. [Oil wells] (1982)

A description is given of the HACP drilling fluid which is highly shear-thinning and has good API filtration control. These properties are maintained in the presence of various additives, contaminants and cuttings. The system is stable at temperatures up to 250/degree/F. for 16 hours. Because of these properties, drilling rates are expected to be significantly faster than the rates obtained with conventional fluids. Because of lost circulation problems, increased drilling rates could not be demonstrated. 6 refs.
Synthesis and properties of sulfonated and crosslinked poly[(vinylidene fluoride)-graft-styrene] membranes (1998)

Crosslinked proton exchange membranes were prepared by electron beam grafting of styrene with divinylbenzene, DVB, or bis(vinyl phenyl)ethane, BVPE, on to poly(vinylidene fluoride), PVDF, followed by sulfonation. The area and thickness increase, crystallinity and mechanical properties of the membranes were investigated. All these properties were influenced by the crosslinker structure and its concentration. The crosslinkers increase the final degree of grafting. For noncrosslinked membranes it was about 80% and with 10% of BVPE crosslinker about 180% after 8 hr. The area increase with grafting is very similar for the noncrosslinked membranes and the differently crosslinked membranes, but the crosslinkers reduce swelling for sulfonated membranes swelled in boiling water. DVB reduces swelling more than BVPE. With grafting, the crystallinity of the PVDF phase decreases; with 10% BVPE the decrease is smallest and with 10% DVB largest. The mechanical properties of the sulfonated swelled membranes decrease with the degree of grafting, for a 10% DVB crosslinked membrane the strength decreases to zero at degrees of grafting higher than 75%. © 1998 John Wiley & Sons, Ltd.
1-aminocyclopropane-1-carboxylic acid (ACC) in plants: more than just the precursor of ethylene! (2014)

Ethylene is a simple two carbon atom molecule with profound effects on plants. There are quite a few review papers covering all aspects of ethylene biology in plants, including its biosynthesis, signaling and physiology. This is merely a logical consequence of the fascinating and pleiotropic nature of this gaseous plant hormone. Its biochemical precursor, 1-aminocyclopropane-1-carboxylic acid (ACC) is also a fairly simple molecule, but perhaps its role in plant biology is seriously underestimated. This triangularly shaped amino acid has many more features than just being the precursor of the lead-role player ethylene. For example, ACC can be conjugated to three different derivatives, but their biological role remains vague. ACC can also be metabolized by bacteria using ACC-deaminase, favoring plant growth and lowering stress susceptibility. ACC is also subjected to a sophisticated transport mechanism to ensure local and long-distance ethylene responses. Last but not least, there are now a few exciting studies where ACC has been reported to function as a signal itself, independently from ethylene. This review puts ACC in the spotlight, not to give it the lead-role, but to create a picture of the stunning co-production of the hormone and its precursor.
Mesomorphism in the System Disodium Chromoglycate (DSCG)-Water (1981)

Abstract A recent letter to this journal by Dr John E Lydon1 criticises the conclusions drawn by us in some earlier work on this subject2 and proposes new structures for the mesophases. In particular, he suggests that the rods in the “middle”-type M phase are square-sectioned boxes containing water as well as being arrayed hexagonally in a water continuum, instead of the cylindrical rods pictured by us. He quotes our figure of 16 Å for the diameter of the rods, which we obtained in an early calculation, but he omits to state that this was based on a hypothetical structure in which there was complete separation between the water and the DSCG, ie, a structure in which there was no water in the rods. (Actually, we mainly referred to this calculation because we thought it afforded some evidence that the structure was not of the inverse type, ie, one in which the rods are in a lipophilic continuum.)
CODEX: a normalization and copy number variation detection method for whole exome sequencing (2015)

High-throughput sequencing of DNA coding regions has become a common way of assaying genomic variation in the study of human diseases. Copy number variation (CNV) is an important type of genomic variation, but detecting and characterizing CNV from exome sequencing is challenging due to the high level of biases and artifacts. We propose CODEX, a normalization and CNV calling procedure for whole exome sequencing data. The Poisson latent factor model in CODEX includes terms that specifically remove biases due to GC content, exon capture and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data. CODEX is compared to existing methods on a population analysis of HapMap samples from the 1000 Genomes Project, and shown to be more accurate on three microarray-based validation data sets. We further evaluate performance on 222 neuroblastoma samples with matched normals and focus on a well-studied rare somatic CNV within the ATRX gene. We show that the cross-sample normalization procedure of CODEX removes more noise than normalizing the tumor against the matched normal and that the segmentation procedure performs well in detecting CNVs with nested structures.
Case‐control single‐marker and haplotypic association analysis of pedigree data (2004)

Related individuals collected for use in linkage studies may be used in case-control linkage disequilibrium analysis, provided one takes into account correlations between individuals due to identity-by-descent (IBD) sharing. We account for these correlations by calculating a weight for each individual. The weights are used in constructing a composite likelihood, which is maximized iteratively to form likelihood ratio tests for single-marker and haplotypic associations. The method scales well with increasing pedigree size and complexity, and is applicable to both autosomal and X chromosomes. We apply the approach to an analysis of association between type 2 diabetes and single-nucleotide polymorphism markers in the PPAR-gamma gene. Simulated data are used to check validity of the test and examine power. Analysis of related cases has better power than analysis of population-based cases because of the increased frequencies of disease-susceptibility alleles in pedigrees with multiple cases compared to the frequencies of these alleles in population-based cases. Also, utilizing all cases in a pedigree rather than just one per pedigree improves power by increasing the effective sample size. We demonstrate that our method has power at least as great as that of several competing methods, while offering advantages in the ability to handle missing data and perform haplotypic analysis.
10-Gbit/s soliton propagation over 5250 km in standard fiber with dispersion compensation (2002)

We have previously proposed the concept of soliton transmission in dispersion-compensated standard fiber systems and shown experimentally that it is possible to propagate solitons over 2022 km in such a system. Here we present experimental results showing 10-Gbit/s data transmission, with acceptable Q values, over 5000 km. The advantages of using solitons are that they are resilient to polarization-mode dispersion, which is relatively high in standard fiber, and that they are compatible with the all-optical processing technologies currently being developed.
Palladium-Catalyzed Decarboxylative Arylation of C−H Bonds by Aryl Acylperoxides (2009)

A Pd(OAc)(2)-catalyzed protocol for decarboxylative arylation of aromatic C-H bond was developed using aryl acylperoxides as inexpensive aryl sources. Substrates containing pyridyl, oxime, and oxazoline groups undergo effectively ortho-selective C-H arylation with excellent functional group tolerance. This arylation should begin by directing-group-assisted cyclopalladation, followed by the reaction of the palladacycle with aryl radicals generated in situ by thermal decomposition of the peroxides.
Real-time simulation of physically realistic global deformations (2000)

In this thesis, we model and simulate large global deformations of linear viscous materials. Furthermore, we simulate the dynamic behaviors of such deformations using finite element methods (FEM). 
Real-time simulation and animation of global deformation of 3D objects, using the finite element method, is difficult due to the following 3 fundamental problems: (1) The linear elastic model is inappropriate for simulating large motions and large deformations (unacceptable distortion will occur); (2) The time step for dynamic integration has to be drastically reduced to simulate collisions, if the traditional penalty methods are applied; (3) The size of the problem (the number of elements in the FEM mesh) is in n magnitude larger than that of a 2D problem. 
In this thesis, we counter these 3 difficulties as following: (1) using quadratic strain instead of the popular linear strain to simulate arbitrarily large motions and global deformations of a 3D object; (2) applying an efficient collision constraint to a decoupled system, which makes an integration step for collision as cheap as a regular dynamic integration step; (3) using a graded mesh instead of a uniform mesh, which reduces the asymptotic complexity of a 3D problem to that, of a 2D problem. 
In order to preserve some of the subtle material properties such as viscous elasticity, we also present an alternative real-time solution without compromising the mass matrix in the FEM system. Instead of decoupling the system by diagonalizing the mass and damping matrix, we preprocess the system using modified nested dissection, which improves the sparsity of the system. 
In this thesis, we also present how we can apply the same FEM model to simulate haptic feedback to a human operation in the virtual environment.
Ambroxol effects in glucocerebrosidase and α‐synuclein transgenic mice (2016)

Our work supports the proposition that ambroxol should be further investigated as a potential novel disease-modifying therapy for treatment of Parkinson disease and neuronopathic Gaucher disease to increase glucocerebrosidase activity and decrease α-synuclein and phosphorylated α-synuclein protein levels. Ann Neurol 2016;80:766-775.
Helicobacter canis sp. nov., a new species from dogs: an integrated study of phenotype and genotype (1993)

A group of Campylobacter-like organisms (CLOs) were isolated from the faeces of diarrhoeic or healthy dogs, constituting 4% of all CLOs from this source. Since they formed a unique DNA homology group within the genus Helicobacter, and exhibited distinctive phenotypic properties, they were collectively termed the HC group. A polyphasic taxonomic analysis was made of this group. The phenotype of four dog isolates and a single human isolate was unique and could be distinguished bacteriologically from other helicobacters. Electron microscopic ultrastructure revealed defining characteristics of Helicobacter. The 16S rRNA gene of the nominated type strain NCTC 12739T was sequenced, and its analysis delineated the group as a new species of Helicobacter. This conclusion was supported by relative DNA homology and whole-cell protein electrophoretic patterns. We therefore propose the name Helicobacter canis sp. nov. for this group. The species most closely related to H. canis sp. nov. were H. cinaedi, 'Flexispira rappini' and H. fennelliae. A species-specific recombinant DNA probe was cloned from NCTC 12739T for use in routine laboratory identification and epidemiological studies. The faecal source, bile tolerance and lack of urease activity of H. canis sp. nov. suggest that this new Helicobacter species colonizes the lower bowel rather than the stomach.
Preparation of Substituted Compounds of Lithium Indium Bromide and Fabrication of All Solid-State Battery (2017)

Background and Objective: Li3InBr6-yXy (X=F, I) was synthesized and the substitution effect on ionic conductivity was investigated. Method: An all solid state secondary battery was fabricated using Li3InBr6-yXy (X=F, Cl, I) and evaluated. Li3InBr6-yFy was single phase at y ≤ 3. The lattice constants for both compounds were decreased with an amount of F. The conductivity of Li3InBr6-yFy was decreased with y and electrochemical stability was improved by the substitution. The conductivity in Li3InBr6-yIy(y ≤ 3) was changed with y and Li3InBr3I3 showed the highest value in these compounds to be 3 ×10-3 Scm-1 at 333 K. 7Li NMR spectra in Li3InBr6-yIy was sharp and it was confirmed the diffusion of Li ion was fast at room temperature. Batteries using Li3InBr5F could be stably charged and discharged for 10 cycles. Results and Conclusion: The discharge capacity increased in the first few cycles and the maximum value of 81 mAhg-1 was obtained in the fourth cycle. Keywords: Solid electrolyte, ionic conductivity, Li-ion secondary battery, all solid-state battery, substitution effect, phase transition.
Photoinduced Giant Dielectric Constant in Lead Halide Perovskite Solar Cells (2014)

Organic-inorganic lead trihalide perovskites have emerged as an outstanding photovoltaic material that demonstrated a high 17.9% conversion efficiency of sunlight to electricity in a short time. We have found a giant dielectric constant (GDC) phenomenon in these materials consisting on a low frequency dielectric constant in the dark of the order of ε0 = 1000. We also found an unprecedented behavior in which ε0 further increases under illumination or by charge injection at applied bias. We observe that ε0 increases nearly linearly with the illumination intensity up to an additional factor 1000 under 1 sun. Measurement of a variety of samples of different morphologies, compositions, and different types of contacts shows that the GDC is an intrinsic property of MAPbX3 (MA = CH3NH3(+)). We hypothesize that the large dielectric response is induced by structural fluctuations. Photoinduced carriers modify the local unit cell equilibrium and change the polarizability, assisted by the freedom of rotation of MA. The study opens a way for the understanding of a key aspect of the photovoltaic operation of high efficiency perovskite solar cells.
Using machine learning to improve automatic vectorization (2012)

Automatic vectorization is critical to enhancing performance of compute-intensive programs on modern processors. However, there is much room for improvement over the auto-vectorization capabilities of current production compilers through careful vector-code synthesis that utilizes a variety of loop transformations (e.g., unroll-and-jam, interchange, etc.). As the set of transformations considered is increased, the selection of the most effective combination of transformations becomes a significant challenge: Currently used cost models in vectorizing compilers are often unable to identify the best choices. In this paper, we address this problem using machine learning models to predict the performance of SIMD codes. In contrast to existing approaches that have used high-level features of the program, we develop machine learning models based on features extracted from the generated assembly code. The models are trained offline on a number of benchmarks and used at compile-time to discriminate between numerous possible vectorized variants generated from the input code. We demonstrate the effectiveness of the machine learning model by using it to guide automatic vectorization on a variety of tensor contraction kernels, with improvements ranging from 2× to 8× over Intel ICC's auto-vectorized code. We also evaluate the effectiveness of the model on a number of stencil computations and show good improvement over auto-vectorized code.
CXCL12/CXCR4-Mediated Procollagen Secretion Is Coupled To Cullin-RING Ubiquitin Ligase Activation (2018)

Tissue fibrosis is mediated by the actions of multiple pro-fibrotic proteins that can induce myofibroblast phenoconversion through diverse signaling pathways coupled predominantly to Smads or MEK/Erk proteins. The TGFβ/TGFβR and CXCL12/CXCR4 axes induce myofibroblast phenoconversion independently through Smads and MEK/Erk proteins, respectively. To investigate these mechanisms at the genetic level, we have now elucidated the TGFβ/TGFβR and CXCL12/CXCR4 transcriptomes in human fibroblasts. These transcriptomes are largely convergent, and up-regulate transcripts encoding proteins known to promote myofibroblast phenoconversion. These studies also revealed a molecular signature unique to CXCL12/CXCR4 axis activation for COPII vesicle formation, ubiquitination, and Golgi/ER localization/targeting. In particular, both CUL3 and KLHL12, key members of the Cullin-RING (CRL) ubiquitin ligase family of proteins involved in procollagen transport from the ER to the Golgi, were highly up-regulated in CXCL12-, but repressed in TGFβ-, treated cells. Up-regulation of CUL3 and KLHL12 was correlated with higher procollagen secretion by CXCL12-treated cells, and this affect was ablated upon treatment with inhibitors specific for CXCR4 or CUL3 and repressed by TGFβ/TGFβR axis activation. The results of these studies show that activation of the CXCL12/CXCR4 axis uniquely facilitates procollagen I secretion through a COPII-vesicle mediated mechanism to promote production of the ECM characteristic of fibrosis.
Traffic shaping system for ATM networks — supporting PC interface functions (2001)

An ATM traffic shaper is presented which regulates the traffic injected into the ATM networks by enforcing specific traffic parameter values that have been agreed upon between the user and the network. It realises preventive flow control functions through a new effective rate control algorithm, adaptive to traffic characteristics. It has been designed to support data communication services. The proposed scheme is presented in detail, and its system functionality and implementation aspects are discussed. Possible applications and model extensions are also discussed.