Miracle-dz/UniFAR-FTUs huggingface dataset:
Emu: Rapid Prototyping of Networking Services

Due to their performance and flexibility, FPGAs are an attractive platform for the execution of network functions. It has been a challenge for a long time though to make FPGA programming accessible to a large audience of developers. An appealing solution is to compile code from a general-purpose language to hardware using high-level synthesis. Unfortunately, current approaches to implement rich network functionality are insufficient because they lack: (i) libraries with abstractions for common network operations and data structures, (ii) bindings to the underlying "substrate" on the FPGA, and (iii) debugging and profiling support. This paper describes Emu, a new standard library for an FPGA hardware compiler that enables developers to rapidly create and deploy network functionality. Emu allows for high-performance designs without being bound to particular packet processing paradigms. Furthermore, it supports running the same programs on CPUs, in Mininet, and on FPGAs, providing a better development environment that includes advanced debugging capabilities. We demonstrate that network functions implemented using Emu have only negligible resource and performance overheads compared with natively-written hardware versions.
Ownership Domains in the Real World

The Ownership Domains type system has had publicly available tool support for a few years. However, the previous implementation used non-backwards compatible language extensions to Java and ran on a research infrastructure, which made it difficult to conduct substantial case studies on interesting systems. We first present a re-implementation of ownership domains using Java 1.5 annotations and the Eclipse infrastructure. We then use the improved tool to annotate two real 15,000-line Java programs while using refactoring tool support, generics and external libraries. Ownership domains, as most other ownership type systems, provide useful encapsulation properties. We illustrate using actual examples from the subject systems how ownership domains also express and enforce design intent regarding object encapsulation and communication and help identify tight coupling. Finally, we mention some expressiveness gaps that we encountered.
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome

SUMMARY SPrCY is a web-accessible database which provides comparison of structure prediction results for the Saccharomyces cerevisiae genome. This web service offers the ability to search, analyze and compare the yeast structural predictions from sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mGenTHREADER) methods. AVAILABILITY The service is freely available via web at http://agave.wustl. edu/yeast/
Engineering a PVD based graphene synthesis method

Graphene is an important nano-material with extraordinary properties. An established PVD based Graphene synthesis method is engineered in order to demonstrate the versatility of the growth method with respect to the quality and number of layers of synthesized Graphene. Annealing temperature and annealing duration are varied to study their effect on the growth. The quality and number of layers of Graphene are verified by Raman characterization.
Influence of chemical and mechanical stress on precision-cut lung slices

Dassow C. , Wiechert L. , Martin C. , Schumann S. , Müller-Newen G. , Guttmann J., Wall WA. , Uhlig S (2009): Biomechanics of Precision-Cut Lung Slices during Biaxial Distension. Am J Respir Crit Care Med, Apr 2009, 179: A1243 Dassow C. , Martin C. , Barrenschee M. , Uhlig S. (2008): Induction of Amphiregulin in Precision-Cut Lung Slices. Am J Respir Crit Care Med, Apr 2008, 177: A195 Dassow C. , Martin S. , Schumann S. , Guttmann J., Uhlig S. (2007): Stretching precisioncut lung slices as a new model to investigate overexpansion of the lung. Perspektiven der pneumologischen Pharmakotherapie, Symposium der Paul-Martini-Stiftung
Open virtual reality

The ICT Mixed Reality Lab is leveraging an open source philosophy to influence and disrupt industry. Projects spun out of the lab's efforts include the VR2GO smartphone based viewer, the inVerse tablet based viewer, the Socket HMD reference design, the Oculus Rift and the Project Holodeck gaming platforms, a repurposed FOV2GO design with Nokia Lumia phones for a 3D user interface course at Columbia University, and the EventLab's Socket based HMD at the University of Barcelona. A subset of these will be demonstrated. This open approach is providing low cost yet surprisingly compelling immersive experiences.
Uncovering Short-Time Correlations between Multichannel Recordings of Brain Activity: a Phase-Space Approach

Short-time correlations in multivariate time series are notoriously difficult to detect. Extending the classical concept of correlation, we present a method to tackle this problem with little computational cost. In essence, the method uncovers multidimensional phase-locking and is especially useful for revealing changes of the dynamical coupling between different brain areas. The approach also permits us to estimate the shortest time-window in which the coupling occurs. Furthermore, the coupling can be quantified by a measure that defines a metric space. Therefore it may be used to identify task-dependent coupling hierarchies between two brain areas. We illustrate the analysis technique by studying the dynamical coupling between two brain regions involved in olfactory processing in the honeybee. We show that the neural activity in both areas is coupled with each other and that the coupling increases significantly during odor processing.
Orthogonally oriented coils for minimization of cross-coupling in cortical implants

This article presents the design of the inductive links of remotely powered wireless cortical implants for minimum interference from the power link to the data link. This interference is minimized by changing the orientation of the inductors. Different orientation types are investigated and compared. Orthogonally oriented coils with high interference suppression and better reproducibility has been proposed. From the simulations, 29% power efficiency and 46 dB interference suppression is achieved for these coils. The spiral inductors are fabricated on PCBs and results of preliminary measurements are presented. Moreover, a conceptual cortical implant prototype is proposed.
Development of high temperature/oxidation-resistant PVD coatings for cutting tools using HIPIMS

A series of high temperature and oxidation resistant, nanoscale, multilayer PVD, hard coatings have been developed through combine DC Unbalanced Magnetron (UBM) and High Power Impulse Magnetron Sputtering (HIPIMS) deposition technologies. The properties of the coatings lend themselves to the application of protecting cutting tools exposed to harsh environment such as the dry, high-speed machining of abrasive materials. This thesis discusses the literature supporting the project and pays tribute to the development of coatings that formed the foundation for the CrAlYBCN/AlSiCN coating series. Plasma diagnostics optimised the process conditions for deposition; a highly ionised metal rich plasma was generated to investigate the effect of process conditions during the pretreatment step. It was found that metal ion implantation into the substrate was successful and that ramping the cathode charge had little effect of the sputter rate of the substrate. Ion etching removed loosely bound surface grain to improve adhesion. A series of coatings were developed that were deposited at different levels of target poisoning, in an attempt to improve coating properties by process control and stoichiometry. Superhard coatings able to withstand temperatures of over 800 °C were produced. The coatings were subjected to a series of mechanical and thermal testing using pin on disk, microhardness, scratch test, Rockwell indentation, isothermal heat treatment and thermogravimetric analysis. Mechanisms of wear and oxidation process have been proposed based on the evidence given. Through coating development two coatings were indicated as having the desired chemical, thermal and mechanical properties suitable for cutting tests. The coating that was deposited at higher bias improved the tool lifetime by 5 times.
Bactericidal and Sterilizing Activity of a Novel Regimen with Bedaquiline, Pretomanid, Moxifloxacin, and Pyrazinamide in a Murine Model of Tuberculosis

ABSTRACT New regimens based on 2 or more novel agents are sought to shorten or to simplify treatment of tuberculosis (TB), including drug-resistant forms. Prior studies showed that the novel combinations of bedaquiline (BDQ) plus pretomanid (PMD) plus pyrazinamide (PZA) and PMD plus moxifloxacin (MXF) plus PZA shortened the treatment duration necessary to prevent relapse by 2 to 3 months and 1 to 2 months, respectively, compared with the current first-line regimen, in a murine TB model. These 3-drug combinations are now being studied in clinical trials. Here, the 4-drug combination of BDQ+PMD+MXF+PZA was compared to its 3-drug component regimens and different treatment durations of PZA and MXF were explored, to identify the optimal regimens and treatment times and to estimate the likelihood of success against drug-resistant strains. BDQ+PMD+MXF+PZA rendered all mice relapse-free after 2 months of treatment. PZA administration could be discontinued after the first month of treatment without worsening outcomes, whereas the absence of MXF, PZA, or BDQ administration from the beginning necessitated approximately 0.5, 1, or 2 months, respectively, of additional treatment to attain the same outcome.
ImageNet pre-trained models with batch normalization

Convolutional neural networks (CNN) pre-trained on ImageNet are the backbone of most state-of-the-art approaches. In this paper, we present a new set of pre-trained models with popular state-of-the-art architectures for the Caffe framework. The first release includes Residual Networks (ResNets) with generation script as well as the batch-normalization-variants of AlexNet and VGG19. All models outperform previous models with the same architecture. The models and training code are available at this http URL and this https URL
Frequency sampling design of prototype filters for nearly perfect reconstruction cosine-modulated filter banks

A new approach to the design of prototype filters for conventional nearly perfect reconstruction (N-PR) cosine-modulated filter banks is presented. The new method is based on the frequency sampling approach for the design of finite-impulse response filters. In the proposed approach, the magnitude response values of samples in the transition band of the prototype filter are the only parameters to be optimized. The analytical and simulation results show that despite there being no direct control over the stopband attenuation of the prototype filter, the performance of the filter bank is extremely good, and in several cases, the whole system closely satisfies the PR property.
Feline respiratory disease

Practical relevance: Non-hemotropic Mycoplasma species are frequently implicated in cases of respiratory disease, and also conjunctivitis, in cats. Clinical challenges: Mycoplasma species are considered commensal bacteria of the conjunctiva and the upper respiratory tract of cats, and hence their role as a primary pathogen is difficult to determine. These organisms certainly appear to play a significant role as a secondary pathogen in the upper airways, and there is increasing evidence that in some animals they may represent a primary infection. However, mycoplasmas have not been found in the lower airways of clinically healthy cats – suggesting that, when present, they likely represent a pathologic process. Diagnostic challenges exist as well; Mycoplasma species are not typically identified via cytology due to their small size, and culture of these organisms requires special media and handling. Although PCR has improved identification and allowed for speciation, conflicting culture and PCR results can create a dilemma regarding the clinical relevance of infection. Evidence base: This article draws on original research and case reports to provide information about the role of Mycoplasma species in thefeline upper and lower respiratory tract, diagnostic methods and associated challenges, and treatment options. Audience: The goal is to provide small animal practitioners with a current and organized review of the often-conflicting literature regarding the role of Mycoplasma species in feline respiratory infections.
Virtual Hematoxylin and Eosin Transillumination Microscopy Using Epi-Fluorescence Imaging

We derive a physically realistic model for the generation of virtual transillumination, white light microscopy images using epi-fluorescence measurements from thick, unsectioned tissue. We demonstrate this technique by generating virtual transillumination H&E images of unsectioned human breast tissue from epi-fluorescence multiphoton microscopy data. The virtual transillumination algorithm is shown to enable improved contrast and color accuracy compared with previous color mapping methods. Finally, we present an open source implementation of the algorithm in OpenGL, enabling real-time GPU-based generation of virtual transillumination microscopy images using conventional fluorescence microscopy systems.
AlvisAE: a collaborative Web text annotation editor for knowledge acquisition

AlvisAE is a text annotation editor aimed at knowledge acquisition projects. An expressive annotation data model allows AlvisAE to support various knowledge acquisition tasks like construction gold standard corpus, ontology population and assisted reading. Collaboration is achieved through a workflow of tasks that emulates common practices (e.g. automatic pre-annotation, adjudication). It is implemented as a Web application requiring no installation by the end-user, thus facilitating the participation of domain experts. AlvisAE is used in several knowledge acquisition projects in the domains of biology and crop science.
Procurement with Reverse Auction and Flexible Noncompetitive Contracts

This article investigates a hybrid procurement mechanism that combines a reverse auction with flexible noncompetitive contracts. A buyer adopts such mechanism to procure multiple units of a product from a group of potential suppliers. Specifically, the buyer first offers contracts to some suppliers who, if accepting the contract, do not participate in the auction while committing to selling a unit to the buyer at the price of the subsequent auction. For the suppliers rejecting the offers, they can join the subsequent auction with the other suppliers to compete on the remaining units. When the buyer offers only one flexible noncompetitive contract, we find that the selected supplier may accept the offer regardless of whether he knows his exact cost information. Meanwhile, the buyer can benefit from offering such a contract, as opposed to solely conducting a regular reverse auction or offering a noncompetitive contract that does not allow suppliers declining offers to join the subsequent auction. Moreover, we find that the suppliers' information about their own costs has a significant impact on the buyer's decision. When the buyer makes multiple offers, we analyze the resulting game behavior of the selected suppliers and demonstrate that the buyer can benefit more than just offering one such contract. Therefore, the hybrid procurement mechanism can be mutually beneficial for both the buyer and the selected suppliers.
Large Deviations Performance of Consensus+Innovations Distributed Detection With Non-Gaussian Observations

We establish the large deviations asymptotic performance (error exponent) of consensus+innovations distributed detection over random networks with generic (non-Gaussian) sensor observations. At each time instant, sensors 1) combine theirs with the decision variables of their neighbors (consensus) and 2) assimilate their new observations (innovations). This paper shows for general non-Gaussian distributions that consensus+innovations distributed detection exhibits a phase transition behavior with respect to the network degree of connectivity. Above a threshold, distributed is as good as centralized, with the same optimal asymptotic detection performance, but, below the threshold, distributed detection is suboptimal with respect to centralized detection. We determine this threshold and quantify the performance loss below threshold. Finally, we show the dependence of the threshold and of the performance on the distribution of the observations: the asymptotic performance of distributed detectors over the same random network with different observations' distributions, for example, Gaussian, Laplace, or quantized, may be different, even though the asymptotic performance of the corresponding centralized detectors is the same.
Heterogeneity of vitamin D receptor gene association with celiac disease and type 1 diabetes mellitus

Objective: Vitamin D has been shown to exert multiple immunomodulatory effects and is known to suppress T-cell activation by binding to the vitamin D receptor (VDR). To determine whether VDR gene polymorphisms are related to the susceptibility to celiac disease, we investigated its implication as a candidate gene in the Basque population. Because celiac disease and type 1 diabetes share common susceptibility loci, we also analyzed families with type 1 diabetes mellitus. Methods: A total of 37 families with celiac disease and 64 type 1 diabetic families of Basque origin with at least one affected offspring were genotyped for four VDR restriction-site polymorphisms (Fok I, Bsm I, Apa I and Taq I). The AFBAC approach was used to test for association. Results: Comparison of VDR genotypes of the patients with those of 88 healthy individuals identified “ff” as a risk genotype for celiac disease [p = 0.01; OR = 3.45 (1.12–10.79)]. On the other hand, a significantly higher frequency of haplotype “fBAt” was observed in the type 1 diabetic group [pc = 0.02; OR = 4.4 (1.5–15.3)]. Conclusion: Our findings suggest that polymorphisms within the vitamin D receptor gene are markers of susceptibility to or protection from autoimmune diseases, although, at least in the Basque population, association of VDR variants with celiac disease and type 1 diabetes seems to be heterogeneous.
BATCH/SEMI-BATCH PROCESS FAULT DETECTION AND DIAGNOSIS USING ORTHOGONAL NONLINEAR MULTI-WAY PCA: Application to an emulsion co-polymerization process

Abstract In this paper, a fault detection and diagnosis for batch/semi-batch processes by utilizing the PCA scores subspace is proposed. To develop the diagnosis model, first the multi-way unfolding is utilised to transform 3-dimensional batches data onto 2-dimensional data. The process of extracting linear and nonlinear correlations from process data is performed by sequentially applying a linear PCA and an orthogonal nonlinear PCA. As a result the nonlinear structures become more apparent. In addition, the sequential approach reduces the complexity of nonlinear PCA development and compact the information to a very low dimension. The trajectory-boundary-limit crossing point discriminant analysis is proposed to diagnose the fault at the instance of being detected and to improve the diagnostic performance. The validity of the proposed strategy is demonstrated by application to the emulsion copolymerization of styrene/MMA semi-batch process.
Morphology cluster and prediction of growth of human brain pyramidal neurons

Predicting neuron growth is valuable to understand the morphology of neurons, thus it is helpful in the research of neuron classification. This study sought to propose a new method of predicting the growth of human neurons using 1 907 sets of data in human brain pyramidal neurons obtained from the website of NeuroMorpho.Org. First, we analyzed neurons in a morphology field and used an expectation-maximization algorithm to specify the neurons into six clusters. Second, naive Bayes classifier was used to verify the accuracy of the expectation-maximization algorithm. Experiment results proved that the cluster groups here were efficient and feasible. Finally, a new method to rank the six expectation-maximization algorithm clustered classes was used in predicting the growth of human pyramidal neurons.
Weighing the Giants – II. Improved calibration of photometry from stellar colours and accurate photometric redshifts

We present improved methods for using stars found in astronomical exposures to calibrate both star and galaxy colours as well as to adjust the instrument flat-field. By developing a spectroscopic model for the Sloan Digital Sky Survey (SDSS) stellar locus in colour–colour space, synthesizing an expected stellar locus, and simultaneously solving for all unknown zero-points when fitting to the instrumental locus, we increase the calibration accuracy of stellar locus matching. We also use a new combined technique to estimate improved flat-field models for the Subaru SuprimeCam camera, forming ‘star flats’ based on the magnitudes of stars observed in multiple positions or through comparison with available measurements in the SDSS catalogue. These techniques yield galaxy magnitudes with reliable colour calibration (≲0.01–0.02 mag accuracy) that enable us to estimate photometric redshift probability distributions without spectroscopic training samples. We test the accuracy of our photometric redshifts using spectroscopic redshifts z_s for ∼5000 galaxies in 27cluster fields with at least five bands of photometry, as well as galaxies in the Cosmic Evolution Survey (COSMOS) field, finding σ((z_p − z_s)/(1 + z_s)) ≈ 0.03 for the most probable redshift z_p. We show that the full posterior probability distributions for the redshifts of galaxies with five-band photometry exhibit good agreement with redshifts estimated from thirty-band photometry in the COSMOS field. The growth of shear with increasing distance behind each galaxy cluster shows the expected redshift–distance relation for a flat Λ cold dark matter (Λ-CDM) cosmology. Photometric redshifts and calibrated colours are used in subsequent papers to measure the masses of 51 galaxy clusters from their weak gravitational shear and determine improved cosmological constraints. We make our python code for stellar locus matching publicly available at http://big-macs-calibrate.googlecode. com; the code requires only input catalogues and filter transmission functions.