Miracle-dz/UniFAR-FTUs huggingface dataset:
Elastography: Elasticity Imaging Using Ultrasound with Application to Muscle and Breast in Vivo

Changes in tissue elasticity are generally correlated with its pathological state. In many cases, despite the difference in elasticity, the small size of a lesion or its location deep in the body preclude its detection by palpation. In general, such a lesion may or may not posses echogenic properties that would make it ultrasonically detectable. Elastography is an ultrasonic method for imaging the elasticity of compliant tissues. The method estimates the local longitudinal strain of tissue elements by ultrasonically assessing the one dimensional local displacements. This information can be combined with first order theoretical estimates of the local stress to yield a quantitative measure of the local elastic properties of tissue. The elasticity information is displayed in the form of a gray scale image called an elastogram. An experimental system for elastography in phantoms based on a single element transducer has been described previously [1]. Here we introduce a new elastography system based on a linear array transducer that is suitable for in vivo scanning. We describe tissue mimicking phantom experiments and preliminary in vivo breast and muscle elastograms confirming the feasibility of performing elastography in vivo. An elastogram of a breast containing an 8 mm palpable cancer nodule clearly shows the lesion. Elastograms and their corresponding sonograms show some similarities and differences in the depiction of tissue structures.
Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding

Methylation, the addition of methyl groups to cytosine (C), plays an important role in the regulation of gene expression in both normal and dysfunctional cells. During bisulfite conversion and subsequent PCR amplification, unmethylated Cs are converted into thymine (T), while methylated Cs will not be converted. Sequencing of this bisulfite-treated DNA permits the detection of methylation at specific sites. Through the introduction of next-generation sequencing technologies (NGS) simultaneous analysis of methylation motifs in multiple regions provides the opportunity for hypothesis-free study of the entire methylome. Here we present a whole methylome sequencing study that compares two different bisulfite conversion methods (in solution versus in gel), utilizing the high throughput of the SOLiD™ System. Advantages and disadvantages of the two different bisulfite conversion methods for constructing sequencing libraries are discussed. Furthermore, the application of the SOLiD™ bisulfite sequencing to larger and more complex genomes is shown with preliminary in silico created bisulfite converted reads.
Amortized Dynamic Cell-Probe Lower Bounds from Four-Party Communication

This paper develops a new technique for proving amortized, randomized cell-probe lower bounds on dynamic data structure problems. We introduce a new randomized nondeterministic four-party communication model that enables "accelerated", error-preserving simulations of dynamic data structures. We use this technique to prove an Ω(n(log n/log log n)2) cell-probe lower bound for the dynamic 2D weighted orthogonal range counting problem (2D-ORC) with n/poly log n updates and n queries, that holds even for data structures with exp(-Ω̃(n)) success probability. This result not only proves the highest amortized lower bound to date, but is also tight in the strongest possible sense, as a matching upper bound can be obtained by a deterministic data structure with worst-case operational time. This is the first demonstration of a "sharp threshold" phenomenon for dynamic data structures. Our broader motivation is that cell-probe lower bounds for exponentially small success facilitate reductions from dynamic to static data structures. As a proof-of-concept, we show that a slightly strengthened version of our lower bound would imply an Ω((log n/log log n)2) lower bound for the static 3D-ORC problem with O(n logO(1) n) space. Such result would give a near quadratic improvement over the highest known static cell-probe lower bound, and break the long standing Ω(log n) barrier for static data structures.
Period-Based Load Partitioning and Assignment for Large Real-Time Applications

We propose a new approach to the problem of workload partitioning and assignment for very large distributed real-time systems, in which software components are typically organized hierarchically, and hardware components potentially span several shared and/or dedicated links. Existing approaches for load partitioning and assignment are based on either schedulability or communication. The first category attempts to construct a feasible schedule for various assignments and chooses the one that minimizes task lateness (or other similar criteria), while the second category partitions the workload heuristically in accordance with the amount of intertask communication. We propose, and argue for, a (new) third category based on task periods, which, among others, combines the ability of handling heterogeneity with excellent scalability. Our algorithm is a recursive invocation of two stages: clustering and assignment. The clustering stage partitions tasks and processors into clusters. The assignment stage maps task clusters to processor clusters. A later scheduling stage will compute a feasible schedule, if any, when the size of processor clusters reduces to one at the bottom of the recursion tree. We introduce a new clustering heuristic and evaluate elements of the period-based approach using simulations to verify its suitability for large real-time applications. Also presented is an example application drawn from the field of command and control that has the potential to benefit significantly from the proposed approach.
In vitro myelin formation using embryonic stem cells

Myelination in the central nervous system is the process by which oligodendrocytes form myelin sheaths around the axons of neurons. Myelination enables neurons to transmit information more quickly and more efficiently and allows for more complex brain functions; yet, remarkably, the underlying mechanism by which myelination occurs is still not fully understood. A reliable in vitro assay is essential to dissect oligodendrocyte and myelin biology. Hence, we developed a protocol to generate myelinating oligodendrocytes from mouse embryonic stem cells and established a myelin formation assay with embryonic stem cell-derived neurons in microfluidic devices. Myelin formation was quantified using a custom semi-automated method that is suitable for larger scale analysis. Finally, early myelination was followed in real time over several days and the results have led us to propose a new model for myelin formation. Highlighted article: The quantitative analysis of mouse ESC-derived neurons and oligodendrocytes co-cultured in a microfluidic device provides insights into the temporal sequence of the myelination process.
Model-driven Deployment of Distributed Components-based Software

Software deployment encompasses all post-development activities that make an application operational. The development of system-based components has made it possible to better highlight this piece of the global software lifecycle, as illustrated by numerous industrial and academic studies. However these are generally developed ad hoc and, consequently platform-dependent. Deployment systems supported by middleware environments (CCM, .Net and EJB), specifically develop mechanisms and tools related to pre-specified deployment strategies. For this topic of distributed component-based software applications, our goal is to define what could be a unified meta modeling architecture for deployment of distributed components based software systems. To illustrate the feasibility of the approach, we introduce a tool called UDeploy (Unified Deployment architecture) which firstly, manages the planning process from meta-information related to the application, the infrastructure and the deployment strategies; secondly, the generation of specific deployment descriptors related to the application and the environment (i.e. the machines connected to a network where a software system is deployed); and finally, the execution of a plan produced by means of deployment strategies used to elaborate a deployment plan.
Efficient phrase-based document indexing for Web document clustering

Document clustering techniques mostly rely on single term analysis of the document data set, such as the vector space model. To achieve more accurate document clustering, more informative features including phrases and their weights are particularly important in such scenarios. Document clustering is particularly useful in many applications such as automatic categorization of documents, grouping search engine results, building a taxonomy of documents, and others. This article presents two key parts of successful document clustering. The first part is a novel phrase-based document index model, the document index graph, which allows for incremental construction of a phrase-based index of the document set with an emphasis on efficiency, rather than relying on single-term indexes only. It provides efficient phrase matching that is used to judge the similarity between documents. The model is flexible in that it could revert to a compact representation of the vector space model if we choose not to index phrases. The second part is an incremental document clustering algorithm based on maximizing the tightness of clusters by carefully watching the pair-wise document similarity distribution inside clusters. The combination of these two components creates an underlying model for robust and accurate document similarity calculation that leads to much improved results in Web document clustering over traditional methods.
Infliximab plus azathioprine for steroid-dependent Crohn's disease patients: a randomized placebo-controlled trial.

BACKGROUND & AIMS The aim of this study was to evaluate the usefulness of short-term infliximab combined with azathioprine (AZA) or 6-mercaptopurine (6-MP) in steroid-dependent Crohn's disease patients. METHODS Patients with active disease despite prednisone given for more than 6 months were eligible and were stratified as follows: the failure stratum consisted of patients receiving AZA/6-MP at a stable dose for more than 6 months, and the naive stratum consisted of patients not treated previously with AZA/6-MP. Patients were randomized to infliximab 5 mg/kg or placebo at weeks 0, 2, and 6. All patients were treated with AZA/6-MP maintained at a stable dose throughout the 52 weeks of the study. The primary end point was remission off steroids at week 24. RESULTS Among the 113 enrolled patients (55 in the failure stratum), 57 were assigned to infliximab. At week 24, the success rate (intent-to-treat analysis) was higher in the infliximab group than in the placebo group (57% vs 29%; P = .003); at weeks 12 and 52, the corresponding rates were 75% vs 38% (P < .001) and 40% vs 22% (P = .04), respectively. In each stratum, the success rate was significantly higher in the infliximab group at weeks 12 and 24, and a trend was found at week 52. In the failure stratum, only 27% of the patients in the infliximab group were still in remission off steroids, compared with 52% in the naive stratum. Steroid resistance was less common and the cumulative dose of prednisone was lower in the infliximab group. CONCLUSIONS Infliximab plus AZA/6-MP is more effective than AZA/6-MP alone in steroid-dependent Crohn's disease patients.
Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains

Typically, eukaryotic nuclei contain 10–30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain “choice” appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3–4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments (∼5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic “neighborhoods. ”
A Study of CO Emission in High-Redshift QSOs Using the Owens Valley Millimeter Array

Searches for CO emission in high-redshift objects have traditionally suffered from the accuracy of optically derived redshifts for lack of bandwidth in correlators at radio observatories. This problem has motivated the creation of the new COBRA continuum correlator with 4 GHz available bandwidth at the Owens Valley Radio Observatory Millimeter Array. Presented here are the first scientific results from COBRA. We report detections of redshifted CO (J = 3 → 2) emission in the QSOs SMM J04135+10277 and VCV J140955.5+562827, as well as a probable detection in RX J0911.4+0551. At redshifts of z = 2.846, 2.585, and 2.796, we find integrated CO flux densities of 5.4, 2.4, and 2.9 Jy km s-1 for SMM J04135+10277, VCV J140955.5+562827, and RX J0911.4+0551, respectively, over line widths of ΔVFWHM ~ 350 km s-1. These measurements, when corrected for gravitational lensing, correspond to molecular gas masses of order M(H2) ~ 109.6-1011.1 M☉ and are consistent with previous CO observations of high-redshift QSOs. We also report 3 σ upper limits on CO (3 → 2) emission in the QSO LBQS 0018-0220 of 1.3 Jy km s-1. We do not detect significant 3 mm continuum emission from any of the QSOs, with the exception of a tentative (3 σ) detection in RX J0911.4+0551 of S3 mm = 0.92 mJy beam-1.
NICSLU: An Adaptive Sparse Matrix Solver for Parallel Circuit Simulation

The sparse matrix solver has become a bottleneck in simulation program with integrated circuit emphasis (SPICE)-like circuit simulators. It is difficult to parallelize the solver because of the high data dependency during the numeric LU factorization and the irregular structure of circuit matrices. This paper proposes an adaptive sparse matrix solver called NICSLU, which uses a multithreaded parallel LU factorization algorithm on shared-memory computers with multicore/multisocket central processing units to accelerate circuit simulation. The solver can be used in all the SPICE-like circuit simulators. A simple method is proposed to predict whether a matrix is suitable for parallel factorization, such that each matrix can achieve optimal performance. The experimental results on 35 matrices reveal that NICSLU achieves speedups of 2.08× ~ 8.57×(on the geometric mean), compared with KLU, with 1-12 threads, for the matrices which are suitable for the parallel algorithm. NICSLU can be downloaded from http://nicslu.weebly. com.
LAMA: Optimized Locality-aware Memory Allocation for Key-value Cache

The in-memory cache system is a performance-critical layer in today's web server architecture. Memcached is one of the most effective, representative, and prevalent among such systems. An important problem is memory allocation. The default design does not make the best use of the memory. It fails to adapt when the demand changes, a problem known as slab calcification. This paper introduces locality-aware memory allocation (LAMA), which solves the problem by first analyzing the locality of the Memcached requests and then repartitioning the memory to minimize the miss ratio and the average response time. By evaluating LAMA using various industry and academic workloads, the paper shows that LAMA outperforms existing techniques in the steady-state performance, the speed of convergence, and the ability to adapt to request pattern changes and overcome slab calcification. The new solution is close to optimal, achieving over 98% of the theoretical potential.
Tunable left-handed material with wire array in a ferrite rectangular waveguide

A Tunable left-handed material (LHM) which is composed of a metallic wire array in a TE10 rectangular waveguide filled with ferrite has been demonstrated by simulations. The left-handed passband can be dynamically and continuously tuned in a wide frequency region by an externally imposed magnetic field. The tunability of the passband is attributed to that of the negative permeability induced by ferromagnetic resonance in the ferrite. The authors proposed a convenient means to design tunable LHM based on the ferromagnetic materials as an alternative to tunable split ring resonators.
The Twins Corpus of Museum Visitor Questions

The Twins corpus is a collection of utterances spoken in interactions with two virtual characters who serve as guides at the Museum of Science in Boston. The corpus contains about 200,000 spoken utterances from museum visitors (primarily children) as well as from trained handlers who work at the museum. In addition to speech recordings, the corpus contains the outputs of speech recognition performed at the time of utterance as well as the system interpretation of the utterances. Parts of the corpus have been manually transcribed and annotated for question interpretation. The corpus has been used for improving performance of the museum characters and for a variety of research projects, such as phonetic-based Natural Language Understanding, creation of conversational characters from text resources, dialogue policy learning, and research on patterns of user interaction. It has the potential to be used for research on children's speech and on language used when talking to a virtual human.
A Bridging Cell Multiscale Methodology to Model the Structural Behaviour of Polymer Matrix Composites

Composite and nanocomposite materials exhibit behaviour which is inherently multiscale, extending from the atomistic to continuum levels. In composites, damage growth tends to occur at the nano and microstructural scale by means of crack growth and fibre-matrix debonding. Concurrent multiscale modeling provides a means of efficiently solving such localized phenomena, however its use in this application has been limited due to a number of existing issues in the multiscale field. These include the seamless transfer of information between continuum and atomistic domains, the small timesteps required for dynamic simulation, and limited research into concurrent multiscale modeling of amorphous polymeric materials. The objective of this thesis is thus twofold: to formulate a generalized approach to solving a coupled atomistic-to-continuum system that addresses these issues and to extend the application space of concurrent multiscale modeling to damage modeling in composite microstructures. To achieve these objectives, a finite element based multiscale technique termed the Bridging Cell Method (BCM), has been formulated with a focus on crystalline material systems. Case studies are then presented that show the effectiveness of the developed technique with respect to full
Interfacing with address events

Address event representation (AER)1 has long been considered a convenient transmission protocol for neuromorphic devices. This is because messages are transmitted by an asynchronous sequence of all-or-nothing ‘digital’ spikes, carrying information in the (analog) pattern of inter-spike time intervals. One evolution of the originally proposed point-to-point AER protocol is a many-to-many, fully-arbitrated protocol that supports the design of fairly general-purpose prototyping systems (as in the Silicon Cortex project2). One missing and long-needed feature of AER-based systems is the ability to acquire data from complex neuromorphic systems, to stimulate them using suitable data, and to support the design and operation of multi-chip AER-based systems. Such needs have been only partially met so far through commercial or homemade hardware and software built for a particular purpose and idiosyncratically dependent on the specific system. We have implemented a general-purpose solution to this problem in the form of a PCI (peripheral component interconnect) board,3 developed at the Italian Institute of Health, supported by software developed at the Insitute for Neuroinformatics. The use of the this board with VLSI networks of spiking neurons is illustrated elsewhere.4 The PCI-AER board can handle up to four sender and four receiver chips. Figure 1 illustrates the three main functions that the board can perform independently in a typical environment: monitoring, sequencing, and mapping. The monitoring function involves reading and time-stamping events from the AER bus, and making them available to the host PC for further processing. The monitor taps any AER transaction and, as the transaction is detected, stores a time label and the address in the FIFO (first in, first out). This decouples the management of AER events from the PCI read operation. Extra bits are used to identify time labels and address words so that the software can recover if words are missing due to FIFO overruns. Figure 2, left, illustrates the monitor data path. Another function that is performed is sequencing: generating spike traffic on the AER bus on the basis of pre-computed inforFigure 1. Multi-chip AER communication framework based on the PCI-AER board. Colored arrows indicate, diagrammatically, the information flow for the different operating modes of the board.
The electrophysiology of language production: what could be improved

Recently, the field of spoken-word production has seen an increasing interest in the use of the electroencephalogram (EEG), mainly for event-related potentials (ERPs). These are exciting times to be a language production researcher. However, no matter how much we would like our results to speak to our theories, they can only do so if our methods are formally correct and valid, and reported in ways that allow replicability. Inappropriate practices in signal processing and statistical testing, when applied to our investigations, may render our conclusions invalid or non-generalizable. Here, we first present some issues in signal processing and statistical testing that we think deserve more attention when analysing data, reporting results, and making inferences. These issues are not new to electrophysiology, so our sole contribution is to reiterate them in order to provide pointers to literature where they have been discussed in more detail and solutions have been proposed. We then discuss other issues pertinent to our investigations of overt word-production because of the effects (and potential confounds) that speaking will have on the signal. Although we cannot provide answers to some of the issues raised, we invite researchers in the field to jointly work on solutions so that the topic of the electrophysiology of word production can thrive on solid grounds.