Miracle-dz/UniFAR-FTUs huggingface dataset:
IC DEFECTS-BASED TESTABILITY ANALYSIS

High quality IC design involves not only performance and silicon area, but also testability. Product quality, measured by low dejects levels (as low as 100 p.p.m.), requires that test patterns must detect nearly all circuit faults caused by likely physical defects. This requires a careful examination of the testability of the physical design, and its enhancement. The purpose of this contribution is to present a methodology for physical testability evaluation, and to demonstrate its usefulness. The methodology allows realistic fault extraction and classification, and the identification of hard to detect faults, their layout location and physical origin, prior to simulation. Measures of physical testability and fault hardness are introduced. When possible, suggestions for design improvement by layout reconfiguration, are provided, as a better solution than simple test improvement, either by test pattern refinement, or by using more sophisticated detection techniques, like current testing. Simulation results, with several design examples, show that layout styles exhibit characteristic pat.terns, in terms of t,he incidence of faults caused by the different, physical defects. Hence, for each layout style, the sensivity of physical designs to each physical defect can be analysed and decreased. Moreover, simulation results with a new cell library demonstrate that physical design improvements can significantly enhance the circuit’s qualit,y and testability.
A Guide to Quantitative Biomarker Assay Development using Whispering Gallery Mode Biosensors

Whispering gallery mode (WGM) sensors are a class of powerful analytical techniques defined by the measurement of changes in the local refractive index at or near the sensor surface. When functionalized with target‐specific capture agents, analyte binding can be measured with very low limits of detection. There are many geometric manifestations of WGM sensors, with chip‐integrated silicon photonic devices first commercialized because of the robust, wafer‐scale device fabrication, facile optical interrogation, and amenability to the creation of multiplexed sensor arrays. Using these arrays, a number of biomolecular targets have been detected in both label‐free and label‐enhanced assay formats. For example, sub‐picomolar detection limits for multiple cytokines were achieved using an enzymatically enhanced sandwich immunoassay that showed high analyte specificity suitable for detection in complex, clinical matrices. This protocol describes a generalizable approach for the development of quantitative, multiplexed immunoassays using silicon photonic microrings as an example WGM platform. © 2017 by John Wiley & Sons, Inc.
Analysis of the Effect of Natural Sequence Variation in Tat and in Cyclin T on the Formation and RNA Binding Properties of Tat-Cyclin T Complexes

ABSTRACT The biological activity of the human immunodeficiency virus type 1 (HIV-1) Tat (Tat1) transcriptional activator requires the recruitment of a Tat1-CyclinT1 (CycT1) complex to the TAR RNA target encoded within the viral long terminal repeat (LTR). While other primate immunodeficiency viruses, such as HIV-2 and mandrill simian immunodeficiency virus (SIVmnd), also encode Tat proteins that activate transcription via RNA targets, these proteins differ significantly, both from each other and from Tat1, in terms of their ability to activate transcription directed by LTR promoter elements found in different HIV and SIV isolates. Here, we show that CycT1 also serves as an essential cofactor for HIV-2 Tat (Tat2) and SIVmnd Tat (Tat-M) function. Moreover, the CycT1 complex formed by each Tat protein displays a distinct RNA target specificity that accurately predicts the level of activation observed with a particular LTR. While Tat2 and Tat-M share the ability of Tat1 to bind to CycT1, they differ from Tat1 in that they are also able to bind to the related but distinct CycT2. However, the resultant Tat-CycT2 complexes fail to bind TAR and are therefore abortive. Surprisingly, mutation of a single residue in CycT2 (asparagine 260 to cysteine) rescues the ability of CycT2 to bind Tat1 and also activates not only TAR binding by all three Tat-CycT2 complexes but also Tat function. Therefore, the RNA target specificity of different Tat-CycT1 complexes is modulated by natural sequence variation in both the viral Tat transcriptional activator and in the host cell CycT molecule recruited by Tat. Further, the RNA target specificity of the resultant Tat-CycT1 complex accurately predicts the ability of that complex to activate transcription from a given LTR promoter element.
The influence of cultural values on U.S. and Danish students’ digital behavior: Exploring culture, new media, and social context

ABSTRACT This study explores the intersection of culture, new media, and social context—an essential component of intercultural new media studies—by investigating the social uses of smartphones, tablets, and laptops in university classrooms in Denmark and the US. American and Danish university students differed significantly in (1) frequency of new media use, (2) preferred classroom policies regulating use, (3) perceived impact of use on learning, attention, and student participation, and (4) preferred instructor strategies for handling distracting uses. Danes and Americans also differed significantly in authority values that are linked to students' new media use in the classroom.
Top‐down influences on lexical selection during spoken word production: A 4T fMRI investigation of refractory effects in picture naming

Spoken word production is assumed to involve stages of processing in which activation spreads through layers of units comprising lexical‐conceptual knowledge and their corresponding phonological word forms. Using high‐field (4T) functional magnetic resonance imaging (fMRI), we assessed whether the relationship between these stages is strictly serial or involves cascaded‐interactive processing, and whether central (decision/control) processing mechanisms are involved in lexical selection. Participants performed the competitor priming paradigm in which distractor words, named from a definition and semantically related to a subsequently presented target picture, slow picture‐naming latency compared to that with unrelated words. The paradigm intersperses two trials between the definition and the picture to be named, temporally separating activation in the word perception and production networks. Priming semantic competitors of target picture names significantly increased activation in the left posterior temporal cortex, and to a lesser extent the left middle temporal cortex, consistent with the predictions of cascaded‐interactive models of lexical access. In addition, extensive activation was detected in the anterior cingulate and pars orbitalis of the inferior frontal gyrus. The findings indicate that lexical selection during competitor priming is biased by top‐down mechanisms to reverse associations between primed distractor words and target pictures to select words that meet the current goal of speech. Hum Brain Mapp, 2006. © 2006 Wiley‐Liss, Inc.
MODp-tests, almost independence and small probability spaces

In this paper, we consider approximations of probability distributions over ZZ p . We present an approach to estimate the quality of approximations of probability distributions towards the construction of small probability spaces. These are used to derandomize algorithms. In contrast to results by Even, Goldreich, Luby, Nisan and Veli ckovi c [EGLNV], our methods are simple, and for reasonably small p, we get smaller sample spaces. Our considerations are motivated by a problemwhich was mentioned in recent work of Azar, Motwani and Naor [AMN], namely, how to construct in time polynomial in n a good approximation to the joint probability distribution of the random variables X1; X2; : : : ; Xn where each Xi has values in f0; 1g and satis es Xi = 0 with probability q and Xi = 1 with probability 1 q where q is arbitrary. Our considerations improve on results by [EGLNV] and [AMN].
The organisms and biological processes involved in asymbiotic nitrogen fixation in waterlogged soil amended with straw 1 ?

The acetylene reduction assay was used to determine nitrogenase activity in a waterlogged soil-straw system. Nitrogenase activity was related to the number of nitrogen-fixing clostridia. The patterns of respiration, microbial numbers, and nitrogenase activity indicated a change in the microbial activity at about the 8th day of incubation. This was attributed to the sequential use of the different straw components, with a short lag in activity between the periods of maximum hemicellulose and cellulose utilization. Two layers of microbial activity were observed in waterlogged soil-straw mixtures, an aerobic layer extending from the surface to a depth of 2 mm, and an anaerobic layer below this. The organisms in the aerobic layer were responsible for the partial degradation of straw and the release of metabolites; the metabolites were used by the nitrogen-fixing organisms in the anaerobic layer. Anaerobic organisms of the genus Clostridi~rn were found to be the only active nitrogen fixers in the waterlogged systems. The physiological and morphological characteristics of the organisms isolated from the waterlogged soil are similar to those of C . butylicurn.
Characterization of a Campylobacter fetus‐like strain isolated from the faeces of a sick leopard tortoise (Stigmochelys pardalis) using matrix‐assisted laser desorption/ionization time of flight as an alternative to bacterial 16S rDNA phylogeny

This article describes the isolation and characterization of a Campylobacter‐like isolate originating from the faeces of a sick leopard tortoise. Molecular as well as matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) characterization suggests that it could correspond to a new Campylobacter species.
Identifying conservation units within captive chimpanzee populations.

One of the primary objectives in the captive management of any endangered primate is to preserve as much as possible the genetic diversity that has evolved and still exists in wild gene pools. The rationale for this is based on the theoretical understanding of the relationship between genetic diversity and fitness in response to selection. There remains little consensus, however, as to the type of genetic data that should be used to monitor captive populations. In order to develop a deeper understanding of the degree and nature of genetic diversity among "wild" chimpanzee gene pools, as well as to determine if one type of genetic data is more useful than others, DNA sequence data were generated at three unlinked, nonrepetitive nuclear loci, one polymorphic microsatellite, and the mitochondrial D-loop for 59 unrelated common and pygmy chimpanzees. The results suggest that: 1) data from nuclear loci can be used to differentiate common chimpanzee subspecies; 2) pygmy chimpanzees may have less genetic diversity than common chimpanzees; 3) shared microsatellite alleles do not always indicate identity by descent; and 4) nonrepetitive loci provide unique insights into evolutionary relationships and provide useful information for captive management programs.
On System Capabilities and Customer Requirements in ERP Implementations

As pre-packaged solutions developed for a generic customer, Enterprise Resource Planning (ERP) systems cannot satisfy ‘out of the box’ all the specific requirements of every entity where they are deployed, due to differences between the ERP application and the business model. The identification of disparities between the organization requirements and the ERP system capabilities allows determining adjustments expected in organizational practices to match the way the ERP application works, as well as modifications, customizations, or extensions needed in the software to fit inadequately addressed business processes. This article focuses on this issue by reviewing current methods that try to identify and bridge gaps between business requirements and system capabilities in ERP implementations.
Low Energy yet Reliable Data Communication Scheme for Network-on-Chip

In this paper, a low energy yet reliable communication scheme for network-on-chip is suggested. To reduce the communication energy consumption, we invoke low-swing signals for transmitting data, as well as data encoding techniques, for minimizing both self and coupling switching capacitance activity factors. To maintain the communication reliability of communication at low-voltage swing, an error control coding (ECC) technique is exploited. The decision about end-to-end or hop-to-hop ECC schemes and the proper number of detectable errors are determined through high-level mathematical analysis on the energy and reliability characteristics of the techniques. Based on the analysis, the extended single error correction double-error detecting end-to-end coding technique with three bits of error detection is used in the network layer. For minimization of the self and coupling switching capacitance activity factors, the odd, even, full invert scheme is employed in the data link layer. This coding has an inherent error detection probability for the flits, which is exploited in the suggested technique. The efficiency of the scheme is studied by using both synthetic and real traffic scenarios. The study reveals savings of up to 43% and 58%, for power dissipation and energy consumption, respectively, without any significant performance degradation and overhead in the network interface.
A recursive nonlinear filter for removal of impulse noise

We present a new algorithm for suppression of impulse noise which is based on a special combination of impulse detection and nonlinear filtering. The nonlinear filter possesses a recursive structure and provides an estimate of the original sample and the impulse height. The impulse detector is realized as a radial basis function network and yields a fuzzy decision about the impulsivity of a sample. Due to the special combination of both systems, we need only a small number of parameters which can be computed recursively using a procedure derived from a joint optimality criterion. Thereby, we achieve a dramatic gain in performance over other existing methods for both weakly and highly corrupted signals. Further, the algorithm preserves signal details and edges and is applicable to arbitrary impulse distributions.
Long-term memory guidance of visuospatial attention in a change-detection paradigm

Visual task performance is generally stronger in familiar environments. One reason for this familiarity benefit is that we learn where to direct our visual attention and effective attentional deployment enhances performance. Visual working memory plays a central role in supporting long-term memory guidance of visuospatial attention. We modified a change detection task to create a new paradigm for investigating long-term memory guidance of attention. During the training phase, subjects viewed images in a flicker paradigm and were asked to detect between one and three changes in the images. The test phase required subjects to detect a single change in a one-shot change detection task in which they held all possible locations of changes in visual working memory and deployed attention to those locations to determine if a change occurred. Subjects detected significantly more changes in images for which they had been trained to detect the changes, demonstrating that memory of the images guided subjects in deploying their attention. Moreover, capacity to detect changes was greater for images that had multiple changes during the training phase. In Experiment 2, we observed that capacity to detect changes for the 3-studied change condition increased significantly with more study exposures and capacity was significantly higher than 1, indicating that subjects were able to attend to more than one location. Together, these findings suggest memory and attentional systems interact via working memory such that long-term memory can be used to direct visual spatial attention to multiple locations based on previous experience.
Strategic Application of Feedforward Neural Networks to Large-Scale Classification

Feedforward neural networks have been successfully applied to a variety of classification problems, but th e number of classes used for experiments was too small to app ly the results directly to large-scale problems. This pap er presents several st rategies for applying feedforward neur al networks to large-scale, complex classificat ion problems: a two-stage classification scheme, a rapid learn ing met hod, a t raining schedul e called select ive reinforcement learning, a t raining scheme including syst ematic noise, and a weight matrix redu ction scheme. These st rategies have been applied to the design of a printed Hangul (Korean script) recognition system. Exp erim ent s with the 990 most frequently used pri nt ed Hangul syllables confirm the usefulness of th e present ed str at egies.
Matrix metalloproteinase 13 loss associated with impaired extracellular matrix remodeling disrupts chondrocyte differentiation by concerted effects on multiple regulatory factors.

OBJECTIVE To link matrix metalloproteinase 13 (MMP-13) activity and extracellular matrix (ECM) remodeling to alterations in regulatory factors leading to a disruption in chondrocyte homeostasis. METHODS MMP-13 expression was ablated in primary human chondrocytes by stable retrotransduction of short hairpin RNA. The effects of MMP-13 knockdown on key regulators of chondrocyte differentiation (SOX9, runt-related transcription factor 2 [RUNX-2], and beta-catenin) and angiogenesis (vascular endothelial growth factor [VEGF]) were scored at the protein level (by immunohistochemical or Western blot analysis) and RNA level (by real-time polymerase chain reaction) in high-density monolayer and micromass cultures under mineralizing conditions. Effects on cellular viability in conjunction with chondrocyte progression toward a hypertrophic-like state were assessed in micromass cultures. Alterations in SOX9 subcellular distribution were assessed using confocal microscopy in micromass cultures and also in osteoarthritic cartilage. RESULTS Differentiation of control chondrocyte micromasses progressed up to a terminal phase, with calcium deposition in conjunction with reduced cell viability and scant ECM. MMP-13 knockdown impaired ECM remodeling and suppressed differentiation in conjunction with reduced levels of RUNX-2, beta-catenin, and VEGF. MMP-13 levels in vitro and ECM remodeling in vitro and in vivo were linked to changes in SOX9 subcellular localization. SOX9 was largely excluded from the nuclei of chondrocytes with MMP-13-remodeled or -degraded ECM, and exhibited an intranuclear staining pattern in chondrocytes with impaired MMP-13 activity in vitro or with more intact ECM in vivo. CONCLUSION MMP-13 loss leads to a breakdown in primary human articular chondrocyte differentiation by altering the expression of multiple regulatory factors.
Granzyme B: a natural born killer

Summary: A main pathway used by cytotoxic T lymphocytes (CTLs) and natural killer cells to eliminate pathogenic cells is via exocytosis of granule components in the direction of the target cell, delivering a lethal hit of cytolytic molecules. Amongst these, granzyme B and perforin have been shown to induce CTL‐mediated target cell DNA fragmentation and apoptosis. Once released from the CTL, granzyme B binds its receptor, the mannose‐6‐phosphate/insulin‐like growth factor II receptor, and is endocytosed but remains arrested in endocytic vesicles until released by perforin. Once in the cytosol, granzyme B targets caspase‐3 directly or indirectly through the mitochondria, initiating the caspase cascade to DNA fragmentation and apoptosis. Caspase activity is required for apoptosis to occur; however, in the absence of caspase activity, granzyme B can still initiate mitochondrial events via the cleavage of Bid. Recent work shows that granzyme B‐mediated release of apoptotic factors from the mitochondria is essential for the full activation of caspase‐3. Thus, granzyme B acts at multiple points to initiate the death of the offending cell. Studies of the granzyme B death receptor and internal signaling pathways may lead to critical advances in cell transplantation and cancer therapy.
Binary Constraint System Games and Locally Commutative Reductions

A binary constraint system game is a two-player one-round non-local game defined by a system of Boolean constraints. The game has a perfect quantum strategy if and only if the constraint system has a quantum satisfying assignment [R. Cleve and R. Mittal, arXiv:1209.2729]. We show that several concepts including the quantum chromatic number and the Kochen-Specker sets that arose from different contexts fit naturally in the binary constraint system framework. The structure and complexity of the quantum satisfiability problems for these constraint systems are investigated. Combined with a new construct called the commutativity gadget for each problem, several classic NP-hardness reductions are lifted to their corresponding quantum versions. We also provide a simple parity constraint game that requires $\Omega(\sqrt{n})$ EPR pairs in perfect strategies where $n$ is the number of variables in the constraint system.
Retinal Nerve Fiber Layer Thickness in Parkinson Disease

Abstract:Dopaminergic neuronal cells have been identified in the inner nuclear and inner plexiform layers of the human retina. The dopaminergic content of the retina is reduced in patients with idiopathic Parkinson disease (PD). These observations led us to study the retinal nerve fiber layer (RNFL) thickness in patients with PD without visual impairment compared to healthy controls using spectral-domain optical coherence tomography (SD-OCT). Eighty-two subjects, including 42 patients with PD, newly diagnosed and untreated (24 men, 18 women, age range: 47–66 years), and 40 healthy controls, were enrolled. Both eyes of patients with PD and controls were imaged with SD-OCT. The mean RNFL thickness was 77 ± 11.5 &mgr;m in PD patients and 89 ± 8.7 &mgr;m in healthy controls (P = 0.001). Selective thinning of the RNFL was found in the temporal region with mean temporal RNFL thickness of 66 ± 6.7 &mgr;m in PD patients and 75 ± 4.8 &mgr;m in controls (P = 0.001). The thickness of the RNFL is decreased in PD patients. Demonstrating progressive thinning of RNFL over time will be critical for validating optical coherence tomography as a viable biomarker of patients with PD.
AirFlow: designing immersive breathing training games for COPD

Chronic Obstructive Pulmonary Disease (COPD) refers to a collection of lung diseases that result in breathing difficulties. In some cases, the symptoms of COPD can be reduced, by engaging in breathing exercises. Technology can support, and we are developing AirFlow, a suite of interactive computer games, to guide breathing exercises and promote learning. To establish requirements, we interviewed 20 people with COPD, in China, to understand their use of breathing exercises, and learn how technology might fit their lifestyle. The findings informed our design goals. We outline a prototype system, where respiration rate, waveform, and amplitude are captured and used to control a virtual environment. The system will guide users through breathing exercises, and provide training instructions, using a series of games. The immersive environment aims to support a fun and motivating experience, therefore underpinning user confidence.