Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytoplasmic Domain Signal Sequences That Mediate Transport of Varicella-Zoster Virus gB from the Endoplasmic Reticulum to the Golgi

ABSTRACT Normal herpesvirus assembly and egress depend on the correct intracellular localization of viral glycoproteins. While several post-Golgi transport motifs have been characterized within the cytoplasmic domains of various viral glycoproteins, few specific endoplasmic reticulum (ER)-to-Golgi transport signals have been described. We report the identification of two regions within the 125-amino-acid cytoplasmic domain of Varicella-Zoster virus gB that are required for its ER-to-Golgi transport. Native gB or gB containing deletions and specific point mutations in its cytoplasmic domain was expressed in mammalian cells. ER-to-Golgi transport of gB was assessed by indirect immunofluorescence and by the acquisition of Golgi-dependent posttranslational modifications. These studies revealed that the ER-to-Golgi transport of gB requires a nine-amino-acid region (YMTLVSAAE) within its cytoplasmic domain. Mutations of individual amino acids within this region markedly impaired the transport of gB from the ER to the Golgi, indicating that this domain functions by a sequence-dependent mechanism. Deletion of the C-terminal 17 amino acids of the gB cytoplasmic domain was also shown to impair the transport of gB from the ER to the Golgi. However, internal mutations within this region did not disrupt the transport of gB, indicating that its function during gB transport is not sequence dependent. Native gB is also transported to the nuclear membrane of transfected cells. gB lacking as many as 67 amino acids from the C terminus of its cytoplasmic domain continued to be transported to the nuclear membrane at apparently normal levels, indicating that the cytoplasmic domain of gB is not required for nuclear membrane localization.
Bayesian Joint Topic Modelling for Weakly Supervised Object Localisation

We address the problem of localisation of objects as bounding boxes in images with weak labels. This weakly supervised object localisation problem has been tackled in the past using discriminative models where each object class is localised independently from other classes. We propose a novel framework based on Bayesian joint topic modelling. Our framework has three distinctive advantages over previous works: (1) All object classes and image backgrounds are modelled jointly together in a single generative model so that "explaining away" inference can resolve ambiguity and lead to better learning and localisation. (2) The Bayesian formulation of the model enables easy integration of prior knowledge about object appearance to compensate for limited supervision. (3) Our model can be learned with a mixture of weakly labelled and unlabelled data, allowing the large volume of unlabelled images on the Internet to be exploited for learning. Extensive experiments on the challenging VOC dataset demonstrate that our approach outperforms the state-of-the-art competitors.
during zebrafish embryogenesis Systematic identification of long noncoding RNAs expressed Material

Material Supplemental http://genome.cshlp. org/content/suppl/2011/11/23/gr.133009. 111.DC1. html References http://genome.cshlp. org/content/22/3/577.full. html#ref-list-1 This article cites 66 articles, 25 of which can be accessed free at: License Commons Creative http://creativecommons.org/licenses/by-nc/3.0/. described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as ). After six months, it is available under http://genome.cshlp. org/site/misc/terms.xhtml first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the
On False Data Injection Attacks Against Railway Traction Power Systems

Modern urban railways extensively use computerized-sensing and control technologies to achieve safe, reliable, and well-timed operations. However, the use of these technologies may provide a convenient leverage to cyber-attackers who have bypassed the air gaps and aim at causing safety incidents and service disruptions. In this paper, we study false data injection (FDI) attacks against railways' traction power systems (TPSes). Specifically, we analyze two types of FDI attacks on the train-borne voltage, current, and position sensor measurements -- which we call efficiency attack and safety attack -- that (i) maximize the system's total power consumption and (ii) mislead trains' local voltages to exceed given safety-critical thresholds, respectively. To counteract, we develop a global attack detection system that serializes a bad data detector anda novel secondary attack detector designed based on unique TPS characteristics. With intact position data of trains, our detection system can effectively detect the FDI attacks ontrains' voltage and current measurements even if the attacker has full and accurate knowledge of the TPS, attack detection, and real-time system state. Extensive simulations driven by realistic running profiles of trains verify that a TPS setup isvulnerable to the FDI attacks, but these attacks can be detected effectively by the proposed global monitoring.
Exploring changes over time in habilitation professionals' perceptions and applications of the International Classification of Functioning, Disability and Health, version for Children and Youth (ICF-CY).

OBJECTIVE This study explored how professionals in inter-disciplinary teams perceived the implementation of the World Health Organization's International Classification of Functioning, Disability and Health, version for Children and Youth (ICF-CY) in Swedish habilitation services. DESIGN Descriptive longitudinal mixed-methods design. METHODS Following participation in a 2-day in-service training on the ICF-CY, 113 professionals from 14 interdisciplinary teams described their perceptions of the implementation of the ICF-CY at 3 consecutive time-points: during in-service training, after 1 year, and after 2.5 years. RESULTS Implementation of the ICF-CY in daily work focused on assessment and habilitation planning and required adaptations of routines and materials. The ICF-CY was perceived as useful in supporting analyses and in communication about children's needs. Professionals also perceived it as contributing to new perspectives on problems and a sharpened focus on participation. CONCLUSION Professionals indicated that the ICF-CY enhanced their awareness of families' views of child participation, which corresponded to organizational goals for habilitation services. An implementation finding was a lack of tools fitting the comprehensive ICF-CY perspective. The study points to the need for ICF-CY-based assessment and intervention methods focusing on child participation.
Specific alignment of structured RNA: stochastic grammars and sequence annealing

MOTIVATION Whole-genome screens suggest that eukaryotic genomes are dense with non-coding RNAs (ncRNAs). We introduce a novel approach to RNA multiple alignment which couples a generative probabilistic model of sequence and structure with an efficient sequence annealing approach for exploring the space of multiple alignments. This leads to a new software program, Stemloc-AMA, that is both accurate and specific in the alignment of multiple related RNA sequences. RESULTS When tested on the benchmark datasets BRalibase II and BRalibase 2.1, Stemloc-AMA has comparable sensitivity to and better specificity than the best competing methods. We use a large-scale random sequence experiment to show that while most alignment programs maximize sensitivity at the expense of specificity, even to the point of giving complete alignments of non-homologous sequences, Stemloc-AMA aligns only sequences with detectable homology and leaves unrelated sequences largely unaligned. Such accurate and specific alignments are crucial for comparative-genomics analysis, from inferring phylogeny to estimating substitution rates across different lineages. AVAILABILITY Stemloc-AMA is available from http://biowiki.org/StemLocAMA as part of the dart software package for sequence analysis.
Apriori-based frequent itemset mining algorithms on MapReduce

Many parallelization techniques have been proposed to enhance the performance of the Apriori-like frequent itemset mining algorithms. Characterized by both map and reduce functions, MapReduce has emerged and excels in the mining of datasets of terabyte scale or larger in either homogeneous or heterogeneous clusters. Minimizing the scheduling overhead of each map-reduce phase and maximizing the utilization of nodes in each phase are keys to successful MapReduce implementations. In this paper, we propose three algorithms, named SPC, FPC, and DPC, to investigate effective implementations of the Apriori algorithm in the MapReduce framework. DPC features in dynamically combining candidates of various lengths and outperforms both the straight-forward algorithm SPC and the fixed passes combined counting algorithm FPC. Extensive experimental results also show that all the three algorithms scale up linearly with respect to dataset sizes and cluster sizes.
Automatic Generation of Music for Inducing Emotive and Physiological Responses

Automatic Generation of Music for Inducing Emotive and Physiological Responses Kristine P. Monteith Department of Computer Science, BYU Doctor of Philosophy Music and emotion are two realms traditionally considered to be unique to human intelligence. This dissertation focuses on furthering artificial intelligence research, specifically in the area of computational creativity, by investigating methods of composing music that elicits desired emotional and physiological responses. It includes the following: • An algorithm for generating original musical selections that effectively elicit targeted emotional and physiological responses, • A description of some of the musical features that contribute to the conveyance of a given emotion or the elicitation of a given physiological response, and • An account of how this algorithm can be used effectively in two different situations: the generation of soundtracks for fairy tales and the generation of melodic accompaniments for lyrics. This dissertation also presents research on more general machine learning topics. These include: • A method of combining output from base classifiers in an ensemble that improves accuracy over a number of different baseline strategies, and • A description of some of the problems inherent in the Bayesian model averaging strategy and a novel algorithm for improving it.
Line Transects by Design: The Influence of Study Design, Spatial Distribution and Density of Objects on Estimates of Abundance

The line transect distance sampling method provides unbiased estimates of abundance when organisms are distributed randomly or line transects are laid out randomly, sample sizes are large and other assumptions of the method are met; such, however, is rarely the case in real life. We conducted a simulation study to investigate how spatial distribution and density of objects, and total length, layout and number of transects influence bias, precision, and accuracy of estimates of abundance obtained by distance sampling along line transects. Overall, density estimated using the distance sampling method was within 4.9% of the true density, but it varied substantially depending upon spatial distribution of objects. Of the three spatial distribution patterns considered, estimates of density were least biased, and most precise and accurate when objects were distributed randomly; they were most biased, and least precise and accurate when objects followed a clumped distribution. The estimated bias (% difference between true density and estimated density) for clumped, random and uniform distribution was 13.1%, -0.4%, and 2.1%, respectively; precision (% coefficient of variation, CV( ˆ D )) was 13.7%, 9.1%, and 9.2%; and accuracy (root mean-squared error, RMSE) was 27.9%, 7.4%, and 11.7% for clumped, random, and uniform distribution, respectively. Increasing total transect length and using several short transects (as opposed to few long transects) generally reduced bias, and increased accuracy and precision of estimates of abundance. A systematic layout of transects worked as well as, or better than, random layout, except when objects were distributed uniformly in space. This study advances the utility of the line transect method by providing information both on how study design affects accuracy and precision of abundance estimates, and how it can be improved when assumptions of the method are not strictly met based on a priori knowledge of the spatial distribution and presumed density of the target organism through appropriate changes in the study design.
Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences

Burkholderia pseudomallei (Bp), the agent of melioidosis, causes disease ranging from acute and rapidly fatal to protracted and chronic. Bp is highly infectious by aerosol, can cause severe disease with nonspecific symptoms, and is naturally resistant to multiple antibiotics. However, no vaccine exists. Unlike many Bp strains, which exhibit random variability in traits such as colony morphology, Bp strain MSHR5848 exhibited two distinct and relatively stable colony morphologies on sheep blood agar plates: a smooth, glossy, pale yellow colony and a flat, rough, white colony. Passage of the two variants, designated “Smooth” and “Rough”, under standard laboratory conditions produced cultures composed of > 99.9% of the single corresponding type; however, both could switch to the other type at different frequencies when incubated in certain nutritionally stringent or stressful growth conditions. These MSHR5848 derivatives were extensively characterized to identify variant-associated differences. Microscopic and colony morphology differences on six differential media were observed and only the Rough variant metabolized sugars in selective agar. Antimicrobial susceptibilities and lipopolysaccharide (LPS) features were characterized and phenotype microarray profiles revealed distinct metabolic and susceptibility disparities between the variants. Results using the phenotype microarray system narrowed the 1,920 substrates to a subset which differentiated the two variants. Smooth grew more rapidly in vitro than Rough, yet the latter exhibited a nearly 10-fold lower lethal dose for mice than Smooth. Finally, the Smooth variant was phagocytosed and replicated to a greater extent and was more cytotoxic than Rough in macrophages. In contrast, multiple locus sequence type (MLST) analysis, ribotyping, and whole genome sequence analysis demonstrated the variants’ genetic conservation; only a single consistent genetic difference between the two was identified for further study. These distinct differences shown by two variants of a Bp strain will be leveraged to better understand the mechanism of Bp phenotypic variability and to possibly identify in vitro markers of infection.
An ultra-low-power SAR ADC with an area-efficient DAC architecture

An ultra-low-power area-efficient 8-bit successive approximation register (SAR) analog-to-digital converter (ADC) is presented. To achieve ultra-low-power performance a DAC architecture is proposed that employs two rail-to-rail low-power unity-gain buffers and only 4 minimum-size capacitors instead of the conventional binary-weighted capacitor array. Thereby, power consumption and area are drastically reduced by virtue of lower switching activity and smaller size capacitor array. The proposed 8-bit SAR ADC is designed and simulated in a 0. 13µm CMOS process. Simulation results show that for a 2.4 kHz (12.4 kHz) input signal while sampling at 25 kHz, the ADC achieves an ENOB of 7.9 (7.8), consumes 290 nW (350 nW) form a 0.8 V analog supply and a 0.6 V digital supply, and achieves a FoM of 48 fJ/conversion-step (62 fJ/conversion-step).
Assessment of myocardial infarction by CT angiography and cardiovascular MRI in patients with cocaine-associated chest pain: a pilot study.

OBJECTIVES Cocaine is a commonly used illicit drug that leads to the most emergency department (ED) visits. Chest pain is the most common presentation, reported in 40% of patients. Our aim was to evaluate the incidence of previous myocardial infarction among young cocaine users (18-40 years) with cocaine-associated chest pain by the assessment of myocardial fibrosis by cardiovascular MRI. Second, we also intended to evaluate the coronary tree by CT angiography (CTA). METHODS 24 cocaine users (22 males) who frequently complained about cocaine-associated chest pain underwent CTA and cardiovascular MRI. Mean age of patients was 29.7 years and most of them (79%) had frequently used inhalatory cocaine. RESULTS The calcium score turned out to be positive in only one patient (Agatston=54). Among the coronary segments evaluated, only one patient had calcified plaques at the anterior descending coronary artery (proximal and medium segments). Assessment of regional ventricular function by the evaluation of 17 segments was normal in all patients. None of the patients showed myocardial delayed enhancement, indicative of myocardial fibrosis. CTA therefore confirmed the low cardiovascular risk of these patients, since most of them (96%) had no atherosclerosis detected by this examination. Only one patient (4%) had coronary atherosclerosis detected, without significant coronary stenosis. CONCLUSION Cardiovascular MR did not detect the presence of delayed enhancement indicative of myocardial fibrosis among young cocaine users with low cardiovascular risk who had complained of cocaine-associated chest pain.
Solid-State Drives: Memory Driven Design Methodologies for Optimal Performance

Solid-state drives (SSDs) faced an astonishing development in the last few years, becoming the cornerstone to new paradigms and markets of the information technology, such as cloud computing and big data centers. So far, the SSD design approach has focused on the optimization of the Flash translation layer, the firmware devoted to fulfill the compatibility with traditional hard-disk drives. For hyperscaled SSDs this strategy is no longer valid since their performance and reliability are strictly linked to that of the NAND Flash memories that constitute the storage medium, in particular when the multilevel cell paradigm is considered. For this reason, the design flow must follow a bottom-up approach that, starting from an accurate knowledge of the time and use dependent reliability of the NAND Flash memories, selects the most appropriate error correction strategy to extend the SSD lifetime while reducing its performance degradation. Then, the design flow moves to that of the SSD controller and of the interface toward the host where the application is running. This paper will thoroughly discuss this bottom-up approach, and finally, it will show how it is possible to leverage new approaches, such as the software-defined storage system that, by exploiting a hardware/software codesign of the SSD controller architecture and of the host application, will be able to revolutionize the traditional computer/memory interaction.
Anesthesia reduces discharge rates in the human pallidum without changing the discharge rate ratio between pallidal segments

Classical rate models of basal ganglia circuitry associate discharge rate of the globus pallidus external and internal segments (GPe, GPi respectively) solely with dopaminergic state and predict an inverse ratio between the discharge rates of the two pallidal segments. In contrast, the effects of other rate modulators such as general anesthesia (GA) on this ratio have been ignored. To respond to this need, we recorded the neuronal activity in the GPe and GPi in awake and anesthetized human patients with dystonia (57 and 53 trajectories respectively) and in awake patients with Parkinson's disease (PD, 16 trajectories) undergoing deep brain stimulation procedures. This triad enabled us to dissociate pallidal discharge ratio from general discharge modulation. An automatic offline spike detection and isolation quality system was used to select 1560 highly isolated units for analysis. The mean discharge rate in the GPi of awake PD patients was dramatically higher than in awake dystonia patients although the firing rate in the GPe was similar. Firing rates in dystonic patients under anesthesia were lower in both nuclei. Surprisingly, in all three groups, GPe firing rates were correlated with firing rates in the ipsilateral GPi. Thus, the firing rate ratio of ipsilateral GPi/GPe pairs was similar in awake and anesthetized patients with dystonia and significantly higher in PD. We suggest that pallidal activity is modulated by at least two independent processes: dopaminergic state which changes the GPi/GPe firing rate ratio, and anesthesia which modulates firing rates in both pallidal nuclei without changing the ratio between their firing rates.
Modularizing Client-Side Web Service Management Aspects

In the short time Web Services have been around, a lot of development tools became available to create and deploy web services. However, typical approaches for the integration of web services require the client applications to hard-wire their references. To improve maintainability and achieve high flexibility in the integration of services we proposed in previous work an intermediate abstraction layer, called Web Services Management Layer (WSML). The WSML allows decoupling services from the application, selecting services depending on specific criteria and monitoring and managing additional service concerns. In this paper we extend that work and present the results of a case study where we implemented the service redirection mechanism extended with a local and global cache. We show how dynamic AOP, and in particularly the JAsCo language, is ideally suited to implement the core functionality of the WSML.
A Framework for Software Architecture Visualisation Assessment

In order to assess software architecture visualisation strategies, we qualitatively characterize then construct an assessment framework with 7 key areas and 31 features. The framework is used for evaluation and comparison of various strategies from multiple stakeholder perspectives. Six existing software architecture visualisation tools and a seventh research tool were evaluated. All tools exhibited shortcomings when evaluated in the framework