Miracle-dz/UniFAR-FTUs huggingface dataset:
The design and application of structured types in Ptolemy II

Ptolemy II is a component-based design and modeling environment. It has a polymorphic type system that supports both the base types and structured types, such as arrays and records. This paper presents the extensions to the base type system that support structured types. In the base type system, all the types are organized into a type lattice, and type constraints in the form of inequalities can be solved efficiently over the lattice. We take a hierarchical and granular approach to add structured types to the lattice, and extend the format of inequality constraints to allow arbitrary nesting of structured types. We also analyze the convergence of the constraint solving algorithm on an infinite lattice after structured types are added. To show the application of structured types, we present a Ptolemy II model that implements part of the IEEE 802.11 specifications. This model makes extensive use of record types to represent the protocol messages in the system.
Non-gaussianity from broken symmetries

Recently we studied inflation models in which the inflation potential is characterized by an underlying approximate global symmetry. In the first work we pointed out that in such a model curvature perturbations are generated after the end of the slow-roll phase of inflation. In this work we develop further the observational implications of the model and compute the degree of non-Gaussianity predicted in the scenario. We find that the corresponding nonlinearity parameter, F{sub NL}, can be as large as 10{sup 2}.
Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus

Availability of computational methods that predict disorder from protein sequences fuels rapid advancements in the protein disorder field. The most accurate predictions are usually obtained with consensus-based approaches. However, their design is performed in an ad hoc manner. We perform first-of-its-kind rational design where we empirically search for an optimal mixture of base methods, selected out of a comprehensive set of 20 modern predictors, and we explore several novel ways to build the consensus. Our method for the prediction of disorder based on Consensus of Predictors (disCoP) combines seven base methods, utilizes custom-designed set of selected 11 features that aggregate base predictions over a sequence window and uses binomial deviance loss-based regression to implement the consensus. Empirical tests performed on an independent benchmark set (with low-sequence similarity compared with proteins used to design disCoP), shows that disCoP provides statistically significant improvements with at least moderate magnitude of differences. disCoP outperforms 28 predictors, including other state-of-the-art consensuses, and achieves Area Under the ROC Curve of . 85 and Matthews Correlation Coefficient of . 5 compared with . 83 and . 48 of the best considered approach, respectively. Our consensus provides high rate of correct disorder predictions, especially when low rate of incorrect disorder predictions is desired. We are first to comprehensively assess predictions in the context of several functional types of disorder and we demonstrate that disCoP generates accurate predictions of disorder located at the post-translational modification sites (in particular phosphorylation sites) and in autoregulatory and flexible linker regions. disCoP is available at http://biomine.ece. ualberta.ca/disCoP/.
Noise-resistant weak-structure enhancement for digital radiography

Today's digital radiography systems mostly use unsharp masking-like image enhancement techniques based on splitting input images into two or three frequency channels. This method allows to enhance very small structures (edge enhancement) as well as enhancement of global contrast (harmonization). However, structures of medium size are not accessible by such enhancement. We develop and test a nonlinear enhancement algorithm based on hierarchically repeated unsharp masking, resulting in a multiscale architecture allowing consistent access to structures of all sizes. The algorithm is noise- resistant in the sense that it prevents unacceptable noise amplification. Clinical tests performed in the radiology departments of two major German hospitals so far strongly indicate the superior performance and high acceptance of the new processing.
The interdependence of the Rho GTPases and apicobasal cell polarity

Signaling via the Rho GTPases provides crucial regulation of numerous cell polarization events, including apicobasal (AB) polarity, polarized cell migration, polarized cell division and neuronal polarity. Here we review the relationships between the Rho family GTPases and epithelial AB polarization events, focusing on the 3 best-characterized members: Rho, Rac and Cdc42. We discuss a multitude of processes that are important for AB polarization, including lumen formation, apical membrane specification, cell-cell junction assembly and maintenance, as well as tissue polarity. Our discussions aim to highlight the immensely complex regulatory mechanisms that encompass Rho GTPase signaling during AB polarization. More specifically, in this review we discuss several emerging common themes, that include: 1) the need for Rho GTPase activities to be carefully balanced in both a spatial and temporal manner through a multitude of mechanisms; 2) the existence of signaling feedback loops and crosstalk to create robust cellular responses; and 3) the frequent multifunctionality that exists among AB polarity regulators. Regarding this latter theme, we provide further discussion of the potential plasticity of the cell polarity machinery and as a result the possible implications for human disease.
Olive Cultivation in the Southern Hemisphere: Flowering, Water Requirements and Oil Quality Responses to New Crop Environments

Olive (Olea europaea L.) is a crop well adapted to the environmental conditions prevailing in the Mediterranean Basin. Nevertheless, the increasing international demand for olive oil and table olives in the last two decades has led to expansion of olive cultivation in some countries of the southern hemisphere, notably in Argentina, Chile, Perú and Australia. While the percentage of world production represented by these countries is still low, many of the new production regions do not have typical Mediterranean climates, and some are located at subtropical latitudes where there is relatively little information about crop function. Thus, the primary objective of this review was to assess recently published scientific literature on olive cultivation in these new crop environments. The review focuses on three main aspects: (a) chilling requirements for flowering, (b) water requirements and irrigation management, and (c) environmental effects on fruit oil concentration and quality. In many arid and semiarid regions of South America, temperatures are high and rainfall is low in the winter and early spring months compared to conditions in much of the Mediterranean Basin. High temperatures have often been found to have detrimental effects on olive flowering in many olive cultivars that have been introduced to South America, and a better understanding of chilling requirements is needed. Lack of rainfall in the winter and spring also has resulted in an urgent need to evaluate water requirements from the flower differentiation period in the winter to early fruit bearing. Additionally, in some olive growing areas of South America and Australia, high early season temperatures affect the timing of phenological events such that the onset of oil synthesis occurs sooner than in the Mediterranean Basin with most oil accumulation taking place in the summer when temperatures are very high. Increasing mean daily temperatures have been demonstrated to decrease fruit oil concentration (%) and negatively affect some aspects of oil quality based on both correlative field studies and manipulative experiments. From a practical standpoint, current findings could be used as approximate tools to determine whether the temperature conditions in a proposed new growing region are appropriate for achieving sustainable oil productivity and quality.
Randomness criteria in terms of α-divergences

Vovk’s randomness criterion characterizes sequences that are random relative to two distinct computable probability measures. The uniqueness of the criterion lies in the fact that, unlike the standard criterion based on the likelihood ratio test, it is expressed in terms of a geometrical quantity, the Hellinger distance, on the space of probability measures. In this paper, we generalize the randomness criterion to a wider class of geometrical quantities, the α-divergences with −1 < α < 1. The non-extendibility of the criterion across the boundaries α = ±1 is investigated in connection with the likelihood ratio test and information geometry.
Deixis and Discourse Processing

Computational approaches to discourse understanding have a two-part goal: (1) identifying those aspects of discourse understanding that require process-based accounts, and (2) characterizing the processes and data structures they involve. To date, in the area of reference, process-based accounts have been developed for reference via anaphoric pronouns and via definite descriptors. In this paper, I propose and argue for a processbased account of deictic reference in text. This account adds precision to common notions of discourse entity, discourse segment and focus and to relationships between the three. Comments University of Pennsylvania Department of Computer and Information Science Technical Report No. MSCIS-88-75. This technical report is available at ScholarlyCommons: http://repository.upenn. edu/cis_reports/610 DISCOURSE DEIXIS AND DISCOURSE PROCESSING Bonnie Lynn Webber MS-CIS-88-75 LINC LAB 133 Department of Computer and Information Science School of Engineering and Applied Science University of Pennsylvania Philadelphia, PA 19104
Demystifying trial networks and network meta-analysis

Networks of randomized clinical trials can be evaluated in the context of a network meta-analysis, a procedure that permits inferences into the comparative effectiveness of interventions that may or may not have been evaluated directly against each other. This approach is quickly gaining popularity among clinicians and guideline decision makers. However, certain methodological aspects are poorly understood. Here, we explain the geometry of a network, statistical and conceptual heterogeneity and incoherence, and challenges in the application and interpretation of data synthesis. These concepts are essential to make sense of a network meta-analysis.
The ascidian Mesp gene specifies heart precursor cells

Understanding the molecular basis of heart development is an important research area, because malformation of the cardiovascular system is among the most frequent inborn defects. Although recent research has identified molecules responsible for heart morphogenesis in vertebrates, the initial specification of heart progenitors has not been well characterized. Ascidians provide an appropriate experimental system for exploring this specification mechanism, because the lineage for the juvenile heart is well characterized, with B7.5 cells at the 110-cell stage giving rise to embryonic trunk ventral cells (TVCs) or the juvenile heart progenitors. Here, we show that Cs-Mesp, the sole ortholog of vertebrate Mesp genes in the ascidian Ciona savignyi, is specifically and transiently expressed in the embryonic heart progenitor cells (B7.5 cells). Cs-Mesp is essential for the specification of heart precursor cells, in which Nkx, HAND and HAND-like (NoTrlc) genes are expressed. As a result, knockdown of Cs-Mesp with specific morpholino antisense oligonucleotides causes failure of the development of the juvenile heart. Together with previous evidence obtained in mice, the present results suggest that a mechanism for heart specification beginning with Mesp through Nkx and HAND is conserved among chordates.
Enabling or Disabling? Increasing Involvement of Charities in Social Housing

Since 1997, there has been a general policy trend towards the inclusion and use of the third sector to provide some public services, services which have traditionally been regarded as the responsibility of the State. Over this time, the Government has viewed the third sector as a, �key partner in a mixed economy of public service provision, alongside the public and private sectors�. The third sector includes organisations, which are charitable, �not for profit�, voluntary and community sector, social enterprise, mutuals, co-operatives, and non-governmental organisations and all work independently of governmental direction. Statistics indicate that there are around 250,000 voluntary and community organisations in addition to the 150,000 general charities in existence.2 It is further thought that the sector contributes at least £7 million to the UK economy.3 In 2002, the Rt Hon Paul Boateng, MP, stated: �[O]ur aim must be to build a new partnership using the sector's strengths to challenge and stimulate new ideas, complement our shared objectives and take forward the development of social policy generally. This partnership is about fresh ways of thinking through the role and structure of government and the voluntary sector and the way we deliver public services. � This paper seeks to consider the role of charities in housing, and the increased focus on charities actively discharging rather than *CONVPL 210 supplementing housing services, as part of government initiatives and beyond. In a sense, there is strong feeling that, at the time of writing, the �credit crunch� in the United Kingdom and impending global recession will lead to a �new dawn� for the social housing sector, in which charities may have a significant role to play. The purpose of this paper is to consider the effect of the wider involvement of charities in public service provision in housing the mentally vulnerable. The focus is narrow to allow for clear exposition of the issues, but many of the issues raised will be of interest to all charities dealing with public services and property. The question ultimately is would charitable involvement as a third arm of public service provision exacerbate the existing problems of fragmentation, as well as destroying some of the key advantages of the charitable sector? Answering the questions posed requires the context of charitable involvement to be established, which involves an examination of the role that the charitable, public and private sectors have played in social housing to identify what is new in current thinking; before analysing how charities as primary, rather than supplementary, providers of public housing services might either enable or disable effective service for the mentally vulnerable.
Secure Outsourced Biometric Authentication With Performance Evaluation on Smartphones

We design privacy-preserving protocols for scaled Manhattan and scaled Euclidean verifiers, secure against malicious clients and honest-but-curious server. We then augment our protocols with principal component analysis (PCA), which can help to improve authentication accuracy. We evaluate the performance of our protocols on an emerging application-namely, continuous authentication of smartphone users. We compare the performance of protocols secure under the malicious client model, with three protocols secure in the honest-but-curious model. We report tradeoffs between computation overhead, communication cost, and authentication accuracy. Our key observations are: 1) scaled Manhattan without PCA gives the best tradeoff between security, accuracy, and overhead and 2) with PCA, memory availability on current smartphones limits the number of features that can be used with scaled Manhattan, and prevents the scaled Euclidean protocol from running. Our extended evaluation on a laptop client shows that PCA with both scaled Manhattan and scaled Euclidean verifiers is feasible given sufficient memory.
Comparison Between the Prognostic Value of Left Ventricular Function and Myocardial Perfusion Reserve in Patients with Ischemic Heart Disease

The purpose of this study was to compare the prognostic value of left ventricular ejection fraction (LVEF) and myocardial perfusion reserve (MPR) assessed with PET in patients with ischemic heart disease (IHD). Myocardial perfusion is the main determinant of left ventricular function in patients with IHD. The prognostic value of LVEF has been widely established. In addition, MPR determines survival in patients with hypertrophic and dilated cardiomyopathies. In the present study, we evaluated whether MPR also determines survival in patients with IHD. Methods: Between 1995 and 2003, 480 consecutive patients with chronic IHD underwent dipyridamole stress and rest 13N-ammonia PET to determine MPR. Additionally, 18F-FDG PET was performed for viability (mismatching defects), infarction (matching defects), and left ventricular function assessment. Patients were followed for all causes of mortality and major cardiovascular events. Results: In 463 of the 480 patients, valid MPR could be measured (368 men; mean age, 66 ± 11 y; LVEF, 35% ± 15%). One hundred nineteen patients underwent a PET-driven revascularization (67 through percutaneous coronary intervention and 52 through coronary artery bypass grafting). The remaining 344 patients were the subject of this study. The overall MPR was 1.71 ± 0.50 (intertertile boundaries, 1.49 and 1.84). After adjustment for age and sex, MPR was associated with a hazard ratio for cardiac death of 4.11 (95% confidence interval, 2.98–5.67) per SD decrease, whereas the risk for LVEF was 2.76 (2.00–3.82) per SD decrease. Conclusion: Patients with IHD with a low MPR are at high risk of cardiac death. MPR is a more sensitive predictor for cardiac death than is LVEF.
Stochastic Mechanics as a Gauge Theory

We show that non-relativistic Quantum Mechanics can be faithfully represented in terms of a classical diffusion process endowed with a gauge symmetry of group Z_4. The representation is based on a quantization condition for the realized action along paths. A lattice regularization is introduced to make rigorous sense of the construction and then removed. Quantum mechanics is recovered in the continuum limit and the full U(1) gauge group symmetry of electro-magnetism appears. Anti-particle representations emerge naturally, albeit the context is non-relativistic. Quantum density matrices are obtained by averaging classical probability distributions over phase-action variables. We find that quantum conditioning can be described in classical terms but not through the standard notion of sub sigma-algebras. Delicate restrictions arise by the constraint that we are only interested in the algebra of gauge invariant random variables. We conclude that Quantum Mechanics is equivalent to a theory of gauge invariant classical stochastic processes we call Stochastic Mechanics.
Cymbidium Ringspot Virus Harnesses RNA Silencing To Control the Accumulation of Virus Parasite Satellite RNA

ABSTRACT Cymbidium ringspot virus (CymRSV) satellite RNA (satRNA) is a parasitic subviral RNA replicon that replicates and accumulates at the cost of its helper virus. This 621-nucleotide (nt) satRNA species has no sequence similarity to the helper virus, except for a 51-nt-long region termed the helper-satellite homology (HSH) region, which is essential for satRNA replication. We show that the accumulation of satRNA strongly depends on temperature and on the presence of the helper virus p19 silencing suppressor protein, suggesting that RNA silencing plays a crucial role in satRNA accumulation. We also demonstrate that another member of the Tombusvirus genus, Carnation Italian ringspot virus (CIRV), supports satRNA accumulation at a higher level than CymRSV. Our results suggest that short interfering RNA (siRNA) derived from CymRSV targets satRNA more efficiently than siRNA from CIRV, possibly because of the higher sequence similarity between the HSH regions of the helper and CIRV satRNAs. RNA silencing sensor RNA carrying the putative satRNA target site in the HSH region was efficiently cleaved when transiently expressed in CymRSV-infected plants but not in CIRV-infected plants. Strikingly, replacing the CymRSV HSH box2 sequence with that of CIRV restores satRNA accumulation both at 24°C and in the absence of the p19 suppressor protein. These findings demonstrate the extraordinary adaptation of this virus to its host in terms of harnessing the antiviral silencing response of the plant to control the virus parasite satRNA.
[Role of autoimmunity in multiple sclerosis].

A number of evidences indicate that an antigen-specific immune reaction is responsible for the formation and/or the maintenance of multiple sclerosis (MS) lesions. This disease is characterized by the following: 1), an infiltration of the white matter of the brain and spinal cord by inflammatory cells; 2), the T and B lymphocytes, present in the lesions or in the cerebrospinal fluid of patients, show signs of activation; i.e., the classic IgG oligoclonal bands of the cerebrospinal fluid (activation of B lymphocytes) and the presence of activation markers on the surface of the T lymphocytes; 3), the presence of an association, and a linkage between the disease and the genes of the HLA complex. The HLA molecules are implicated in the presentation of the antigen to the T lymphocytes; 4), finally, it should be noted that the therapeutic approaches aimed at reducing (immunosuppressants) or at modulating (beta-interferon, copolymer 1) the immune responses have a positive effect on this disease, whereas those treatments which activate the immune system (gamma-interferon) have a negative effect.
Value of superb microvascular imaging ultrasonography in the diagnosis of carpal tunnel syndrome

Abstract The aim of this study was to compare the value of superb microvascular imaging (SMI) in carpal tunnel syndrome (CTS) with that of color Doppler ultrasonography (CDUS) and power Doppler ultrasonography (PDUS). Fifty patients with symptomatic CTS and 25 healthy volunteers were enrolled. The cross-sectional area (CSA), CDUS score, PDUS score, and SMI score of the median nerve (MN) at the carpal tunnel were recorded. The value of different ultrasonography (US) diagnostic strategies was calculated. The blood flow display ratio in the MN of the healthy volunteers had no statistical difference between CDUS, PDUS, and SMI (20%, 32%, and 48%, respectively, P >.05). The blood flow display ratio for SMI in patients was significantly higher than that of CDUS and PDUS (90%, 52%, and 60%, respectively, P <.005). The accuracy of SMI score ≥2 (79%) was much higher than that of CDUS and PDUS (61% and 63%, respectively, P <.05). Comprehensive consideration of SMI and CSA, CSA≥10.5 mm2, and/or SMI score ≥2 has the highest accuracy (83%), significantly higher than that of CSA combination with CDUS or PDUS (68% and 69%, respectively, P <.05). SMI is more sensitive to display the blood flow in the MN with CTS than CDUS and PDUS. It might significantly improve the diagnosis value for CTS.
ASPECTS OF CONTROL AND PERCEPTION

This paper deals with the problem of artistic control in the performance situation and its effect on the perceived and experienced musical sound. This is not a presentation of controllers and control parameters, but a discussion in a wider framework where the description of variables and quantitative measures are emphasized. Models of human interaction in a live acoustical environment are mentioned and some results from MIDI performance analyses are presented. Perceptual issues concerning musical sound variables, visualization of sound attributes (time-varying models), analyses of musical sound, and subjective testing are discussed in the last part.