Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast volumetric visual hull computation

Silhouette-based reconstruction techniques using multiple wide-baseline camera set-ups are popular building blocks to generate models of temporal human action. This contribution reviews visual hull computation algorithms. In particular we focus on the class of volumetric-based algorithms. We identify different processing strategies based on hierarchical, octree-based processing and suggest a new dynamic strategy that can significantly minimise the computational effort. The techniques discussed are evaluated with synthetic and real data sets. The savings demonstrated in computations on the real test sequences are in the order of a factor six on a 512×512×512 volumetric resolution.
Likelihood Approach to Dynamic Panel Models with Interactive Effects

This paper considers dynamic panel models with a factor error structure that is correlated with the regressors. Both short panels (small T) and long panels (large T) are considered. With a small T, consistent estimation requires either a suitable formulation of the reduced form or an appropriate conditional equation for the first observation. Also needed is a suitable control for the correlation between the effects and the regressors. Under the factor error structure, the panel system implies parameter constraints between the mean vector and the covariance matrix. We explore the constraints through a quasi-FIML approach. The factor process is treated as parameters and it can have arbitrary dynamics under both fixed and large T. The large T setting involves incidental parameters because the number of parameters (including the time effects, the factor process, the heteroskedasticity parameters) increases with T. Even though an increasing number of parameters are estimated, we show that there is no incidental parameters bias to affect the limiting distributions; the estimator is centered at zero even scaled by the fast convergence rate of root-NT. We also show that the quasi-FIML approach is efficient under both fixed and large T, despite non-normality, heteroskedasticity, and incidental parameters. Finally we develop a feasible and fast algorithm for computing the quasi-FIML estimators under interactive effects.
Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts

Populations of bacteria acting in collaboration can produce complex behaviors which are not achievable by individual cells. There has, consequently, been considerable interest in the engineering of bacterial populations. Here we describe an approach for the engineering of aspects of bacterial quorum communication, using Standard Virtual Parts, a synthetic biology programming language, dubbed SVPWrite, and an evolutionary algorithm. We apply this system to engineering the output characteristics of the subtilin receiver system of Bacillus subtilis. Simple modifications, such as altering the strength of the output response to a subtilin input, are easily achieved. More complex adaptations, such as modifying the shape of the receiver response curve, necessitate alterations to the topology of the regulatory network. More generally, the use of Standard Virtual Parts and a programming language allow circuit design, simulation and evaluation to easily be automated, permitting exploration of a far larger proportion of design space than would be possible using standard manual design approaches.
Respiratory Syncytial Virus Fusion Protein-Induced Toll-Like Receptor 4 (TLR4) Signaling Is Inhibited by the TLR4 Antagonists Rhodobacter sphaeroides Lipopolysaccharide and Eritoran (E5564) and Requires Direct Interaction with MD-2

ABSTRACT Respiratory syncytial virus (RSV) is a leading cause of infant mortality worldwide. Toll-like receptor 4 (TLR4), a signaling receptor for structurally diverse microbe-associated molecular patterns, is activated by the RSV fusion (F) protein and by bacterial lipopolysaccharide (LPS) in a CD14-dependent manner. TLR4 signaling by LPS also requires the presence of an additional protein, MD-2. Thus, it is possible that F protein-mediated TLR4 activation relies on MD-2 as well, although this hypothesis has not been formally tested. LPS-free RSV F protein was found to activate NF-κB in HEK293T transfectants that express wild-type (WT) TLR4 and CD14, but only when MD-2 was coexpressed. These findings were confirmed by measuring F-protein-induced interleukin 1β (IL-1β) mRNA in WT versus MD-2−/− macrophages, where MD-2−/− macrophages failed to show IL-1β expression upon F-protein treatment, in contrast to the WT. Both Rhodobacter sphaeroides LPS and synthetic E5564 (eritoran), LPS antagonists that inhibit TLR4 signaling by binding a hydrophobic pocket in MD-2, significantly reduced RSV F-protein-mediated TLR4 activity in HEK293T-TLR4–CD14–MD-2 transfectants in a dose-dependent manner, while TLR4-independent NF-κB activation by tumor necrosis factor alpha (TNF-α) was unaffected. In vitro coimmunoprecipitation studies confirmed a physical interaction between native RSV F protein and MD-2. Further, we demonstrated that the N-terminal domain of the F1 segment of RSV F protein interacts with MD-2. These data provide new insights into the importance of MD-2 in RSV F-protein-mediated TLR4 activation. Thus, targeting the interaction between MD-2 and RSV F protein may potentially lead to novel therapeutic approaches to help control RSV-induced inflammation and pathology. IMPORTANCE This study shows for the first time that the fusion (F) protein of respiratory syncytial virus (RSV), a major cause of bronchiolitis and death, particularly in infants and young children, physically interacts with the Toll-like receptor 4 (TLR4) coreceptor, MD-2, through its N-terminal domain. We show that F protein-induced TLR4 activation can be blocked by lipid A analog antagonists. This observation provides a strong experimental rationale for testing such antagonists in animal models of RSV infection for potential use in people. This study shows for the first time that the fusion (F) protein of respiratory syncytial virus (RSV), a major cause of bronchiolitis and death, particularly in infants and young children, physically interacts with the Toll-like receptor 4 (TLR4) coreceptor, MD-2, through its N-terminal domain. We show that F protein-induced TLR4 activation can be blocked by lipid A analog antagonists. This observation provides a strong experimental rationale for testing such antagonists in animal models of RSV infection for potential use in people.
Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data

Despite the central role of quantitative PCR (qPCR) in the quantification of mRNA transcripts, most analyses of qPCR data are still delegated to the software that comes with the qPCR apparatus. This is especially true for the handling of the fluorescence baseline. This article shows that baseline estimation errors are directly reflected in the observed PCR efficiency values and are thus propagated exponentially in the estimated starting concentrations as well as ‘fold-difference’ results. Because of the unknown origin and kinetics of the baseline fluorescence, the fluorescence values monitored in the initial cycles of the PCR reaction cannot be used to estimate a useful baseline value. An algorithm that estimates the baseline by reconstructing the log-linear phase downward from the early plateau phase of the PCR reaction was developed and shown to lead to very reproducible PCR efficiency values. PCR efficiency values were determined per sample by fitting a regression line to a subset of data points in the log-linear phase. The variability, as well as the bias, in qPCR results was significantly reduced when the mean of these PCR efficiencies per amplicon was used in the calculation of an estimate of the starting concentration per sample.
Track—a trace construction kit

TRACK is a kit to interactively construct environments that trace the execution of methods and the flow of messages between SMALLTALK-80 objects. It enables the user to set up traces by means of direct manipulation. This is done by placing obstacles between icons representing specific classes and instances much in the way a jumping course is set up. TRACK may be used to generate multiple visualizations of programs which may be concurrently run. It is a browsing and debugging tool as well as an algorithm animation tool. TRACK is tightly integrated with the standard tools of the SMALL- TALK-80 programming environment.
Data Resource Profile: Cardiovascular disease research using linked bespoke studies and electronic health records (CALIBER)

The goal of cardiovascular disease (CVD) research using linked bespoke studies and electronic health records (CALIBER) is to provide evidence to inform health care and public health policy for CVDs across different stages of translation, from discovery, through evaluation in trials to implementation, where linkages to electronic health records provide new scientific opportunities. The initial approach of the CALIBER programme is characterized as follows: (i) Linkages of multiple electronic heath record sources: examples include linkages between the longitudinal primary care data from the Clinical Practice Research Datalink, the national registry of acute coronary syndromes (Myocardial Ischaemia National Audit Project), hospitalization and procedure data from Hospital Episode Statistics and cause-specific mortality and social deprivation data from the Office of National Statistics. Current cohort analyses involve a million people in initially healthy populations and disease registries with ∼105 patients. (ii) Linkages of bespoke investigator-led cohort studies (e.g. UK Biobank) to registry data (e.g. Myocardial Ischaemia National Audit Project), providing new means of ascertaining, validating and phenotyping disease. (iii) A common data model in which routine electronic health record data are made research ready, and sharable, by defining and curating with meta-data >300 variables (categorical, continuous, event) on risk factors, CVDs and non-cardiovascular comorbidities. (iv) Transparency: all CALIBER studies have an analytic protocol registered in the public domain, and data are available (safe haven model) for use subject to approvals. For more information, e-mail s.denaxas@ucl.ac. uk
Optimization of free viewpoint interpolation by applying adaptive depth plane distributions in plane sweeping a histogram-based approach to a non-uniform plane distribution

In this paper, we present a system to increase performance of plane sweeping for free viewpoint interpolation. Typical plane sweeping approaches incorporate a uniform depth plane distribution to investigate different depth hypotheses to generate a depth map, used in novel camera viewpoint generation. When the scene consists of a sparse number of objects, some depth hypotheses do not contain objects and can cause noise and wasted computational power. Therefore, we propose a method to adapt the plane distribution to increase the quality of the depth map around objects and to reduce computational power waste by reducing the number of planes in empty spaces in the scene. First, we generate the cumulative histogram of the previous frame in a temporal sequence of images. Next, we determine a new normalized depth for every depth plane by analyzing the cumulative histogram. Steep sections of the cumulative histogram will result in a dense local distribution of planes; a flat section will result in a sparse distribution. The results, performed on controlled and on real images, demonstrate the effectiveness of the method over a uniform distribution and allows a lower number of depth planes, and thus a more performant processing, for the same quality.
Research Report SAML Artifact Information Flow Revisited

The standardized OASIS Security Assertion Markup Language (SAML) has become one of the most deployed frameworks in federated identity management even though it focuses only on single sign-on. Answering industry’s pursuit of the reduction of user-management costs and enabling cost-ef(cid:2)cient deployment because of its browser-based pro(cid:2)les, SAML is believed to become widely used soon. With the revision to Version 2.0, especially SAML’s browser/artifact pro(cid:2)le has gained new security measures defeating old vulnerabilities. We analyze this pro(cid:2)le and focus on the problem of artifact information (cid:3)ow. We devise a concrete exploit to demonstrate the impact of this problem. We address this problem by a new browser/artifact pro(cid:2)le called Janus. The innovation is to split the artifact into two independent shares that have different information (cid:3)ow in a standard web browser. This new method defeats artifact information (cid:3)ow ef(cid:2)ciently without relying on assumptions on the artifact lifetime.
A new global localization algorithm based on feature extraction and particle filter

This paper describes a new global localization algorithm based on feature extraction and particle filter. This algorithm uses two kinds of sensors: wheels encoders and a laser scanner. A map of the environment is built by taking laser readings of the environment from well-known poses of the robot. The resulting map is composed by a list of features, representing the position of clusters obtained by using the mean shift algorithm. The mean shift algorithm is also applied for each sampling step in order to calculate the importance factor of the particles. The trials have been conducted by using a simulator of a differential drive robot
A PMOS mm-wave power amplifier at 77 GHz with 90 mW output power and 24% efficiency

In deeply scaled CMOS processes with gate lengths below 40 nm the analog performance of NMOS and PMOS FETs are comparable. At the same time PMOS FETs can typically operate under higher operating voltages than NMOS devices. In this paper, we present the first millimeter-wave power amplifier exclusively employing PMOS. The single stage, 3-stack power amplifier operates at 65 - 92 GHz with more than 35% fractional bandwidth and 12 dB gain. At 78 GHz, the PA achieves a maximum output power of 19.6 dBm and PAE of 18% with class-A bias, and 18.7 dBm and 24% PAE with class-AB bias. The PA has been fabricated in 32 nm CMOS SOI process and occupies 440 μm × 280 μm area (only 0.05 mm2 excluding pads). To the authors' knowledge this PA achieves the highest efficiency for any silicon PA in the 60-90 GHz frequency band. The output power is also the best reported in silicon for this frequency range, for amplifiers that do not use elaborate power-combining approaches.
Social Conventions in Collaborative Tagging

With the increasing popularity of online collaborative tagging services, the study of user tagging behavior is of significant interest. A model of vocabulary evolution is described from the literature, re-interpreted using game theoretic concepts, and tested via simulation. Refinements are motivated in view of the nature of collaborative tagging and in light of recent analyses of real-world collaborative tagging data.
LOW-FREQUENCY QUASI-PERIODIC OSCILLATION FROM THE 11 Hz ACCRETING PULSAR IN TERZAN 5: NOT FRAME DRAGGING

We report on six RXTE observations taken during the 2010 outburst of the 11 Hz accreting pulsar IGR J17480−2446 located in the globular cluster Terzan 5. During these observations we find power spectra which resemble those seen in Z-type high-luminosity neutron star low-mass X-ray binaries, with a quasi-periodic oscillation (QPO) in the 35–50 Hz range simultaneous with a kHz QPO and broadband noise. Using well-known frequency–frequency correlations, we identify the 35–50 Hz QPOs as the horizontal branch oscillations, which were previously suggested to be due to Lense–Thirring (LT) precession. As IGR J17480−2446 spins more than an order of magnitude more slowly than any of the other neutron stars where these QPOs were found, this QPO cannot be explained by frame dragging. By extension, this casts doubt on the LT precession model for other low-frequency QPOs in neutron stars and perhaps even black hole systems.
HAMPI: A solver for word equations over strings, regular expressions, and context-free grammars

Many automatic testing, analysis, and verification techniques for programs can be effectively reduced to a constraint-generation phase followed by a constraint-solving phase. This separation of concerns often leads to more effective and maintainable software reliability tools. The increasing efficiency of off-the-shelf constraint solvers makes this approach even more compelling. However, there are few effective and sufficiently expressive off-the-shelf solvers for string constraints generated by analysis of string-manipulating programs, so researchers end up implementing their own ad-hoc solvers. To fulfill this need, we designed and implemented Hampi, a solver for string constraints over bounded string variables. Users of Hampi specify constraints using regular expressions, context-free grammars, equality between string terms, and typical string operations such as concatenation and substring extraction. Hampi then finds a string that satisfies all the constraints or reports that the constraints are unsatisfiable. We demonstrate Hampi's expressiveness and efficiency by applying it to program analysis and automated testing. We used Hampi in static and dynamic analyses for finding SQL injection vulnerabilities in Web applications with hundreds of thousands of lines of code. We also used Hampi in the context of automated bug finding in C programs using dynamic systematic testing (also known as concolic testing). We then compared Hampi with another string solver, CFGAnalyzer, and show that Hampi is several times faster. Hampi's source code, documentation, and experimental data are available at http://people.csail. mit.edu/akiezun/hampi1
Why Voxel-Based Morphometry Should Be Used

This article has been written in response to Dr. Fred L. Bookstein's article entitled '"Voxel-Based Morphometry" Should Not Be Used with Imperfectly Registered Images' in this issue of NeuroImage. We will address three main issues: (i) Dr. Bookstein appears to have misunderstood the objective of voxel-based morphometry (VBM) and the nature of the continuum we referred to. (ii) We agree with him when he states that findings from VBM can pertain to systematic registration errors during spatial normalization. (iii) His argument about voxelwise tests on smooth data holds in the absence of error variance, but is of no consequence when using actual data. We first review the tenets of VBM, paying particular attention to the relationship between VBM and tensor-based morphometry. The last two sections of this response deal with the specific concerns raised by Dr. Bookstein.
Taming Deadlocks in Multithreaded Programs

Many real-world multithreaded programs contain deadlock bugs. These bugs should be detected and corrected. Many existing detection strategies are not consistently scalable to handle large-scale applications. Many existing dynamic confirmation strategies may not reveal detectable deadlocks with high probability. And many existing runtime deadlock-tolerant strategies may incur high runtime overhead and may not prevent the same deadlock from re-occurring. This paper presents the current progress of our project on dynamic deadlock detection, confirmation, and resolution. It also describes a test harness framework developed to support our proposed approach.
Intelligent system for material quality control using impact-echo testing

This paper introduces an intelligent system to discern the quality of materials inspected by the impact-echo technique. The system includes a hardware setup to inspect parallelepiped-shape materials and a procedure to classify the material depending on its quality condition. Four levels of classification with different grades of knowledge about the material defects are approached: material condition, kind of defect, defect orientation, and defect dimension. The number of classes (material qualities) in the lowest classification level is 12. The procedure is applied on signals coming from 3D finite element simulations and lab experiments with aluminium specimens. The classification procedure is performed using frequency features and the classification algorithms: LDA, MLP, and an algorithm based on mixtures of independent component analyzers. We show the best performance to model the impact-echo data is obtained by the ICA mixture model.
Comparing treatment effects between propensity scores and randomized controlled trials: improving conduct and reporting.

This editorial refers to ‘Do observational studies using propensity score methods agree with randomized trials? A systematic comparison of studies on acute coronary syndrome’†, by I.J. Dahabreh et al. , on page 1893 Evaluating the effectiveness of a therapeutic intervention is ideally carried out in the setting of a randomized controlled trial (RCT). Patients are randomly allocated to the experimental and control groups ensuring that observed, pre-treatment key prognostic characteristics, but also unobserved patient characteristics, are balanced between the treatment groups, minimizing the variability in patient characteristics. Providing a sufficient number of patients have been randomized, this balance in observed and unobserved pre-treatment characteristics between the groups enables unbiased conclusions about the treatment effect to be drawn. There may, however, be instances where randomization is not possible due to, for example, ethical reasons (e.g. emergency surgery,1 transplantation2) or because it is impractical (e.g. rare events, financial reasons). When it is not possible to conduct an adequately powered RCT, observational studies are often carried out to examine and infer treatment effects. In addition, treatment effects observed in RCTs that involve highly selective populations are often examined in different patient populations and settings in observational studies. However, in observational studies, investigators have no control over treatment assignment, which is often part of a patient's routine medical care. In these instances, it is likely that potentially large systematic differences (typically confounding by indication) in observed patient characteristics could lead to large, biased, and ultimately misleading estimates of treatment effect. Propensity scores are increasingly being used to reduce the impact …
A new Unsupervised Clustering-based Feature Extraction Method

In manipulating data such as in supervised or unsupervised learning, we need to extract new features from the original features for the purpose of reducing the dimension of feature space and achieving better performance. In this paper, we investigate a novel schema for unsupervised feature extraction for classification problems. We based our method on clustering to achieve feature extraction. A new similarity measure based on trend analysis is devised to identify redundant information in the data. Clustering is then performed on the feature space. Once groups of similar features are formed, linear transformation is realized to extract a new set of features. The simulation results on classification problems for experimental data sets from UCI machine learning repository and face recognition problem show that the proposed method is effective in almost cases when compared to conventional unsupervised methods like PCA and ICA. General Terms Pattern Recognition, Machine Learning, Feature Extraction, and Data mining.