Miracle-dz/UniFAR-FTUs huggingface dataset:
On the C‐statistics for evaluating overall adequacy of risk prediction procedures with censored survival data

For modern evidence‐based medicine, a well thought‐out risk scoring system for predicting the occurrence of a clinical event plays an important role in selecting prevention and treatment strategies. Such an index system is often established based on the subject's ‘baseline’ genetic or clinical markers via a working parametric or semi‐parametric model. To evaluate the adequacy of such a system, C‐statistics are routinely used in the medical literature to quantify the capacity of the estimated risk score in discriminating among subjects with different event times. The C‐statistic provides a global assessment of a fitted survival model for the continuous event time rather than focussing on the prediction of bit‐year survival for a fixed time. When the event time is possibly censored, however, the population parameters corresponding to the commonly used C‐statistics may depend on the study‐specific censoring distribution. In this article, we present a simple C‐statistic without this shortcoming. The new procedure consistently estimates a conventional concordance measure which is free of censoring. We provide a large sample approximation to the distribution of this estimator for making inferences about the concordance measure. Results from numerical studies suggest that the new procedure performs well in finite sample. Copyright © 2011 John Wiley & Sons, Ltd.
TRAJECTORY GENERATION FOR CAR-LIKE ROBOTS USING CUBIC CURVATURE POLYNOMIALS

Curvature polynomials of cubic order are ideal primitive trajectories for car-like robots. Unlike the clothoids, which are linear curvature polynomials, cubic curves can be used to determine a unique trajectory to an arbitrary target posture using a single continuous primitive. Such curves are also the lowest order curves which are continuous in the torque applied to steering mechanisms, so they generate trajectories which are relatively easily tracked by a real vehicle. Like the clothoids, cubic curvature polynomials are relatively difficult to compute but are easy to execute. A real-time numerical method to compute them is described.
A 2D process-Based model for suspended sediment dynamics: A first step towards ecological modeling

In estuaries suspended sediment concentration (SSC) is one of the most important contributors to turbidity, which influences habitat conditions and ecological functions of the system. Sediment dynamics differs depending on sediment supply and hydrodynamic forcing conditions that vary over space and over time. A robust sediment transport model is a first step in developing a chain of models enabling simulations of contaminants, phytoplankton and habitat conditions. This works aims to determine turbidity levels in the complex-geometry delta of the San Francisco estuary using a process-based approach (Delft3D Flexible Mesh software). Our approach includes a detailed calibration against measured SSC levels, a sensitivity analysis on model parameters and the determination of a yearly sediment budget as well as an assessment of model results in terms of turbidity levels for a single year, water year (WY) 2011. Model results show that our process-based approach is a valuable tool in assessing sediment dynamics and their related ecological parameters over a range of spatial and temporal scales. The model may act as the base model for a chain of ecological models assessing the impact of climate change and management scenarios. Here we present a modeling approach that, with limited data, produces reliable predictions and can be useful for estuaries without a large amount of processes data.
Singular Value Decompositions and Low Rank Approximations of Tensors

The singular value decomposition is among the most important tools in numerical analysis for solving a wide scope of approximation problems in signal processing, model reduction, system identification and data compression. Nevertheless, there is no straightforward generalization of the algebraic concepts underlying the classical singular values and singular value decompositions to multilinear functions. Motivated by the problem of lower rank approximations of tensors, this paper develops a notion of singular values for arbitrary multilinear mappings. We provide bounds on the error between a tensor and its optimal lower rank approximation. Conceptual algorithms are proposed to compute singular value decompositions of tensors.
A Data-Driven Stochastic Approach for Unmixing Hyperspectral Imagery

In this paper, we propose a two-step Bayesian approach to handle the ill-posed nature of the unmixing problem for accurately estimating the abundances. The abundances are dependent on the scene contents and they represent mixing proportions of the endmembers over an area. In this work, a linear mixing model (LMM) is used for the image formation process in order to derive the data term. In the first step, a Huber-Markov random field (HMRF)-based prior distribution is assumed to model the dependencies within the abundances across the spectral space of the data. The threshold used in the HMRF prior is derived from an initial estimate of abundances obtained using the matched filters. This makes the HMRF prior data-driven, i.e., dHMRF. Final abundance maps are obtained in the second step within a maximum a posteriori probability (MAP) framework, and the objective function is optimized using the particle swarm optimization (PSO). Theoretical analysis is carried out to show the effectiveness of the proposed method. The approach is evaluated using the synthetic and real AVIRIS Cuprite data. The proposed method has the following advantages. 1) The estimated abundances are resistant to noise since they are based on an initial estimate that has high signal-to-noise ratio (SNR). 2) The variance in the abundance maps is well preserved since the threshold in the dHMRF is derived from the data.
Vertical profiles of velocity variances and TKE using Doppler-lidar scan data

Application of Doppler lidar scanning wind speed data for measurements of vertical profiles of turbulent quantities and momentum flux for the unstable boundary layer have been reported since the late 1990s by many researches, including Eberhard et at. (1989), Gal-Chen et al. (1992), Banta et al. (1997). Over the last decade, the High-Resolution Doppler Lidar (HRDL), designed and developed at the National Oceanic and Atmospheric Administration (NOAA) Environmental Technology Laboratory (ETL), has been highly effective in the study of dynamic processes in the ABL because of its temporal and spatial resolution (2 Hertz and 30 m), narrow beam, and capability to measure the component of the wind velocity parallel to the lidar beam (radial velocity) with a precision of 10-20 cm/s (Grund et al.2001, Wulfmeyer et al. 2000).
L-selectin-deficient mice have impaired leukocyte recruitment into inflammatory sites

L-selectin, a cell surface adhesion molecule that is expressed by most leukocytes, mediates leukocyte rolling along vascular endothelium at sites of inflammation. The contribution of L-selectin to leukocyte migration in models of chronic inflammation was assessed by using mice that lack cell surface L-selectin expression. Significant inhibition of neutrophil (56-62%), lymphocyte (70-75%), and monocyte (72-78%) migration into an inflamed peritoneum was observed 24 and 48 h after administration of thioglycollate, an inflammatory stimulus. L-selectin- deficient mice were also significantly impaired in delayed-type hypersensitivity reactions. Footpad swelling in response to sheep red blood cell challenge was reduced 75% in L-selectin-deficient mice compared with wild-type mice. Ear swelling in a model of contact hypersensitivity induced by oxazolone challenge was also reduced by 69% compared to wild-type mice. Consistent with L-selectin-mediating leukocyte migration into diverse vascular beds during inflammation, L- selectin-deficient mice were significantly resistant to death resulting from lipopolysaccharide (LPS)-induced toxic shock. LPS administration resulted in a 90% mortality rate in control mice after 24 h, while there was a 90% survival rate in L-selectin-deficient mice. These results demonstrate that L-selectin plays a prominent role in leukocyte homing to nonlymphoid tissues during inflammation and that blocking this process can be beneficial during pathological inflammatory responses.
Code-Mixing in Social Media Text

Automatic understanding of noisy social media text is one of the prime presentday research areas. Most research has so far concentrated on English texts; however, more than half of the users are writing in other languages, making language identification a prerequisite for comprehensive processing of social media text. Though language identification has been considered an almost solved problem in other applications, language detectors fail in the social media context due to phenomena such as code-mixing, code-switching, lexical borrowings, Anglicisms, and phonetic typing. This paper reports an initial study to understand the characteristics of code-mixing in the social media context and presents a system developed to automatically detect language boundaries in code-mixed social media text, here exemplified by Facebook messages in mixed English-Bengali and English-Hindi. RÉSUMÉ. La compréhension automatique du texte bruyant des médias sociaux est l’un des secteurs de recherche contemporaine principaux. Jusqu’ici, la plupart des recherches se sont concentrées sur les textes en anglais ; mais plus de la moitié des utilisateurs écrivent dans d’autres langues, ce qui rend l’identification de la langue préalable au traitement complet du texte des médias sociaux. Bien que l’identification de la langue ait été considérée comme un problème presque résolu dans d’autres applications, les détecteurs de langue échouent dans le contexte des médias sociaux, et cela est dû aux phénomènes tels que le mélange et l’alternance de code linguistique, les emprunts lexicaux, les anglicismes et la dactylographie phonétique. Cet article présente une étude initiale pour comprendre les caractéristiques de mélange des codes dans le contexte des médias sociaux ainsi qu’ un système développé pour détecter automatiquement les barrières linguistiques en texte «code-mélangé» de médias sociaux, ici illustrées par des messages de Facebook en mixte anglais-bengali et anglais-hindi.
Singing Without Hearing: A Comparative Study of Children and Adults Singing a Familiar Tune

The current study had 2 goals: to examine and compare baseline singing accuracy of 3 age-groups of participants (children ages 5–8 years, children ages 9–12, and adults) when performing a familiar song from memory, and to examine all participants’ use of auditory and proprio-kinesthetic feedback in regulating pitch by masking their ability to hear themselves. Pitch accuracy, error variability, and tonal stability were examined. All participants were asked to sing “The Alphabet Song” from memory in 2 conditions: normal auditory feedback and masked auditory feedback. Under both feedback conditions, there was significant improvement between the youngest children (ages 5–8) and the adults on all 3 measures, but not between the older children (ages 9–12) and the adults. Participants in every age-group performed more poorly in terms of interval accuracy and error variability when they could not hear themselves. In terms of tonal stability, however, we found an age by feedback interaction such that auditory masking negatively affected key stability for children ages 9 to 12, but not the younger children or the adults. This suggests that although older children may rely heavily on auditory feedback to control relative pitch accuracy and tonal center, adults and younger children may show a different pattern of feedback monitoring for interval-based singing accuracy and maintaining a consistent tonal center.
The Application of Appearance Models to Martian Impact Craters

This document describes preliminary work regarding a PhD project which seeks to construct automated image analysis systems for use in planetary sciences. Simple linear Active Appearance Models of grey level image patches (AAMs) are used here in an attempt to automatically identify craters in satellite images of the Martian surface. We describe a series of experiments which investigate AAM of various orders, and ﬁnd that they do not provide a suitable solution to this task, due to two features of these approaches. The ﬁrst is that the similarity function used to optimise model location (based on Likelihood) is incapable of distinguishing between evidence for an object and entirely featureless regions of an image. Secondly, Martian craters seem to conform to a class of appearance behaviour for which high order terms of a linear model describe nothing more than a stochastic (essentially noise) process.
Discretionary liquidity : Hedge funds , side pockets , and gates 1

: During the recent financial crisis, more than 30% of hedge fund managers used their discretion to restrict investor liquidity through the use of “gates” or “side pockets. ” Using a database of hedge fund investor interests, this paper is the first to empirically examine the determinants of these discretionary liquidity restrictions (DLRs) and their consequences for hedge fund investors. We find that funds enacted DLRs following poor performance and when their portfolio assets were more illiquid. However, despite claims from managers that DLRs protected investor interests by preventing fire-sales, funds that enacted DLRs continued to underperform comparable funds. Consistent with DLRs reflecting agency problems, we find that restricting investor liquidity during the crisis had a negative impact on fund reputation that spilled over across the hedge fund family. DLR funds and their family affiliates had a more difficult time raising capital and were more likely to cut their fees in the post crisis era.
Therapeutic Impact of Human Serum Albumin–Thioredoxin Fusion Protein on Influenza Virus-Induced Lung Injury Mice

Reactive oxygen species (ROS) are the primary pathogenic molecules produced in viral lung infections. We previously reported on the use of a recombinant human serum albumin (HSA)–thioredoxin 1 (Trx) fusion protein (HSA–Trx) for extending the half-life Trx, an endogenous protein with anti-oxidant properties. As a result, it was possible to overcome the unfavorable pharmacokinetic and short pharmacological properties of Trx. We hypothesized that HSA–Trx would attenuate the enhanced ROS production of species such as hydroxyl radicals by neutrophils during an influenza viral infection. The levels of 8-hydroxy-2′-deoxyguanosine and 3-nitrotyrosine were used as indices of the anti-oxidant activity of HSA–Trx. In addition, the cytoprotective effects of HSA–Trx were examined in PR8 (H1N1) influenza virus-induced lung injured mice. The findings show that HSA–Trx reduced the number of total cells, neutrophils, and total protein in BALF of influenza virus-induced lung injured mice. The HSA–Trx treatment significantly decreased the level of 8-hydroxy-2′-deoxyguanosine and 3-nitrotyrosine, but failed to inhibit inducible nitric oxide synthase expression, in the lungs of the virus-infected mice. On the other hand, Tamiflu® treatment also significantly suppressed the production of inflammatory cells and neutrophil infiltration, as well as the protein level in BALF and lung histopathological alterations caused by the influenza virus. The suppressive effect of Tamiflu® was slightly stronger than that of HSA–Trx. Interestingly, Tamiflu® significantly decreased virus proliferation, while HSA–Trx had no effect. These results indicate that HSA–Trx may be of therapeutic value for the treatment of various acute inflammatory disorders such as influenza-virus-induced pneumonia, by inhibiting inflammatory-cell responses and suppressing the overproduction of NO in the lung.
Family Mealtimes and Family Functioning

ABSTRACT This study contributes to the existing research literature by assessing how the frequency of family mealtimes correlates with family communication and life satisfaction. Participants consisted of 50 families from the Southeastern United States. Parent and child participants completed measures assessing frequency of family mealtime, family communication, and family satisfaction. Results indicated that, based on parent-report, the frequency of all family members eating dinner together was significantly and positively correlated with both family communication and family satisfaction. Implications of findings highlight the importance of encouraging regular mealtime interactions among families.
European red squirrel population dynamics driven by squirrelpox at a gray squirrel invasion interface

Infectious disease introduced by non-native species is increasingly cited as a facilitator of native population declines, but direct evidence may be lacking due to inadequate population and disease prevalence data surrounding an outbreak. Previous indirect evidence and theoretical models support squirrelpox virus (SQPV) as being potentially involved in the decline of red squirrels (Sciurus vulgaris) following the introduction of the non-native gray squirrel (Sciurus carolinensis) to the United Kingdom. The red squirrel is a major UK conservation concern and understanding its continuing decline is important for any attempt to mitigate the decline. The red squirrel–gray squirrel system is also exemplary of the interplay between infectious disease (apparent competition) and direct competition in driving the replacement of a native by an invasive species. Time series data from Merseyside are presented on squirrel abundance and squirrelpox disease (SQPx) incidence, to determine the effect of the pathogen and the non-native species on the native red squirrel populations. Analysis indicates that SQPx in red squirrels has a significant negative impact on squirrel densities and their population growth rate (PGR). There is little evidence for a direct gray squirrel impact; only gray squirrel presence (but not density) proved to influence red squirrel density, but not red squirrel PGR. The dynamics of red SQPx cases are largely determined by previous red SQPx cases, although previous infection of local gray squirrels also feature, and thus, SQPV-infected gray squirrels are identified as potentially initiating outbreaks of SQPx in red squirrels. Retrospective serology indicates that approximately 8% of red squirrels exposed to SQPV may survive infection during an epidemic. This study further highlights the UK red squirrel – gray squirrel system as a classic example of a native species population decline strongly facilitated by infectious disease introduced by a non-native species. It is therefore paramount that disease prevention and control measures are integral in attempts to conserve red squirrels in the United Kingdom.
Characterizing the Production Process: A Disaggregated Analysis of Italian Manufacturing Firms

This paper provides a description of the production process by comparing different frameworks in which to analyze the relations between inputs and output. The analyses are performed on a representative sample of Italian manufacturing firms. We employ both parametric and non-parametric analysis. The latter allows to detect the presence of heterogeneity in the way the production is carried out within each sector. Results of the parametric analysis show that coefficient esti­mates tend to be robust with respect to the different models employed.
Innovation performance and competitive strategies in the Turkish manufacturing industry

In this paper, we report on empirical investigation within the context of the Innovations in Manufacturing Industries in Turkey Study 2004/2005. The data was gathered in nine different cities in Turkey during the period August 2004 – January 2005. The survey was conducted through face-to-face interviews due to the complex nature of the survey and was implemented in 135 manufacturing firms operating in four sectors: Textiles, chemicals, food, and metal. The study has been an extension of the European Manufacturing Survey 2004 (EMS 2004) coordinated by the Fraunhofer Institute for Systems and Innovation Research and covering nine countries: Germany, Turkey, Austria, Switzerland, France, Slovenia, Croatia, Italy, and United Kingdom. An extended version of the questionnaire form used in EMS 2004 has been employed. Some of the basic results concerning competitive priorities, new product development, and operations management are presented.
Independent Component Analysis: A Flexible Nonlinearity and Decorrelating Manifold Approach

Independent component analysis (ICA) finds a linear transformation to variables that are maximally statistically independent. We examine ICA and algorithms for finding the best transformation from the point of view of maximizing the likelihood of the data. In particular, we discuss the way in which scaling of the unmixing matrix permits a static nonlinearity to adapt to various marginal densities. We demonstrate a new algorithm that uses generalized exponential functions to model the marginal densities and is able to separate densities with light tails. We characterize the manifold of decorrelating matrices and show that it lies along the ridges of high-likelihood unmixing matrices in the space of all unmixing matrices. We show how to find the optimum ICA matrix on the manifold of decorrelating matrices, and as an example we use the algorithm to find independent component basis vectors for an ensemble of portraits.
Personalizing Cancer Treatment in the Age of Global Genomic Analyses: PALB2 Gene Mutations and the Response to DNA Damaging Agents in Pancreatic Cancer

Metastasis and drug resistance are the major causes of mortality in patients with pancreatic cancer. Once developed, the progression of pancreatic cancer metastasis is virtually unstoppable with current therapies. Here, we report the remarkable clinical outcome of a patient with advanced, gemcitabine-resistant, pancreatic cancer who was later treated with DNA damaging agents, on the basis of the observation of significant activity of this class of drugs against a personalized xenograft generated from the patient's surgically resected tumor. Mitomycin C treatment, selected on the basis of its robust preclinical activity in a personalized xenograft generated from the patient's tumor, resulted in long-lasting (36+ months) tumor response. Global genomic sequencing revealed biallelic inactivation of the gene encoding PalB2 protein in this patient's cancer; the mutation is predicted to disrupt BRCA1 and BRCA2 interactions critical to DNA double-strand break repair. This work suggests that inactivation of the PALB2 gene is a determinant of response to DNA damage in pancreatic cancer and a new target for personalizing cancer treatment. Integrating personalized xenografts with unbiased exomic sequencing led to customized therapy, tailored to the genetic environment of the patient's tumor, and identification of a new biomarker of drug response in a lethal cancer. Mol Cancer Ther; 10(1); 3–8. ©2010 AACR. Mol Cancer Ther; 10(1); 3–8. ©2010 AACR.