Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Clinically-Attenuated Burkholderia mallei by Whole Genome Sequencing: Candidate Strain for Exclusion from Select Agent Lists

Background Burkholderia mallei is an understudied biothreat agent responsible for glanders which can be lethal in humans and animals. Research with this pathogen has been hampered in part by constraints of Select Agent regulations for safety reasons. Whole genomic sequencing (WGS) is an apt approach to characterize newly discovered or poorly understood microbial pathogens. Methodology/Principal Findings We performed WGS on a strain of B. mallei, SAVP1, previously pathogenic, that was experimentally infected in 6 equids (4 ponies, 1 mule, 1 donkey), natural hosts, for purposes of producing antibodies. Multiple high inocula were used in some cases. Unexpectedly SAVP1 appeared to be avirulent in the ponies and mule, and attenuated in the donkey, but induced antibodies. We determined the genome sequence of SAVP1 and compared it to a strain that was virulent in horses and a human. In comparison, this phenotypic avirulent SAVP1 strain was missing multiple genes including all the animal type III secretory system (T3SS) complex of genes demonstrated to be essential for virulence in mice and hamster models. The loss of these genes in the SAVP1 strain appears to be the consequence of a multiple gene deletion across insertion sequence (IS) elements in the B. mallei genome. Therefore, the strain by itself is unlikely to revert naturally to its virulent phenotype. There were other genes present in one strain and not the other and vice-versa. Conclusion/Significance The discovery that this strain of B. mallei was both avirulent in the natural host ponies, and did not possess T3SS associated genes may be fortuitous to advance biodefense research. The deleted virulence-essential T3SS is not likely to be re-acquired naturally. These findings may provide a basis for exclusion of SAVP1 from the Select Agent regulation or at least discussion of what else would be required for exclusion. This exclusion could accelerate research by investigators not possessing BSL-3 facilities and facilitate the production of reagents such as antibodies without the restraints of Select Agent regulation.
Comparing Risk-Neutral Probability Density Functions Implied by Option Prices - Market Uncertainty and Ecb-Council Meetings

In recent years different techniques to uncover the information on market expectations implicit in option prices have been developed. This paper proposes an approach to highlight statistically significant changes in risk-neutral probability density functions by comparing the distributional characteristics of statistics derived from risk-neutral densities to those of a benchmark sample. In an application we extract risk-neutral probability density functions from LIFFE-Euribor futures options and look for characteristic differences in market expectations related to meetings of the Governing Council of the ECB.
Orphan afterglows in the Universal structured jet model for ?-ray bursts

The paucity of reliable achromatic breaks in γ-ray burst afterglow light curves motivates independent measurements of the jet aperture. Serendipitous searches of afterglows, especially at radio wavelengths, have long been the classic alternative. These survey data have been interpreted assuming a uniformly emitting jet with sharp edges (‘top-hat’ jet), in that case the ratio of weakly relativistically beamed afterglows to GRBs scales with the jet solid angle. In this paper, we consider, instead, a very wide outflow with a luminosity that decreases across the emitting surface. In particular, we adopt the universal structured jet (USJ) model, which is an alternative to the top-hat model for the structure of the jet. However, the interpretation of the survey data is very different: in the USJ model, we only observe the emission within the jet aperture and the observed ratio of prompt emission rate to afterglow rate should solely depend on selection effects. We compute the number and rate of afterglows expected in all-sky snapshot observations as a function of the survey sensitivity. We find that the current (negative) results for OA searches are in agreement with our expectations. In radio and X-ray bands, this was mainly due to the low sensitivity of the surveys, while in the optical band the sky coverage was not sufficient. In general, we find that X-ray surveys are poor tools for OA searches, if the jet is structured. On the other hand, the Faint Images of the Radio Sky at Twenty-cm radio survey and future instruments like the Allen Telescope Array (in the radio band) and especially GAIA, Panoramic Survey Telescope and Rapid Response System and Large Synoptic Survey Telescope (in the optical band) will have chances to detect afterglows.
Biological Convergence of Cancer Signatures

Gene expression profiling has identified cancer prognostic and predictive signatures with superior performance to conventional histopathological or clinical parameters. Consequently, signatures are being incorporated into clinical practice and will soon influence everyday decisions in oncology. However, the slight overlap in the gene identity between signatures for the same cancer type or condition raises questions about their biological and clinical implications. To clarify these issues, better understanding of the molecular properties and possible interactions underlying apparently dissimilar signatures is needed. Here, we evaluated whether the signatures of 24 independent studies are related at the genome, transcriptome or proteome levels. Significant associations were consistently observed across these molecular layers, which suggest the existence of a common cancer cell phenotype. Convergence on cell proliferation and death supports the pivotal involvement of these processes in prognosis, metastasis and treatment response. In addition, functional and molecular associations were identified with the immune response in different cancer types and conditions that complement the contribution of cell proliferation and death. Examination of additional, independent, cancer datasets corroborated our observations. This study proposes a comprehensive strategy for interpreting cancer signatures that reveals common design principles and systems-level properties.
On the asymptotic efficiency of importance sampling techniques

The asymptotic efficiency of importance sampling (IS) techniques for the simulation of rare events in a multidimensional nonlinear setting was studied by J.S. Sadowsky and J.A. Bucklew (see ibid., vol.36, p.579-88, 1990). Fundamental results on the asymptotic efficiency of the mean-value modification (MM) technique were derived. Additionally, a statement was made that other IS techniques cannot be asymptotically efficient. It is shown that for the simulation of digital communication systems with Gaussian input, a broad class of asymptotically efficient IS techniques exists. Necessary and sufficient conditions are provided for the asymptotic efficiency of five different IS techniques (including MM) for one-dimensional linear systems. Multidimensional generalizations of these IS techniques are proposed. A sufficient condition for the asymptotic efficiency of these techniques applied to multidimensional nonlinear systems is provided. >
Study the effect of tissue heterogeneity and anisotropy in atrial fibrillation based on a human atrial model

Atrial fibrillation (AF) is the most common cardiac arrhythmias in clinic, it is characterized by multiple waves of excitation coursing through myocardial tissue. AF disrupts the normal sinus rhythm and may arise from ectopic foci. In right atrium, there are many different conduction bundles which have different action potential morphology, and they provide a substrate for reentrant activity during AF. Fibre orientation is important in electric propagation and maintaining AF, however, most previous simulation studies didn't consider the fibre orientation. In this paper we studied the effect of tissue heterogeneity and anisotropy on initiation and maintaining of AF based on a realistic human atrial model with fibre orientation and detailed conduction system. The results showed that tissue heterogeneity and anisotropy are important for AF, and in some cases AF is transient due to the lack of anisotropy. Fiber orientation is very important in sustaining of re-entry waves. This investigation suggests that a detail atrial anatomical model should be necessary for AF simulation.
Rapid vision loss in a 15-year-old boy.

A 15-year-old boy with a recent diagnosis of T-cell acute lymphoblastic leukaemia (ALL) and a history of factor V Leiden heterozygosity presented with a sudden onset of bilateral vision loss over a 24 h period. 2 weeks prior to presentation he received pegaspargase chemotherapy. During the week preceding admission he had noted mild blurred vision and complained of retro-orbital headaches. Ophthalmic examination revealed visual acuity of 20/800 in the right eye and minimal light perception in the left eye. He had sluggish pupillary reactivity to light with a left relative afferent pupillary defect. Dilated fundoscopic examination demonstrated bilateral florid optic disc swelling with peripapillary and dot-blot haemorrhages in the periphery, and macular oedema of the left eye. Neurological examination demonstrated mild left peripheral seventh nerve palsy. Multiplanar and multisequence MRI of the orbits, face and neck were obtained before and after administration of 20 cc iv contrast (Figures 1–4). Figure 1 Pre-contrast T1 weighted axial MRI of the brain. Figure 4 Post-contrast T1 weighted sagittal MRI. What are the abnormalities seen in Figures 1 and ​and22? Figure 2 Post-contrast fat-saturated T1 weighted axial MRI of the brain. What do you notice in Figure 3? Figure 3 Fat-saturated T2 weighted coronal MRI of the brain. Are there any additional findings in Figure 4? What is the diagnosis?
Effect of One-Handed Pushing and Puling Strength at Different Handle Heights in Vertical Direction

— The purpose of this study was to measure the maximal isometric strength and to investigate the effects of different handle-heights and elbow angles with respect to Mid. sagittal plane on the pushing and pulling strength in vertical direction. Eight male subjects performed a series of static strength measurement for each subject. The highest isometric strength was found in pulling at shoulder height (S.H.) (Mean = 60.29 lb., SD = 16.78 lb.) and the lowest isometric strength was found also in pulling at elbow height (E.H.) (Mean = 33.06 lb., SD = 6.56 lb.). Although the isometric strengths were higher at S.H than at E.H. for both activities, the maximal isometric strengths were compared statistically. ANOVA was performed. The results of the experiment revealed that there was a significant different between handle heights. However, there were no significant different between angles and activities, also no correlation between grip strength and activities.
An Augmented Lagrangian Method for image reconstruction with multiple features

We present an Augmented Lagrangian Method (ALM) for solving image reconstruction problems with a cost function consisting of multiple regularization functions with a data fidelity constraint. The presented technique is used to solve inverse problems related to image reconstruction, including compressed sensing formulations. Our contributions include an improvement for reducing the number of computations required by an existing ALM method, an approach for obtaining the proximal mapping associated with p-norm based regularizers, and lastly a particular ALM for the constrained image reconstruction problem with a hybrid cost function including a weighted sum of the p-norm and the total variation of the image. We present examples from Synthetic Aperture Radar imaging and Computed Tomography.
Essays in sovereign credit risk

This dissertation investigates aspects of sovereign credit risk in advanced and emerging economies. It consists of two chapters. Chapter 1 studies the determinants of sovereign credit default swap (CDS) spreads for 16 advanced economies during the recent financial crisis. We document that the state of the world financial system, and since the beginning of the crisis, the state of a country’s domestic financial system, have strong explanatory power for the behavior of CDS spreads. Furthermore, the magnitude of this effect depends on the relative importance of a country's financial system pre-crisis. Our results suggest the presence of a private-to-public risk transfer through which market participants incorporate their expectations about the potential burden of government intervention. Chapter 2 studies the extent to which macro-economic variables govern the dynamics of emerging market sovereign CDS spreads. In this chapter, I propose a structural model of sovereign credit risk based on a country's access to international capital flows through exports, imports and international reserves. The joint dynamics of the sovereign’s repayment capacity and the amount of outstanding debt determine the level of default risk and thus the sovereign CDS spread. I implement the model for a sample of six emerging economies for a period covering the recent financial crisis. A calibrated version of the model captures the widening of sovereign spreads during the crisis and provides a good fit for their time-series dynamics. Lastly, I find that the market-implied level of country liabilities is on average 13% larger than the reported level of debt. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Finance First Advisor Urban J. Jermann Second Advisor Karen K. Lewis Third Advisor Stephan Dieckmann
Molecular and Cellular Pathobiology In Vivo Regulation of TGF-b by R-Ras 2 Revealed through Loss of the RasGAP Protein NF 1

Ras superfamily proteins participate in TGF-b—mediated developmental pathways that promote either tumor suppression or progression. However, the specific Ras proteins, which integrate in vivo with TGF-b signaling pathways, are unknown. As a general approach to this question, we activated all Ras proteins in vivo by genetic deletion of the RasGAP protein Nf1 and examined mice doubly deficient in a Ras protein to determine its requirement in formation of TGF-b—dependent neurofibromas that arise in Nf1-deficient mice. Animals lacking Nf1 and the Ras-related protein R-Ras2/TC21 displayed a delay in formation of neurofibromas but an acceleration in formation of brain tumors and sarcomas. Loss of R-Ras2 was associated with elevated expression of TGF-b in Nf1-deficient Schwann cell precursors, blockade of a Nf1/TGFbRII/AKT-dependent autocrine survival loop in tumor precursor cells, and decreased precursor cell numbers. Furthermore, the increase in size of sarcomas from xenografts doubly deficient in these geneswas also found to be TGF-b—dependent, in this case resulting from cell nonautonomous effects on endothelial cells and myofibroblasts. Extending these findings in clinical specimens, we documented an increase in TGF-b ligands and an absence of TGF-b receptor II in malignant peripheral nerve sheath tumors, which correspond to tumors in the Nf1-deficient mouse model. Together, our findings reveal R-Ras2 as a critical regulator of TGF-b signaling in vivo. Cancer Res; 72(20); 5317–27. 2012 AACR.
A SURVEY OF COMPUTER VISION METHODS FOR LOCATING FRUIT ON TREES

A review of previous studies to automate the location of fruit on trees using computer vision methods was performed. The main features of these approaches are described, paying special attention to the sensors and accessories utilized for capturing tree images, the image processing strategy used to detect the fruit, and the results obtained in terms of the correct/false detection rates and the ability to detect fruit independent of its maturity stage. The majority of these works use CCD cameras to capture the images and use local or shape-based analysis to detect the fruit. Systems using local analysis, like intensity or color pixel classification, allow for rapid detection and were able to detect fruit at specific maturity stages, i.e., fruit with a color different from the background. However, systems based on shape analysis were more independent of hue changes, were not limited to detecting fruit with a color different from the color of the background; however, their algorithms were more time consuming. The best results obtained indicate that more than 85% of visible fruits are usually detectable, although with CCD sensors there were a number of false detections that in most cases were above >5%. The approaches using range images and shape analysis were capable of detecting fruit of any color, did not generate false alarms, and gave precise information about the fruit three-dimensional position. In spite of these promising results, the problem of total fruit occlusion limits the amount of fruit that can be harvested, ranging from 40 to 100% of total fruit, depending on fruiting and viewing conditions. This fact seriously affects the feasibility of future harvesting robots relying on images that do not contain a high percentage of visible fruit. Therefore, new techniques to reduce total occlusion should be studied in order to make the process feasible.
Random walk based routing protocol for wireless sensor networks

In recent years, design of wireless sensor networks using methodologies and mechanisms from other disciplines has gained popularity for addressing many networking aspects and providing more flexible and robust algorithms. We address in this paper the problem of random walk to model routing for data gathering in wireless sensor networks. While at first glance, this approach may seem to be overly simplistic and highly inefficient, many encouraging results that prove its comparability with other approaches have been obtained over the years. In this approach, a packet generated from a given sensor node performs a random motion until reaching a sink node where it is collected. The objective of this paper is to give an analytical model to evaluate the performance of the envisioned routing scheme with special attention to two metrics: the mean system data gathering delay and the induced spatial distribution of energy consumption. The main result shows that this approach achieves acceptable performance for applications without too stringent QoS requirements provided that the ratio of sink nodes over the total number of sensor nodes is carefully tuned.
Global sliding mode control for uncertain linear systems with input time-delays

The problem of designing global sliding mode controllers for a class of linear and uncertain systems with time delays of control was concerned. Firstly, we proposed a new method for integral sliding surface. It can make up for the deficiencies of the traditional sliding surface, eliminating the process of reaching and ensuring the global robustness of the system. Secondly, this paper gave the process of designing a global sliding mode controller. Based on LMI, it gives and proves a sufficient asymptotic stability condition of the sliding motion. Designed the dynamics and discontinuity of the compensating control law can guarantee the existence of the sliding surface and effectively compensate for the uncertainties. Finally, The efficiency and superiority of the proposed method were demonstrated by simulation study.
Design of tactile sensing systems for dextrous manipulators

Preliminary work aimed at understanding the general issues and tradeoffs governing the design of extended tactile sensing systems is reviewed. General methods for estimating the bandwidths of line-addressed and matrix-addressed systems are presented. The proposed tactile sensing system incorporates four subsystems that permit the high-speed access of tactile data: (1) a transduction scheme; (2) a preprocessing scheme; (3) a multiplexing and transmission subsystem; and (4) tactile data selection techniques. Designs for implementation at each of these levels are presented. The designs emphasize practical necessities such as simplicity, reliability, and economy, along with plans to incorporate a tactile system into the Utah/MIT dextrous hand. <<ETX>>
A virtual environment for simulating manufacturing operations in 3D

The paper presents a method for simulating basic manufacturing operations (unload, load, process, move, and store) in a 3D virtual environment. The virtual environment provides a framework for representing a facility layout in 3D, which encapsulates the static and the dynamic behavior of the manufacturing system. The 3D manufacturing objects in the facility are mapped with the nodes in the framework. The framework, a modified scenegraph structure, is a tree structure which can be manipulated by updating the parent-child relationships and the transformation matrix to simulate the basic manufacturing operations. The method can be easily extended to represent more specific manufacturing operations.
Study on the Effect of Different Frequency Bands of EEG Signals on Mental Tasks Classification

Currently, frequency bands not more than 40 Hz are usually used to perform mental tasks classification in brain-computer interface systems. In this study, by using Keirn's EEG data, we studied the effects of ten 10 Hz-wide subbands between 0 and 100 Hz on mental tasks classification. Features were computed in frequency domain as the sum of weighted power spectral value in each subband at each channel (C3, C4, P3, P4, O1, and O2). Fisher's linear discriminant was used to perform task-pair classification. Our results indicated that subbands ranging from 30 to 100 Hz resulted in relatively greater classification accuracy at many scalp sites. The average classification accuracy of 98.3% across 130 task pairs was achieved by using features including those obtained on gamma bands (30-100 Hz), which is much greater than that of 89.3% by using the frequency band 0-30 Hz only
Controlling nonlocal light-matter interactions via spectral-domain transformation optics

We propose a new transformation-optics framework based on nonlocal coordinate transformations in the spectral (wavenumber) domain. Our approach allows a physically-incisive and powerful geometrical interpretation in terms of deformation of the equi-frequency contours, and sets the stage for new intriguing developments in dispersion engineering of electromagnetic metamaterials.
Eigentransport for efficient and accurate all-frequency relighting

We present a method for creating a geometry-dependent basis for diffuse precomputed radiance transfer. Unlike previous PRT bases, ours is derived from Principal Component Analysis of the sampled transport functions at each vertex, without relying on pre-projections to secondary bases, such as the Spherical Harmonics or Haar wavelets. It allows for efficient evaluation of shading, has low memory requirements and produces accurate results with few coefficients. We are able to capture all-frequency effects from both distant and near-field dynamic lighting in real-time and present a simple and efficient rotation scheme. Reconstruction of the final shading becomes a low-order dot product and is performed on the GPU.