Miracle-dz/UniFAR-FTUs huggingface dataset:
Diiraction Eeects E.2. Scalar Diffraction Theory Results

Diiraction eeects may be signiicant o ver long distances, even for a wide beam. Therefore, unless care is taken, diiraction eeects can seriously degrade the performance of an interfer-ometric array. Previously, Tnago and Twiss 1980 considered diiraction eeects for a small diameter interferometer. Visibility losses were tabulated as a function of the pathlengths of the two combining beams e.g. from 200 and 400 m respectively. The atness of the wavefronts assumed made it possible to calculate the wavefront analytically with only one numerical quadrature. More recently, Hrynevych 1992 has extended these results with more mathematical rigor and experimental veriication, and has considered the speciic case of the SUSI Sydney University Stellar Interferometer. For beams with aberrations due to atmospheric turbulence, analytic solutions seem very diicult, and none have been published to date. Therefore, numerical calculations from scalar diiraction theory including various formulations have been used to estimate visibility losses. An earlier version of this work Bagnuolo 1988 diiracted" model atmospheres numerically to examine the losses in visibility i n a n i n terferometer as a function of beam size. For the CHARA there are two w avebands of interest: 0.5550. 9 m V, R, and I and 2.112. 4 K. Therefore, we need to consider diiraction eeects for three cases: K-band observations, in which w e are in the single-r 0 regime without AO, Visual bands observations with an AO system, Visual bands without AO, limited to 1-2 r 0 " apertures i.e. 20030 cm. Ideally, one would like to reduce the beam size as much as possible in order to reduce the size and cost of the optics, especially the Optical Path Length Equalizer OPLE. There is therefore a trade-oo between the beam reduction factor and the losses in visibility and other eeects due to diiraction. In the CHARA array the beam reduction factor of 8:1 thus represents a compromise. In the rest of this Appendix we will brieey summarize scalar diiraction theory, the simulations , and the implications for the CHARA Array.
A hormone-DNA repair circuit governs the response to genotoxic insult.

UNLABELLED Alterations in DNA repair promote tumor development, but the impact on tumor progression is poorly understood. Here, discovery of a biochemical circuit linking hormone signaling to DNA repair and therapeutic resistance is reported. Findings show that androgen receptor (AR) activity is induced by DNA damage and promotes expression and activation of a gene expression program governing DNA repair. Subsequent investigation revealed that activated AR promotes resolution of double-strand breaks and resistance to DNA damage both in vitro and in vivo. Mechanistically, DNA-dependent protein kinase catalytic subunit (DNAPKcs) was identified as a key target of AR after damage, controlling AR-mediated DNA repair and cell survival after genotoxic insult. Finally, DNAPKcs was shown to potentiate AR function, consistent with a dual role in both DNA repair and transcriptional regulation. Combined, these studies identify the AR-DNAPKcs circuit as a major effector of DNA repair and therapeutic resistance and establish a new node for therapeutic intervention in advanced disease. SIGNIFICANCE The present study identifies for the fi rst time a positive feedback circuit linking hormone action to the DNA damage response and shows the significant impact of this process on tumor progression and therapeutic response. These provocative findings provide the foundation for development of novel nodes of therapeutic intervention for advanced disease.
Analysis of ARX Functions: Pseudo-linear Methods for Approximation, Differentials, and Evaluating Diffusion

This paper explores the approximation of addition mod 2n by addition mod 2w, where 1 ≤ w ≤ n, in ARX functions that use large words (e.g., 32-bit words or 64-bit words). Three main areas are explored. First, pseudo-linear approximations aim to approximate the bits of a w-bit window of the state after some rounds. Second, the methods used in these approximations are also used to construct truncated differentials. Third, branch number metrics for diffusion are examined for ARX functions with large words, and variants of the differential and linear branch number characteristics based on pseudo-linear methods are introduced. These variants are called effective differential branch number and effective linear branch number, respectively. Applications of these approximation, differential, and diffusion evaluation techniques are demonstrated on Threefish-256 and Threefish-512.
Morphological changes in tight junctions of Necturus maculosus proximal tubules undergoing saline diuresis

Tight junctions between epithelial cells are believed to control the paracellular diffusion of substances across epithelia. Epithelia in which tight junctions are poorly developed display a higher paracellular electrical conductance, while those with extensive tight junctions show lower conductance values. We described here a particular epithelium, that of the proximal tubules of the Necturus kidney, in which the development of the tight junctions varies in parallel with a change of paracellular electrical conductance. In control conditions, tight junctions between epithelial cells of the proximal tubules are more developed than in tubules undergoing saline diuresis, a situation which increases the conductance across the paracellular shunt pathway.
Preseismic deformation and coseismic displacements associated With the 1999 Chi-Chi, Taiwan, Earthquake

The destructive 1999 Chi-Chi, Taiwan, earthquake ( M w 7.5) produced an approximately 100-km-long surface rupture, mostly along the previously recognized north-south-trending Chelungpu fault. Preseismic deformation in central Taiwan is realized from annually repeated Global Positioning System (GPS) data acquired during the 1992-1999 period. The total WNW-ESE shortening rate in the vicinity of the epicentral region, that is from the west coast to the western boundary of the Central Range, is up to 25 mm/yr. The crustal deformation before the Chi-Chi earthquake was essentially a uniaxial compressional strain of 0.36 μstrain/yr in the direction of 114°. The GPS measurements taken 0.2-2.7 yr before and within 3 months after the mainshock were utilized to estimate the coseismic displacements. Horizontal movements of 1.1-9.1 m in the NW-NNW directions are observed on the hanging wall (eastern side) of the fault. There is a northward-increasing trend in the magnitude of the displacement vectors and a dramatic change in the direction of about 50° toward the east along the fault strike. In contrast, much smaller SE-SEE movements of 0.1-1.5 m are found on the footwall (western side) of the fault. The GPS data show 2.4-10.1 m of total horizontal offsets across the Chelungpu fault. Vertical offsets of 1.2-4.4 m with the eastern side up are also observed along the surface rupture. The uplift on the hanging wall decreases rapidly toward the east. It becomes subsidence at Sun Moon Lake and in the Puli-Wushe area. The stations on the footwall show subsidence of 0.02-0.26 m. The width of the uplift zone increases from about 10 km in the south to approximately 30 km in the north. Manuscript received 13 October 2000.
AIDS vaccine development and challenge viruses: getting real.

There is consensus that effective AIDS vaccines should induce both cellular and humoral immunity. Challenge of macaques with SIVor constructs of SIVand HIV (SHIV) has been invaluable to test vaccine efficacy; however, the biological relevance of some results is uncertain. Ideally, biologically meaningful challenges should mimic human HIV-1 transmission as closely as possible and will, therefore, involve (a) R5 viruses, (b) mucosal challenge routes, (c) viruses with neutralization profiles resembling those of recently transmitted HIV-1 isolates (for testing neutralizing antibody-based vaccines), and (d) heterologous challenge viruses.
Reinforcement Learning in Large Multi-agent Systems

Enabling reinforcement learning to be eective in large-scale multi-agent Markov Decisions Problems is a challenging task. To address this problem we propose a multi-agent variant of Q-learning: “Q Updates with Immediate Counterfactual Rewards-learning” (QUICR-learning). Given a global reward function over all agents that the large-scale system is trying to maximize, QUICR-learning breaks down the global reward into many agent-specific rewards that have the following two properties: 1) agents maximizing their agentspecific rewards tend to maximize the global reward, 2) an agent’s action has a large influence on its agent-specific reward, allowing it to learn quickly. Each agent then uses standard Q-learning type updates to form a policy to maximize the agent-specific rewards. Results on multi-agent grid-world problems over two topologies, show that QUICRlearning can be eective with hundreds of agents and can achieve up to 300% improvements in performance over both conventional and local Q-learning in the largest tested systems.
TACE Activation by MAPK-Mediated Regulation of Cell Surface Dimerization and TIMP3 Association

A metalloproteinase implicated in inflammation and cancer is inactive as dimers and active as monomers. Falling Apart for Activation The ADAM metalloproteinase TACE [tumor necrosis factor–α (TNF-α)–converting enzyme] mediates the cleavage of several signaling molecules, including TNF-α and transforming growth factor–α (TGF-α), to generate soluble forms. Xu et al. sought to understand the mechanisms by which the MAPKs p38 and ERK activate TACE. Under basal conditions, inactive TACE was present at the cell surface in dimers that interacted preferentially with the metalloproteinase inhibitor TIMP3. Stimulation of p38 or ERK activity resulted in higher relative amounts of TACE monomers at the cell surface, decreased association of TACE with TIMP3, and increased TACE activity. This mechanism of activation may also apply to related ADAM metalloproteinase. Ectodomain shedding mediated by tumor necrosis factor–α (TNF-α)–converting enzyme [TACE; also known as ADAM17 (a disintegrin and metalloproteinase 17)] provides an important switch in regulating cell proliferation, inflammation, and cancer progression. TACE-mediated ectodomain cleavage is activated by signaling of the mitogen-activated protein kinases (MAPKs) p38 and ERK (extracellular signal–regulated kinase). Here, we found that under basal conditions, TACE was predominantly present as dimers at the cell surface, which required its cytoplasmic domain and enabled efficient association with tissue inhibitor of metalloproteinase-3 (TIMP3) and silencing of TACE activity. Upon activation of the ERK or p38 MAPK pathway, the balance shifted from TACE dimers to monomers, and this shift was associated with increased cell surface presentation of TACE and decreased TIMP3 association, which relieved the inhibition of TACE by TIMP3 and increased TACE-mediated proteolysis of transforming growth factor–α. Thus, cell signaling altered the dimer-monomer equilibrium and inhibitor association to promote activation of TACE-mediated ectodomain shedding, a regulatory mechanism that may extend to other ADAM proteases.
Ambulatory Total Extraperitoneal Inguinal Hernia Repair: Feasibility and Impact on Quality of Life

Background and Objectives: Feasibility of ambulatory laparoscopic inguinal hernia repair in developing countries is not known due to lack of dedicated outpatient centers. This study prospectively evaluated the feasibility of outpatient discharge after laparoscopic total extraperitoneal inguinal hernia repair done in combination with in-hospital services and its impact on quality of life. Methods: Forty patients were studied who had uncomplicated inguinal hernias and fulfilled the selection criteria. Quality of life was evaluated by using the SF-12 questionnaire. Results: Ninety percent of patients could be discharged as outpatients. Four patients required admission. No major complications or readmissions occurred. Physical components of quality of life deteriorated in the immediate postoperative period but improved to above preoperative levels within one month. A transient deterioration in subgroups of the mental health component was observed, which recovered to normal in less than a week. There was no significant alteration in the emotional component. There has been no recurrence at a median follow-up of 25 months. Conclusion: It was feasible to safely perform outpatient TEP in combination with routine in-hospital services without increasing complications or causing any adverse impact on quality of life. This was possible subject to adherence to proper selection and discharge criteria.
The three Bacillus anthracis toxin genes are coordinately regulated by bicarbonate and temperature

The two Bacillus anthracis toxins are composed of three proteins, protective antigen, lethal factor, and edema factor. The structural genes for these three components are located on the virulence plasmid pXO1. We constructed transcriptional fusions between the regulatory region of each of these genes and lacZ. Each construct was then inserted as a single copy at the corresponding toxin gene locus on pXO1, resulting in three isogenic strains. Two environmental factors, bicarbonate and temperature, were found to induce beta-galactosidase synthesis in each recombinant strain. Furthermore, the transcription of the three toxin genes appears to be coordinately regulated.
Baseline Distribution of Participants With Depression and Impaired Quality of Life in the Treatment of Preserved Cardiac Function Heart Failure With an Aldosterone Antagonist Trial

Background—Previous studies have demonstrated the psychosocial effect of heart failure in patients with reduced ejection fraction. However, the effects on patients with preserved ejection fraction have not yet been elucidated. This study aimed to determine the baseline characteristics of participants with heart failure with preserved ejection fraction as it relates to impaired quality of life (QOL) and depression, identify predictors of poor QOL and depression, and determine the correlation between QOL and depression. Methods and Results—Among patients enrolled in the Treatment of Preserved Cardiac Function Heart Failure With an Aldosterone Antagonist Trial (TOPCAT), 3400 patients completed the Kansas City Cardiomyopathy Questionnaire, 3395 patients completed European QOL 5D Visual Analog Scale, and 1431 patients in United States and Canada completed the Patient Health Questionnaire-9. The mean summary score on the Kansas City Cardiomyopathy Questionnaire was 54.8, and on European QOL 5D Visual Analog Scale, it was 60.3; 27% of patients had moderate to severe depression. Factors associated with better Kansas City Cardiomyopathy Questionnaire and European QOL 5D Visual Analog Scale via multiple logistic regression analysis were American region, older age, no history of angina pectoris or asthma, no use of hypoglycemic agent, more activity level, and lower New York Heart Association class. Factors associated with depression via multiple logistic regression analysis included younger age, female sex, comorbid angina, chronic obstructive pulmonary disease, use of a hypoglycemic agent, lower activity level, higher New York Heart Association class, and selective serotonin reuptake inhibitor use. There were significant correlations between each of the QOL scores and depression. Conclusions—Patients with heart failure with preserved ejection fraction, who were younger had higher New York Heart Association class or comorbid angina pectoris, had lower activity levels, lived in Eastern Europe or were taking hypoglycemic agents, were more likely to have impaired QOL and depression. Clinical Trial Registration—URL: http://www.clinicaltrials. gov. Unique identifier: NCT00094302.
Routing and Spectrum Allocation in Elastic Optical Networks: A Tutorial

Flexgrid technology is now considered to be a promising solution for future high-speed network design. In this context, we need a tutorial that covers the key aspects of elastic optical networks. This tutorial paper starts with a brief introduction of the elastic optical network and its unique characteristics. The paper then moves to the architecture of the elastic optical network and its operation principle. To complete the discussion of network architecture, this paper focuses on the different node architectures, and compares their performance in terms of scalability and flexibility. Thereafter, this paper reviews and classifies routing and spectrum allocation (RSA) approaches including their pros and cons. Furthermore, various aspects, namely, fragmentation, modulation, quality-of-transmission, traffic grooming, survivability, energy saving, and networking cost related to RSA, are presented. Finally, the paper explores the experimental demonstrations that have tested the functionality of the elastic optical network, and follows that with the research challenges and open issues posed by flexible networks.
Assessment of Knee Implant Alignment Using Coordinate Measurement on Three-Dimensional Computed Tomography Reconstructions

The rapid development of navigation systems designed to improve implant alignment calls for precise methods to verify positioning. One new approach to assess knee implant alignment is coordinate measurement (CM) using reference objects on 3-dimensional reconstructions of computed tomographic (CT) image sequences. The objectives of this study were to determine whether implant alignment can be accurately and precisely examined with CT-based CM, and whether correct positioning of a transversal support implant can be attained using a specially developed aiming instrument. Average deviation of CT measurements from those made with a digital caliper remained within the caliper’s range of error. This level of accuracy was observer independent. CT-based CM can be used for accurate and precise alignment verification. As well, precise alignment of transversal support can be achieved during implantation with a conventional aiming device, assuming the bony landmarks are appropriately recognized.
Channel changes in badlands

Stripping of the vegetation and soil from a 13-hectare site in Virginia underlain by coastal plain sediments created a rapidly evolving badland topography. Two types of channels developed: (1) sand-bed alluvial channels were graded to transport the bed material load supplied from slope erosion with available runoff, but they also generally eroded their beds slowly, and (2) steeper, bedrock-floored channels incised rapidly. In bedrock channels the erosion rate was proportional to the 4/9ths power of drainage area and the 2/3rds power of gradient. These exponents are consistent with a model in which the erosion rate is proportional to the bed shear during high flows. Due to rapid mass wasting and reduced runoff, the alluvial channels became as much as 50% steeper during the winter than the summer, with an attendant yearly cycle of winter aggradation and summer entrenchment. The gradients, their seasonal variability, and their downstream hydraulic geometry were consistent with the predictions of total load transport formulas for sand beds and high loads. The hydraulic geometry of alluvial channels in the Virginia badlands were similar to that on the Morrison Formation in the western United States.
Switched-capacitor decimation filters with direct form polyphase structure having very small sensitivity characteristics

A novel approach for the realization of switched-capacitor decimation filters is proposed. The design process is based on the optimum allocation of poles and zeros of a transfer function, so that the best compromise is achieved between filter complexity and sensitivity with respect to capacitance ratio errors. Analytical boundaries enclosing the feasible frequency responses for a given nominal design and specified capacitance ratio tolerance are used, enabling quick and reliable statistical sensitivity comparisons without the need for Monte Carlo simulations. Results are shown for an illustrative design example of a video-frequency decimation filter. A prototype filter has been built and tested in the laboratory to validate the theory, and measurement results are included.
Numerically Safe Gomory Mixed-Integer Cuts

We describe a simple process for generating numerically safe cutting planes using floating-point arithmetic and the mixed-integer rounding procedure. Applying this method to the rows of the simplex tableau permits the generation of Gomory mixed-integer cuts that are guaranteed to be satisfied by all feasible solutions to a mixed-integer programming problem (MIP). We report on tests with the MIPLIB 3.0 and MIPLIB 2003 test collections as well as with MIP instances derived from the TSPLIB traveling salesman library.
Primary CNS Lymphoma in Children and Adolescents: A Descriptive Analysis from the International Primary CNS Lymphoma Collaborative Group (IPCG)

Purpose: To describe the demographic and clinical features and outcomes for children and adolescents with primary CNS lymphoma (PCNSL). Experimental Design: A retrospective series of children and adolescents with PCNSL was assembled from 10 cancer centers in 3 countries. Results: Twenty-nine patients with a median age of 14 years were identified. Sixteen (55%) had Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 1 or greater. Frontline therapy consisted of chemotherapy only in 20 patients (69%), while 9 (31%) had chemotherapy plus cranial radiotherapy. Most patients received methotrexate (MTX)-based regimens. Overall response rate was 86% (complete remission 69%, partial remission 17%). The 2-year progression-free survival (PFS) and overall survival (OS) rates were 61% and 86%, respectively; the 3-year OS was 82%. Univariate analyses were conducted for age (≤14 vs. >14 years), PS (0 or 1 vs. >1), deep brain lesions, MTX dose, primary treatment with chemotherapy alone, intrathecal chemotherapy, and high-dose therapy. Primary treatment with chemotherapy alone was associated with better overall response rates with an odds ratio (OR) of 0.125 (P = 0.02). There was a marginally significant relationship between higher doses of MTX and response (OR = 1.5, P = 0.06). ECOG-PS of 0 to 1 was the only factor associated with better outcome with hazard ratios of 0.136 (P = 0.017) and 0.073 (P = 0.033) for PFS and OS, respectively. Conclusion: This is the largest series collected of pediatric PCNSL. The outcome of children and adolescents seems to be better than in adults. PS of 0 to 1 is associated with better survival. Clin Cancer Res; 17(2); 346–52. ©2011 AACR.
Detecting botnets using file system indicators Master ’ s thesis

Botnets, large groups of networked zombie computers under centralised control, are recognised as one of the major threats on the internet. There is a lot of research towards ways of detecting botnets, in particular towards detecting Command and Control servers. Most of the research is focused on trying to detect the commands that these servers send to the bots over the network. For this research, we have looked at botnets from a botmaster’s perspective. First, we characterise several botnet enhancing techniques using three aspects: resilience, stealth and churn. We see that these enhancements are usually employed in the network communications between the C&C and the bots. This leads us to our second contribution: we propose a new botnet detection method based on the way C&C’s are present on the file system. We define a set of file system based indicators and use them to search for C&C’s in images of hard disks. We investigate how the aspects resilience, stealth and churn apply to each of the indicators and discuss countermeasures botmasters could take to evade detection. We validate our method by applying it to a test dataset of 94 disk images, 16 of which contain C&C installations, and show that low false positive and false negative ratio’s can be achieved. Approaching the botnet detection problem from this angle is novel, which provides a basis for further research.