Miracle-dz/UniFAR-FTUs huggingface dataset:
A gene expression signature that distinguishes desmoid tumours from nodular fasciitis

Nodular fasciitis (NF) is a rapidly growing cellular mass composed of fibroblasts/myofibroblasts, usually localized in subcutaneous tissues, that typically undergoes fibrosis and almost never recurs. Desmoid tumours (DTs) are rare forms of fibroblastic/myofibroblastic growth that arise in deep soft tissues, display a propensity for local infiltration and recurrence, but fail to metastasize. Given that both entities are primarily fibroblastic/myofibroblastic lesions with overlapping histological features, their gene expression profiles were compared to identify differentially expressed genes that may provide not only potential diagnostic markers, but also clues as to the pathogenesis of each disorder. Differentially expressed transcripts (89 clones displaying increased expression in DTs and 246 clones displaying increased expression in NF) included genes encoding several receptor and non‐receptor tyrosine kinases (EPHB3, PTPRF, GNAZ, SYK, LYN, EPHA4, BIRC3), transcription factors (TWIST1, PITX2, EYA2, OAS1, MITF, TCF20), and members of the Wnt signalling pathway (AXIN2, WISP1, SFRP). Remarkably, almost one‐quarter of the differentially expressed genes encode proteins associated with inflammation and tissue remodelling, including members of the interferon (IFN), tumour necrosis factor (TNF), and transforming growth factor beta (TGF‐β) signalling pathways as well as metalloproteinases (MMP1, 9, 13, 23), urokinase plasminogen activator (PLAU), and cathepsins. The observations provide the first comparative molecular characterization of desmoid tumours and nodular fasciitis and suggest that selected tyrosine kinases, transcription factors, and members of the Wnt, TGF‐β, IFN, and TNF signalling pathways may be implicated in influencing and distinguishing their fate. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Magnification chromoendoscopy for the diagnosis of gastric intestinal metaplasia and dysplasia.

BACKGROUND The aim of this study was to define the reproducibility and accuracy of magnification chromoendoscopy for the diagnosis of lesions associated with gastric cancer (intestinal metaplasia and dysplasia). METHODS A total of 136 patients with previously diagnosed lesions and 5 gastrectomy specimens were studied. Endoscopic examination was performed with a magnification endoscope after methylene blue (1%) spraying. According to differences in color and mucosal pattern, groups and subgroups of endoscopic images were defined, and biopsies taken (n = 462). Five endoscopists were asked to classify individually 2 endoscopic images per subgroup on 2 separate occasions. RESULTS Three groups of endoscopic images were defined: nonmetaplastic, nondysplastic mucosa (I); metaplastic mucosa (II); and dysplastic mucosa (III). Ten subgroups were defined according to pit pattern: round small (IA), round and tubular small (IB), coarse round (IC), and course round pits with a straight pit (ID); blue irregular marks (IIA), blue round and tubular pits (IIB), blue villi (IIC), and blue small pits (IID); and loss of clear pattern, with depression (IIIA) or with slight elevation (IIIB). The kappa statistic for intraobserver agreement on the classification of endoscopic images in groups was 0.86; for interobserver agreement, it was 0.74. For classification into subgroups, kappa values ranged from 0.48 to 0.78. For 85% of the areas classified endoscopically as Group I (n = 146), no mucosal lesions or gastritis was described at histologic examination; for 83% of those in Group II (n = 198), intestinal metaplasia was found. Subgroups IIA and IIB were more often associated with complete intestinal metaplasia (62%), and IIC and IID with incomplete metaplasia (67%); in Group III (n = 118), dysplasia was diagnosed histopathologically in 33%. For the diagnosis of dysplasia, specificity was 81% (95% CI [77%, 85%]) and negative predictive value 99% (95% CI [99%, 100%]). CONCLUSIONS Gastric endoscopic patterns with chromoendoscopy and magnification seem reproducible and valid for the diagnosis of lesions associated with gastric cancer. This procedure may improve the follow-up of individuals at high-risk of gastric cancer, at least for the exclusion of severe lesions.
Correlates of aerobic fitness in urban and rural Portuguese adolescents

Background: Improving physical fitness is often an objective of programmes aimed at preventing obesity among youth. Aim: To evaluate the association between cardiorespiratory fitness (CRF) and area of residence controlling for several correlates in adolescents. Subjects and methods: CRF was assessed with the progressive aerobic cardiovascular endurance run (PACER) test in a cross-sectional sample of 362 Portuguese adolescents (165 males, 197 females) of 13–16 years of age. Youth were classified by area of residence as urban or rural. Gender, age, weight status, parental education, screen time (inactivity) and moderate-to-vigorous physical activity (MVPA) were statistically controlled. Logistic regression analysis was used. Results: Adolescents of both sexes from rural settings were 76% more likely to be classified as aerobically fit compared to those from urban areas. The odds ratio for CRF in the final model was similar in boys (OR = 0.24, 95% CI 0.06–0.99, p < 0.05) and girls (OR = 0.24, 95% CI 0.07–0.76, p < 0.05). MVPA and weight status were important predictors of CRF in Portuguese adolescents of 13–16 years of age. Maternal education was an additional predictor in girls. Conclusion: CRF and rural/urban settings were significantly related in this sample of Portuguese adolescents of both sexes.
Multi-baseline interferometric SAR for iterative height estimation

The tradeoff in choosing baseline length in interferometric SAR is that short baselines allow higher error while long baselines cause greater phase unwrapping problems. Combining information from baselines of different lengths can take advantage of the greater accuracy of long baselines while determining the phase wrapping from shorter baselines. This paper describes an iterative method which starts at the shortest baseline and proceeds to longer and longer baselines. The height is estimated for each baseline, using the previous estimate only to determine the phase wraps. If the signal-to-noise ratio of the interferometer is known and a value for the probability of error in the phase wraps is chosen, an optimal sequence of baseline lengths can be calculated. Simulations show that errors tend to propagate and become worse, so mean or median filters are used between each iteration. This paper will describe the technique and show examples from a simulated scene.
Generation of improved test cases from UML state diagram using genetic algorithm

An UML statechart diagram is used to model the dynamic aspects of object oriented software systems. A Finite State Machine (FSM) and an Extended Finite State Machine (EFSM) are commonly used for Model Based-Testing (MBT). A test case generation from FSM is easy due to unconditional transition from state to state by traversal. A test case generation from EFSM needs to satisfy the guard condition before transition from state to state. Testing from EFSM is difficult due to unfeasible paths and test data. This paper proposes a search-based approach to find feasible transition sequences and test data generation. The Unified Modeling Language specifications are translated into extended flow graphs. An Extended flow graph from EFSM specifies the control and data flow in a statechart diagram. To guide the feasible transition path a genetic algorithm (GA) framework is proposed. It is shown that the test cases so generated yield an improved test set.
Detection of Pilot Contamination Attack for Multi-Antenna Based Secrecy Systems

This paper considers the problem of detecting the pilot contamination attack for multi-antenna secrecy systems. The detection problem is formulated as a binary hypothesis problem and the likelihood ratio or the generalized likelihood ratio is employed as a decision statistic for the detection of the pilot contamination. Using the Neyman-Pearson criterion, we then develop several detection methods under the different assumptions of the channel and noise statistics. To be specific, the cases of interest are as follows: (i) exact knowledge of all covariance matrices, (ii) exact knowledge of the legitimate channel and noise covariance matrices, but no knowledge of the jamming channel covariance matrix and (iii) no knowledge of all covariance matrices. The performance comparison of the proposed schemes with the conventional scheme is performed by simulations.
Identifying Buyer Market Areas and the Impact of Buyer Concentration in Feeder Cattle Markets Using Mapping and Spatial Statistics

The size and shape of market areas for buyers from four major cattle feeding areas are determined by mapping data from the nation's largest video auction. Spatial statistics are also examined to determine their ability to identify market areas for feeder cattle. Mapping shows that procurement areas for feeder cattle buyers are large, irregularly shaped, and overlap substantially. A new statistic was developed to determine primary market areas. Feeder cattle buyers behave as oligopsonists in counties where most buyers are from one feeding area, and prices are higher for feeder cattle in counties where two or more market areas overlap.
Japanese and U.S. Exports and Investment as Conduits of Growth

We develop a simple model of the choice between exploiting a technology in another country via export and via direct foreign investment. The model points to the destination country's size, level of technological sophistication, and distance from the source as factors in the decision. Moreover, it suggests that the effects of these variables may not only be nonhomogeneous but nonmonotonic as well. We use the model as a basis for estimating Japanese and U.S. exports and DFI positions around the world. Consistent with the theory we find that the importance of DFI relative to exports grows with population, although, contrary to our theory, the elasticity of DFI, as well as exports, with respect to population is less than one. We find that distance tends to inhibit DFI much less than it inhibits exports, as our theory predicts. We find some tendency for Japanese exports to rise relative to DFI as countries become more advanced with U.S. exports and DFI exhibiting the opposite tendency. Taking population, per capita income, factor endowments, and distance into account, we find Japan to be more open to U.S. exports than any region in the world except East Asia.
The Impossibility of Philanthropic Funding Decisions: The Australian Non‐Government Funder Experience

Non‐government funders (NGFs) are major contributors to the third sector. Literature on this private philanthropic world is limited and access to stakeholders and practices within these institutions is a barrier to empirical research. With public oversight limited to nominal federal tax law disclosure, issues of accountability are under‐researched. We examine how NGFs ‘account’ for their grant making decisions in an Australian context. Focused on how NGFs assess likely success, it finds that assurance is constructed as part of the decision‐making process through a more socialising form of accountability, based on personal interaction, in contrast to a reliance on hierarchical accountability and transparency.
Building an electric model vehicle and implementing an obstacle avoidance algorithm

The present paper it presents an electric model vehicle with its own system of acquisition and computation of the information, on which we will test the collision control algorithms in indoors and outdoors with GPS localization. The algorithm used in this project is the Potential Field method. We chose to use a LIDAR sensor that can acquire distance data from the environment in 2D. The main objective of these tests is to make obstacle avoidance with mobile robot in Real-Time.
AROSICS: An Automated and Robust Open-Source Image Co-Registration Software for Multi-Sensor Satellite Data

Geospatial co-registration is a mandatory prerequisite when dealing with remote sensing data. Inter- or intra-sensoral misregistration will negatively affect any subsequent image analysis, specifically when processing multi-sensoral or multi-temporal data. In recent decades, many algorithms have been developed to enable manual, semi- or fully automatic displacement correction. Especially in the context of big data processing and the development of automated processing chains that aim to be applicable to different remote sensing systems, there is a strong need for efficient, accurate and generally usable co-registration. Here, we present AROSICS (Automated and Robust Open-Source Image Co-Registration Software), a Python-based open-source software including an easy-to-use user interface for automatic detection and correction of sub-pixel misalignments between various remote sensing datasets. It is independent of spatial or spectral characteristics and robust against high degrees of cloud coverage and spectral and temporal land cover dynamics. The co-registration is based on phase correlation for sub-pixel shift estimation in the frequency domain utilizing the Fourier shift theorem in a moving-window manner. A dense grid of spatial shift vectors can be created and automatically filtered by combining various validation and quality estimation metrics. Additionally, the software supports the masking of, e.g., clouds and cloud shadows to exclude such areas from spatial shift detection. The software has been tested on more than 9000 satellite images acquired by different sensors. The results are evaluated exemplarily for two inter-sensoral and two intra-sensoral use cases and show registration results in the sub-pixel range with root mean square error fits around 0.3 pixels and better.
In vitro activity of hexadecylphosphocholine (miltefosine) against metronidazole-resistant and -susceptible strains of Trichomonas vaginalis.

OBJECTIVES Trichomonas vaginalis is the causative agent of trichomoniasis, a sexually transmitted disease with worldwide significance. Trichomoniasis can be treated with metronidazole; however, resistant strains of T. vaginalis have been isolated and there is a lack of useful alternative drugs. The aim of the present study was to examine the activity of hexadecylphosphocholine (HePC; miltefosine), a membrane-active alkylphospholipid, that is licensed as an antileishmanial agent against T. vaginalis. METHODS The efficacy of HePC after 30 min, 1 h, 16 h and 24 h against four different T. vaginalis strains (with varying resistance to metronidazole) was evaluated. RESULTS It was shown that all isolates, including the metronidazole-resistant strains, were susceptible to HePC, with EC50s of between 8 and 40 microM and EC90s of between 8 and 80 microM depending on time and on the medium used for the experiments. Treatment of trichomonads with HePC resulted in rounding up and, at concentrations of >or=40 microM, in subsequent total lysis of the organisms. CONCLUSIONS HePC may be a promising new candidate for the treatment of trichomoniasis.
A TRMM-Based Tropical Cyclone Cloud and Precipitation Feature Database

AbstractThe Tropical Rainfall Measuring Mission (TRMM) satellite has provided invaluable data for tropical cyclone (TC) research since December 1997. The challenge, however, is how to analyze and efficiently utilize all of the information from several instruments on TRMM that observe the same target. In this study, a tropical cyclone precipitation, cloud, and convective cell feature (TCPF) database has been developed by using observations of the TRMM precipitation radar (PR), Microwave Imager (TMI), Visible and Infrared Scanner (VIRS), Lightning Imaging System (LIS), and the TRMM 3B42 rainfall product. The database is based on an event-based method that analyzes the measurements from multiple sensors. This method condenses the original information of pixel-level measurements into the properties of events, which can significantly increase the efficiency of searching and sorting the observed historical TCs. With both convective and rainfall properties included, the database offers the potential to aid the r.
Post-Rendering 3D Image Warping: Visibility, Reconstruction, and Performance for Depth-Image Warping

William R. Mark POST-RENDERING 3D IMAGE WARPING: VISIBILITY, RECONSTRUCTION, AND PERFORMANCE FOR DEPTH-IMAGE WARPING (Under the direction of Dr. Gary Bishop) The images generated by real-time 3D graphics systems exhibit enormous frame-to-frame coherence, which is not exploited by the conventional graphics pipeline. I exploit this coherence by decoupling image rendering from image display. My system renders every Nth frame in the conventional manner, and generates the in-between frames with an image warper. The image warper modifies a rendered image so that it is approximately correct for a new viewpoint and view direction. My image warper uses McMillan’s 3D image warp. Unlike perspective image warps, the 3D image warp can correct for changes in viewpoint, even for objects at different depths. As a result, my system does not require the application programmer to segment the scene into different depth layers, as is required by systems that use a perspective image warp. I attack three major challenges associated with using 3D warping for rendering acceleration: visibility, reconstruction, and performance. I describe how to choose pairs of rendered images so that most of the needed portions of the scene are visible in these images. I describe a framework for the 3D warp reconstruction problem, and develop reconstruction algorithms that produce good quality images. Finally, I describe properties of the 3D warp that could be used to build efficient 3D image warpers in hardware. My technique can also compensate for rendering-system latency and network latency. I have built a real-time system that demonstrates this capability by displaying rendered images at a remote location, with low latency.
Investigating China's Disaggregated Processed Exports: Evidence that Both the RMB and Exchange Rates in Supply Chain Countries Matter

China's trade surplus is entirely in processing trade. Processed exports are final goods produced using parts and components coming from supply chain countries. Many claim that because much of the value added of China's processed exports comes from other countries, the renminbi should not affect China's processed exports. To investigate these issues, this paper disaggregates processed exports into their two main categories, processing with imported materials (PWIM) exports and processing and assembly (PAA) exports. For PWIM exports, much of the value added comes from China while for PAA exports most of the value added comes from supply chain countries. DOLS results indicate that exchange rates in supply chain countries affect both types of exports and that the renminbi significantly affects PWIM exports, but not PAA exports. These results indicate that both the renminbi and exchange rates in supply chain countries matter for processed exports.
Involvement of serine 96 in the catalytic mechanism of ferredoxin-NADP+ reductase: structure--function relationship as studied by site-directed mutagenesis and X-ray crystallography.

The crystal structure of ferredoxin-NADP+ reductase (FNR) suggests that Ser96 is directly involved in hydride transfer between the isoalloxazine moiety of FAD and the nicotinamide ring of NADP(H). To probe its role, Ser96 has been mutated to valine (S96V) and glycine (S96G). These mutations primarily affected the interaction of the nicotinamide ring with the flavin. Absorbance, fluorescence, and circular dichroism spectra and the crystal structure of FNR-S96V indicate that this mutant folds properly. FNR-S96V shows only 0.05% of wild-type activity, while the affinities for both ferredoxin and NADP+ are virtually unchanged. However, spectral perturbations induced by NADP+ binding to FNR-S96V strongly resemble those elicited by the binding of 2'-monophosphoadenosine-5'-diphosphoribose, a substrate analog lacking the nicotinamide ring, both to the mutant and wild-type enzymes. Rapid reaction studies on the valine mutant failed to detect charge-transfer intermediates during flavin reduction by NADPH. In addition, no semiquinone formation was seen during photoreduction of FNR-S96V. The three-dimensional structure of the valine mutant shows small, albeit definite, changes only in the isoalloxazine microenvironment. The glycine mutant of FNR displays behavior intermediate between that of wild-type enzyme and that of the valine mutant. It maintains ca. 2% of the wild-type activity as well as the ability to form the charge-transfer species between reduced FNR and NADP+. In photoreduction experiments, the same degree of flavin semiquinone stabilization was observed with FNR-S96G and with the wild-type enzyme. NADP+ binding to the glycine mutant was very similar to that observed in the case of the valine mutant. (ABSTRACT TRUNCATED AT 250 WORDS)
Hepatitis C Virus Impairs p53 via Persistent Overexpression of 3β-Hydroxysterol Δ24-Reductase*

Persistent infection with hepatitis C virus (HCV) induces tumorigenicity in hepatocytes. To gain insight into the mechanisms underlying this process, we generated monoclonal antibodies on a genome-wide scale against an HCV-expressing human hepatoblastoma-derived cell line, RzM6-LC, showing augmented tumorigenicity. We identified 3β-hydroxysterol Δ24-reductase (DHCR24) from this screen and showed that its expression reflected tumorigenicity. HCV induced the DHCR24 overexpression in human hepatocytes. Ectopic or HCV-induced DHCR24 overexpression resulted in resistance to oxidative stress-induced apoptosis and suppressed p53 activity. DHCR24 overexpression in these cells paralleled the increased interaction between p53 and MDM2 (also known as HDM2), a p53-specific E3 ubiquitin ligase, in the cytoplasm. Persistent DHCR24 overexpression did not alter the phosphorylation status of p53 but resulted in decreased acetylation of p53 at lysine residues 373 and 382 in the nucleus after treatment with hydrogen peroxide. Taken together, these results suggest that DHCR24 is elevated in response to HCV infection and inhibits the p53 stress response by stimulating the accumulation of the MDM2-p53 complex in the cytoplasm and by inhibiting the acetylation of p53 in the nucleus.
Human Interactive Patterns in Temporal Networks

Modern information and communication technologies provide digital traces of human interactive activities, which offer novel avenues to map and analyze temporal features of human interaction networks. This paper explores mesoscopic patterns of human interactive activities from six real-world interaction networks with temporal-topological isomorphic subgraphs, i.e., temporal motifs. We discover two dominant mutual motifs, “Star,” “Ordered-chain,” and one dominant directed motif, “Ping-Pong,” which characterize the interactive patterns of “Leader,” “Queue,” and “Feedback,” respectively. Moreover,temporal dynamics shows that bursts are universal in human mesoscopic patterns, and the evolution of three dominant temporal motifs indicates the existence of characteristic time. Finally, we analyze temporal robustness and generalization to verify that 3-event temporal motifs are a simple yet powerful tool to capture the mesoscopic patterns of human interactive activities.