Miracle-dz/UniFAR-FTUs huggingface dataset:
Stereotactic Body Radiotherapy-Induced Arterial Hypervascularity of Non-Tumorous Hepatic Parenchyma in Patients with Hepatocellular Carcinoma: Potential Pitfalls in Tumor Response Evaluation on Multiphase Computed Tomography

Purpose To evaluate temporal changes in contrast enhancement patterns of non-tumorous hepatic parenchyma with a focus on arterial hypervascularity on multiphase computed tomography (CT) in patients with hepatocellular carcinoma (HCC) treated with stereotactic body radiotherapy (SBRT). Methods We retrospectively identified 61 patients who had undergone multiphase contrast-enhanced CT at one, three, and six months after SBRT. Irradiated versus non-irradiated liver parenchyma was delineated by cross-correlation with the dose-volume histogram of SBRT plan. Serial changes in the contrast enhancement patterns of the irradiated versus non-irradiated liver parenchyma were evaluated by two abdominal radiologists in consensus. We compared the frequency of the contrast enhancement patterns according to the follow-up period using the Fisher-Freeman-Halton exact test. Results The irradiated non-tumorous hepatic parenchyma showed that the prevalence of arterial hypervascularity increased during the follow-up period (P<.01): 11.5% (7/61) in one, 45.9% (28/61) in three, and 54.1% (33/61) in six months. Contrast wash-out on the delayed phase was uncommon: 1.6% (1/61) in one, 3.3% (2/61) in three, and 0% in six months. Conclusion The incidence of arterial hypervascularity of the irradiated hepatic parenchyma gradually increased until six months after SBRT, which could interfere with the accurate evaluation of treatment response. The lack of wash-out on the delayed phase in the hypervascular area would distinguish SBRT-related change from residual/recurred HCC.
Health-e-Child : An Integrated Biomedical Platform for Grid-Based Paediatrics

There is a compelling demand for the integration and exploitation of heterogeneous biomedical information for improved clinical practice, medical research, and personalised healthcare across the EU. The Health-e-Child project aims at developing an integrated healthcare platform for European Paediatrics, providing seamless integration of traditional and emerging sources of biomedical information. The long-term goal of the project is to provide uninhibited access to universal biomedical knowledge repositories for personalised and preventive healthcare, large-scale information-based biomedical research and training, and informed policy making. The project focus will be on individualised disease prevention, screening, early diagnosis, therapy and follow-up of paediatric heart diseases, inflammatory diseases, and brain tumours. The project will build a Gridenabled European network of leading clinical centres that will share and annotate biomedical data, validate systems clinically, and diffuse clinical excellence across Europe by setting up new technologies, clinical workflows, and standards. This paper outlines the design approach being adopted in Health-e-Child to enable the delivery of an integrated biomedical information platform.
Low ectomycorrhizal inoculum potential and diversity from soils in and near ancient forests of bristlecone pine (Pinus longaeva)

Intersite variation in ectomycorrhizal (ECM) inoculum potential in soils from 16 sites located in arid subal - pine areas of the White Mountains of California was quantified. The study sites included valleys dominated by big sagebrush (Artemisia tridentata Nutt.) and mountainsides dominated by ancient Great Basin bristlecone pine (Pinus longaeva Bailey). ECM inoculum potential was not detected at three of four valley sites nor in 42% of forest soil sam- ples. Only 10 mycorrhizal species were detected in bioassays, and four of those accounted for 94.5% of all colonized seedlings, in order of decreasing abundance these were Pyronemataceae sp. , Rhizopogon sp. , Wilcoxina rehmii Yang & Korf, and Cenococcum sp. These species were identified also from in situ mycorrhizal roots. The abundance of the dominant Pyronemataceae sp. was significantly positively correlated with pH, which at all forest sites was high com- pared with typical conifer forest soils. Our results show that the ECM inoculum potential of soils is low, homogeneous, and spatially restricted in these ancient high-elevation forests.
Language input and semantic categories: a relation between cognition and early word learning

Variations in the amount and nature of early language to which children are exposed have been linked to their subsequent ability (e.g. Huttenlocher, Haight, Bryk, Seltzer & Lyons, 1991; Hart & Risley, 1995). In three computational simulations, we explore how differences in linguistic experience can explain differences in word learning ability due to changes in the development of semantic category structure. More specifically, we manipulate the amount of language input, sentential complexity, and the frequency distribution of words within categories. In each of these simulations, improvements in category structure, are tightly correlated with subsequent improvements in word learning ability even when the nature of the input remains the same over time. These simulations suggest that variation in early language environments may result in differences in lexical proficiency by altering underlying cognitive abilities like categorization.
Layered shortest path (LASH) routing in irregular system area networks

In recent years we have seen a growing interest in irregular network topologies for cluster interconnects. One problem related to such topologies is that the combination of shortest path and deadlock free routing is difficult. As a result of this the existing solutions for routing in irregular networks either guarantee shortest paths relative to some constraint (like up*/down*), or have to resort to deadlock recovery through non-minimal escape channels. In this paper we propose a method that guarantees shortest path routing and in-order delivery, and that uses virtual channels for deadlock avoidance. We present a theoretical upper bound on the number of virtual channels needed, and through extensive empirical testing we demonstrate that the actual number of virtual channels is very low even for large networks.
Editorial response: hyperlactatemia and hepatic steatosis as features of mitochondrial toxicity of nucleoside analogue reverse transcriptase inhibitors.

The long-term toxicity of highly active antiretroviral therapy (HAART), especially the development of both the lipodystrophy syndrome and hyperlipidemia, has been linked to the use of HIV protease inhibitors in most studies. However, the broad spectrum of toxicities associated with one of the other classes of drugs, the nucleoside analogue reverse transcriptase inhibitors (NRTIs), can display complications almost as serious and with more fatal outcomes. The common pathway of NRTI toxicities is induction of mitochondrial dysfunction [1, 2], because NRTIs inhibit DNA polymerase-y, an essential enzyme for the replication of mitochondrial DNA (mtDNA). Depletion of mtDNA will follow, successively leading to depletion of mtDNA-encoded proteins and to mitochondrial dysfunction. All long-term side effects of NRTIs that have been described can be attributed to this mitochondrial toxicity, and recently we hypothesized that the HAART-related lipodystrophy is induced via this mechanism as well [3].
Laser removal of foreign materials from semiconductor wafers

Removal of foreign materials formed during VLSI/ULSI processing, is one of the challenges of advanced semiconductor technology. As device geometries continue to shrink, microcontaminants such as particles, metallic contaminants, photoresists and other organic residues have an increasing impact on yield. As wafer processing becomes more aggressive and contaminants which are yield limiting become much smaller, traditional cleaning techniques based on wet-chemistry cleaning become less adequate. Only a completely dry cleaning process can overcome all the drawbacks associated with the problematic wet chemistry cleaning. A novel DUV-Excimer laser Dry removal method allows the elimination of these contaminants, in a single step process.
The Part-Of-Speech Tagging Guidelines for the Penn Chinese Treebank (3.0)

This document describes the Part-of-Speech (POS) tagging guidelines for the Penn Chinese Treebank Project. The goal of the project is the creation of a 100-thousand-word corpus of Mandarin Chinese text with syntactic bracketing. The Chinese Treebank has been released via the Linguistic Data Consortium (LDC) and is available to the public. The POS tagging guidelines have been revised several times during the two-year period of the project. The previous two versions were completed in December 1998 and March 1999, respectively. This document is the third and final version. We have added an introduction chapter in order to explain some rationale behind certain decisions in the guidelines. We also include the English gloss to the Chinese words in the guidelines. In this document, we first discuss the criteria for POS tagging and other factors that we considered when designing our POS tagset. Second, we describe each of the thirty-three POS tags in detail. Third, we provide tests to distinguish certain POS tag pairs and specify the treatment for some common collocations. Fourth, we list a number of words with each POS tag. Finally, we compare our tagset with three tagsets: the tagset for the Academia Sinica Balanced Corpus in Taiwan (CKIP, 1995), the tagset for the Grammatical Knowledge Base developed by Peking University in China (Yu et al., 1998), and the tagset for the English Penn Treebank (Santorini, 1990).
A revival of the landscape paradigm: Large scale data harvesting provides access to fitness landscapes

T he first large-scale fitness analysis of HIV in presence and absence of antiviral drugs has been presented in a recent publication [1]. This study confirms expectations, in particular ruggedness and neutrality of the HIV fitness landscape, but it provides at the same time also unexpected results like long-range correlations and surprisingly little influence of antiviral agents on the landscape structure. Here, we make use of this occasion to present a brief account on the development of the landscape concept from a pure metaphor to an experimentally assisted tool for modeling and understanding evolution. Sewall Wright [2], one of the three great scholars of population genetics conceived the idea of a fitness landscape as a metaphor for the evolutionary process: species or subspecies are occupying local fitness optima in a rugged landscape (Fig. 1). Fitness is plotted upon genotype space, which is a high-dimensional space with individual genotypes differing in the recombination pattern of genes as elements. The metaphor was introduced as a visualization of his theory of shifting balance as a model of evolution that in a nutshell may be formulated as a process in three logical steps [3, 4]: (i) Random drift leads to semi-isolated subpopulations or demes within the global population, which are losing fitness because of accidental loss of fittest genotypes known as Muller’s ratchet [5], (ii) mass selection acts on complex genetic interaction networks and raises the fitness of subpopulations, and (iii) interdemic selection raises the fitness of the global population. Environmental change shifts the adaptive peaks on the landscape and drives evolutionary dynamics. Clearly, the landscape concept is suggestive for the Wright model and facilitates its understanding. Wright’s model of evolution has been heavily criticized by Ronald Fisher and others. Apart from the practical impossibility to measure fitness in the first half of the 20th century and the apparent lack of knowledge on the nature of genes and genotypes that rendered void any attempt to quantify fitness on landscapes, Fisher’s and Wright’s views on evolution differed in many aspects. Fisher’s concept called large population size theory assumes that (i) the ecological context of evolution is large panmictic populations rather than small subpopulations, (ii) the PETER SCHUSTER
Wage-Tenure Contracts, Experience and Employment Status

The objective of this paper is to study equilibrium in a labour market with search frictions a la Burdett and Mortensen (1998). Identical firms post wage-contracts and ex-ante identical workers search for a job while unemployed and for a better one while employed. Although this situation has been analysed before, Stevens (2004) and Burdett and Coles (2003), the main novelty of this paper is to allow firms to offer contracts according to the worker's initial experience and employment status. We construct an equilibrium in which firms compete in 'promotion' contracts and offer unemployed workers longer 'probation' periods than to employed workers. An interesting feature of this equilibrium is that outside offers become more generous with experience. This generates workers cohort effects within a firm that depend on the level of experience at which they where hired. The distribution of earnings within the firm is then such that workers who have acquired more 'outside' firm experience and more tenure are higher in the earnings scale.
The Potential of Sentinel Satellites for Burnt Area Mapping and Monitoring in the Congo Basin Forests

In this study, the recently launched Sentinel-2 (S2) optical satellite and the active radar Sentinel-1 (S1) satellite supported by active fire data from the MODIS sensor were used to detect and monitor forest fires in the Congo Basin. In the context of a very strong El Nino event, an unprecedented outbreak of fires was observed during the first months of 2016 in open forests formations in the north of the Republic of Congo. The anomalies of the recent fires and meteorological situation compared to historical data show the severity of the drought. Burnt areas mapped by the S1 SAR and S2 Multi Spectral Instrument (MSI) sensors highlight that the fires occurred mainly in Marantaceae forests, characterized by open tree canopy cover and an extensive tall herbaceous layer. The maps show that the origin of the fires correlates with accessibility to the forest, suggesting an anthropogenic origin. The combined use of the two independent and fundamentally different satellite systems of S2 and S1 captured an extent of 36,000 ha of burnt areas, with each sensor compensating for the weakness (cloud perturbations for S2, and sensitivity to ground moisture for S1) of the other.
In situ high resolution transmission electron microscopy investigation of deformation mechanism in sub-10-nm Au crystals

Abstract In situ high resolution transmission electron microscopy investigations were performed on sub-10-nm Au crystals. The effects of tensile loading direction and crystal size on the deformation mechanism of Au crystals were analysed. For the Au crystals with a width below 2 nm, the surface atom diffusion with a phenomenon of layer by layer peeling is the main deformation mechanism and the tensile loading direction plays negligible effect. For the Au crystals with a width over 7 nm, the dislocations generated form surface and gliding into crystal dominate the plastic deformation and the tensile loading direction plays important role. Lomer dislocations are produced and destructed by dislocation reaction during tensile strain process in <001> oriented Au crystal. The Schmid law is the key intrinsic issue controlling the deformation mechanism for the nanowires with a size larger than 7 nm.
Applying Scheduling and Tuning to On-Line Parallel Tomography

Tomography is a popular technique to reconstruct the three-dimensional structure of an object from a series of two-dimensional projections. Tomography is resource-intensive and deployment of a parallel implementation onto Computational Grid platforms has been studied in previous work. In this work, we address on-line execution of the application where computation is performed as data is collected from an on-line instrument. The goal is to compute incremental 3-D reconstructions that provide quasi-real-time feedback to the user. We model on-line parallel tomography as a tunable application: trade-offs between resolution of the reconstruction and frequency of feedback can be used to accommodate various resource availabilities. We demonstrate that application scheduling/tuning can be framed as multiple constrained optimization problems and evaluate our methodology in simulation. Our results show that prediction of dynamic network performance is key to efficient scheduling and that tunability allows for production runs of on-line parallel tomography in Computational Grid environments.
R-PF: Enhancing Service Regularity for Legacy Scheduling Policy

We present a novel scheduling policy, regularity-aware proportional fair (R-PF) that enhances service regularity for the legacy proportional fair (PF) scheduling policy. R-PF addresses the challenge that clients may have different preferences between service regularity and long-term average throughput. R-PF allows clients to specify their own preferences, and then provides services tailored to clients' specifications. R-PF preserves the advantages of PF, including high spectrum efficiency, fairness among clients, minimal coordination between the base station and clients, and low complexity. We analytically study the performance of R-PF under an i.i. d. channel model. We prove that each client achieves its optimal tradeoff between service regularity and throughput by reporting its true preference. We also prove that the total throughput under R-PF is almost the same as that under PF. Furthermore, we compare the performance of R-PF against other state-of-the-art scheduling policies using trace-based simulations. Simulation results demonstrate that our policy provides the optimal performance for all kinds of clients with different preferences between service regularity and throughput. Simulation results also show that R-PF is backward compatible in that it enhances service regularity for clients who prefer high regularity without sacrificing the throughput for those who prefer high throughput.
sclerosis Meta-analysis of the efficacy and safety of Sativex (nabiximols), on spasticity in people with multiple

Objective: To determine the efficacy of Sativex (USAN: nabiximols) in the alleviation of spasticity in people with multiple sclerosis. Methods: The results from three randomized, placebo-controlled, double-blind parallel group studies were combined for analysis. Patients: 666 patients with multiple sclerosis and spasticity. Measures: A 0–100 mm Visual Analogue Scale (VAS, transformed to a 0–10 scale) or a 0–10 Numerical Rating Scale (0–10 NRS) was used to measure spasticity. Patients achieving a 30% improvement from baseline in their spasticity score were defined as ‘responders’. Global impression of change (GIC) at the end of treatment was also recorded. Results: The patient populations were similar. The adjusted mean change of the numerical rating scale from baseline in the treated group was 1.30 compared with 0.97 for placebo. Using a linear model, the treatment difference was 0.32 (95% CI 0.61, 0.04, p1⁄4 0.026). A statistically significant greater proportion of treated patients were responders (odds ratio (OR)1⁄4 1.62, 95% CI 1.15, 2.28; p1⁄4 0.0073) and treated patients also reported greater improvement: odds ratio 1.67 (95% CI 1.05, 2.65; p1⁄4 0.030). High numbers of subjects experienced at least one adverse event, but most were mild to moderate in severity and all drug-related serious adverse events resolved. Conclusion: The meta-analysis demonstrates that nabiximols is well tolerated and reduces spasticity.
Miniature Multileaf Collimator as an Alternative to Traditional Circular Collimators for Stereotactic Radiosurgery and Stereotactic Radiotherapy

Purpose: To evaluate the miniature multileaf collimator (MMLC) as an alternative to traditional circular collimators for radiosurgery. Materials and Methods: ‘Circular’ fields were created with the Radionics MMLC (leaf width 3.53 mm at isocenter). Beam data, including tissue maximum ratios, output factors, penumbrae and isodose distributions of these fields were measured. These were compared to the Radionics circular collimators traditionally used for radiosurgery. The MMLC data were input to the XKnife Treatment Planning System. Treatment plans were completed and evaluated using both the MMLC ‘circular’ fields and the circular collimators. Results: MMLC fields using 3, 5, 7, 9, 11, and 13 leaves on each side of the Radionics MMLC were created to approximate circular fields. The TMRs are essentially identical to those of comparable-size circular collimators. Measured at isocenter at 5-cm depth for 6 MV, the 80–20% penumbra widths are comparable to circular collimators, but are increased by as much as 1 mm at the leaf intersections (steps) where scalloping occurs. Isodose distributions were matched to those of circular collimators with comparable 50% isodose widths. Treatment plans for the MMLC ‘circular’ fields with four arcs (totaling 360Conclusions: With the MMLC simulating circular fields, dose distributions may be obtained which are essentially identical to comparable-size circular collimators. The mechanical accuracy of the MMLC is as good as that of the circular collimators, and the leakage dose is less. The diameter of ‘circular’ fields is limited by the MMLC leaf width to 1 cm and greater in increments of 7 mm. Attention needs to be paid to mechanical collisions because the MMLC is bulkier than the circular collimators.
Extension to Nonconforming Meshes of the Combined Current and Charge Integral Equation

We bring out some mathematical properties of the current and charge boundary integral equation when it is posed on a surface without geometrical singularities. This enables us to show that it is then possible to solve this equation by a boundary element method that requires no interelement continuity. In particular, this property allows the use of meshes on various parts of the surface obtained independently of each other. The extension to surfaces with geometrical singularities showed that acute dihedral angles can lead to inaccuracies in the results. We built a two-dimensional version of this equation which brought out that the wrong results are due to spurious oscillations concentrating around the singular points of the geometry. Noticing that the system linking the current and the charge is a saddle-point problem, we have tried augmenting the approximation of the charge to stabilize the numerical scheme. We show that this stabilization procedure, when coupled with a refinement of the mesh in the proximity of the geometrical singularities, obtained by a simple subdivision of the triangles, greatly reduces the effect of these instabilities.
Hierarchical Phrase-Based MT at the Charles University for the WMT 2010 Shared Task

We describe our experiments with hierarchical phrase-based machine translation for WMT 2010 Shared Task. We provide a detailed description of our configuration and data so the results are replicable. For English-to-Czech translation, we experiment with several datasets of various sizes and with various preprocessing sequences. For the other 7 translation directions, we just present the baseline results.
Improved Unsupervised POS Induction through Prototype Discovery

We present a novel fully unsupervised algorithm for POS induction from plain text, motivated by the cognitive notion of prototypes. The algorithm first identifies landmark clusters of words, serving as the cores of the induced POS categories. The rest of the words are subsequently mapped to these clusters. We utilize morphological and distributional representations computed in a fully unsupervised manner. We evaluate our algorithm on English and German, achieving the best reported results for this task.