Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation of 4D CT Image Data and Analysis of Lung Tumour Mobility during the Breathing Cycle

The mobility of lung tumours during the breathing cycle is a source of error in radiotherapy treatment planning. Spatio-temporal CT data sets can be used to measure the movement of lung tumours caused by breathing. Because modern CT scanners can only scan a limited region of the body simultaneously at different times, patients have to be scanned in segments consisting of multiple slices. For studying free breathing motion multislice CT scans can be collected simultaneously with digital spirometry over several breathing cycles. The image data set is assembled by sorting the free breathing multislice CT scans according to the couch position and the tidal volume. But artefacts can occur because there are no data segments for exactly the same tidal volume and all couch positions. In this paper, a non-linear registration method is used to interpolate and reconstruct 4D CT data sets from multislice CT scans in high quality. The non-linear registration estimates a velocity field between successive scans, which is used to reconstruct a 4D CT data set by interpolating data at user-defined tidal volumes. By this technique, artefacts can be reduced significantly. Furthermore, the reconstructed 4D CT data sets are used for studying the motion of lung tumours during the respiratory cycle. The reconstructed 4D data sets of 4 patients were used to quantify the individual lung tumour motion as well as to estimate the tumour's appearance probability during a breathing cycle.
Bovine Papillomavirus E7 Oncoprotein Inhibits Anoikis

ABSTRACT The bovine papillomavirus type 1 (BPV-1) E7 oncoprotein is required for the full transformation activity of the virus. Although BPV-1 E7 by itself is not sufficient to induce cellular transformation, it enhances the abilities of the other BPV-1 oncogenes to induce anchorage independence. We have been exploring the mechanisms by which E7 might affect the transformation efficiency of other viral oncoproteins and in particular whether it might protect cells from apoptosis. We report here that BPV-1 E6 and E7 can each independently inhibit anoikis, a type of apoptosis that is induced upon cell detachment. Using site-directed mutagenesis, we determined regions of the E7 protein that were essential for its antiapoptotic activity. The ability of E7 to inhibit anoikis did partially correlate with an ability to enhance anchorage independence of BPV-1 E6-transformed cells. In addition, the antiapoptotic activity of E7 also only partially correlated with its ability to bind p600, a cellular protein that has previously been reported to play a role in anoikis. We conclude that the contribution of E7 to BPV-induced cellular transformation may involve its ability to inhibit anoikis but that additional functional activities must also be involved.
Heavy Metal Tolerance in Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an aerobic, non-fermentative Gram-negative bacterium widespread in the environment. S. maltophilia Sm777 exhibits innate resistance to multiple antimicrobial agents. Furthermore, this bacterium tolerates high levels (0.1 to 50 mM) of various toxic metals, such as Cd, Pb, Co, Zn, Hg, Ag, selenite, tellurite and uranyl. S. maltophilia Sm777 was able to grow in the presence of 50 mM selenite and 25 mM tellurite and to reduce them to elemental selenium (Se0) and tellurium (Te0) respectively. Transmission electron microscopy and energy dispersive X-ray analysis showed cytoplasmic nanometer-sized electron-dense Se0 granules and Te0 crystals. Moreover, this bacterium can withstand up to 2 mM CdCl2 and accumulate this metal up to 4% of its biomass. The analysis of soluble thiols in response to ten different metals showed eightfold increase of the intracellular pool of cysteine only in response to cadmium. Measurements by Cd K-edge EXAFS spectroscopy indicated the formation of Cd-S clusters in strain Sm777. Cysteine is likely to be involved in Cd tolerance and in CdS-clusters formation. Our data suggest that besides high tolerance to antibiotics by efflux mechanisms, S. maltophilia Sm777 has developed at least two different mechanisms to overcome metal toxicity, reduction of oxyanions to non-toxic elemental ions and detoxification of Cd into CdS.
Corotated SPH for Deformable Solids

Smoothed Particle Hydrodynamics (SPH) is a powerful technique for the animation of natural phenomena. While early SPH approaches in Computer Graphics have mainly been concerned with liquids or gases, recent research also focuses on the dynamics of deformable solids using SPH. In this paper, we present a novel corotational SPH formulation for deformable solids. The rigid body modes are extracted from the deformation field which allows to use a linear strain tensor. In contrast to previous rotationally invariant meshless approaches, we show examples using coplanar and collinear particle data sets. The presented approach further allows for a unified meshfree representation of deformable solids and fluids. This enables the animation of sophisticated phenomena, such as phase transitions. The versatility and the efficiency of the presented SPH scheme for deformable solids is illustrated in various experiments.
KronoMiner: using multi-foci navigation for the visual exploration of time-series data

The need for pattern discovery in long time-series data led researchers to develop interactive visualization tools and analytical algorithms for gaining insight into the data. Most of the literature on time-series data visualization either focus on a small number of tasks or a specific domain. We propose KronoMiner, a tool that embeds new interaction and visualization techniques as well as analytical capabilities for the visual exploration of time-series data. The interface's design has been iteratively refined based on feedback from expert users. Qualitative evaluation with an expert user not involved in the design process indicates that our prototype is promising for further research.
PRD125, a Potent and Selective Inhibitor of Sterol O-Acyltransferase 2 Markedly Reduces Hepatic Cholesteryl Ester Accumulation and Improves Liver Function in Lysosomal Acid Lipase-Deficient Mice

In most organs, the bulk of cholesterol is unesterified, although nearly all possess a varying capability of esterifying cholesterol through the action of either sterol O-acyltransferase (SOAT) 1 or, in the case of hepatocytes and enterocytes, SOAT2. Esterified cholesterol (EC) carried in plasma lipoproteins is hydrolyzed by lysosomal acid lipase (LAL) when they are cleared from the circulation. Loss-of-function mutations in LIPA, the gene that encodes LAL, result in Wolman disease or cholesteryl ester storage disease (CESD). Hepatomegaly and a massive increase in tissue EC levels are hallmark features of both disorders. While these conditions can be corrected with enzyme replacement therapy, the question arose as to whether pharmacological inhibition of SOAT2 might reduce tissue EC accretion in CESD. When weaned at 21 days, Lal−/− mice, of either gender, had a whole liver cholesterol content that was 12- to 13-fold more than that of matching Lal+/+ littermates (23 versus 1.8 mg, respectively). In Lal−/− males given the selective SOAT2 inhibitor PRD125 1,11-O-o-methylbenzylidene-7-O-p-cyanobenzoyl-1,7,11-trideacetylpyripyropene A in their diet (∼10 mg/day per kg body weight) from 21 to 53 days, whole liver cholesterol content was 48.6 versus 153.7 mg in untreated 53-day-old Lal−/− mice. This difference reflected a 59% reduction in hepatic EC concentration (mg/g), combined with a 28% fall in liver mass. The treated mice also showed a 63% reduction in plasma alanine aminotransferase activity, in parallel with decisive falls in hepatic mRNA expression levels for multiple proteins that reflect macrophage presence and inflammation. These data implicate SOAT2 as a potential target in CESD management.
Construction of multiple-rate quasi-cyclic LDPC codes via the hyperplane decomposing

This paper presents an approach to the construction of multiple-rate quasi-cyclic low-density parity-check (LDPC) codes. Parity-check matrices of the proposed codes consist of q X q square submatrices. The block rows and block columns of the parity-check matrix correspond to the hyperplanes (μ-flats) and points in Euclidean geometries, respectively. By decomposing the μ -flats, we obtain LDPC codes of different code rates and a constant code length. The code performance is investigated in term of the bit error rate and compared with those of LDPC codes given in IEEE standards. Simulation results show that our codes perform very well and have low error floors over the additive white Gaussian noise channel.
Normalizing traffic pattern with anonymity for mission critical applications

Intruders often want to analyze traffic pattern to get information for his some malicious activities in ultra-secure network. This work presents a general approach to prevent traffic pattern of IP-based network from being analyzed. It is an isolated scheme which can be used to prevent traffic analysis in overall network by achieving the same goal in each network segment independently. On each network segment, complementary traffic is generated according to its real traffic, and the combination of these two kinds of traffic constitutes the normalized traffic on each link. Main advantages of our approach are, from the performance viewpoint, 1) complementary traffic does not compete on the bandwidth with real traffic actively, and 2) complementary traffic does not consume the bandwidth of other network segment at all. In addition, by encrypting source and destination IP addresses of each packet, anonymous communication can be achieved and anonymous normalized traffic loses its value for the analysis of eavesdropped traffic by intruders.
Evaluation of variants of the SGM algorithm aimed at implementation on embedded or reconfigurable devices

Inferring dense depth from stereo is crucial for several computer vision applications and stereo cameras based on embedded systems and/or reconfigurable devices such as FPGA became quite popular in the past years. In this field Semi Global Matching (SGM) is, in most cases, the preferred algorithm due to its good trade-off between accuracy and computation requirements. Nevertheless, a careful design of the processing pipeline enables significant improvements in terms of disparity map accuracy, hardware resources and frame rate. In particular factors like the amount of matching costs and parameters, such as the number/selection of scanlines, and so on have a great impact on the overall resource requirements. In this paper we evaluate different variants of the SGM algorithm suited for implementation on embedded or reconfigurable devices looking for the best compromise in terms of resource requirements, accuracy of the disparity estimation and running time. To assess quantitatively the effectiveness of the considered variants we adopt the KITTI 2015 training dataset, a challenging and standard benchmark with ground truth containing several realistic scenes.
Unifying Nuclear Norm and Bilinear Factorization Approaches for Low-Rank Matrix Decomposition

Low rank models have been widely used for the representation of shape, appearance or motion in computer vision problems. Traditional approaches to fit low rank models make use of an explicit bilinear factorization. These approaches benefit from fast numerical methods for optimization and easy kernelization. However, they suffer from serious local minima problems depending on the loss function and the amount/type of missing data. Recently, these low-rank models have alternatively been formulated as convex problems using the nuclear norm regularizer, unlike factorization methods, their numerical solvers are slow and it is unclear how to kernelize them or to impose a rank a priori. This paper proposes a unified approach to bilinear factorization and nuclear norm regularization, that inherits the benefits of both. We analyze the conditions under which these approaches are equivalent. Moreover, based on this analysis, we propose a new optimization algorithm and a "rank continuation'' strategy that outperform state-of-the-art approaches for Robust PCA, Structure from Motion and Photometric Stereo with outliers and missing data.
Is All “Communicating” Hydrocephalus Really Communicating? Prospective Study on the Value of 3D-Constructive Interference in Steady State Sequence at 3T

BACKGROUND AND PURPOSE: 3D-constructive interference in steady state (3D-CISS) sequence has been used to assess the CSF pathways. The aim of this study was to investigate the additive value of 3D-CISS compared with conventional sequences in the diagnosis of obstructive membranes in hydrocephalus. MATERIALS AND METHODS: A total of 134 patients with hydrocephalus underwent MR imaging examination with a 3T unit consisting of turbo spin-echo, 3D-CISS, and cine phase-contrast (cine PC) sequences. 3D-CISS was used to assess obstructive membranes in CSF pathways compared with other sequences. Cine PC, follow-up imaging, and surgical findings were used to confirm obstructive membranes. RESULTS: Comparing the number of noncommunicating cases by using the conventional and 3D-CISS images, we found 26 new cases (19.4%) of 134 cases that were previously misdiagnosed as communicating hydrocephalus by conventional images. 3D-CISS sequence identified obstructive membranes invisible in other sequences, which facilitated selection of neuroendoscopy in the treatment of 31 patients (23.1%) in total who would have been otherwise treated with shunt insertion. These patients included 26 newly diagnosed noncommunicating cases after demonstration of intraventricular and/or fourth ventricular outlet membranes and 5 cases of communicating hydrocephalus with obstructing cisternal membranes. There were obstructions of the foramina of Luschka in 22 of 26 newly found noncommunicating cases. CONCLUSIONS: Conventional sequences are insensitive to obstructive membranes in CSF pathways, especially in the fourth ventricular exit foramina and the basal cisterns. 3D-CISS sequence, revealing these obstructive membranes, can alter patient treatment and prognosis.
Fast shadows and lighting effects using texture mapping

Generating images of texture mapped geometry requires projecting surfaces onto a two-dimensional screen. If this projection involves perspective, then a division must be performed at each pixel of the projected surface in order to correctly calculate texture map coordinates. We show how a simple extension to perspective-comect texture mapping can be used to create various lighting effects, These in- clude arbitrary projection of two-dimensional images onto geom- etry, realistic spotlights, and generation of shadows using shadow maps( 10). These effects are obtained in real time using hardware that performs correct texture mapping.
A radio-frequency reconfigurable CMOS-GaN class-E Chireix power amplifier

A new load-insensitive class-E power amplifier mode is presented that that enables frequency reconfigurability by statically changing the switch duty-cycle without compromising its tuned efficiency performance. The technique is tested on a prototype CMOS-GaN class-E Chireix power amplifier designed for 1.8-2.2 GHz. The drain efficiency is more than 55% at 8dB back-off and more than 60% at 6dB back-off across the band by reconfiguring the duty-cycle at each frequency via the pulse-width controlled CMOS drivers.
Axonal Targeting of Trk Receptors via Transcytosis Regulates Sensitivity to Neurotrophin Responses

Axonal targeting of trophic receptors is critical for neuronal responses to extracellular developmental cues, yet the underlying trafficking mechanisms remain unclear. Here, we report that tropomyosin-related kinase (Trk) receptors for target-derived neurotrophins are anterogradely trafficked to axons via transcytosis in sympathetic neurons. Using compartmentalized cultures, we show that mature receptors on neuronal soma surfaces are endocytosed and remobilized via Rab11-positive recycling endosomes into axons. Inhibition of dynamin-dependent endocytosis disrupted anterograde transport and localization of TrkA receptors in axons. Anterograde TrkA delivery and exocytosis into axon growth cones is enhanced by nerve growth factor (NGF), acting locally on distal axons. Perturbing endocytic recycling attenuated NGF-dependent signaling and axon growth while enhancing recycling conferred increased neuronal sensitivity to NGF. Our results reveal regulated transcytosis as an unexpected mode of Trk trafficking that serves to rapidly mobilize ready-synthesized receptors to growth cones, thus providing a positive feedback mechanism by which limiting concentrations of target-derived neurotrophins enhance neuronal sensitivity.
Panel-Data Estimates of the Production Function and the Revenue Function: What Difference Does it Make?

The lack of individual firm information on output prices is a major problem in the econometrics of production. In particular, it may be expected to account for a significant share of the large discrepancies found between the cross-sectional and time-series estimates of capital and scale elasticities. However, taking advantage of two panel-data samples for which we had such information, we find that estimating the revenue function (using a nominal output measure) or the production function proper (using a real output measure) makes very little difference for our results. The biases due to other sources of specification errors are probably more important.
Clustering and Classifying Person Names by Origin

In natural language processing, information about a person's geographical origin is an important feature for name entity transliteration and question answering. We propose a language-independent name origin clustering and classification framework. Provided with a small amount of bilingual name translation pairs with labeled origins, we measure origin similarities based on the perplexities of name character language and translation models. We group similar origins into clusters, then train a Bayesian classifier with different features. It achieves 84% classification accuracy with source names only, and 91% with both source and target name pairs. We apply the origin clustering and classification technique to a name transliteration task. The cluster-specific transliteration model dramatically improves the transliteration accuracy from 3.8% to 55%, reducing the transliteration character error rate from 50.3 to 13.5. Adding more unlabeled name pairs to the cluster-specific name transliteration model further improves the transliteration accuracy.
Efficient Parallel Subgraph Counting Using G-Tries

Finding and counting the occurrences of a collection of subgraphs within another larger network is a computationally hard problem, closely related to graph isomorphism. The subgraph count is by itself a very powerful characterization of a network and it is crucial for other important network measurements. G-tries are a specialized data-structure designed to store and search for subgraphs. By taking advantage of subgraph common substructure, g-tries can provide considerable speedups over previously used methods. In this paper we present a parallel algorithm based precisely on g-tries that is able to efficiently find and count subgraphs. The algorithm relies on randomized receiver-initiated dynamic load balancing and is able to stop its computation at any given time, efficiently store its search position, divide what is left to compute in two halfs, and resume from where it left. We apply our algorithm to several representative real complex networks from various domains and examine its scalability. We obtain an almost linear speedup up to 128 processors, thus allowing us to reach previously unfeasible limits. We showcase the multidisciplinary potential of the algorithm by also applying it to network motif discovery.
Transcriptome response of Lolium arundinaceum to its fungal endophyte Epichloë coenophiala.

Tall fescue (Lolium arundinaceum) is one of the primary forage and turf grasses in temperate regions of the world. A number of favourable characteristics of tall fescue are enhanced by its seed-transmissible fungal symbiont (endophyte) Epichloë coenophiala. Our approach was to assemble the tall fescue transcriptome, then identify differentially expressed genes (DEGs) for endophyte-symbiotic (E+) vs endophyte-free (E-) clones in leaf blades, pseudostems, crowns and roots. RNA-seq reads were used to construct a tall fescue reference transcriptome and compare gene expression profiles. Over all tissues examined, 478 DEGs were identified between the E+ and E- clones for at least one tissue (more than two-fold; P < 0.0001, 238 E+ > E- and 240 E- > E+), although no genes were differentially expressed in all four tissues. Gene ontology (GO) terms, GO:0010200 (response to chitin), GO:0002679 (respiratory burst during defence response) and GO:0035556 (intracellular signal transduction) were significantly overrepresented among 25 E- > E+ DEGs in leaf blade, and a number of other DEGs were associated with defence and abiotic response. In particular, endophyte effects on various WRKY transcription factors may have implications for symbiotic stability, endophyte distribution in the plant, or defence against pathogens.
Modeling of Human Prokineticin Receptors: Interactions with Novel Small-Molecule Binders and Potential Off-Target Drugs

Background and Motivation The Prokineticin receptor (PKR) 1 and 2 subtypes are novel members of family A GPCRs, which exhibit an unusually high degree of sequence similarity. Prokineticins (PKs), their cognate ligands, are small secreted proteins of ∼80 amino acids; however, non-peptidic low-molecular weight antagonists have also been identified. PKs and their receptors play important roles under various physiological conditions such as maintaining circadian rhythm and pain perception, as well as regulating angiogenesis and modulating immunity. Identifying binding sites for known antagonists and for additional potential binders will facilitate studying and regulating these novel receptors. Blocking PKRs may serve as a therapeutic tool for various diseases, including acute pain, inflammation and cancer. Methods and Results Ligand-based pharmacophore models were derived from known antagonists, and virtual screening performed on the DrugBank dataset identified potential human PKR (hPKR) ligands with novel scaffolds. Interestingly, these included several HIV protease inhibitors for which endothelial cell dysfunction is a documented side effect. Our results suggest that the side effects might be due to inhibition of the PKR signaling pathway. Docking of known binders to a 3D homology model of hPKR1 is in agreement with the well-established canonical TM-bundle binding site of family A GPCRs. Furthermore, the docking results highlight residues that may form specific contacts with the ligands. These contacts provide structural explanation for the importance of several chemical features that were obtained from the structure-activity analysis of known binders. With the exception of a single loop residue that might be perused in the future for obtaining subtype-specific regulation, the results suggest an identical TM-bundle binding site for hPKR1 and hPKR2. In addition, analysis of the intracellular regions highlights variable regions that may provide subtype specificity.