Miracle-dz/UniFAR-FTUs huggingface dataset:
On the lower envelope of bivariate functions and its applications

We consider the problem of obtaining sharp (nearly quadratic) bounds for the combinatorial complexity of the lower envelope (i.e. pointwise minimum) of a collection of n bivariate (or generally multi-variate) continuous and "simple" functions, and of designing efficient algorithms for the calculation of this envelope. This problem generalizes the well-studied univariate case (whose analysis is based on the theory of Davenport-Schinzel sequences), but appears to be much more difficult and still largely unsolved. It is a central problem that arises in many areas in computational and combinatorial geometry, and has numerous applications including generalized planar Voronoi diagrams, hidden surface elimination for intersecting surfaces, purely translational motion planning, finding common transversals of polyhedra, and more. In this abstract we provide several partial solutions and generalizations of this problem, and apply them to the problems mentioned above. The most significant of our results is that the lower envelope of n triangles in three dimensions has combinatorial complexity at most O(n2α(n)) (where α(n) is the extremely slowly growing inverse of Ackermann's function), that this bound is tight in the worst case, and that this envelope can be calculated in time O(n2α(n)).
CFBDS J005910.90-011401.3: Reaching the T-Y Brown Dwarf transition?

the date of receipt and acceptance should be inserted later Abstract. We report the discovery of CFBDS J005910.90-011401.3 (hereafter CFBDS0059), the coolest brown dwarf iden- tified to date. We found CFBDS0059 using iand zimages from the Canada-France-Hawaii Telescope (CFHT), and present optical and near-infrared photometry, Keck laser guide sta r adaptive optics imaging, and a complete near-infrared spe ctrum, from 1.0 to 2.2� m. A side to side comparison of the near-infrared spectra of CFBDS0059 and ULAS J003402.77-005206.7 (hereafter ULAS0034), previously the coolest known brown dwarf, indicates that CFBDS0059 is∼ 50 ± 15K cooler. We estimate a temperature of Teff∼ 620K and gravity of log g∼ 4.75. Evolutionary models translate these parameters into an age of 1-5 Gyr and a mass of 15− 30 MJup. We estimate a photometric distance of∼13pc, which puts CFBDS0059 within easy reach of accurate parallax measurements. Its large proper m otion suggests membership in the older population of the thin disk. The spectra of both CFBDS0059 and ULAS J0034 shows probable absorption by a wide ammonia band on the blue side of the H-band flux peak. If, as we expect, that feature deepens furthe r for still lower effective temperatures, its appearance will become a natural breakpoint for the transition between the T spectr al class and the new Y spectral type. CFBDS0059 and ULAS J0034 would then be the first Y0 dwarfs.
Genetic variability of Schistosoma bovis cercarial production according to miracidial dose

ABSTRACT Cercarial production related to miracidial dose variation with Schistosoma bovis strains from Sudan and Spain in Bulinus truncatus from Tunisia was studied. Results showed that an increase in the miracidial dose proposed to the host-mollusc (1 and 5 miracidia) gave rise to a decrease in cercarial productivity of Sudanese S. bovis and to an increase for Spanish s. bovis. It is concluded that this response difference tothe miracidial dose variation depends on genetic characters peculiar to the parasite strain and represents a new aspect of genetic variability of schistosome populations.
Repurposing Drugs in Oncology (ReDO)—mebendazole as an anti-cancer agent

Mebendazole, a well-known anti-helminthic drug in wide clinical use, has anti-cancer properties that have been elucidated in a broad range of pre-clinical studies across a number of different cancer types. Significantly, there are also two case reports of anti-cancer activity in humans. The data are summarised and discussed in relation to suggested mechanisms of action. Based on the evidence presented, it is proposed that mebendazole would synergise with a range of other drugs, including existing chemotherapeutics, and that further exploration of the potential of mebendazole as an anti-cancer therapeutic is warranted. A number of possible combinations with other drugs are discussed in the Appendix.
Logical aspects of rates of convergence in metric spaces

Abstract In this paper we develop a method for finding, under general conditions, explicit and highly uniform rates of convergence for the Picard iteration sequences for selfmaps on bounded metric spaces from ineffective proofs of convergence to a unique fixed point. We are able to extract full rates of convergence by extending the use of a logical metatheorem recently proved by Kohlenbach. In recent case studies we were able to find such explicit rates of convergence in two concrete cases. Our novel method now provides an explanation in logical terms for these findings. This amounts, loosely speaking, to general conditions under which we in this specific setting can transform a ∀∃∀-sentence into a ∀∃-sentence via an argument involving product spaces. This reduction in logical complexity allows us to use the existing machinery to extract quantitative bounds of the sort we need.
Simultaneous generation of fra‐2 conditional and fra‐2 knock‐out mice

Loss of function mouse models comprise knock‐out mice, where a gene is deleted in the germline, and conditional knock‐out mice with somatic deletion of a floxed allele in defined tissues. Both types of mice are used for comprehensive studies of gene functions in vivo. Here, we describe a simple method for simultaneous generation of mice with conditional or knock‐out alleles for the transcription factor fra‐2 (Fos‐related antigen 2) using a single embryonic stem (ES) cell clone. ES cells with a floxed fra‐2 allele were transiently transfected with a Cre‐recombinase expression plasmid and plated at low density. Most of the resulting ES cell colonies consisted of a mixture of cells that have either retained or lost the conditional allele. We demonstrate that these mixed ES cell clones can be directly used for generation of chimeras that give rise to offspring with conditional or knock‐out alleles simultaneously. This strategy shortens the time and reduces the number of germline transmission events to generate genetically modified mice. genesis 45:447–451, 2007. © 2007 Wiley‐Liss, Inc.
Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo

Hox transcription factors control many aspects of animal morphogenetic diversity. The segmental pattern of Drosophila larval muscles shows stereotyped variations along the anteroposterior body axis. Each muscle is seeded by a founder cell and the properties specific to each muscle reflect the expression by each founder cell of a specific combination of ‘identity’ transcription factors. Founder cells originate from asymmetric division of progenitor cells specified at fixed positions. Using the dorsal DA3 muscle lineage as a paradigm, we show here that Hox proteins play a decisive role in establishing the pattern of Drosophila muscles by controlling the expression of identity transcription factors, such as Nautilus and Collier (Col), at the progenitor stage. High-resolution analysis, using newly designed intron-containing reporter genes to detect primary transcripts, shows that the progenitor stage is the key step at which segment-specific information carried by Hox proteins is superimposed on intrasegmental positional information. Differential control of col transcription by the Antennapedia and Ultrabithorax/Abdominal-A paralogs is mediated by separate cis-regulatory modules (CRMs). Hox proteins also control the segment-specific number of myoblasts allocated to the DA3 muscle. We conclude that Hox proteins both regulate and contribute to the combinatorial code of transcription factors that specify muscle identity and act at several steps during the muscle-specification process to generate muscle diversity.
Voxel-Based Analysis of Gray Matter and CSF Space in Idiopathic Normal Pressure Hydrocephalus

Aims: To investigate regional morphologic changes in idiopathic normal pressure hydrocephalus (INPH) based on diagnosis with INPH Guidelines using voxel-based morphometry. Method: Three-dimensional magnetic resonance imaging was performed in 34 INPH patients, who met probable INPH criteria, probable 34 Alzheimer disease patients, and 34 normal control subjects. Results: Statistical parametric mapping was used to conduct voxel-based morphometry analysis of the morphologic data and revealed enlarged ventricles and sylvian fissures and stenotic sulci of high convexity, especially in the precuneus in the INPH group, with decreased gray matter density in the insula, caudate and thalamus. Conclusion: In INPH, morphologic change occurs in the frontoparietal high convexity with ventricular dilatations, dilated sylvian fissures and tight sulci in the medial parietal lobes.
SerbGO: searching for the best GO tool

In recent years, the scientific community has provided many tools to assist with pathway analysis. Some of these programs can be used to manage functional annotation of gene products, others are oriented to exploring and analyzing data sets and many allow both possibilities. Potential users of these tools are faced with the necessity to decide which of the existing programs are the most appropriate for their needs. SerbGO is a user-friendly web tool created to facilitate this task. It can be used (i) to search for specific functionalities and determine which applications provide them and (ii) to compare several applications on the basis of different types of functionalities. Iterating and combining both functionalities can easily lead to selecting an appropriate tool. Data required by SerbGO is either the desired capabilities within a defined Standard Functionalities Set or the list of the tools to be compared. The analysis performed carries out a cross-classification that produces an easily readable output with the list of tools that implement the capabilities demanded or a table with the categorization of the GO tools that one wishes to compare. SerbGO is freely available and does not require a login. It can be accessed either directly at our server (http://estbioinfo.stat.ub.es/apli/serbgo) or at the GO Consortium website (http://www.geneontology.org/GO.tools.microarray.shtml#serbgo).
Determining the convergence of variance in Gaussian belief propagation via semi-definite programming

In order to compute the marginal distribution from a high dimensional distribution with loopy Gaussian belief propagation (BP), it is important to determine whether Gaussian BP would converge. In general, the convergence condition for Gaussian BP variance and mean are not necessarily the same, and this paper focuses on the convergence condition of Gaussian BP variance. In particular, by describing the message-passing process of Gaussian BP as a set of updating functions, the necessary and sufficient convergence condition of Gaussian BP variance is derived, with the converged variance proved to be independent of the initialization as long as it is greater or equal to zero. It is further proved that the convergence condition can be verified efficiently by solving a semi-definite programming (SDP) optimization problem. Numerical examples are presented to corroborate the established theories.
paraganglioma: relation to adverse tumor phenotype and predisposing mutation

Recurrent alterations in promoter methylation of tumor suppressor genes (TSGs) and LINE1 (L1RE1) repeat elements were previously reported in pheochromocytoma and abdominal paraganglioma. This study was undertaken to explore CpG methylation abnormalities in an extended tumor panel and assess possible relationships between metastatic disease and mutation status. CpG methylation was quantified by bisulfite pyrosequencing for selected TSG promoters and LINE1 repeats. Methylation indices above normal reference were observed for DCR2 (TNFRSF10D), CDH1, P16 (CDKN2A), RARB, and RASSF1A. Z-scores for overall TSG, and individual TSG methylation levels, but not LINE1, were significantly correlated with metastatic disease, paraganglioma, disease predisposition, or outcome. Most strikingly, P16 hypermethylation was strongly associated with SDHB mutation as opposed to RET/MEN2, VHL/VHL, or NF1-related disease. Parallel analyses of constitutional, tumor, and metastasis DNA implicate an order of events where constitutional SDHB mutations are followed by TSG hypermethylation and 1p loss in primary tumors, later transferred to metastatic tissue. In the combined material, P16 hypermethylation was prevalent in SDHB-mutated samples and was associated with short disease-related survival. The findings verify the previously reported importance of P16 and other TSG hypermethylation in an independent tumor series. Furthermore, a constitutional SDHB mutation is proposed to predispose for an epigenetic tumor phenotype occurring before the emanation of clinically recognized malignancy.
Cardiorespiratory Fitness and Digestive Cancer Mortality: Findings from the Aerobics Center Longitudinal Study

Although higher levels of physical activity are inversely associated with risk of colon cancer, few prospective studies have evaluated overall digestive system cancer mortality in relation to cardiorespiratory fitness (CRF). The authors examined this association among 38,801 men ages 20 to 88 years who performed a maximal treadmill exercise test at baseline in the Aerobics Center Longitudinal Study (Dallas, TX) during 1974 to 2003. Mortality was assessed over 29 years of follow-up (1974-2003). Two hundred eighty-three digestive system cancer deaths occurred during a mean 17 years of observation. Age-adjusted mortality rates per 10,000 person-years according to low, moderate, and high CRF groups were 6.8, 4.0, and 3.3 for digestive system cancer (Ptrend < 0.001). After adjustment for age, examination year, body mass index, smoking, drinking, family history of cancer, personal history of diabetes, hazard ratios (95% confidence intervals) for overall digestive cancer deaths for those in the middle and upper 40% of the distribution of CRF relative to those in the lowest 20% were 0.66 (0.49-0.88) and 0.56 (0.40-0.80), respectively. Being fit (the upper 80% of CRF) was associated with a lower risk of mortality from colon [0.61 (0.37-1.00)], colorectal [0.58 (0.37-0.92)], and liver cancer [0.28 (0.11-0.72)] compared with being unfit (the lowest 20% of CRF). These findings support a protective role of CRF against total digestive tract, colorectal, and liver cancer deaths in men. (Cancer Epidemiol Biomarkers Prev 2009;18(4):1111–7)
Investcoin: A System for Privacy-Preserving Investments

This work presents a new framework for Privacy-Preserving Investment systems in a distributed model. In this model, independent investors can transfer funds to independent projects, in the same way as it works on crowdfunding platforms. The framework protects the investors' single payments from being detected (by any other party), only the sums of each investor's payments are revealed. Likewise, the projects' single incoming payments are concealed and only the final sums of the incoming payments for every project are revealed. In this way, no other party than the investor (not even the system administration) can detect how much she paid to any single project. Though it is still possible to confidentially exchange any part of an investment between any pair of investors, such that market liquidity is unaffected by the system. On top, our framework allows a privacy-preserving return of a multiple of all the held investments (e.g. interest payments or dividends) to the indivdual investors while still revealing nothing else than the sum of all returns for every investor. We provide reasonable security guarantees for this framework that are based on common notions from the Secure Multi-Party Computation literature. As instantiation for this framework we present Investcoin. It is a proper combination of three cryptographic protocols, namely a Private Stream Aggregation scheme, a Commitment scheme and a Range test and it is usable in connection with any existing currency. The security of these protocols is based on the DDH assumption. By a composition theorem from the SMPC literature, the security of the resulting Investcoin protocol is also based on the DDH assumption. Furthermore, we provide a simple decentralised key generation protocol for Investcoin supporting dynamic join/leave and fault-tolarance of investors and moreover achieves some security guarantees against malicious investors.
Sentiment Analysis: A tool for Rating Attribution to Content in Recommender Systems

Collaborative filtering techniques are commonly used in social networking environ- ments for proposing user connections or interesting shared resources. While metrics based on ac- cess patterns and user behavior produce interesting results, they do not take into account qualitative information, i.e. the actual opinion of a user that used the resource and whether or not he would propose it for use to other users. This is of particular importance on educational repositories, where the users present significant deviations in goals, needs, interests and expertise level. In this paper, we propose the introduction of sentiment analysis techniques on user comments regarding an edu- cational resource in order to extract the opinion of a user for the quality of the latter and take into account its quality as perceived by the community before proposing the resource to another user.
Feature subset selection for support vector machines through discriminative function pruning analysis

In many pattern classification applications, data are represented by high dimensional feature vectors, which induce high computational cost and reduce classification speed in the context of support vector machines (SVMs). To reduce the dimensionality of pattern representation, we develop a discriminative function pruning analysis (DFPA) feature subset selection method in the present study. The basic idea of the DFPA method is to learn the SVM discriminative function from training data using all input variables available first, and then to select feature subset through pruning analysis. In the present study, the pruning is implement using a forward selection procedure combined with a linear least square estimation algorithm, taking advantage of linear-in-the-parameter structure of the SVM discriminative function. The strength of the DFPA method is that it combines good characters of both filter and wrapper methods. Firstly, it retains the simplicity of the filter method avoiding training of a large number of SVM classifier. Secondly, it inherits the good performance of the wrapper method by taking the SVM classification algorithm into account.
The effect of sulfinpyrazone on platelet economy and thrombus formation in rabbits.

Platelet survival was prolonged in rabbits which had been on sulfinpyrazone for 30 days or more. This was not accompanied by changes in tests of blood coagulation in vitro. Thrombus formation in flowing blood was on the average less, but not significantly so. The mechanism of the change in platelet economy is unknown. It does not appear to depend on blood coagulation and cannot be explained by serum uric acid which does not occur in the rabbit. It may be attributable to changes in the platelet membrane which may also account for the increase in serotonin uptake.
Morphological characterization of Recherchefjorden (Bellsund, Svalbard) using marine geomorphometry

Geomorphological research based on geomorphological mapping seeks to identify the origins and age of forms as well as to describe the process that created or transformed a particular form. One of the most important aspects of this study is the morphometry and morphology of the landscape. This also applies to the submarine areas, and issues related to marine geomorphometry. Bathymetric data used in this study were obtained from the measurements of the Norwegian Hydrographic Service and measurements conducted by the authors. Its main goal was: to determine the bathymetry of the Recherchefjorden (Bellsund, Svalbard), establish morphometric parameters for the analysis of the morphology of the bottom. The boundaries of zones, related to the specific character of bottom geomorphology linked with geological structure, tectonics and, in particular, the impact of glacial system, was delineated. The sets of landforms (areas) were distinguished based on the morphometric analysis resulting from the determined parameters: slopes, its aspects, curvatures and Bathymetric Position Index. Basically, this areas are concentrated in two zones: the main Recherchefjorden and its surroundings. The delimitation also takes into account the origins and location of theme in relation to the glacial systems. On this basis, moraine areas were distinguished. They are linked with the Holocene advances of two glaciers, Renardbeen and Recherchebreen, mainly during the Little Ice Age. They constitute boundary zones between areas with different morphometric parameters: outer fjord and inner fjord. Moreover, taking into account geology and terrestrial geomorphology it was possible to describe paraglacial processes in this area.
Region Adaptive Unsharp Masking based DCT Interpolation for Efficient Video Intra Frame Up-Sampling

Most of the existing interpolation techniques available in the literature produce a blurring effect while converting a low resolution video to its high resolution counterpart. The blurring results in the loss of fine details and critical edge information of a video intra frame. In order to resolve this problem, an efficient, no reference, hybrid interpolation technique is proposed here. The proposed method makes use of a combination of anticipatory, spatial domain, region adaptive unsharp masking operation with the discrete cosine transform (DCT) based interpolation technique for retaining some of the fine details and critical edge information in the reconstructed video frame. The region adaptive unsharp masking is a preprocessing step which sharpens the intra frame regions locally as per their statistical local variance so as to compensate the blurring caused by the subsequent DCT based interpolation technique. The degree of sharpening is proportionately increased if the local variance is greater than the global variance on the contrary the sharpening will be proportionately reduced, if the local variance is less than the global threshold value. Experimental results reveal that the proposed method outperforms most of the existing interpolation techniques in terms of peak-signal-to-noise-ratio (PSNR) as well as visual quality for different types of video sequences. General Terms Video restoration, video resizing, interpolation.
Grand Challenge: Understanding Survival Paradoxes in Epidemiology

Survival paradoxes are commonly observed in the literature. This phenomenon describes the association of certain risk factors with negative outcomes in the general population and the opposite effect in certain subpopu-lations and vice versa. Overall, the field is poorly understood. The counter-intuitive findings reported in the literature have contributed to confusion among clinicians regarding the appropriate treatment of conventional risk factors in patients with chronic diseases. Below we review two such paradoxes in kidney and cardiovascular disease epidemiology and discuss possible explanations of these findings.