Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of Cancer-Associated Genes via Epigenetic Derepression Mechanisms in Gynecologic Cancer

Like other cancers, most gynecologic cancers are caused by aberrant expression of cancer-related genes. Epigenetics is one of the most important gene expression mechanisms, which contribute to cancer development and progression by regulating cancer-related genes. Since the discovery of differential gene expression patterns in cancer cells when compared with normal cells, extensive efforts have been made to explore the origins of abnormal gene expression in cancer. Epigenetics, the study of inheritable changes in gene expression that do not alter DNA sequence is a key area of this research. DNA methylation and histone modification are well-known epigenetic mechanisms, while microRNAs and alternative splicing have recently been identified as important regulators of epigenetic mechanisms. These mechanisms not only affect specific target gene expression but also regulate the functioning of other epigenetic mechanisms. Moreover, these diverse epigenetic regulations occur simultaneously. Epigenetic regulation of gene expression is extraordinarily complicated and all epigenetic mechanisms to be studied at once to determine the exact gene regulation mechanisms. Traditionally, the contribution of epigenetics to cancer is thought to be mediated through the inactivation of tumor suppressor genes expression. But recently, it is arising that some oncogenes or cancer-promoting genes (CPGs) are overexpressed in diverse type of cancers through epigenetic derepression mechanism, such as DNA and histone demethylation. Epigenetic derepression arises from diverse epigenetic changes, and all of these mechanisms actively interact with each other to increase oncogenes or CPGs expression in cancer cell. Oncogenes or CPGs overexpressed through epigenetic derepression can initiate cancer development, and accumulation of these abnormal epigenetic changes makes cancer more aggressive and treatment resistance. This review discusses epigenetic mechanisms involved in the overexpression of oncogenes or CPGs via epigenetic derepression in gynecologic cancers. Therefore, improved understanding of these epigenetic mechanisms will provide new targets for gynecologic cancer treatment.
Feature-Based Estimation of Radial Basis Mappings for Non-Rigid Registration

We study the challenging problem of registering images of a non-rigid surface by estimating a Radial Basis Mapping from feature matches. We cast the problem as a Maximum Likelihood Estimation coupled with nested model selection. We propose an algorithm based on dynamically inserting centres and refining the transformation parameters under the control of a selection model criterion. We validate the algorithm using extensive simulations and by building on recent feature extraction and matching techniques, we report convincing results on real data.
On Computer-Assisted Orchestration

In 2003, I presented to Ircam a proposal for a long-term research project on the subject of computer-assisted orchestration. The results of this research project lead to the prototype softwares, ‘Orchidee’ and now, ‘Ato-ms’, both used by numerous composers. With these systems, composers can specify a target sound and replicate it with a given, predetermined orchestra. The target sound, defined as a set of audio and symbolic features, can be constructed either by analysing a pre-recorded sound, or through a compositional process. The orchestration procedure uses large pre-analysed instrumental sound databases to offer composers a set of sound combinations. This procedure relies on a set of features that describe different aspects of the sound. Almost 10 years after the start of this project, it is time to look back at what was accomplished from the musical stand point, and to open some new perspectives on the subject, like the introduction of target descriptors for orchestral qualities, and orchestral layers.
Influence of fatty liver on plasma small, dense LDL- cholesterol in subjects with and without metabolic syndrome.

AIM Small, dense low density lipoprotein (sLDL) is known as an atherogenic lipoprotein and is often associated with metabolic syndrome (MS). A high frequency of sLDL is found in hypertriglyceridemic subjects. Also, fatty liver (FL) is often associated with MS; therefore, we studied whether the association of FL increases sLDL- cholesterol (C) in subjects with MS. METHODS In total, 207 patients were enrolled in this study and FL was estimated by echogram. The presence of MS was diagnosed according to the Japanese Guidelines for the Definition of Metabolic Syndrome. RESULTS sLDL-C and sLDL-C/LDL-C in the MS group were higher than in the non-MS group. Also, sLDL-C and sLDL-C/LDL-C in the FL group were higher than in the non-FL group. The simple correlation coefficient (r) between plasma triglyceride and sLDL-C or sLDL-C/LDL-C in all subjects was 0.36 and 0.51. In the MS group, r values were 0.32 and 0.52 while, in the non-FL group, r was 0.32 and 0.38, respectively. Two-way ANOVA revealed that FL was a powerful determinant of plasma sLDL-C and sLDL-C/LDL-C, but MS was not. When we divided all subjects into four groups, i.e., MS(-)FL(-), MS(-)FL(+), MS(+)FL(-) and MS(+)FL(+), sLDL-C/LDL-C of MS(+)FL(+) was significantly higher than all other groups. CONCLUSION Association of MS and FL significantly increased sLDL-C and sLDL-C/LDL-C. The significant relationship between sLDL-C/LDL-C and plasma triglyceride in the FL group indicates that FL may produce triglyceriderich VLDL, a precurser of sLDL, thereby contributing to the appearance of sLDL particles in the plasma of MS patients with FL.
The Effects of Teaching Method and Students' Interest on Students' Achievement in Volleyball (An Experimental Study)

The objective of the study was to find out the effect of volleyball teaching methods --studen-oriented, teacher-oreiented, and convensional- tower the students‘ achievement in learning volley ball. Besides that, it also aimed to know the effect of students‘ interest, higt interest, low interest-- on their learning achievement. The experiment was conducted at FIK-UNP in Padang using 3 X 2 factorial design. The sample consisted of 84 students taken randomly.The students were divided into three groups of treatment (two groups for experiment and the other for control). There were two kinds of instruments used, one measuring skills in volleyball and the other for measuring students‘interest. By using analysis of variance the testing of hypotheses concluded that five null hypotheses were rejected and other five were accepted. Therefore, it can be concluded that: (1) the student-oriented method was better than the teacher-oriented and the conventional method; (2) there were interactions found between teaching method and students'interest which exist differences on student achievement in volleyball; (3) the teacher-oriented and the conventional method resulted in not different effect; (4) highly interested students using the teacher-oriented method would produce higher achievement than using the conventional one; (5) there was no different effect among the three methods for students with lower interest. The student-oriented method is worth using to teach volleyball especially for students‘ having high interest
The watershed concept and its use in segmentation : a brief history

The watershed is one of the most used tools in image segmentation. We present how its concept is born and developed over time. Its implementation as an algorithm or a hardwired device evolved together with the technology which allowed it. We present also how it is used in practice, first together with markers, and later introduced in a multiscale framework, in order to produce not a unique partition but a complete hierarchy.
Incremental evaluation of a monotone XPath fragment

This paper shows a scheme for incremental evaluation of XPath queries. Here, we focus on a monotone fragment of XPath, i.e., when a data is deleted from (or inserted to) the database, only deletion (insertion, resp.) may occur to query answers. For efficiently processing deletions, we store information on partial matchings, i.e., which elements were participating in matchings for which query answers, and also store counters showing how many matchings each query answer had. We use the information on the partial matchings also for skipping a part of computation upon data insertion. We investigate properties of the XPath fragment in order to keep the amount of information we store as small as possible.
Semiorders and a Theory of Utility Discrimination

In the theory of preferences underlying utility theory i t is generally assumed that the indifference relation is transitive, and this leads t o equivalence classes of indifferent elements or, equally, t o indifference curves. It has been pointed out that this assumption is contrary to experience and that utility is not perfectly discriminable, as such a theory necessitates. In this paper intransitive indifference relations are admitted and a class of them are axiomatized. This class is shown t o be substantially equivalent t o a utility theory in which there are just noticeable difference functions which state for any value of utility the change in utility so that the change is just noticeable. In the case of risk represented by a linear utility function over a mixture space, the precise form of the function is examined in detail.
Extracting the knowledge embedded in support vector machines

One of the main challenges in support vector machine (SVM) for data mining applications is to obtain explicit knowledge from the solutions of SVM for explaining classification decisions. This paper exploits the fact that the decisions from a non-linear SVM could be decoded into linguistic rules based on the information provided by support vectors and its decision function. Given a support vector of a certain class, cross points between each line, which is extended from the support vector along each axis, and SVM decision hyper-curve are searched first. A hyper-rectangular rule is derived from these cross points. The hyper-rectangle is tuned by a tuning phase in order to exclude those out-class data points. Finally, redundant rules are merged to produce a compact rule set. Simultaneously, important attributes could be highlighted in the extracted rules. Rule extraction results from our proposed method could follow decisions of SVM classifiers very well. Comparisons between our method and other rule extraction methods are also carried out on several benchmark data sets. Higher rule accuracy is obtained in our method with fewer number of premises in each rule.
The Politics of Exclusion: Institutions and Immigration Policy in Contemporary Germany

Immigration is one of the most sensitive issues of modern European politics. Nowhere is this more the case than in Germany, as a result of its history and the sheer scale of immigration it has experienced since 1945. Yet despite this background, Germany's immigration, residence and citizenship policy has been more restrictive when compared to that of many other countries; indeed, official policy long maintained that Germany was not a 'country of immigration'. But why has this been the case? The politics of exclusion provides a new analytical perspective on immigration in Germany, tracing the country's immigration and citizenship policy since the Second World War. The book argues that institutional politics are central to understanding why Germany's policy structures have experienced only incremental change over the past 20 years, and have remained comparatively restrictive. With its lively and accessible style, the book will appeal to advanced scholars and students of immigration and Germany.
Using Multi-Objective Optimization for the Selection of Ensemble Members

2 Institute of Molecular Genetics of the ASCR, v. v. i. Videˇ nska 1083, 142 20 Prague 4, Czech Republic Abstract: In this paper we propose a clustering process which uses a multi-objective evolution to select a set of diverse clusterings. The selected clusterings are then com- bined using a consensus method. This approach is com- pared to a clustering process where no selection is applied. We show that careful selection of input ensemble members can improve the overall quality of the final clustering. Our algorithm provides more stable clustering results and in many cases overcomes the limitations of base algorithms.
Genomic Diversity at Thirteen Short Tandem Repeat Loci in a Substructured Caste Population, Golla, of Southern Andhra Pradesh, India

AbstractGenomic diversity based on 13 short tandem repeat (STR) loci was studied in seven population groups of a substructured Golla caste from Chittoor district in southern Andhra Pradesh, India. These groups are traditionally pastoral, culturally homogeneous, and strictly endogamous. Blood samples were drawn from 317 individuals from 30 Golla villages. The 13 STR loci analyzed in five standard multiplex polymerase chain reactions were: (1) CSF1R, TH01, and PLA2A; (2) F13A1, CYP19, and LPL; (3) D21S1446 and D21S1435; (4) D20S481, D20S473, and D20S604; and (5) D5S1453 and D6S1006. The average heterozygosity was found to be low among the Golla subgroups (0.64-0.70) in comparison to that of groups at the upper levels of the hierarchy. The coefficient of gene differentiation was found to be moderate (average GST = 0.031; range between 0.018 and 0.049 among the loci) when compared to that observed for a similar class of markers among populations with relatively higher levels of hierarchy, for example, among castes. It is, however, much higher when compared to the average observed for Indian caste and tribal populations, based on classical markers. Genetic distance measures revealed clusters of populations that are consistent with the known ethnohistorical and geographical backgrounds of the groups. We claim that these hypervariable markers are quite useful in understanding the process of substructuring within the Indian castes, leading to the formation of smaller breeding isolates, the basic Mendelian units within which microevolutionary forces operate.
Network Design and Architectures for Highly Dynamic Next-Generation IP-Over-Optical Long Distance Networks

The DARPA CORONET project seeks to develop the target network architectures and technologies needed to build next-generation long-distance IP-over-Optical-Layer (IP/OL) networks. These next-generation networks are expected to scale 10-100 times larger than today's largest commercial IP/OL network. Furthermore, DARPA has established advanced objectives for very rapid provisioning of new IP or private line connections, very rapid restoration against up to three simultaneous network failures, and future dynamic ldquowavelengthrdquo services ranging from speeds of 40-800 Gigabits per second. Besides these ambitious goals, the CORONET project seeks to establish a commercially-viable network architecture that supports both commercial and government services. In this paper, we describe the CORONET program requirements, and present our initial architectures and analysis of the early phases of this long-term project. We propose a novel 2-Phase Fast Reroute restoration method that achieves 50-100 ms restoration in the IP-Layer in a cost-effective manner, and a commercially viable OL restoration method that can meet the rapid CORONET requirements. We also estimate the magnitude of the extra capacity needed to provide dynamic wavelength services compared to that of static services, and show that the extra capacity to restore a small percentage of high priority traffic against multiple failures requires a small amount of extra capacity compared to that of single failures.
Named Entity Disambiguation using Freebase and Syntactic Parsing

Named Entity Disambiguation (NED) is a fundamental task of semantic annotation for the Semantic Web. The task of Word Sense Disambiguation (WSD) in Ontology-Based Information Extraction (OBIE) aims to establish a link between the textual entity mention and the corresponding class in the ontology. In this paper, we propose a NED process integrated in a rule-based OBIE system for French. We show that our SVM approach can improve disambiguation efficiency using syntactic features provided by the Fips parser and popularity score features extracted from the Freebase knowledge base.
LAPS - localisation using appearance of prior structure: 6-DoF monocular camera localisation using prior pointclouds

This paper is about pose estimation using monocular cameras with a 3D laser pointcloud as a workspace prior. We have in mind autonomous transport systems in which low cost vehicles equipped with monocular cameras are furnished with preprocessed 3D lidar workspaces surveys. Our inherently cross-modal approach offers robustness to changes in scene lighting and is computationally cheap. At the heart of our approach lies inference of camera motion by minimisation of the Normalised Information Distance (NID) between the appearance of 3D lidar data reprojected into overlapping images. Results are presented which demonstrate the applicability of this approach to the localisation of a camera against a lidar pointcloud using data gathered from a road vehicle.
A Previously Unrecognized Protein-Protein Interaction between TWEAK and CD163: Potential Biological Implications1

TWEAK (TNF-like weak inducer of apoptosis) is a TNF superfamily member implicated in several mechanisms. Although fibroblast growth factor inducible 14 (Fn14)/TweakR has been reported as its receptor, an as yet unrecognized surface molecule(s) might modulate TWEAK function(s). Thus, we set out to identify TWEAK-binding proteins by screening a combinatorial peptide library. Cyclic peptides containing a consensus motif (WXDDG) bound to TWEAK specifically. These peptides were similar to CD163, a scavenger receptor cysteine-rich domain family member, restricted to the monocyte/macrophage lineage and responsible for the uptake of circulating haptoglobin-hemoglobin (Hp-Hb) complexes. Sequence profile analysis suggested that TWEAK mimicked the CD163 natural ligand (Hp-Hb). Consistently, we show dose-dependent TWEAK binding to CD163 and blockade by an anti-CD163 Ab. In a competition assay, both soluble CD163 and Fn14/TweakR were able to compete off TWEAK binding to coated Fn14/TweakR or CD163, respectively. Flow-cytometry and immunofluorescence assays showed that human monocytes (Fn14/TweakR negative and CD163 positive) bind TWEAK, thus blocking the recognition of CD163 and reducing the activation mediated by a specific mAb in these cells. We demonstrate that monocytes can sequester TWEAK from supernatants, thus preventing tumor cell apoptosis; this effect was reverted by preincubation with the peptide mimicking CD163 or with a mAb anti-CD163, indicating specificity. Finally, we show that recombinant human TWEAK binding to CD163-transfected Chinese hamster ovary cells is inhibited by the presence of either unlabeled TWEAK or the Hp-Hb complex. Together, these data are consistent with the hypothesis that CD163 either acts as a TWEAK scavenger in pathological conditions or serves as an alternate receptor for TWEAK in cells lacking Fn14/TweakR.
Radial evolution of solar wind intermittency in the inner heliosphere

[1] We analyzed intermittency in the solar wind, as observed on the ecliptic plane, looking at magnetic field and velocity fluctuations between 0.3 and 1 AU, for both fast and slow wind and for compressive and directional fluctuations. Our analysis focused on the property that probability distribution functions of a fluctuating field affected by intermittency become more and more peaked at smaller and smaller scales. Since the peakedness of a distribution is measured by its flatness factor we studied the behavior of this parameter for different scales to estimate the degree of intermittency of our time series. We confirmed that both magnetic field and velocity fluctuations are rather intermittent and that compressive magnetic fluctuations are generally more intermittent than the corresponding velocity fluctuations. In addition, we observed that compressive fluctuations are always more intermittent than directional fluctuations and that while slow wind intermittency does not depend on the radial distance from the Sun, fast wind intermittency of both magnetic field and velocity fluctuations clearly increases with the heliocentric distance. We propose that the observed radial dependence can be understood if we imagine interplanetary fluctuations made of two main components: one represented by coherent, nonpropagating structures convected by the wind and, the other one made of propagating, stochastic fluctuations, namely Alfven waves. While the first component tends to increase the intermittency level because of its coherent nature, the second one tends to decrease it because of its stochastic nature. As the wind expands, the Alfvenic contribution is depleted because of turbulent evolution and, consequently, the underlying coherent structures convected by the wind, strengthen further on by stream-stream dynamical interaction, assume a more important role increasing intermittency, as observed. Obviously, slow wind does not show a similar behavior because Alfvenic fluctuations have a less dominant role than within fast wind and the Alfvenicity of the wind has already been frozen by the time we observe it at 0.3 AU. Finally, our analysis suggests that the most intermittent magnetic fluctuations are distributed along the local interplanetary magnetic field spiral direction while, those relative to wind velocity seem to be located along the radial direction.
In Vivo Protein Interactions and Complex Formation in the Pectobacterium atrosepticum Subtype I-F CRISPR/Cas System

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their associated proteins (Cas; CRISPR associated) are a bacterial defense mechanism against extra-chromosomal elements. CRISPR/Cas systems are distinct from other known defense mechanisms insofar as they provide acquired and heritable immunity. Resistance is accomplished in multiple stages in which the Cas proteins provide the enzymatic machinery. Importantly, subtype-specific proteins have been shown to form complexes in combination with small RNAs, which enable sequence-specific targeting of foreign nucleic acids. We used Pectobacterium atrosepticum, a plant pathogen that causes soft-rot and blackleg disease in potato, to investigate protein-protein interactions and complex formation in the subtype I-F CRISPR/Cas system. The P. atrosepticum CRISPR/Cas system encodes six proteins: Cas1, Cas3, and the four subtype specific proteins Csy1, Csy2, Csy3 and Cas6f (Csy4). Using co-purification followed by mass spectrometry as well as directed co-immunoprecipitation we have demonstrated complex formation by the Csy1-3 and Cas6f proteins, and determined details about the architecture of that complex. Cas3 was also shown to co-purify all four subtype-specific proteins, consistent with its role in targeting. Furthermore, our results show that the subtype I-F Cas1 and Cas3 (a Cas2-Cas3 hybrid) proteins interact, suggesting a protein complex for adaptation and a role for subtype I-F Cas3 proteins in both the adaptation and interference steps of the CRISPR/Cas mechanism.
Coupled gating between individual skeletal muscle Ca2+ release channels (ryanodine receptors)

Excitation-contraction coupling in skeletal muscle requires the release of intracellular calcium ions (Ca2+) through ryanodine receptor (RyR1) channels in the sarcoplasmic reticulum. Half of the RyR1 channels are activated by voltage-dependent Ca2+ channels in the plasma membrane. In planar lipid bilayers, RyR1 channels exhibited simultaneous openings and closings, termed "coupled gating. " Addition of the channel accessory protein FKBP12 induced coupled gating, and removal of FKBP12 uncoupled channels. Coupled gating provides a mechanism by which RyR1 channels that are not associated with voltage-dependent Ca2+ channels can be regulated.