Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns and Processes of Genome-Wide Divergence Between North American and African Drosophila melanogaster

Genomic tools and analyses are now being widely used to understand genome-wide patterns and processes associated with speciation and adaptation. In this article, we apply a genomics approach to the model organism Drosophila melanogaster. This species originated in Africa and subsequently spread and adapted to temperate environments of Eurasia and the New World, leading some populations to evolve reproductive isolation, especially between cosmopolitan and Zimbabwean populations. We used tiling arrays to identify highly differentiated regions within and between North America (the United States and Caribbean) and Africa (Cameroon and Zimbabwe) across 63% of the D. melanogaster genome and then sequenced representative fragments to study their genetic divergence. Consistent with previous findings, our results showed that most differentiation was between populations living in Africa vs. outside of Africa (i.e., “out-of-Africa” divergence), with all other geographic differences being less substantial (e.g., between cosmopolitan and Zimbabwean races). The X chromosome was much more strongly differentiated than the autosomes between North American and African populations (i.e., greater X divergence). Overall differentiation was positively associated with recombination rates across chromosomes, with a sharp reduction in regions near centromeres. Fragments surrounding these high FST sites showed reduced haplotype diversity and increased frequency of rare and derived alleles in North American populations compared to African populations. Nevertheless, despite sharp deviation from neutrality in North American strains, a small set of bottleneck/expansion demographic models was consistent with patterns of variation at the majority of our high FST fragments. Although North American populations were more genetically variable compared to Europe, our simulation results were generally consistent with those previously based on European samples. These findings support the hypothesis that most differentiation between North America and Africa was likely driven by the sorting of African standing genetic variation into the New World via Europe. Finally, a few exceptional loci were identified, highlighting the need to use an appropriate demographic null model to identify possible cases of selective sweeps in species with complex demographic histories.
Comparison of Agglomerative and Partitional Document Clustering Algorithms

Abstract : Fast and high-quality document clustering algorithms play an important role in providing intuitive navigation and browsing mechanisms by organizing large amounts of information into a small number of meaningful clusters, and in greatly improving the retrieval performance either via cluster-driven dimensionality reduction, term-weighting, or query expansion. This ever-increasing importance of document clustering and the expanded range of its applications led to the development of a number of novel algorithms and new clustering criterion functions, especially in the context of partitional clustering. The focus of this paper is to experimentally evaluate the performance of seven different global criterion functions in the context of agglomerative clustering algorithms and compare the clustering results of agglomerative algorithms and partitional algorithms for each one of the criterion functions. Our experimental evaluation shows that for every criterion function, partitional algorithms always lead to better clustering results than agglomerative algorithms, which suggests that partitional clustering algorithms are well-suited for clustering large document datasets due to not only their relatively low computational requirements, but also comparable or even better clustering performance.
CheckViz: Sanity Check and Topological Clues for Linear and Non‐Linear Mappings

Multidimensional scaling is a must‐have tool for visual data miners, projecting multidimensional data onto a two‐dimensional plane. However, what we see is not necessarily what we think about. In many cases, end‐users do not take care of scaling the projection space with respect to the multidimensional space. Anyway, when using non‐linear mappings, scaling is not even possible. Yet, without scaling geometrical structures which might appear do not make more sense than considering a random map. Without scaling, we shall not make inference from the display back to the multidimensional space. No clusters, no trends, no outliers, there is nothing to infer without first quantifying the mapping quality. Several methods to qualify mappings have been devised. Here, we propose CheckViz, a new method belonging to the framework of Verity Visualization. We define a two‐dimensional perceptually uniform colour coding which allows visualizing tears and false neighbourhoods, the two elementary and complementary types of geometrical mapping distortions, straight onto the map at the location where they occur. As examples shall demonstrate, this visualization method is essential to help users make sense out of the mappings and to prevent them from over interpretations. It could be applied to check other mappings as well.
Oxidative Stress Caused by Inactivation of Glutathione Peroxidase and Adaptive Responses

Abstract Reactive oxygen species (ROS) are generated as by-products of cellular metabolism, primarily in the mitochondria. When the cellular production of ROS exceeds the cell's antioxidant capacity, cellular macromolecules such as lipids, proteins and DNA can be damaged. Because of this, 'oxidative stress' is thought to contribute to aging and pathogenesis of a variety of human diseases. However, in the last 10-15 years, a considerable body of evidence has accumulated that ROS serve as subcellular messengers, and play a role in gene regulation and signal transduction pathways, which may be involved in defensive mechanisms against oxidative stress. This review focuses on oxidative stress caused by the inactivation of glutathione peroxidase (GPx), a major peroxide scavenging enzyme. GPx is inactivated by a variety of physiological substances, including nitric oxide and carbonyl compounds in vitro and in cell culture. Decreased GPx activity has also been reported in tissues where oxidative stress occurs in several pathological animal models. The accumulation of increased levels of peroxide resulting from inactivation of GPx may act as a second messenger and regulate expression of antiapoptotic genes and the GPx itself to protect against cell damage. These findings suggest that GPx undergoes inactivation under various conditions such as nitroxidative stress and glycoxidative stress, and that these changes are a common feature of various types of oxidative stress which may be associated with the modification of redox regulation and cellular function.
On the design of optimized projections for sensing sparse signals in overcomplete dictionaries

Sparse signals can be sensed with a reduced number of random projections and then reconstructed if compressive sensing (CS) is employed. Traditionally, the projection matrix has been chosen as a random Gaussian matrix, but improved reconstruction performance can be obtained by optimizing the projection matrix. In this paper, we are interested in projection matrix designs for sensing sparse signals in overcomplete dictionaries. In particular, we put forth a closed form design that stems from the formulation of an optimization problem, which bypasses the complexity of iterative design approaches.
The evolution of Freud's theory about dreaming.

: Freud revised his theory of dreams significantly. First, he discovered the role of the id in dreaming. He hypothesized that the function of dreaming is to gratify an infantile sexual wish, in accordance with the pleasure principle, and thereby to preserve sleep. However, he learned later that anxiety generated by recent events plays a greater role in stimulating dream formation than he had thought and that some dreams actually generate anxiety. These clinical observations caused him, in large part, to revise his theories of dreaming, of anxiety, and of the mental apparatus.
Persistence of impaired PRL responses to sulpiride in patients with PRL secreting pituitary adenomas after successful hypophysectomy.

TRH, arginine, L-dopa, and sulpiride tests for PRL secretion were carried out in 18 control subjects and 20 patients with pituitary PRL-secreting adenomas before and after hypophysectomy. After the hypophysectomy PRL levels fell to normal ranges in 9 cases (categorized as Group I), and remained high in 11 other cases (categorized as Group II). After the operation, there were no alterations of PRL responsiveness to TRH, arginine, or to L-dopa in terms of percent change from the basal value, in either Group I or Group II. No significant differences were found in PRL responses to the above three agents between operated Group I patients and normal subjects even when expressed in absolute values. On the other hand, the PRL responses to sulpiride in both Groups I and II improved markedly after the hypophysectomy, but the absolute response in operated Group I patients was still lower than that in normal subjects. The mean PRL value in operated Group I (mean +/- S.E., 13.2 +/- 0.8 ng/ml, n = 9) was significantly (p less than 0.01) higher than in normal subjects (5.1 +/- 0.4 ng/ml, n = 18). It is concluded 1) that even in hypophysectomized normoprolactinemic patients the circulating PRL may originate mainly from the residual tumor cells, and 2) that the sulpiride test is useful to detect the abnormalities of hypothalamo-pituitary axis in operated patients with PRL-secreting adenomas, whereas TRH, arginine, and L-dopa tests are less useful for such purposes.
Comparative expressed sequence hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression

Altered expression of genes can have phenotypic consequences in cancer development and treatment, developmental abnormalities, and differentiation processes. Here we describe a rapid approach, termed comparative expressed sequence hybridization (CESH), which gives a genome-wide view of relative expression patterns within tissues according to chromosomal location. No prior knowledge of genes or cloning is required, and minimal amounts of tissue can be used. Expression profiles are achieved in a manner similar to the identification of chromosomal imbalances by comparative genomic hybridization analysis. The approach is demonstrated to indicate a chromosomal region that harbors overexpressed genes that may be associated with a drug-resistant phenotype. In addition, known and new regions of differential gene expression in both normal tissues and tumor samples from the soft tissue sarcoma group of rhabdomyosarcoma (RMS) are indicated. These regions included 2p24; overexpression of MYCN at 2p24 was confirmed by quantitative reverse transcription–PCR for all of the alveolar RMS cases and did not necessarily correspond to genomic amplification. Evidence including region specific microarray analysis indicated that overexpression of several genes from a region may be required for detection by CESH. This evidence is consistent with clusters of functionally related genes and mechanisms that affect the expression of a number of genes at a particular genomic location. The distinctive CESH profiles demonstrated in different subtypes of RMS show potential for tumor classification.
Anti-Peptide Monoclonal Antibodies Generated for Immuno-Multiple Reaction Monitoring-Mass Spectrometry Assays Have a High Probability of Supporting Western blot and ELISA*

Immunoaffinity enrichment of peptides coupled to targeted, multiple reaction monitoring-mass spectrometry (immuno-MRM) has recently been developed for quantitative analysis of peptide and protein expression. As part of this technology, antibodies are generated to short, linear, tryptic peptides that are well-suited for detection by mass spectrometry. Despite its favorable analytical performance, a major obstacle to widespread adoption of immuno-MRM is a lack of validated affinity reagents because commercial antibody suppliers are reluctant to commit resources to producing anti-peptide antibodies for immuno-MRM while the market is much larger for conventional technologies, especially Western blotting and ELISA. Part of this reluctance has been the concern that affinity reagents generated to short, linear, tryptic peptide sequences may not perform well in traditional assays that detect full-length proteins. In this study, we test the feasibility and success rates of generating immuno-MRM monoclonal antibodies (mAbs) (targeting tryptic peptide antigens) that are also compatible with conventional, protein-based immuno-affinity technologies. We generated 40 novel, peptide immuno-MRM assays and determined that the cross-over success rates for using immuno-MRM monoclonals for Western blotting is 58% and for ELISA is 43%, which compare favorably to cross-over success rates amongst conventional immunoassay technologies. These success rates could most likely be increased if conventional and immuno-MRM antigen design strategies were combined, and we suggest a workflow for such a comprehensive approach. Additionally, the 40 novel immuno-MRM assays underwent fit-for-purpose analytical validation, and all mAbs and assays have been made available as a resource to the community via the Clinical Proteomic Tumor Analysis Consortium's (CPTAC) Antibody (http://antibodies.cancer.gov) and Assay Portals (http://assays.cancer.gov), respectively. This study also represents the first determination of the success rate (92%) for generating mAbs for immuno-MRM using a recombinant B cell cloning approach, which is considerably faster than the traditional hybridoma approach.
Role of Survivin Phosphorylation by Aurora B in Mitosis

The chromosomal protein passenger complex, a key mitotic regulator, consists of at least four proteins, INCENP, Aurora B, Survivin and Borealin. Survivin, in contrast to the other members of the chromosomal protein passenger complex (CPC), is mobile at metaphase. This protein is also phosphorylated by Aurora B at Threonine 117. In this work we have studied the role of the phosphorylation of Survivin in mitotosis by using non phosphorylable T117A and phosphomimic T117E silent resistant Survivin mutants, inducible cell lines expressing these mutants and a combination of siRNA, time-lapse microscopy and FRAP analysis. Time lapse microscopy and FRAP analysis show that Survivin T117A mutant is very stably associated with centromeres and its expression induces a prometaphasic arrest in endogenous survivin depleted cells. In addition, Survivin T117A was unable to rescue the phenotypes of the endogenous survivin depleted cells. Expressed in these cells, the phosphomimic Survivin T117E mutant exhibits a very weak interaction with the centromeres and behaves as a dominant negative mutant inducing severe mitotic defects. Our data suggest that the Aurora B generated phosphorylation/dephosphorylation cycle of Survivin is required for proper proceeding of mitosis.
Next-Generation Mapping of Complex Traits with Phenotype-Based Selection and Introgression

Finding the genes underlying complex traits is difficult. We show that new sequencing technology combined with traditional genetic techniques can efficiently identify genetic regions underlying a complex and quantitative behavioral trait. As a proof of concept we used phenotype-based introgression to backcross loci that control innate food preference in Drosophila simulans into the genomic background of D. sechellia, which expresses the opposite preference. We successfully mapped D. simulans introgression regions in a small mapping population (30 flies) with whole-genome resequencing using light coverage (∼1×). We found six loci contributing to D. simulans food preference, one of which overlaps a previously discovered allele. This approach is applicable to many systems, does not rely on laborious marker development or genotyping, does not require existing high quality reference genomes, and needs only small mapping populations. Because introgression is used, researchers can scale mapping population size, replication, and number of backcross generations to their needs. Finally, in contrast to more widely used mapping techniques like F2 bulk-segregant analysis, our method produces near-isogenic lines that can be kept and reused indefinitely.
The caries-preventive effect of xylitol/maltitol and erythritol/maltitol lozenges: results of a double-blinded, cluster-randomized clinical trial in an area of natural fluoridation.

OBJECTIVE Xylitol studies suggest caries reductions in the order of 50%. Based on animal/microbial studies, erythritol potentially has caries-preventive properties. However, clinical studies are required to confirm this. The aim of the study was to investigate the additional caries-preventive effect of xylitol/maltitol and erythritol/maltitol lozenges delivered at school, relative to controls receiving comprehensive prevention, in a low-caries prevalence population. METHODS A 4-year, cluster-randomized, double-blinded clinical trial. Five hundred and seventy-nine 10-year-old consenting subjects from 21 schools were randomly assigned to one of five groups. Four groups used the lozenges on school days, in three teacher-supervised sessions daily, over 1 or 2 years. The daily amount was 4.7 g/4.6 g for xylitol/maltitol and 4.5 g/4.2 g for erythritol/maltitol. The groups received free examinations and care in the public health centre. Four hundred and ninety-six children were analysed. The main outcome measure was dentin caries increment based on a clinical examination at 4 years since the start. The groups were compared in relation to the increment using hierarchical logistic regression to adjust for potential clustering. RESULTS Use of xylitol/maltitol or erythritol/maltitol lozenges did not result in caries reduction. A strong relationship between baseline caries prevalence and the 4-year increment was observed (OR = 7.38; 95% CI: 3.78-14.41). CONCLUSIONS The results suggest that in relatively low-caries conditions the school-based use of xylitol/maltitol or erythritol/maltitol lozenges would not have additional caries-preventive effect when compared with comprehensive prevention.
FERMI LARGE AREA TELESCOPE OBSERVATIONS OF TWO GAMMA-RAY EMISSION COMPONENTS FROM THE QUIESCENT SUN

We report the detection of high-energy γ-rays from the quiescent Sun with the Large Area Telescope on board the Fermi Gamma-Ray Space Telescope (Fermi) during the first 18 months of the mission. These observations correspond to the recent period of low solar activity when the emission induced by cosmic rays (CRs) is brightest. For the first time, the high statistical significance of the observations allows clear separation of the two components: the point-like emission from the solar disk due to CR cascades in the solar atmosphere and extended emission from the inverse Compton (IC) scattering of CR electrons on solar photons in the heliosphere. The observed integral flux (⩾100 MeV) from the solar disk is (4.6 ± 0.2[statistical error]+1.0 − 0.8[systematic error]) × 10−7 cm−2 s−1, which is ∼7 times higher than predicted by the “nominal” model of Seckel et al. In contrast, the observed integral flux (⩾100 MeV) of the extended emission from a region of 20° radius centered on the Sun, but excluding the disk itself, (6.8 ± 0.7[stat.]+0.5 − 0.4[syst.]) × 10−7 cm−2 s−1, along with the observed spectrum and the angular profile, is in good agreement with the theoretical predictions for the IC emission.
The typology and diachrony of higher numerals in Indo-European: a phylogenetic comparative study

Numerals have fascinated and mystified linguists, mathematicians and lay persons alike for centuries. The productive use of numerals (in languages where this happens) exploits recursivity to give rise to what we call the ‘the number line’. While the smaller numerals 1–10 have enjoyed intense scrutiny, the typological study of the formation of the higher numerals has received comparatively less attention. This article contains a comprehensive typological account of how languages in the Indo-European language family code numerals beyond 10 (10–99, 100s, 1,000s), the morphemes involved, and how these are ordered. We use this dataset from eighty-one Indo-European languages with phylogenetic comparative methods to propose diachronic reconstructions of these patterns in the Proto-Indo-European language. Our findings indicate that small numerals (11–19) show the widest cross-linguistic variation, and that higher numerals exhibit more consistency in both component parts and their ordering. Additionally, we show statistical evidence of correlations between the ordering of base and atom morphemes and other word order patterns (noun-postposition, noun-genitive, and verb-object order).
Embedded Model Predictive Control on a PLC using a primal-dual first-order method for a subsea separation process

The results of a PLC implementation of embedded Model Predictive Control (MPC) for an industrial problem are presented in this paper. The embedded MPC developed is based on the linear MPC module in SEPTIC (Statoil Estimation and Prediction Tool for Identification and Control), and it combines custom ANSI C code generation with problem size reduction methods, embedded real-time considerations, and a primal-dual first-order method that provides a fast and light QP solver obtained from the FiOrdOs code generator toolbox. Since the primal-dual first-order method proposed in this paper is new in the control community, an extensive comparison study with other state-of-the-art first-order methods is conducted to underline its potential. The embedded MPC was implemented on the ABB AC500 PLC, and its performance was tested using hardware-in-the-loop simulation of Statoil's newly patented subsea compact separation process. A warm-start variant of the proposed first-order method outperforms a tailored interior-point method by a factor of 4 while occupying 40% less memory.
A mere metaphor? Framings of the concept of metaphor in biological specialist communication

This chapter presents a discourse analytical study of explicit reference to theconcept of metaphor within a broad range of biological disciplines. The aim ofthe analysis was to study in what capacity the term ‘metaphor’ was conceptualizedand framed in actual scientific research writing, and whether the differentframings were related to the specific discipline or genre or even stage ofscientific development. Though the concept of metaphor is generally valued as ascientific heuristic resource, two distinct positions on the specific values of metaphorin science are represented in the material. The dominant position criticizesmetaphor for its open-endedness and aims at either empirically sanitizingor discarding the metaphor. A less dominant and more social-constructivepositionembraces the open-endedness as a valuable and dynamic scientific drivingforce suitable for scientific communication as well as heuristics. In either case,the explicit reference to metaphor functions as a rhetorical strategy for promotingand positioning the author’s own research.