Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomics advances the study of inbreeding depression in the wild

Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high‐throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
High speed fuzzy learning machine with guarantee of global minimum and its applications to chaotic system identification and medical image processing

The paper describes a generalized fuzzy learning machine, which is a generalised and modified type of the neo-fuzzy-neuron presented by the authors in 1992. This machine can well grasp the nonlinear correlation of each input. It has a very high nonlinear mapping ability compared with the conventional neural network and it guarantees the global minimum. Furthermore, learning speed and its accuracy are improved drastically. It was successfully applied to the identification of the nonlinear dynamical system, e.g. two dimensional Lorenz chaotic model, and to the automatic detection of landmark location in the roentgenographic cephalogram for orthodontic treatment. The results were promising.
The eclipsing, double-lined, Of supergiant binary Cygnus OB2-B17

Context. Massive, eclipsing, double-lined, spectroscopic binarie s are not common but are necessary to understand the evolution of massive stars as they are the only direct way to determine stellar masses. They are also the progenitors of energetic phenomena such as X-ray binaries and -ray bursts. Aims. We present a photometric and spectroscopic analysis of the candidate binary system Cyg OB2-B17 to show that it is indeed a massive evolved binary. Methods. We utilise V band and white-light photometry to obtain a light curve and period of the system, and spectra at different resolutions to calculate preliminary orbital parameters and spectral cla sses for the components. Results. Our results suggest that B17 is an eclipsing, double-lined, spectroscopic binary with a period of 4.0217�0.0004 days, with two massive evolved components with preliminary classificatio ns of O7 and O9 supergiants. The radial velocity and light curves are consistent with a massive binary containing components with similar luminosities, and in turn with the preliminary spectral types and a ge of the association.
The menu-size complexity of revenue approximation

We consider a monopolist that is selling n items to a single additive buyer, where the buyer's values for the items are drawn according to independent distributions F1,F2,…,Fn that possibly have unbounded support. It is well known that - unlike in the single item case - the revenue-optimal auction (a pricing scheme) may be complex, sometimes requiring a continuum of menu entries. It is also known that simple auctions with a finite bounded number of menu entries can extract a constant fraction of the optimal revenue. Nonetheless, the question of the possibility of extracting an arbitrarily high fraction of the optimal revenue via a finite menu size remained open. In this paper, we give an affirmative answer to this open question, showing that for every n and for every ε>0, there exists a complexity bound C=C(n,ε) such that auctions of menu size at most C suffice for obtaining a (1-ε) fraction of the optimal revenue from any F1,…,Fn. We prove upper and lower bounds on the revenue approximation complexity C(n,ε), as well as on the deterministic communication complexity required to run an auction that achieves such an approximation.
The Application of Ant Colony Optimization in Wireless Sensor Network Routing

The paper proposes wireless sensor clustering routing protocol based on ant colony algorithm(ACO). The method firstly uses the network self-topology to get a stable cluster structure based on modularity clustering algorithm; secondly make a new cluster-head selection function according to each cluster node residual energy and the distribution of cluster node; then we propose inter-cluster multi-hop routing algorithm based on ant colony optimization, which in order to balance the energy between consumption on the transmission path and residual one of cluster-head node, developing new ant transmission probability and pheromone updating strategy, we verify the validity of algorithm through simulation.
ICMM - a maturity model for software inspections

Software inspection is widely acknowledged as an important method in software engineering. However, there is a need to better understand how to implement and improve inspection practices. This paper introduces Inspection Capability Maturity Model (ICMM), which provides support for assessment and improvement of software inspection practices in a software organization. The model has been developed iteratively based on a comprehensive literature survey and experiences from eight case organizations. This paper includes a detailed description of the used followed research process, the structure of ICMM and the rationale for the defined criteria. Additionally, the role of this kind of model in inspection process improvement is discussed. Copyright © 2010 John Wiley & Sons, Ltd.
3D Plant Modelling via Hyperspectral Imaging

Plant phenomics research requires different types of sensors be employed to measure the physical traits of plant surface and to estimate the plant biomass. Of particular interest is the hyperspectral imaging device which captures wavelength indexed band images that characterise material properties of objects under study. In this paper, we introduce a proof of concept research that builds 3D plant model directly from hyperspectral images captured in a controlled lab environment. We show that hyperspectral imaging has shown clear advantages in segmenting plant from its background and is promising in generating comprehensive 3D plant models.
Dolphin-Few - An Architecture for Compilers Development, Monitoring and Use on the Web

DOLPHIN is a framework for the development of high performance, multi-language and multiarchitecture compilers. This framework contains several components, but is specially prepared to help the development of the middle-level task of the compilation process. It contains a large set of analysis and optimizations routines, several front-ends and back-ends, and a set of tools to help the development of new routines. This paper focus the DOLPHIN – Front-End for the Web, a project based on the DOLPHIN framework, to build a set of applications, to make available some new services on the web, namely an integrated development environment, a system for monitoring and analyze the behavior of the compilation tasks and also, an environment for the development of compiler components. Keys words: Compilers development, frameworks, web applications
Resource Space Management Systems

Liquidpub 1 is an EU project within the “future and emerging technologies” category whose goal is to capture the lessons learned and opportunities provided by the Web and open source, agile software development to develop concepts, models, metrics, and science support services for an efficient (for people), effective (for science), and sustainable (for publishers and the community) way of creating, disseminating, evaluating, and consuming scientific knowledge [1]. Novel services for science are a hot topic these days. From social bookmarking sites to online ranking of scientists, these services try to assist scientists in sharing content and assessing people and their scientific contributions. These services are however still very much anchored to a traditional notion of publication and are only scratching the surface of what can be done to help scientists collaborate for the greater good. Examples of Scientific Services. An example of services that Liquidpub intends to deliver is that of Liquid Journals (LJ), that redefines the traditional notion of journal which was born at a time where the paper was the only possible form of non-verbal knowledge dissemination, printing was the scarce resource, and therefore peer review and pre-publication filtering was necessary. Liquid journals are based on these notions i) separation of publication from inclusion in a journal: contributions are posted online (without any review) or published in traditional journals following a traditional process, and then they can be included in an arbitrarily high number of LJs. Each LJ decides policies and rules to determine if a contribution is included. Essentially, LJs are ways to aggregate all sort of available content based on what is interesting and relevant for its readers. This can be done via review, collaborative filtering, looking at journals of people we consider highly, etc; ii) Everybody (even individuals) can create and run LJs; iii) Papers are not the only source of knowledge. Blogs, experiments, datasets, slides, comments/feedback and the like are valid and useful forms of dissemination, some of them having the additional benefits of allowing early dissemination and therefore better collaboration. Including feedback as a form of contribution has the effect that it is considered as part of what is evaluated from a scientist and therefore it encourages giving feedback, which is fundamental to the scientific creation process. All is driven towards what the purpose of a journal should be: providing people with interesting content to read, minimizing the dissemination overhead, and maximizing the collaboration. Current journals are a
Prognostic significance of p53, Her‐2, and EGFR overexpression in borderline and epithelial ovarian cancer

The objective of the study was to evaluate the prognostic effect of p53, Her-2, and EGFR in borderline and epithelial ovarian cancer. Tumor tissue from 85 patients with borderline and 783 patients with epithelial ovarian cancer stage I-IV were analyzed immunohistochemically for p53 positivity and over-expression of Her-2 and EGFR. In the ovarian cancer (OC) group 415 patients (53%) had p53-positive tumors, 272 (35%) had tumors with Her-2 over-expression, and 483 (62%) had over-expression of EGFR. In the OC group the classical prognostic factors (older age, higher FIGO stage, and poorer differentiated stage) had significant prognostic value in both uni- and multivariate analyses. Multivariate analyses in the OC group proved p53 positivity to increase mortality significantly depending on the grade of the tumor. Her-2 likewise increased the risk of mortality significantly in this group depending on the grade of the tumor. EGFR on the other hand did not have any additional prognostic effect in the OC group after adjustment for the classical prognostic and molecular factors was made. In the borderline group Her-2 and EGFR over-expression in combination, adjusted for age and p53, significantly improved the prognosis.
Lasing from dye-doped planar cholesteric liquid crystal devices

The lasing action of dye doped cholesteric liquid crystal (CLC) cell was investigated in this work. A planar state was prepared by antiparallel rubbing process ITO glasses with polymide layer coating. The dye doped cholesteric liquid crystal mixture was used by mixing a laser dye DCM, a chiral agent CB15 and a nematic liquid crystal TEB30A. A second harmonic Q-switched Nd:YAG pulsed laser (λ=532nm) was used as the pumping source. A sharp peak was measured at 611 nm in the cell-normal direction and cell-plane direction after reaching threshold pump energy. The least full width of half maximum (FWHM) were about 10 nm and 12 nm. The optical structure of the device was investigated upon applied voltage. The results show that planar state of the CLCs is a prerequisite for the generation of lasing emission. So laser emission attributed to the photonic band gap (Bragg mode) in the cell-normal direction in which the helical axis exists. Due to the waveguide structure formed by the liquid crystal sandwiched between glass substrates (ne=1.522, no=1.692>ng=1.50), quasi-in-plane leaky lasing modes exist in the cell-plane direction.
Scalable Parallel Application Launch on Cplant ™

This paper describes the components of a runtime system for launching parallel applications and presents performance results for starting a job on more than a thousand nodes of a workstation cluster. This runtime system was developed at Sandia National Laboratories as part of the Computational Plant (Cplant™) project, which is deploying large-scale parallel computing clusters using commodity hardware and the Linux operating system. We have designed and implemented a flexible runtime system that allows for launching parallel jobs on thousands of nodes in a matter of seconds. The interactions of the components are described, and the key issues that address the scalability and performance of the runtime system are discussed. We also present performance results of launching executables of varying sizes on more than a thousand nodes.
Opportune Job Shredding: An Effective Approach for Scheduling Parameter Sweep Appli

A method for decontaminating uranium product from the Purex process comprises addition of hydrazine to the product uranyl nitrate stream from the Purex process, which contains hexavalent (UO22+) uranium and heptavalent technetium (TcO4-). Technetium in the product stream is reduced and then complexed by the addition of oxalic acid (H2C2O4), and the Tc-oxalate complex is readily separated from the uranium by solvent extraction with 30 vol. % tributyl phosphate in n-dodecane.
An Incremental Principal Component Analysis for Chunk Data

This paper presents a new algorithm of dynamic feature selection by extending the algorithm of Incremental Principal Component Analysis (IPCA), which has been originally proposed by Hall and Martin. In the proposed IPCA, a chunk of training samples can be processed at a time to update the eigenspace of a classification model without keeping all the training samples given so far. Under the assumption that L of training samples are given in a chunk, first we derive a new eigenproblem whose solution gives us a rotation matrix of eigen-axes, then we introduce a new algorithm of augmenting eigen-axes based on the accumulation ratio. We also derive the one-pass incremental update formula for the accumulation ratio. The experiments are carried out to verify if the proposed IPCA works well. Our experimental results demonstrate that it works well independent of the size of data chunk, and that the eigenvectors for major components are obtained without serious approximation errors at the final learning stage. In addition, it is shown that the proposed IPCA can maintain the designated accumulation ratio by augmenting new eigen-axes properly. This property enables a learning system to construct an informative eigenspace with minimum dimensionality.
Efficient design and generation of a multi-facet arbiter

Based on the arbiter template developed in [1], we presented an efficient, modular, and scalable decentralized parallel design of a new multi-facet arbiter. Moreover, with this modular and reusable hardware design, we have implemented a parametric arbiter generator that automatically generates various multi-facet arbiters. With the decentralized parallel design and the generator, not only a fastest and smallest round-robin arbiter but also other type arbiters were designed and generated on the fly. The experiment results were given to show the designs' excellent performances.
Synergistic Toughening in Ternary Silica/Hollow Glass Spheres/Epoxy Nanocomposites

Herein, the fracture toughness of ternary epoxy systems containing nanosilica and hollow glass microspheres (HGMS) is investigated. The experimental measurements reveal synergistic fracture toughness in some hybrid compositions: The incorporation of 10 phr of HGMS and nanosilica alone modify the fracture toughness of epoxy by 39% and 91%, respectively. However, use of 10 phr hybrid modifier can enhance the fracture toughness of the resin up to 120%. Observations reveal different toughening mechanisms for the blends i.e., plastic deformation for silica nanoparticles and crack bifurcation for HGMS. Both of these toughening mechanisms additively contribute to the synergism in ternary epoxies. GRAPHICAL ABSTRACT
Flexible Non-Terminals for Dependency Tree-to-Tree Reordering

A major beneﬁt of tree-to-tree over tree-to-string translation is that we can use target-side syntax to improve reordering. While this is relatively simple for binarized constituency parses, the reordering problem is considerably harder for dependency parses, in which words can have arbitrarily many children. Previous approaches have tackled this problem by restricting grammar rules, reducing the expressive power of the translation model. In this paper we propose a general model for dependency tree-to-tree reordering based on ﬂexible non-terminals that can compactly encode multiple insertion positions. We explore how insertion positions can be selected even in cases where rules do not entirely cover the children of input sentence words. The proposed method greatly improves the ﬂexibility of translation rules at the cost of only a 30% increase in decoding time, and we demonstrate a 1.2–1.9 BLEU improvement over a strong tree-to-tree baseline.
Crystal structure of human platelet‐derived growth factor BB.

The crystal structure of the homodimeric BB isoform of human recombinant platelet‐derived growth factor (PDGF‐BB) has been determined by X‐ray analysis to 3.0 A resolution. The polypeptide chain is folded into two highly twisted antiparallel pairs of beta‐strands and contains an unusual knotted arrangement of three intramolecular disulfide bonds. Dimerization leads to the clustering of three surface loops at each end of the elongated dimer, which most probably form the receptor recognition sites.
Prognostic significance of human epidermal receptor (HER)- 3 immunohistochemical expression in patients with metastatic breast cancer.

BACKGROUND Previous reports have shown that human epidermal receptor (HER)-3 overexpression may be associated with poor prognosis in patients with breast cancer, but results have been conflicting. In this study, we sought to investigate the prognostic significance of HER-3 immunohistochemical expression in patients with metastatic breast cancer. METHODS We retrospectively analyzed HER-3 immunohistochemical expression profiles in 45 paraffin-embedded specimens from patients who had been treated between 1996 and 2006 in the Department of Oncology of the Uludag University School of Medicine, Bursa, Turkey. Membranous or cytoplasmic dominant expression patterns of HER-3 were analyzed using the Rajkumar score and a cytoplasmic 4-point scoring system, respectively. Progression-free survival (PFS) and overall survival (OS) served as the main outcome measures. RESULTS The median PFS in the study participants was 9 months (interquartile range: 4.5-13 months), whereas the median OS was 20 months (interquartile range: 7.5-28 months). Categorization of the patient population according to HER-3 positive immunohistochemical expression did not reveal any statistically significant difference in terms of both PFS (p=0.70) and OS (p=0.81). The results of multivariable Cox regression analysis indicated that tumor size was the only independent predictor of PFS, whereas estrogen and progesterone receptor status was independently associated with OS. CONCLUSIONS HER-3 immunohistochemical expression did not correlate with outcomes in Turkish patients with metastatic breast cancer. Although our results suggest that HER-3 expression in cancer specimens is not of prognostic significance, further prospective studies are warranted to confirm these results.
Pattern formation during development of the embryonic cerebellum

The patterning of the embryonic cerebellum is vital to establish the elaborate zone and stripe architecture of the adult. This review considers early stages in cerebellar Purkinje cell patterning, from the organization of the ventricular zone to the development of Purkinje cell clusters—the precursors of the adult stripes.
Disruption of Wnt/β-catenin Signaling in Odontoblasts and Cementoblasts Arrests Tooth Root Development in Postnatal Mouse Teeth

Tooth development undergoes a series of complex reciprocal interactions between dental epithelium and the underlying mesenchymal cells. Compared with the study in tooth crown formation, little is known about the molecular mechanism underlying the development of tooth roots. In the present study, we conditionally knock out β-catenin gene (Ctnnb1) within developing odontoblasts and cementoblasts during the development of tooth roots, and observed rootless molars as well as incomplete incisors. Histological analyses revealed intact structure of molar crown and labial side of incisor, however, as for the molar roots and the lingual portion of incisor, the formation of dentin and periodontal tissues were greatly hampered. In situ hybridization experiments using probes of odontoblastic marker genes collagen type I, alpha 1 (Col1a1), osteocalcin (OC) and dentin sialophosphoprotein (Dspp) manifested striking undifferentiation of root odontoblasts in which Ctnnb1 was eliminated. Bromodeoxyuridine (BrdU) labeling and proliferating cell nuclear antigen (PCNA) immunohistochemical experiments also showed retarded proliferation of pre-odontoblasts in mutant mice. However, cell apoptosis was not affected. Additionally, a disrupted formation of cementoblasts, suggested by the absence of transcripts of bone sialoprotein (Bsp) in follicle mesenchyme, was also evident in mutant mice. Our study provides strong in vivo evidence to confirm that Wnt/β-catenin signaling is functionally significant to root odontogenesis and cementogenesis during the tooth root development.
Dmp1 Promoter-Driven Diphtheria Toxin Receptor Transgene Expression Directs Unforeseen Effects in Multiple Tissues

Mice harbouring a dentin matrix protein 1 (Dmp1) promoter-driven human diphtheria toxin (DT) receptor (HDTR) transgene (Tg) have recently been used to attain targeted ablation of osteocytes by diphtheria toxin (DT) treatment in order to define osteocyte function. Use of these Tg mice has asserted mechano- and novel paracrine regulatory osteocyte functions. To explore osteocyte roles fully, we sought to confirm the selectivity of DT effects in these transgenic mice. However, our findings revealed incomplete DT-induced osteocyte ablation, prevalent HDTR misexpression, as well as more prominent histopathological DT-induced changes in multiple organs in Tg than in wild-type (WT) littermate mice. Mechanistic evidence for DT action, via prominent regulation of phosphorylation status of elongation factor-2 (EF-2), was also found in many non-skeletal tissues in Tg mice; indicative of direct “off-target” DT action. Finally, very rapid deterioration in health and welfare status in response to DT treatment was observed in these Tg when compared to WT control mice. Together, these data lead us to conclude that alternative models for osteocyte ablation should be sought and caution be exercised when drawing conclusions from experiments using these Tg mice alone.