Miracle-dz/UniFAR-FTUs huggingface dataset:
A general species delimitation method with applications to phylogenetic placements

Motivation: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. The OTU-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets. Results: We introduce the Poisson tree processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our evolutionary placement algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches with popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GYMC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data. Availability and implementation: The code is freely available at www.exelixis-lab.org/software.html. Contact: Alexandros.Stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of PWM Techniques Using Uniform Sampling in Variable-Speed Electrical Drives with Large Speed Range

In order to minimize motor losses and avoid torque pulsations in a variable-speed electric drives, it is necessary that, at low speeds, the output voltage of the inverter is characterized as far as possible by a sinusoidal shape with variable amplitude and frequency. To this aim, inverters controlled by pulsewidth modulation techniques are employed. In particular, when the subharmonic method is used in an asynchronous way utilizing the natural sampling, a dc component and subharmonics may be present, with dangerous consequences to the electric motor. To overcome these drawbacks, one can use a modulation method called ``uniform sampling,'' with symmetrical or asymmetrical modulation. Single-and three-phase analytical solutions to cover also overmodulation conditions are presented for uniform sampling, and comparisons are made between the natural and the symmetrical and asymmetrical uniform-sampling methods. The harmonic content obtainable under overmodulation conditions is investigated, useful information about the first-harmonic behavior is provided as a function of the modulating depth, and the influence of the displacement angle between the modulating and carrier waves on the first harmonic of the output voltage is evidenced particularly at low frequency values.
Differentiation of dendritic cell populations in macrophage colony‐stimulating factor‐deficient mice homozygous for the osteopetrosis (op) mutation

In op/op mice, immunohistochemical and electron microscopic techniques were used to examine the effects of the OP mutation on dendritic cell populations in lymphoid tissues and skin. In the thymic medulla, T cell zone of lymph nodes, and splenic white pulp of op/op mice, numbers of NLDC‐145‐positive dendritic cells were not decreased. Compared to the normal litter‐ mates, numbers of BM8‐positive macrophages were reduced in various tissues of the mutant mice, including the lymphoid tissues. These dendritic cells of op/op mice expressed la antigens but not F4/80 and BM8 antigens. Ultrastructurally, the dendritic cells developed a tubulo‐ vesicular system typical of interdigitating cells, but they were abnormal in that interdigitation of their cytoplasmic processes was not prominent. In the epidermis of the op/op mice, dendritic cells expressed NLDC‐145, F4/80, la antigens, and adenosine diphosphatase or adenosine triphosphatase activity, and numbers of NLDC‐145‐, la‐, or ADPase‐positive dendritic cells were reduced slightly, but these reductions were not significant statistically. Bir‐ beck granules were detected in most of them electron microscopically. These results indicate that nonlymphoid dendritic cells develop in the lymphoid tissues and skin of op/op mouse, suggesting that they are differentiated from granulocyte‐macrophage colony‐forming cells or earlier hematopoietic cell precursors.
The efficient memory-based VLSI array designs for DFT and DCT

Efficient memory-based VLSI arrays and a new design approach for the discrete Fourier transform (DFT) and discrete cosine transform (DCT) are presented. The DFT and DCT are formulated as cyclic convolution forms and mapped into linear arrays which characterize small numbers of I/O channels and low I/O bandwidth. Since the multipliers consume much hardware area, the designs utilize small ROMs and adders to implement the multiplications. Moreover, the ROM size can be reduced effectively by arranging the data in the designs appropriately. The arrays outperform others in the architectural topology (local and regular connection), computing speeds, hardware complexity, the number of I/O channels, and I/O bandwidth. They benefit from the advantages of both systolic array and the memory-based architectures. >
Political scandals, “black materials,” and changing backstage imaginary in the Hong Kong press, 2001–2015

This article examines changes in political communication in Hong Kong in the past 15 years by analyzing the portrayals in mainstream newspapers of the political “backstage,” that is, the part of the political process that is kept from public view. Specifically, the empirical analysis focuses on how the media have utilized the phrase “black materials” in association with political scandals. Based on the qualitative textual analysis of news and commentary articles published in six local newspapers, the findings showed that a significant change occurred in media portrayals of “black material collection” during the study period. Before 2012, the practice was largely ad hoc or tied to elections, and the collection of black materials followed largely legal means. After 2012, the practice was portrayed as routinized, pervasive, and illegal. The changes in the media portrayals both reflected and constructed China as a powerful state with increasing levels of intrusion on Hong Kong affairs.
A Metabolomic Approach to Target Compounds from the Asteraceae Family for Dual COX and LOX Inhibition

The application of metabolomics in phytochemical analysis is an innovative strategy for targeting active compounds from a complex plant extract. Species of the Asteraceae family are well-known to exhibit potent anti-inflammatory (AI) activity. Dual inhibition of the enzymes COX-1 and 5-LOX is essential for the treatment of several inflammatory diseases, but there is not much investigation reported in the literature for natural products. In this study, 57 leaf extracts (EtOH-H2O 7:3, v/v) from different genera and species of the Asteraceae family were tested against COX-1 and 5-LOX while HPLC-ESI-HRMS analysis of the extracts indicated high diversity in their chemical compositions. Using O2PLS-DA (R2 > 0.92; VIP > 1 and positive Y-correlation values), dual inhibition potential of low-abundance metabolites was determined. The O2PLS-DA results exhibited good validation values (cross-validation = Q2 > 0.7 and external validation = P2 > 0.6) with 0% of false positive predictions. The metabolomic approach determined biomarkers for the required biological activity and detected active compounds in the extracts displaying unique mechanisms of action. In addition, the PCA data also gave insights on the chemotaxonomy of the family Asteraceae across its diverse range of genera and tribes.
Pre-Processing Of Automatic Skin Cancer Detection System: Comparative Study

abstract Skin cancer is increasing and effect many people in different part of the world. Malignant melanoma as the deadliest type of skin cancer can be treated successfully if it detected early. Automatic detection is one of the most challenging research areas that can be used for early detection of such vital cancer. Over the last few years, many automatic diagnosis systems been suggested by different researchers targeting increasing of the diagnosis accuracy. This paper presents a quick review on the design of whole system and focus in preprocessing step of the automatic system. Preprocessing as the basis of automation system plays a vital role for accurate detection. This paper implements three techniques of contrast enhancement in the framework of three methodologies to find out the most effective one for further processing. The quality of resulted images in each methodology has been found based on testing the skin cancer images database using three image quality measurements.
Breaking - that's me!: meaning, identity, gender constructions among young break(danc)ers living in Oslo, Norway

The hip-hop culture has evolved from the ghettos of The Bronx, New York in the 1970s, into a global phenomenon. Despite such prominence there is an absence of academic research on the hip-hop culture element: breakdance. Through eight months of participant observations and 17 qualitative interviews, this study investigates the identity construction process among breakdancers with diverse ethnic backgrounds in Norway. The aim is to provide an insight into the lives of young people and their impression management in constructing a breaker identity. The analysis highlights the complex and contested nature of breakdance as it is experienced and viewed by young people performing breakdance in Norway. Through deliberate impression management the breakdancers construct an alternative identity detached from other social categories. As a result, breakdance seems to counter social oppression and to have an empowering and liberating potential different from the common stigmatization and stereotypical prejudices regarding gender and ethnicity that many have experienced.
Toward Multi-Layer Holistic Evaluation of System Designs

The common practice for quantifying the benefit(s) of design-time architectural choices of server processors is often limited to the chip- or server-level. This quantification process invariably entails the use of salient metrics, such as performance, power, and reliability, which capture-in a tangible manner-a designs overall ramifications. This paper argues for the necessity of a more holistic evaluation approach, which considers metrics across multiple integration levels (chip, server and datacenter). In order to facilitate said comprehensive evaluation, we utilize an aggregate metric, e.g. the Total Cost of Ownership (TCO), to harness the complexly of comparing multiple metrics at multiple levels. We motivate our proposition for holistic evaluation with a case study that compares a 2D processor to a 3D processor at various design integration levels. We show that while a 2D processor is clearly the best choice at the processor level, the conclusion is reversed at the data-center level, where the 3D processor becomes a better choice. This result emanates mainly from the performance benefits of processor-DRAM 3D integration, and the ability to amortize (at the datacenter-level) the higher 3D per-server cost and lower reliability by requiring fewer 3D servers to match the same performance.
Tfs the Typed Feature Structure Representation Formalism Delis Stands for \descriptive Lexical Speciications and Tools for Corpus-based Lexicon Building". Delis

The Typed Feature Structure (TFS) representation formalism deenes the data model of the lexical knowledge base developed within the Delis 1 project. The inheritance-based constraint architecture embodied in the TFS system integrates two computational paradigms: the object-oriented approach ooers complex, recursive, possibly nested, record objects represented as typed feature structures with attribute-value restrictions and (in)equality constraints, and multiple inheritance; the relational programming approach ooers declarativity, logical variables, non-determinism with back-tracking, and existential query evaluation. The constraint-based properties of the TFS formalism are fully exploited in the Delis lexicon model and pertaining tools. These include corpus search and support for the major steps and types of activity in lexicon building: creation, population and modiication of lexical models; exportation towards formats for both NLP and human use. 1 Overview The Delis project is building a generic toolbox for the interactive corpus based construction of lexical speciications which deal with the levels of lexical semantics, syntax and morphosyntax. The tools are used to build monolingual lexicon fragments for perception and speech act verbs and nouns of English, French, Italian, Danish and Dutch, as well as experimental bi-and multilingual fragments. Users from publishing and transla-tion/documentation participate in the tool speciication work and in practical evaluation. The author would like to thank Ulrich Heid and the other project members for their discussion of the contents of this paper presented in earlier versions. Any infelicities or errors are the author's.
Rotor Retaining Sleeve Design for a 1.12-MW High-Speed PM Machine

Permanent-magnet (PM) synchronous machines (PMSMs) can provide excellent performance in terms of torque density, energy efficiency, and controllability. However, PMs on the rotor are prone to centrifugal force, which may break their physical integrity, particularly at high-speed operation. Typically, PMs are bound with carbon fiber or retained by alloy sleeves on the rotor surface. This paper is concerned with the design of a rotor retaining sleeve for a 1.12-MW 18-kr/min PM machine; its electromagnetic performance is investigated by the 2-D finite-element method (FEM). Theoretical and numerical analyses of the rotor stress are carried out. For the carbon fiber protective measure, the stresses of three PM configurations and three pole filler materials are compared in terms of operating temperature, rotor speed, retaining sleeve thickness, and interference fit. Then, a new hybrid protective measure is proposed and analyzed by the 2-D FEM for operational speeds up to 22 kr/min (1.2 times the rated speed). The rotor losses and machine temperatures with the carbon fiber retaining sleeve and the hybrid retaining sleeve are compared, and the sleeve design is refined. Two rotors using both designs are prototyped and experimentally tested to validate the effectiveness of the developed techniques for PM machines. The developed retaining sleeve makes it possible to operate megawatt PM machines at high speeds of 22 kr/min. This opens doors for many high-power high-speed applications such as turbo-generator, aerospace, and submarine motor drives.
The relationship between perceived effective entrepreneurship education and entrepreneurial intention: the role of perception of university support, perceived creativity disposition and entrepreneurial passion

Entrepreneurship has led to the ever increasing and continuous growing field of entrepreneurship education. However, there are growing concerns about the effectiveness of the programme in forming entrepreneurial intention and the ultimate advancement of enterprising behaviour. Hence, this study investigated the relationship between perceived effective entrepreneurship education and entrepreneurial intention, while considering the role of perception of university support, perceived creativity disposition, entrepreneurial passion for inventing, and entrepreneurial passion for founding a business venture. To validate the model, data from 595 university students were analysed using the Partial Least Squares Structural Equation Modelling (PLS-SEM). The findings showed that all the hypothesised direct relationships were supported except for the relationship between perceived effective entrepreneurship education and entrepreneurial intention. Similarly, the hypothesized mediating relationships were supported. In addition, only two hypothesized moderating relationships were supported, but not the moderating effect of perception of university support on perceived effective entrepreneurship education and entrepreneurial passion for founding. Based on the findings, this study contributes theoretically by extending the use of both the theory of planned behaviour and Shapero’s entrepreneurial event model framework to increase the understanding of the relationship between entrepreneurship education and entrepreneurial intention. Methodologically, this study contributes by employing the hierarchical modelling using PLS-SEM to explain the relationships developed. In practical terms, the findings provide the stakeholders responsible for entrepreneurship development a better picture of the formation of entrepreneurial intentions, as well as the impact of potential venture initiators’ beliefs and perceptions on their intention to commence a business. Overall, it enables the government and the policy-makers to direct thoughts and resources on young adults who are likely to form entrepreneurial intentions, and consequently, create business ventures
Attentional bias following frustration in youth with psychopathic traits

The emotional deficit perspective predicts that youth with psychopathic traits are relatively unresponsive to negative affective cues and display smaller attentional biases for affective stimuli following negative experiences than youth without psychopathic traits. In contrast, because the negative preception hypothesis predicts that youth with psychopathic traits learn to tune out negative affective experiences, it predicts that such youth exhibit greater attentional biases away from sadness-related stimuli following negative experiences than youth without psychopathic traits, and that these biases increase with age. This study was designed to test the conflicting predictions of the emotional deficit perspective and the negative preception hypothesis by administering an affective dot probe task to 135 male and female detained adolescents (13.06 to 17.62 years of age) following a frustration experience. Analyses showed that age moderated the impact of psychopathic traits: as age increased, higher levels of the affective-interpersonal component of psychopathy were associated with increasing attentional bias away from both sadness-related and happiness-related stimuli. These findings provide initial evidence corroborating the negative preception hypothesis in youth with psychopathic traits.
Unbounded Fredholm Operators and Spectral Flow

Abstract We study the gap (= “projection norm” = “graph distance”) topology of the space of all (not necessarily bounded) self-adjoint Fredholm operators in a separable Hilbert space by the Cayley transform and direct methods. In particular, we show the surprising result that this space is connected in contrast to the bounded case. Moreover, we present a rigorous definition of spectral flow of a path of such operators (actually alternative but mutually equivalent definitions) and prove the homotopy invariance. As an example, we discuss operator curves on manifolds with boundary.
Chronic chemotherapeutic stress promotes evolution of stemness and WNT/beta-catenin signaling in colorectal cancer cells: implications for clinical use of WNT-signaling inhibitors

Most solid tumors contain a subfraction of cells with stem/progenitor cell features. Stem cells are naturally chemoresistant suggesting that chronic chemotherapeutic stress may select for cells with increased “stemness”. We carried out a comprehensive molecular and functional analysis of six independently selected colorectal cancer (CRC) cell lines with acquired resistance to three different chemotherapeutic agents derived from two distinct parental cell lines. Chronic drug exposure resulted in complex alterations of stem cell markers that could be classified into three categories: 1) one cell line, HT-29/5-FU, showed increased “stemness” and WNT-signaling, 2) three cell lines showed decreased expression of stem cell markers, decreased aldehyde dehydrogenase activity, attenuated WNT-signaling and lost the capacity to form colonospheres and 3) two cell lines displayed prominent expression of ABC transporters with a heterogeneous response for stem cell markers. While WNT-signaling could be attenuated in the HT-29/5-FU cells by the WNT-signaling inhibitors ICG-001 and PKF-118, this was not accompanied by any selective growth inhibitory effect suggesting that the cytotoxic activity of these compounds is not directly linked to WNT-signaling inhibition. We conclude that classical WNT-signaling inhibitors have toxic off-target activities that need to be addressed for clinical development.
Bypassing a Kinase Activity with an ATP-Competitive Drug

Unfolded proteins in the endoplasmic reticulum cause trans-autophosphorylation of the bifunctional transmembrane kinase Ire1, which induces its endoribonuclease activity. The endoribonuclease initiates nonconventional splicing of HAC1 messenger RNAto trigger the unfolded-protein response (UPR). We explored the role of Ire1's kinase domain by sensitizing it through site-directed mutagenesis to the ATP-competitive inhibitor 1NM-PP1. Paradoxically, rather than being inhibited by 1NM-PP1, drug-sensitized Ire1 mutants required 1NM-PP1 as a cofactor for activation. In the presence of 1NM-PP1, drug-sensitized Ire1 bypassed mutations that inactivate its kinase activity and induced a full UPR. Thus, rather than through phosphorylation per se, a conformational change in the kinase domain triggered by occupancy of the active site with a ligand leads to activation of all known downstream functions.