Miracle-dz/UniFAR-FTUs huggingface dataset:
Higher Criticism for Large-Scale Inference: especially for Rare and Weak effects

In modern high-throughput data analysis, researchers perform a large number of statistical tests, expecting to find perhaps a small fraction of significant effects against a predominantly null background. Higher Criticism (HC) was introduced to determine whether there are any nonzero effects; more recently, it was applied to feature selection, where it provides a method for selecting useful predictive features from a large body of potentially useful features, among which only a rare few will prove truly useful. In this article, we review the basics of HC in both the testing and feature selection settings. HC is a flexible idea, which adapts easily to new situations; we point out simple adaptions to clique detection and bivariate outlier detection. HC, although still early in its development, is seeing increasing interest from practitioners; we illustrate this with worked examples. HC is computationally effective, which gives it a nice leverage in the increasingly more relevant "Big Data" settings we see today. We also review the underlying theoretical "ideology" behind HC. The Rare/Weak (RW) model is a theoretical framework simultaneously controlling the size and prevalence of useful/significant items among the useless/null bulk. The RW model shows that HC has important advantages over better known procedures such as False Discovery Rate (FDR) control and Family-wise Error control (FwER), in particular, certain optimality properties. We discuss the rare/weak phase diagram, a way to visualize clearly the class of RW settings where the true signals are so rare or so weak that detection and feature selection are simply impossible, and a way to understand the known optimality properties of HC.
Long-Term Reward Prediction in TD Models of the Dopamine System

This article addresses the relationship between long-term reward predictions and slow-timescale neural activity in temporal difference (TD) models of the dopamine system. Such models attempt to explain how the activity of dopamine (DA) neurons relates to errors in the prediction of future rewards. Previous models have been mostly restricted to short-term predictions of rewards expected during a single, somewhat artificially defined trial. Also, the models focused exclusively on the phasic pause-and-burst activity of primate DA neurons; the neurons' slower, tonic background activity was assumed to be constant. This has led to difficulty in explaining the results of neurochemical experiments that measure indications of DA release on a slow timescale, results that seem at first glance inconsistent with a reward prediction model. In this article, we investigate a TD model of DA activity modified so as to enable it to make longer-term predictions about rewards expected far in the future. We show that these predictions manifest themselves as slow changes in the baseline error signal, which we associate with tonic DA activity. Using this model, we make new predictions about the behavior of the DA system in a number of experimental situations. Some of these predictions suggest new computational explanations for previously puzzling data, such as indications from microdialysis studies of elevated DA activity triggered by aversive events.
In vivo bone-specific EphB4 overexpression in mice protects both subchondral bone and cartilage during osteoarthritis.

OBJECTIVE In vitro activation of the receptor EphB4 positively affects human osteoarthritis (OA) articular cell metabolism. However, the specific in vivo role of this ephrin receptor in OA remains unknown. We investigated in mice the in vivo effect of bone-specific EphB4 overexpression on OA pathophysiology. METHODS Morphometric, morphologic, and radiologic evaluations were performed on postnatal day 5 (P5) mice and on 10-week-old mice. Knee OA was induced surgically by destabilization of the medial meniscus (DMM) in 10-week-old male EphB4 homozygous transgenic (EphB4-Tg) and wild-type (WT) mice. Medial compartment evaluations of cartilage were performed using histology and immunohistochemistry, and evaluations of subchondral bone using histomorphometry, osteoclast staining, and micro-computed tomography. RESULTS There was no obvious phenotype difference in skeletal development between EphB4-Tg mice and WT mice at P5 or at 10 weeks. At 8 and 12 weeks post-DMM, the EphB4-Tg mice demonstrated significantly less cartilage alteration in the medial tibial plateau and the femoral condyle than did the WT mice. This was associated with a significant reduction of aggrecan and type II collagen degradation products, type X collagen, and collagen fibril disorganization in the operated EphB4-Tg mice. The medial tibial subchondral bone demonstrated a significant reduction in sclerosis, bone volume, trabecular thickness, and number of tartrate-resistant acid phosphatase-positive osteoclasts at both times assessed post-DMM in the EphB4-Tg mice than in the WT mice. CONCLUSION This is the first in vivo evidence that bone-specific EphB4 overexpression exerts a protective effect on OA joint structural changes. The findings of this study stress the in vivo importance of subchondral bone biology in cartilage integrity.
Embodied Design Ideation Methods: Analysing the Power of Estrangement

Embodied design ideation practices work with relationships between body, material and context to enliven design and research potential. Methods are often idiosyncratic and due to their physical nature not easily transferred. This presents challenges for designers wishing to develop and share techniques or contribute to research. We present a framework that enables designers to understand, describe and contextualise their embodied design ideation practices in ways that can be understood by peers, as well as those new to embodied ideation. Our framework developed over two conference workshops provides a frame for discussion of embodied design actions that leverage the power of estrangement. We apply our framework to eight embodied design ideation methods. Our contribution is thus twofold: (1) a framework to understand and leverage the power of estrangement in embodied design ideation, and (2) an inspirational catalogue demonstrating the diversity of ideas that embodied design ideation methods can foster.
Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome

Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.
Emotion in motion.

Background: Individuals with heightened anxiety vulnerability demonstrate a bias favouring attention to negative information, and it has been argued that this reflects a difficulty to disengage from negative information. Methods to manipulate attentional bias have demonstrated inconsistent effectiveness, however such methods have not targeted biases in attentional disengagement specifically. A recently developed approach to attentional bias modification, labelled Emotion-in-Motion, has been proposed to result in facilitated attentional disengagement from information. Thus, the present study empirically investigated whether the Emotion-in-Motion task modifies biased attentional disengagement from negative information using eye-movement recordings. Methods: Forty-four participants completed the Emotion-in-Motion attention manipulation task under conditions designed to enhance attention (Attend Negative) or attenuate attention (Avoid Negative) to negative information. Biased attentional engagement with, and attentional disengagement from, negative information was examined subsequently. Results: Participants in the Avoid Negative condition demonstrated lower levels of biased attentional disengagement from negative information as compared to participants in the Attend Negative condition. No difference in biased attentional engagement with negative information was observed. Conclusions: It is concluded that the Emotion-in-Motion task serves to independently manipulate selective attentional disengagement from negative information and may be useful in investigating the specific role of biased attentional disengagement in emotional vulnerability.
Power and sample size calculations for generalized regression models with covariate measurement error

Covariate measurement error is often a feature of scientific data used for regression modelling. The consequences of such errors include a loss of power of tests of significance for the regression parameters corresponding to the true covariates. Power and sample size calculations that ignore covariate measurement error tend to overestimate power and underestimate the actual sample size required to achieve a desired power. In this paper we derive a novel measurement error corrected power function for generalized linear models using a generalized score test based on quasi‐likelihood methods. Our power function is flexible in that it is adaptable to designs with a discrete or continuous scalar covariate (exposure) that can be measured with or without error, allows for additional confounding variables and applies to a broad class of generalized regression and measurement error models. A program is described that provides sample size or power for a continuous exposure with a normal measurement error model and a single normal confounder variable in logistic regression. We demonstrate the improved properties of our power calculations with simulations and numerical studies. An example is given from an ongoing study of cancer and exposure to arsenic as measured by toenail concentrations and tap water samples. Copyright © 2003 John Wiley & Sons, Ltd.
Cyberscience and the Knowledge-Based Economy. Open Access and Trade Publishing: From Contradiction to Compatibility with Non-Exclusive Copyright Licensing

Open source, open content and open access are set to fundamentally alter the conditions of knowledge production and distribution. Open source, open content and open access are also the most tangible result of the shift towards e-science and digital networking. Yet, widespread misperceptions exist about the impact of this shift on knowledge distribution and scientific publishing. It is argued, on the one hand, that for the academy there principally is no digital dilemma surrounding copyright and there is no contradiction between open science and the knowledge-based economy if profits are made from non-exclusive rights. On the other hand, pressure for the ‘digital doubling’ of research articles in open access repositories (the ‘green road’) is misguided and the current model of open access publishing (the ‘gold road’) has not much future outside biomedicine. Commercial publishers must understand that business models based on the transfer of copyright have not much future either. Digital technology and its economics favour the severance of distribution from certification. What is required of universities and governments, scholars and publishers, is to clear the way for digital innovations in knowledge distribution and scholarly publishing by enabling the emergence of a competitive market that is based on non-exclusive rights. This requires no change in the law but merely an end to the praxis of copyright transfer and exclusive licensing. The best way forward for research organisations, universities and scientists is the adoption of standard copyright licences that reserve some rights, namely Attribution and No Derivative Works, but otherwise will allow for the unlimited reproduction, dissemination and re-use of the research article, commercial uses included.
Robust vehicle edge detection by cross filter method

In visual surveillance, vehicle tracking and identification is very popular and applied in many applications such as traffic incident detection, traffic control and management. Edge detection is the key to the success of vehicle tracking and identification. Edge detection is to identify edge locations or geometrical shape changes in term of pixel value along a boundary of two regions in an image. This paper aims to investigate different edge detection methods and introduce a Cross Filter (CF) method, with a two-phase filtering approach, for vehicle images in a given database. First, four classical edge detectors namely the Canny detector, Prewitt detector, Roberts detector and Sobel detector are tested on the vehicle images. The Canny detected image is found to offer the best performance in Phase 1. In Phase 2, the robust CF, based on a spatial relationship of intensity change on edges, is applied on the Canny detected image as a second filtering process. Visual and numerical comparisons among the classical edge detectors and CF detector are also given. The average DSR of the proposed CF method on 10 vehicle images is 95.57%.
Mitochondrial support of persistent presynaptic vesicle mobilization with age-dependent synaptic growth after LTP

Mitochondria support synaptic transmission through production of ATP, sequestration of calcium, synthesis of glutamate, and other vital functions. Surprisingly, less than 50% of hippocampal CA1 presynaptic boutons contain mitochondria, raising the question of whether synapses without mitochondria can sustain changes in efficacy. To address this question, we analyzed synapses from postnatal day 15 (P15) and adult rat hippocampus that had undergone theta-burst stimulation to produce long-term potentiation (TBS-LTP) and compared them to control or no stimulation. At 30 and 120 min after TBS-LTP, vesicles were decreased only in presynaptic boutons that contained mitochondria at P15, and vesicle decrement was greatest in adult boutons containing mitochondria. Presynaptic mitochondrial cristae were widened, suggesting a sustained energy demand. Thus, mitochondrial proximity reflected enhanced vesicle mobilization well after potentiation reached asymptote, in parallel with the apparently silent addition of new dendritic spines at P15 or the silent enlargement of synapses in adults. DOI: http://dx.doi. org/10.7554/eLife.15275. 001
Neuropeptides Control the Dynamic Behavior of Airway Mucosal Dendritic Cells

The airway mucosal epithelium is permanently exposed to airborne particles. A network of immune cells patrols at this interface to the environment. The interplay of immune cells is orchestrated by different mediators. In the current study we investigated the impact of neuronal signals on key functions of dendritic cells (DC). Using two-photon microscopic time-lapse analysis of living lung sections from CD11c-EYFP transgenic mice we studied the influence of neuropeptides on airway DC motility. Additionally, using a confocal microscopic approach, the phagocytotic capacity of CD11c+ cells after neuropeptide stimulation was determined. Electrical field stimulation (EFS) leads to an unspecific release of neuropeptides from nerves. After EFS and treatment with the neuropeptides vasoactive intestinal peptide (VIP) or calcitonin gene-related peptide (CGRP), airway DC in living lung slices showed an altered motility. Furthermore, the EFS-mediated effect could partially be blocked by pre-treatment with the receptor antagonist CGRP8–37. Additionally, the phagocytotic capacity of bone marrow-derived and whole lung CD11c+ cells could be inhibited by neuropeptides CGRP, VIP, and Substance P. We then cross-linked these data with the in vivo situation by analyzing DC motility in two different OVA asthma models. Both in the acute and prolonged OVA asthma model altered neuropeptide amounts and DC motility in the airways could be measured. In summary, our data suggest that neuropeptides modulate key features motility and phagocytosis of mouse airway DC. Therefore altered neuropeptide levels in airways during allergic inflammation have impact on regulation of airway immune mechanisms and therefore might contribute to the pathophysiology of asthma.
[Systematic review with meta-analysis: Subcutaneous insulin glargine coadministration for diabetic ketoacidosis].

BACKGROUND The standard treatment of diabetic ketoacidosis involves intravenous infusion of regular insulin until recovery of the episode: this is associated with high costs. Coadministration of insulin glargine from the onset of management may prove beneficial, potentially avoiding rebound hyperglycemia, and hopefully improving the time to resolution of the disease. METHODS We searched MEDLINE, EMBASE, and CENTRAL for randomized controlled trials comparing coadministration of insulin glargine versus standard treatment in patients with diabetic ketoacidosis. To be eligible, studies must assess the efficacy of insulin glargine and report clinically important outcomes. Two reviewers extracted data, assessed risk of bias and summarized strength of evidence using the GRADE approach. RESULTS Four studies (135 participants during hospital follow-up) were included in this review. Low-quality evidence from three trials suggested that subcutaneously administered insulin glargine, in addition to the standard treatment, significantly reduces the time to resolution of diabetic ketoacidosis (MD -4.19 hours; 95% CI: -7.81 to 0.57; p = 0.02). There was neutral difference between the two groups regarding length of hospital stay and hypoglycemic episodes. CONCLUSIONS subcutaneously administered insulin glargine, in addition to standard treatment, significantly reduces the time to resolution of diabetic ketoacidosis, with neutral effects on hypoglycemic episodes.
Peer-learning between pre-service teachers: embracing Lesson Study

Purpose – The purpose of this paper is to explore a model of Lesson Study owned entirely by pre-service teachers (PSTs), conveying its potential to facilitate mutual spaces of learning between peers beyond formal hierarchical relationships with expert teachers. Fuller’s (1969) conceptual framework of teacher development informed the study, consisting of self, task and impact “phases of concern”. Design/methodology/approach – Participants were secondary physical education PSTs (n=17), completing a university-led postgraduate certificate in education course. Action research methodology was adopted during school placements, when PSTs engaged in Lesson Study with peers. Data obtained through a group discussion board, individual questionnaires and interviews, were subjected to inductive analysis, with key patterns compared to locate themes. Findings – All PSTs felt Lesson Study contributed positively to their training, reinforcing perceived benefits of cycles of action for planning, observing a lesson, reviewi.
Competências emocionais: estudo de validação de um instrumento de medida

espanolEste trabajo tuvo como objetivo la construccion y evaluacion de las propiedades psicometricas de un Inventario de Competencias Emocionales (ICE). Los 76 items del instrumento representaban cuatro habilidades relacionadas con la inteligencia emocional: percepcion de emociones, uso de emociones para facilitar el pensamiento, comprension de emociones y regulacion de emociones. Se aplico el instrumento a 409 adultos brasilenos, predominantemente mujeres (76,5 %) con edad media de 30,2 anos (DE=11,5) que respondieron a traves de una escala Likert de 5 puntos. Un analisis factorial exploratoria revelo una estructura con cinco factores: percepcion de emociones, regulacion de emociones de baja potencia, expresividad emocional, regulacion de emociones en los otros y regulacion de emociones de alta potencia. Ademas, se observo un patron de correlaciones positivas y significativas con diversos aspectos de la calidad de vida. Se concluyo que el instrumento tiene condiciones psicometricas favorables para recomendar su uso en la investigacion EnglishThis work aimed at the construction and evaluation of the psychometric properties of an Emotional Competence Inventory (ECI). The 76 items of the instrument were constructed to represent four skills related to emotional intelligence: emotional perception, the usage of emotion to facilitating thought, emotional understanding and emotional regulation. The instrument was administered to 409 Brazilian adults, predominantly female (76.5%), with a mean age of 30.2 (SD=11.5), who answered via a five-point Likert scale. An exploratory factor analysis revealed a structure with five factors: emotional perception, regulation of low potency emotions, emotional expressivity, emotional regulation in other people and regulation of high potency emotion. Furthermore, it was observed a pattern of positive and significant correlations with many aspects of quality of life. It was concluded that the instrument has favorable psychometric conditions to recommend its use in research portuguesEste trabalho teve como objetivos a construcao e avaliacao das propriedades psicometricas de um Inventario de Competencias Emocionais (ICE). Os 76 itens do instrumento foram construidos para representar quatro habilidades relacionadas a inteligencia emocional: percepcao de emocoes, uso da emocao para facilitacao do pensamento, compreensao de emocoes e regulacao de emocoes. O instrumento foi aplicado a 409 brasileiros adultos, predominantemente do sexo feminino (76,5%), com idade media de 30,2 anos (DP=11,5), que o responderam em uma escala Likert de cinco pontos. Uma analise fatorial exploratoria revelou uma estrutura com cinco fatores: percepcao de emocoes, regulacao de emocoes de baixa potencia, expressividade emocional, regulacao de emocoes em outras pessoas e regulacao de emocoes de alta potencia. Alem disso, observou-se um padrao de correlacoes positivas e significativas com diversos aspectos da qualidade de vida. Concluiu-se que o instrumento apresenta condicoes psicometricas favoraveis para a recomendacao de seu uso em pesquisas
Attachment styles and relationship quality: Actual, perceived, and ideal partner matching

Attachment dimension matching in dating relationships and how matching relates to relationship quality were investigated. Across 2 studies, individuals preferred similar but more secure partners (lower anxiety and lower avoidance) as reflected by their ideals. In Study 1, greater similarity between the self and perceptions of the partner’s anxiety predicted more positive relationship outcomes (e.g., relationship satisfaction, trust). Similar results were found for ideal–perceived partner avoidance similarity, whereas ideal–perceived partner anxiety similarity was less important. Study 2 involved both partners in the relationship and indicated that relationship outcomes were predicted by the actor’s and partner’s attachment dimensions as well as by ideal–perceived partner similarity and self–perceived partner similarity.