Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting chemical–protein relations with ensembles of SVM and deep learning models

Abstract Mining relations between chemicals and proteins from the biomedical literature is an increasingly important task. The CHEMPROT track at BioCreative VI aims to promote the development and evaluation of systems that can automatically detect the chemical–protein relations in running text (PubMed abstracts). This work describes our CHEMPROT track entry, which is an ensemble of three systems, including a support vector machine, a convolutional neural network, and a recurrent neural network. Their output is combined using majority voting or stacking for final predictions. Our CHEMPROT system obtained 0.7266 in precision and 0.5735 in recall for an F-score of 0.6410 during the challenge, demonstrating the effectiveness of machine learning-based approaches for automatic relation extraction from biomedical literature and achieving the highest performance in the task during the 2017 challenge. Database URL: http://www.biocreative. org/tasks/biocreative-vi/track-5/
Ultrastructural alterations in the retinal pigment epithelium and photoreceptors of a Stargardt patient and three Stargardt mouse models: indication for the central role of RPE melanin in oxidative stress

Background Stargardt disease (SD) is characterized by the accumulation of the age-pigment lipofuscin in the retinal pigment epithelium (RPE) and subsequent neuroretinal degeneration. The disease leads to vision loss early in life. Here, we investigate age-dependent ultrastructural changes in three SD mouse models: albino Abca4-/- and pigmented Abca4-/- and Abca4-/-. Rdh8-/- mice. Since we found indications for oxidative stress primarily in albino SD mice, we tested RPE melanin for its antioxidative capabilities. Methods SD mouse eyes were investigated by light, fluorescence and electron microscopy and were compared to the respective albino and pigmented wild type mice and to a human donor SD eye. To confirm the role of RPE melanin in scavenging oxidative stress, melanin from S. officinalis as a standard and porcine RPE were tested for their capability to quench superoxide anions. Results Histological alterations indicative of oxidative stress and/or lysosomal dysfunction were present in albino Abca4-/- and Abca4-/-. Rdh8-/- mice. Retinal damage, such as inner segment rupture and pyknotic or free photoreceptor nuclei in the subretinal space and RPE vacuolization were exclusively found in albino Abca4-/- mice. Shortened and disorganized photoreceptor outer segments and dead RPE cells were found in albino Abca4-/- and Abca4-/-. Rdh8-/- mice, with earlier onset in albino Abca4-/- mice. Undegraded phagosomes and lipofuscin accumulation were present in the RPE of all three SD strains, but numbers were highest in Abca4-/-. Rdh8-/- mice. Lipofuscin morphology differed between SD strains: (melano-)lipofuscin granules in pigmented Abca4-/- mice had a homogenous electron density and sharp demarcations, while lipofuscin in albino Abca4-/- mice had a flocculent electron density and often lacked a surrounding membrane, indicating loss of lysosomal integrity. Young Abca4-/-. Rdh8-/- mice showed (melano-)lipofuscin granules with homogenous electron density, while in aged animals granules with flocculent electron density predominated. Both strains of pigmented SD mice had melanolipofuscin clusters as found in the human SD eye. Like melanin from S. officinalis, porcine RPE melanin can also quench superoxide anions. Discussion The presented pathologies in albino Abca4-/- and Abca4-/-. Rdh8-/- mice suggest oxidative stress and/or lysosomal dysfunction within the RPE. Since albino Abca4-/- mice have the earliest onset and severest damage and as absence of melanin and also melanin turnover with age are known to diminish RPEs anti-oxidative properties, we assume that RPE melanin plays a role in SD related damages. A lack of pathology in pigmented Abca4-/- mice due to lower stress levels as compared to the Abca4-/-. Rdh8-/- mice underlines this hypothesis. It is also supported by the finding that RPE melanin can quench superoxide anions. We therefore suppose that RPE melanin is important in retinal health and we discuss its role as an oxidative stress scavenger.
The Functional Neuroanatomy of Lexical Tone Perception: An Activation Likelihood Estimation Meta-Analysis

In tonal language such as Chinese, lexical tone serves as a phonemic feature in determining word meaning. Meanwhile, it is close to prosody in terms of suprasegmental pitch variations and larynx-based articulation. The important yet mixed nature of lexical tone has evoked considerable studies, but no consensus has been reached on its functional neuroanatomy. This meta-analysis aimed at uncovering the neural network of lexical tone perception in comparison with that of phoneme and prosody in a unified framework. Independent Activation Likelihood Estimation meta-analyses were conducted for different linguistic elements: lexical tone by native tonal language speakers, lexical tone by non-tonal language speakers, phoneme, word-level prosody, and sentence-level prosody. Results showed that lexical tone and prosody studies demonstrated more extensive activations in the right than the left auditory cortex, whereas the opposite pattern was found for phoneme studies. Only tonal language speakers consistently recruited the left anterior superior temporal gyrus (STG) for processing lexical tone, an area implicated in phoneme processing and word-form recognition. Moreover, an anterior-lateral to posterior-medial gradient of activation as a function of element timescale was revealed in the right STG, in which the activation for lexical tone lied between that for phoneme and that for prosody. Another topological pattern was shown on the left precentral gyrus (preCG), with the activation for lexical tone overlapped with that for prosody but ventral to that for phoneme. These findings provide evidence that the neural network for lexical tone perception is hybrid with those for phoneme and prosody. That is, resembling prosody, lexical tone perception, regardless of language experience, involved right auditory cortex, with activation localized between sites engaged by phonemic and prosodic processing, suggesting a hierarchical organization of representations in the right auditory cortex. For tonal language speakers, lexical tone additionally engaged the left STG lexical mapping network, consistent with the phonemic representation. Similarly, when processing lexical tone, only tonal language speakers engaged the left preCG site implicated in prosody perception, consistent with tonal language speakers having stronger articulatory representations for lexical tone in the laryngeal sensorimotor network. A dynamic dual-stream model for lexical tone perception was proposed and discussed.
Information in Stock and Bond Markets

In the paper, the proxy for trading intensity activity is the time between trades (Dufour and Engle 2000). Furfine and Remolona state that trades during crisis periods may reflect far more information above and beyond the information being conveyed by their increased rate of arrival. It is not clear, however, what kind of information is conveyed by rate of arrival of trades in the government bond markets.
International Association for Chinese Management Research Dissertation Grant and Workshop Topic: Indigenous Management Research in China

In general terms, indigenous research is any study about a uniquely local phenomenon that examines its local (emic) implications and/or its global (etic) implications. Whether a study is indigenous or not can be judged by a simple rule that the study involves at least one construct or variable unique to a local phenomenon. Further, the quality of an indigenous study can be assessed by the novel contribution of such unique construct or variable in terms of building new theories or revising the extant theories. This can be a working definition of indigenous research with two central features: providing unique and novel perspectives concerning a local phenomenon.
Proton Mr Spectroscopy in Brain Metabolic Disorders Diagnostic-specific H-mrs Changes

Metabolic disorders of the central nervous system (CNS) include pathologies with extremely different pathogenesis. The clinical diagnosis of these disorders is often very difficult and requires sophisticated laboratory investigations. Proton magnetic resonance (MR) spectroscopy (1H-MRS) has been recently used in a number of clinical studies to supplement conventional MRI as it is able to provide in vivo biochemical assay of a given brain tissue. Brain data on several neurometabolic diseases suggest that 1H-MRS can provide in vivo chemical-pathological characterization of the abnormality detected by MRI and can detect metabolic alterations in tissue appearing normal on conventional MRI. This may help for differential diagnosis and can be important in the evaluation of disease outcome. Indices provided by 1H-MRS have been demonstrated to be relevant to patients’ clinical status, to represent sensitive indicators of early neurological involvement and to be helpful in monitoring effects of therapeutic interventions. This suggests that, in the next future, a more extensive use of brain 1H-MRS in the management of patients with metabolic disorders affecting CNS should be encouraged.
Cs/cns/ee 253: Advanced Topics in Machine Learning Topic: When Precisely Does Active Learning Help?

Definition 11.1. 2 (Volume of a version space) The volume of the version space is the total prior probability mass of its hypotheses. Thus, given a prior Pr[·] on H, we have vol(V) = h∈V Pr[h] (11.1.2) Recall from last lecture that the goal of the myopic strategy is to maximize the expected shrinkage of the version space. Formally, this can be done by picking max i min b∈{−1,1} As shown in the last lecture, if a random hypothesis h ∈ H is drawn according to the prior Pr[·], then the the myopic strategy makes at most 4 log 1 min Pr[h] times as many queries in expectation as any possible strategy makes in expectation. Example in 1D: Suppose our data lie in [0, 1]. Consider the following threshold hypotheses H := {h τ : τ ∈ [0, 1]} where h τ (x) := 1 if x ≥ τ −1 otherwise Suppose we have a uniform prior on hypotheses. Refer to the accompanying figures. If we have evenly spaced unlabeled data points along the interval [0, 1], then the myopic strategy is just ordinary binary search.
Impact of breast milk on IQ , brain size and white matter development

Although observational findings linking breast milk to higher scores on cognitive tests may be confounded by factors associated with mothers’ choice to breastfeed, it has been suggested that one or more constituents of breast milk facilitate cognitive development, particularly in preterms. Because cognitive scores are related to head size, we hypothesised that breast milk mediates cognitive effects by affecting brain growth. We used detailed data from a randomized feeding trial to calculate percentage of breast milk (%EBM) in the infant diet of 50 adolescents. MRI scans were obtained (mean age=15y9m), allowing volumes of total brain (TBV), white and grey matter (WMV, GMV) to be calculated. In the total group %EBM correlated significantly with Verbal IQ (VIQ); in boys, with all IQ scores, TBV and WMV. VIQ was, in turn, correlated with WMV and, in boys only, additionally with TBV. No significant relationships were seen in girls or with grey matter. These data support the hypothesis that breast milk promotes brain development, particularly white matter growth. The selective effect in males accords with animal and human evidence regarding gender effects of early diet. Our data have important neurobiological and public health implications and identify areas for future mechanistic study. Numerous studies report that breastfeeding is associated with higher scores on tests of neurodevelopment and cognition in later life (1,2), suggesting that breast milk may impact early brain development, with potentially important biological, medical and social Copyright © 2009 International Pediatric Research Foundation, Inc. All rights reserved. Corresponding Author: Elizabeth Isaacs PhD Nutrition Unit UCL Institute of Child Health 30 Guilford Street London WC1N 1EH, UK Telephone: 44 (0)20 795
What are inflectional paradigms

In this chapter, I examine the defining characteristics of inflectional paradigms (Section 1.1). A central issue in morphological theory is whether inflectional paradigms have theoretical significance. According to paradigm-based theories of inflection (e.g. those of Stump 2001, Blevins 2006, Ackerman, Blevins and Malouf 2009, Brown and Hippisley 2012), the definition of a language's inflectional morphology makes essential reference to the structure of paradigms; but according to morpheme-based theories (e.g. those of Halle and Marantz 1993, Bobaljik 2002, Muller 2002), paradigms are instead merely an epiphenomenal effect of principles of morpheme combination, having no essential role in the definition of a language's inflectional morphology. I compare the morpheme-based perspective (Section 1.2) with the paradigm-based approach (Section 1.3); of these, only the latter is compatible with two central hypotheses for which I argue in this book: the irreducibility hypothesis and the interface hypothesis. What is an inflectional paradigm? In a language with inflectional morphology, morphosyntactic properties are grammatical properties to which the language's syntax and morphology are both sensitive. In French, for example, the gender properties “feminine” and “masculine” and the number properties “singular” and “plural” are morphosyntactic properties. On one hand, syntactic agreement relations are sensitive to contrasts in gender and number; thus, the noun phrase in (1) is grammatical because its constituents agree in gender and number, and the noun phrase in (2) is ungrammatical because its constituents fail to agree in this way. At the same time, rules of inflectional morphology are likewise sensitive to contrasts in gender and number; thus, the French adjective national has distinct feminine and masculine forms in the plural (feminine plural nationales /nasjɔnal/, masculine plural nationaux /nasjɔno/), while in the singular, the feminine and masculine forms of national are distinguished orthographically though not phonologically (feminine singular nationale , masculine singular national , both /nasjɔnal/). (1) les musees nationaux the. pl museum. masc.pl national. masc.pl ‘the national museums’ (2) *le musees nationales the. masc.sg museum. masc.pl national. fem.pl Some morphosyntactic properties have specific semantic correlates; thus, noun phrases with singular reference tend to be headed by nouns in their singular form. But morphosyntactic properties may also lack any obvious semantic correlate; thus, while noun phrases with female reference may tend to be headed by feminine nouns, some feminine nouns (e.g. recrue ‘recruit,’ sentinelle ‘sentinel’) ordinarily have male reference and others – in fact, the large majority – fail to refer specifically to either sex ( souris ‘mouse,’ table ‘table,’ invention ‘invention,’ and so on).
Reflections On Symmetry In Chemistry And Elsewhere

reflections on symmetry in chemistry and elsewhere is available in our book collection an online access to it is set as public so you can get it instantly. Our digital library saves in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Merely said, the reflections on symmetry in chemistry and elsewhere is universally compatible with any devices to read.
The dynamical Mordell-Lang problem for Noetherian spaces

Let X be a Noetherian space, let Φ : X −→ X be a continuous function, let Y ⊆ X be a closed set, and let x ∈ X. We show that the set S := {n ∈ N : Φn(x) ∈ Y } is a union of at most finitely many arithmetic progressions along with a set of Banach density zero. In particular, we obtain that given any quasi-projective variety X, any rational map Φ : X −→ X, any subvariety Y ⊆ X, and any point x ∈ X whose orbit under Φ is in the domain of definition for Φ, the set S is a finite union of arithmetic progressions together with a set of Banach density zero. This answers a question posed by Laurent Denis [7]. We prove a similar result for the backward orbit of a point and provide some quantitative bounds.
Objeto de aprendizagem para o ensino de química : alotropia e a história da áfrica

Este trabalho tem como proposito descrever e analisar o processo de elaboracao do objeto de aprendizagem Alotropia e Africa, proposto por alunos do curso de Licenciatura em Quimica, da Universidade Federal de Uberlândia, Minas Gerais, Brasil, para ensinar conceitos ligados a Quimica articulados a conhecimentos de matriz africana e da cultura afro-brasileira. O material foi projetado no intuito de contribuir para por em pratica a Lei 10. 639/2003, que trata da obrigatoriedade de inclusao da tematica "Historia e Cultura Afro-Brasileira" no ensino fundamental e medio. Alem disso, quer possibilitar, nos licenciandos envolvidos no projeto, olhares para a Africa que possibilitem romper com o silencio, desconhecimento e representacoes eurocentricas.
Machine Learning for the Knowledge Plane

The field of machine learning has made major strides over the last 20 years. This document summarizes the major problem formulations that the discipline has studied, then reviews three tasks in cognitive networking and briefly discusses how aspects of those tasks fit these formulations. After this, it discusses challenges for machine learning research raised by Knowledge Plane applications and closes with proposals for the evaluation of learning systems developed for these problems. B1. Background and Motivation Recently, Clark (2002) and Partridge (2003) have proposed a new vision for computer network management—the Knowledge Plane—that would augment the current paradigm of low-level data collection and decision making with higher-level processes. One key idea is that the Knowledge Plane would learn about its own behavior over time, making it better able to analyze problems, tune its operation, and generally increase its reliability and robustness. This suggests the incorporation of concepts and methods from machine learning (Langley, 1995; Mitchell, 1997), an established field that is concerned with such issues. Machine learning aims to understand computational mechanisms by which experience can lead to improved performance. In everyday language, we say that a person has `learned' something from an experience when he can do something he could not, or could not do as well, before that experience. The field of machine learning attempts to characterize how such changes can occur by designing, implementing, running, and analyzing algorithms that can be run on computers. The discipline draws on ideas from many other fields, including statistics, cognitive psychology, information theory, logic, complexity theory, and operations research, but always with the goal of understanding the computational character of learning.
On Circuits and Subgraphs of Chromatic Graphs 9. Erd~s

A graph is said to be k-chromatic if its vertices can be split into k classes so that two vertices of the same class ase not connected (by an edge) and such a splitting is not possible for 7c-1 classes. Tutte was the first to show that for every k there is a k-chromatic graph which contains no triangle [l]. The lower girth of a graph is defined as the smallest integer t so that our graph has a circuit oft edges. J. B. Kelly and L. M. Kelly [2] showed that there exist graphs of arbitrarily high chromatic number and lower girth 6. I proved [3] that for every t and Ic there is a graph of chromatic number L and lower girth t. In fact I showed the following sharper result : To every k there is an E so that for n > q,(c, Ic) there is a Gcn) (GC”) will denote a graph of n vertices, Glfi) will denote a graph with n vertices and 1 edges) of chromatic number Ic and lower girth > E logn. We shall show that in some sense this result is best possible. First we introduce some notations, f(m, L ; n) denotes the maximum of the chromatic number of all graphs G”), every subgraph of m vertices of which has chromatic number not exceeding k ; g,(n) is the largest integer for which there is a I? (~) of chromatic number k and lower girth g,(n). Clearly g,(a) is the largest odd integer not exceeding n (since every odd circuit has chromatic number 3). For k > 3 the determination of g,+(N) seems very difficult. In [3] I proved? CC,, cg, . will denote suitable positive constants) log n src(n) > CllogE * (1)
St Reading Rotated Problems and Rotationally Invariant Crossover in Evolutionary Multi-objective Optimization

Problems that are not aligned with the coordinate system can present difficulties to many 15 optimization algorithms, including evolutionary algorithms, by trapping the search on a ridge. The ridge problem in single-objective optimization is understood, but until now 17 little work has been done on understanding this issue in the multi-objective domain. Multiobjective problems withparameter interactions present difficulties to an optimization algo19 rithm,which are not present in the single-objective domain. In this work,we have explained the nature of these difficulties, and investigated the behavior of the NSGA-II, which has 21 difficulties with problems not aligned with the principle coordinate system. This study has investigated Simplex Crossover (SPX), Unimodal Normally Distributed Crossover 23 (UNDX), Parent-Centric Crossover (PCX), and Differential Evolution (DE), as possible alternatives to the Simulated Binary Crossover (SBX) operator within the NSGA-II, on 25 problems exhibiting parameter interactions through a rotation of the coordinate system. An analysis of these operators on three rotated bi-objective test problems, and a four27 and eight-objective problem is provided. New observations on the behavior of rotationally invariant crossover operators in the multi-objective problem domain have been reported. 29