Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the consequences of redirecting an exocytic Rab onto endocytic vesicles

Bidirectional vesicular traffic links compartments along the exocytic and endocytic pathways. Rab GTPases have been implicated in specifying the direction of vesicular transport. To explore this possibility, we sought to redirect an exocytic Rab, Sec4, onto endocytic vesicles by fusing the catalytic domain of the Sec4 GEF, Sec2, onto the CUE localization domain of Vps9, a GEF for the endocytic Rab Ypt51. The Sec2GEF-GFP-CUE construct localized to bright puncta predominantly near sites of polarized growth, and this localization was dependent on the ability of the CUE domain to bind to the ubiquitin moieties added to the cytoplasmic tails of proteins destined for endocytic internalization. Sec4 and Sec4 effectors were recruited to these puncta with various efficiencies. Cells expressing Sec2GEF-GFP-CUE grew surprisingly well and secreted protein at near-normal efficiency, implying that Golgi-derived secretory vesicles were delivered to polarized sites of cell growth despite the misdirection of Sec4 and its effectors. A low efficiency mechanism for localization of Sec2 to secretory vesicles that is independent of known cues might be responsible. In total, the results suggest that while Rabs may play a critical role in specifying the direction of vesicular transport, cells are remarkably tolerant of Rab misdirection.
Estatísticas Cardiovasculares do Programa Boas Práticas em Cardiologia – Dados de um Hospital Público Terciário Brasileiro

Resumo Fundamento O Programa Boas Práticas em Cardiologia é uma iniciativa da Sociedade Brasileira de Cardiologia (SBC) destinada à melhoria do cuidado cardiovascular nos hospitais públicos brasileiros. Objetivos Descrever características dos pacientes internados com Síndrome Coronariana Aguda (SCA) e Insuficiência Cardíaca (IC) e avaliar os indicadores de desempenho alcançados nos braços (SCA e IC) em um hospital público terciário, com uma meta pré-estabelecida de 85% de aderência às recomendações da SBC. Métodos Estudo do tipo transversal descritivo realizado por meio da coleta de dados de pacientes que estiveram internados entre maio de 2016 e setembro de 2019. Resultados Foram incluídos 1036 pacientes, 273 pacientes no braço IC e 763 no braço SCA. A média de idade foi de 59,8 ± 12,0 anos na SCA e 57,0 ± 14,1 anos na IC, com predomínio do sexo masculino em ambos os grupos. Mais da metade dos pacientes não tinham ensino fundamental completo e mais de 90% declararam renda mensal inferior a cinco salários-mínimos. Na SCA, predominou o diagnóstico de SCA com supradesnivelamento do segmento ST (66,3%) e 2,9% dos pacientes foram a óbito. Na IC, a etiologia mais comum foi a Doença de Chagas (25,8%) e 17,9% dos pacientes foram a óbito. Na avaliação dos indicadores de desempenho, nove dos 12 indicadores tiveram taxas de aderência acima de 85%. Conclusão Programas de qualidade são essenciais à melhoria do cuidado e os indicadores de desempenho do hospital apontam para uma boa adesão às diretrizes assistenciais da SBC, particularmente no braço da SCA.
Geometric Optimization of the MSSM Gough-Stewart Platform

This work focuses on analyzing the effects of the geometric parameters on the singularity-free workspace in order to determine the optimal architecture for the minimal simplified symmetric manipulator Gough-Stewart platform. To this end, the reference orientation is taken as the considered orientation because it is an impartial orientation. In this orientation, the singularity surface becomes a plane coinciding with the base plane. Accordingly, an analytic algorithm is developed to determine the singularity-free workspace. The analysis shows that: (1) for similar isosceles triangle base and platform, the optimal architecture is one for which both the base and the platform are equilateral triangles, and the size ratio between the platform and the base is 1/2; and (2) if the base and the platform are not similar triangles, the global optimal architecture is difficult to determine. Only an approximate optimal architecture is available.
Magnesium-25 hyperfine confirmation of the localized-ground-state model of the V$sup -$ center in MgO

The localized-hole model of the ${V}^{\ensuremath{-}}$ center in the alkaline earth oxides is represented as a positive hole trapped on one oxygen atom adjacent to a positive-ion vacancy (in the ground state and on the time scale of an ESR experiment). Upon trapping the hole, the oxygen atom is presumed to relax away from the vacancy, thus lowering the symmetry from octahedral to tetragonal. The validity of this model has recently been challenged on the basis that a proper description of the ground state is a molecular orbital representing a linear combination of states with the hole on either of the two oxygen atoms opposite one another about the vacancy. We present the analysis of some ESR spectra in which we observed the resolved hyperfine splitting due to a single $^{25}\mathrm{Mg}^{2+}$ ion adjacent to the trapped hole and on the axis of the defect. From the natural abundance of the $^{25}\mathrm{Mg}$ isotope one can calculate the expected hyperfine line intensities relative to that of the central line arising from ${V}^{\ensuremath{-}}$ centers having only $^{24}\mathrm{Mg}$ or $^{26}\mathrm{Mg}$ atoms in the axial positions, for the localized and for the delocalized models. The measured relative intensities agree with those calculated for the localized model. An analysis of the axial spectrum indicates the presence of an unusually intense forbidden line at $X$ band. This becomes relatively more intense at the $\mathrm{Ku}$ band, as expected. Shifts of line position and intensity relative to the lines of an allowed hyperfine sextet agree with those predicted. The values of the hyperfine parameters are found to be $A=+2.84$ MHz and $B=\ensuremath{-}0.86$ MHz. The quadrupole parameter is found to be +0.18 MHz. The sign of $A$ is anomalous in that a contact interaction is expected to give an isotropic parameter with the sign of the nuclear magnetic moment. This may result from exchange polarization. The magnitude of $B$ is interpreted as indicating a compact unpaired charge distribution. The ${V}^{\ensuremath{-}}$ centers studied here were generated by fast-neutron irradiation, and there is no confusion with impurity-associated hole centers; the former have a long-term stability in MgO, while the latter decay rapidly to negligible levels at room temperature.
Creatine Deficiency Disorders: Phenotypes, Genotypes, Diagnosis, and Treatment Outcomes

Creatine is synthetized from arginine and glycine. There are two enzymes in the synthesis: l-arginine:glycine amidinotransferase and guanidinoacetate methyltransferase. After the synthesis, it is taken up by high-energy-requiring organs using creatine transporter. Biallelic pathogenic variants in GAMT result in guanidinoacetate methyltransferase deficiency and biallelic pathogenic variants in GATM result in l-arginine:glycine amidinotransferase deficiency. Hemizygous pathogenic variant in males and heterozygous pathogenic variant in females in SLC6A8 result in creatine transporter deficiency. Patients with these disorders present with a wide range of symptoms, including developmental delay, seizures, movement disorder, behavioral problems, and hypotonia. The diagnosis can be suspected by elevated guanidinoacetate and low creatine levels in body fluids in guanidinoacetate methyltransferase deficiency, low guanidinoacetate and low creatine levels in body fluids in l-arginine:glycine amidinotransferase deficiency, and elevated creatine-to-creatinine ratio in urine in creatine transporter deficiency in males as well as absent or significantly decreased creatine level in brain proton magnetic resonance spectroscopy. Genetic investigations such as targeted next-generation sequencing panel or exome sequencing can also identify these disorders; however, metabolite measurements and creatine in proton magnetic resonance spectroscopy are crucial to confirm the diagnosis. While all 3 disorders are currently treated with creatine supplementation, guanidinoacetate methyltransferase deficiency is also treated with ornithine supplementation and a protein- or arginine-restricted diet, and creatine transporter deficiency is treated with arginine and glycine supplementation (with no proven improvements).
Complete Genome Sequence of an Escherichia coli Strain Isolated from Laboratory Mouse Stool for Use as a Chassis for Transgene Delivery to the Murine Microbiome

Tools to explore functional changes in the microbiome are limited. Here, we report the complete genome sequence of a strain of Escherichia coli that was isolated from murine stool. This sequence will provide essential information to further develop this tool, and similar tools, to explore the complex murine microbiome. ABSTRACT Tools to explore functional changes in the microbiome are limited. Here, we report the complete genome sequence of a strain of Escherichia coli that was isolated from murine stool. This sequence will provide essential information to further develop this tool, and similar tools, to explore the complex murine microbiome.
Causes of death of patients with non-valvular atrial fibrillation in Asians

Objectives The aim of this study was to determine the causes of death among Asian non-valvular atrial fibrillation (AF) patients who were registered in a nationwide AF registry, and to investigate the differences in the causes of death in AF patients compared between those who were taking and not taking oral anticoagulant (OAC). Methods The COhort of antithrombotic use and Optimal INR Level in patients with non-valvular Atrial Fibrillation in Thailand (COOL-AF) study enrolled non-valvular AF patients from 27 centers in Thailand during 2014–2017 to create the COOL-AF Thailand registry. Cause of death was classified as cardiovascular (CV) death, non-CV death, or undetermined cause of death. All events were evaluated and verified by an independent adjudication committee. Results There was a total of 3,405 patients (mean age: 67.8 years, 41.8% female), and the mean follow-up duration was 31.8±8.7 months. Three hundred and eighty patients (11.2%) died during follow-up. CV death, non-CV death, and undetermined cause accounted for 121 (31.8%), 189 (49.7%), and 70 (18.4%) patients, respectively. Of those with a known cause of death, heart failure (10%), intracranial hemorrhage (ICH; 10%), sudden cardiac death (6.8%), and ischemic stroke (5.8%) were the most often observed causes of death. Concerning non-CV death, infection/sepsis (27.7%), cancer (5.5%), respiratory (5.2%), and major bleeding (4.5%) were the most prevalent causes of death. The use and type of OAC were found to be major determinants of ICH and major bleeding incidence. Conclusion Death due to ischemic stroke was responsible for only 4.7% of all deaths in Asian AF patients. Non-CV death, such as infection/sepsis or malignancy, was more far more prevalent than CV death in Asian AF patients. An improved integrated care approach is needed to reduce the prevalence of non-CV death in Asian AF patients.
The scalar product in two‐particle relativistic quantum mechanics

In the framework of two‐particle relativistic quantum mechanics, a Poincare‐invariant scalar product and the corresponding physical Hilbert space of states are constructed. This is achieved by finding a tensor current of rank 2, jμν(x1,x2), satisfying two independent conservation laws, relative to particles 1 and 2, respectively. Then the scalar product is obtained by integrating the current jμν over two three‐dimensional spacelike hypersurfaces. The Hermiticity of the Poincare group generators is ensured by the fact that the kernel of the current jμν is translation invariant and covariant. A simple expression of the scalar product is obtained when one chooses for the two spacelike hypersurfaces two constant parallel hyperplanes. The positivity of the norm is, in general, ensured if the spectrum of the eigenvalues of the total mass squared operator comes out to be positive.
Numerical analysis of indirect Auger transitions in InGaN

Indirect phonon-assisted Auger recombination mechanisms in bulk InGaN are investigated in the framework of perturbation theory, using first-principles phonon spectral density functions and electronic structures obtained by nonlocal empirical pseudopotential calculations. Nonpolar carrier-phonon interactions are treated within the rigid pseudoion framework, thus avoiding the introduction of empirical deformation potentials. The calculated indirect Auger coefficients exhibit a weak temperature dependence and dominate over direct processes for alloy compositions corresponding to the entire visible spectrum. The present results suggest that indirect Auger processes may be relevant in the operation of InGaN-based light-emitting diodes and lasers, at least in the yellow-green spectral region.
The effect of 4 weeks of high‐intensity interval training and 2 weeks of detraining on cardiovascular disease risk factors in male adolescents

What is the central question of this study? What is the effect of 4 weeks of high‐intensity interval training (HIIT) and 2 weeks of detraining on vascular function and traditional cardiovascular disease (CVD) risk factors in male adolescents? What is the main finding and its importance? Four weeks of HIIT improved macrovascular function in adolescents. However, this training period did not measurably change microvascular function, body composition or blood biomarkers. Following 2 weeks of detraining, the improvement in flow‐mediated dilatation (FMD) was lost. This highlights the importance of the continuation of regular exercise for the primary prevention of CVD.
On the orthogonality of anti-leakage Fourier transform based seismic trace interpolation

Summary Seismic data regularization, which aims to estimate the seismic traces on a spatially regular grid using the a cquired irregular sampled data, is an interpolation/extrapolation problem. Sampling theory offers the basic conditions for all the seismic data regularization implementations. In sampling theory, Fourier transform plays a crucial role in the analysis of the reconstruction/interpolation basis (interpolant); it estimates the frequency components in frequency/wave-number domain, and its inverse transform creates the seismic data on the desired regular grid. Difficulties arise from the non-orthogonality of the global Fourier basis on an irregular grid, which results in the energy from one frequency component leaks onto others. This well-known phenomenon is called “spectral leakage”. The updated Fourier transform: Anti-leakage Fourier transform (ALFT) offers to overcome the above mentioned difficulties. It estimates the spatial frequency content on a n irregularly sampled grid with significantly reduced frequency leakage. In this paper, we investigate the properties of ALFT and give an insight on how it works. The interpolants are numerically calculated and analyzed in detail. The orthogonality condition of the interpolants is discussed, which demonstrates that the ALFT data reconstruction meets the two most important interpolation conditions (e.g. orthogonal condition and unity condition). With the amplitude analysis on interpolants, the stability of ALFT algorithm is also addressed.
A note on the image system for a stokeslet in a no-slip boundary

Abstract The velocity and pressure fields for Stokes's flow due to a point force (‘stokeslet’) in the vicinity of a stationary plane boundary are analysed, using Fourier transforms, to obtain the image system required to satisfy the no-slip condition on the boundary. The image system, which is illustrated by diagrams, is found to consist of a stokeslet equal in magnitude but opposite in sign to the initial stokeslet, a stokes-doublet and a source-doublet, the displacement axes for the doublets being in the original direction of the force. The influence of the wall on the near and far fields is discussed. In the far field it is found that a stokeslet aligned parallel to the wall produces a stokes-doublet far-field, whereas a stokeslet normal to the wall produces a combination of a source-doublet and a stokes-quadrupole far-field. Although results can be alternatively derived by the method of Lorentz (7) using a reciprocal theorem, the present method yields much more clearly the form of the image system.
Constructivist Tokenization for English

This paper revisits tokenization from a theoretical perspective, and argues for the necessity of a constructivist approach to tokenization for semantic parsing and modeling language acquisition. We consider two problems: (1) (semi-) automatically converting existing lexicalist annotations, e.g. those of the Penn TreeBank, into constructivist annotations, and (2) automatic tokenization of raw texts. We demonstrate that (1) a heuristic rule-based constructivist tokenizer is able to yield relatively satisfactory accuracy when gold standard Penn TreeBank part-of-speech tags are available, but that some manual annotations are still necessary to obtain gold standard results, and (2) a neural tokenizer is able to provide accurate automatic constructivist tokenization results from raw character sequences. Our research output also includes a set of high-quality morpheme-tokenized corpora, which enable the training of computational models that more closely align with language comprehension and acquisition.
Analyse syntaxique de langues faiblement dotées à partir de plongements de mots multilingues [Syntactic analysis of under-resourced languages from multilingual word embeddings]

RÉSUMÉ. Cet article présente une tentative pour appliquer des méthodes d’analyse syntaxique performantes, à base de réseaux de neurones récursifs, à des langues pour lesquelles on dispose de très peu de ressources. Nous proposons une méthode originale à base de plongements de mots multilingues obtenus à partir de langues plus ou moins proches typologiquement, aﬁn de déterminer la meilleure combinaison de langues possibles pour l’apprentissage. L’approche a permis d’obtenir des résultats encourageants dans des contextes considérés comme linguisti-quement difﬁciles. Le code source est disponible en ligne (voir ABSTRACT. This article presents an attempt to apply efﬁcient parsing methods based on recur-sive neural networks to languages for which very few resources are available. We propose an original approach based on multilingual word embeddings acquired from different languages so as to determine the best language combination for learning. The approach yields competitive results in contexts considered as linguistically difﬁcult. nord,
Semgrex and Ssurgeon, Searching and Manipulating Dependency Graphs

Searching dependency graphs and manipulating them can be a time consuming and challenging task to get right. We document Semgrex, a system for searching dependency graphs, and introduce Ssurgeon, a system for manipulating the output of Semgrex. The compact language used by these systems allows for easy command line or API processing of dependencies. Additionally, integration with publicly released toolkits in Java and Python allows for searching text relations and attributes over natural text.
Predicates and entities in Abstract Meaning Representation

Nodes in Abstract Meaning Representation (AMR) are generally thought of as neo-Davidsonian entities. We review existing translation into neo-Davidsonian representations and show that these translations inconsistently handle copula sentences. We link the problem to an asymmetry arising from a problematic handling of words with no associated PropBank frames for the underlying predicate. We introduce a method to automatically and uniformly decompose AMR nodes into an entity-part and a predicative part, which offers a consistent treatment of copula sentences and quasi- predicates such as brother or client.
Apprentissage profond pour le traitement automatique des langues [Deep Learning for Natural Language Procesing]

RÉSUMÉ. Ces dernières décennies, les réseaux de neurones artiﬁciels et plus généralement leur apprentissage dit profond ont renouvelé les perspectives de recherche en traitement automa-tique des langues (TAL). Par leur capacité en termes d’apprentissage de représentations, les réseaux neuronaux ont permis des avancées importantes pour le TAL et ce pour de nombreuses tâches par exemple l’analyse syntaxique, la classiﬁcation de documents, la reconnaissance au-tomatique de la parole et la traduction automatique. Néanmoins, ces évolutions récentes posent de nombreuses questions scientiﬁques. Si les performances obtenues par les modèles neuronaux impressionnent souvent, les architectures déployées sont complexes à concevoir et à optimiser. La vision de ces modèles comme une boîte noire est problématique tant l’interprétation des résultats et la compréhension de ce qui est appris restent obscures. Ce numéro spécial propose donc d’explorer les apports de l’apprentissage profond pour le TAL, d’en montrer à la fois les promesses, les limites et les singularités. ABSTRACT. During the last decades, artiﬁcial neural networks and deep learning approaches have strongly renewed the research perspectives in Natural Language Processing (NLP). Neural networks provide an efﬁcient way for representation learning, yielding important improvement in several tasks. These tasks include document classiﬁcation, syntactic parsing, automatic speech recognition and machine translation. Whereas the performances achieved by neural networks are impressive, their conception and optimization are still challenging. Moreover, these architectures are merely understood as efﬁcient black boxes and their results remain difﬁcult to interpret and explain. This special issue explores contributions of deep learning to NLP, their promises along with their limits and peculiarities. MOTS-CLÉS
Character-level Dependency Annotation of Chinese

In this paper, we propose a new model for annotating dependency relations at the Mandarin character level with the aim of building treebanks to cope with the unsatisfactory performance of existing word segmentation and syntactic analysis models in specific scientific domains, such as Chinese patent texts. The result is a treebank of 100 sentences annotated according to our scheme, which also serves as a training corpus that facilitates the subsequent development of a joint word segmenter and dependency analyzer that enables downstream tasks in Chinese to be separated from the non-standardized pre-processing step of word segmentation.
Measure words are measurably different from sortal classifiers

Nominal classifiers categorize nouns based on salient semantic properties. Past studies have long debated whether sortal classifiers (related to intrinsic semantic noun features) and mensural classifiers (related to quantity) should be considered as the same grammatical category. Suggested diagnostic tests rely on functional and distributional criteria, typically evaluated in terms of isolated example sentences obtained through elicitation. This paper offers a systematic re-evaluation of this long-standing question: using 981,076 nominal phrases from a 489 MB dependency-parsed word corpus, corresponding extracted contextual word embeddings from a Chinese BERT model, and information-theoretic measures of mutual information, we show that mensural classifiers can be distributionally and functionally distinguished from sortal classifiers justifying the existence of distinct syntactic categories for mensural and sortal classifiers. Our study also entails broader implications for the typological study of classifier systems.
Préface [Foreword]

En linguistique, et à plus forte raison en morphologie, ces quarante dernières années ont vu revenir au devant de la scène des principes théoriques et descriptifs qu’avaient partiellement occultés plusieurs décennies d’hégémonie du courant générativiste. Plusieurs événements ont directement ou indirectement, contribué à ce revirement, la période charnière étant la reconnaissance, de la part de Noam Chomsky, de l’indépendance de la morphologie, qu’il n’assimile plus, à partir de (Chomsky 1970), à une branche de la syntaxe :