Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient Loss-Based Decoding On Graphs For Extreme Classification

In extreme classification problems, learning algorithms are required to map instances to labels from an extremely large label set. We build on a recent extreme classification framework with logarithmic time and space, and on a general approach for error correcting output coding (ECOC) with loss-based decoding, and introduce a flexible and efficient approach accompanied by theoretical bounds. Our framework employs output codes induced by graphs, for which we show how to perform efficient loss-based decoding to potentially improve accuracy. In addition, our framework offers a tradeoff between accuracy, model size and prediction time. We show how to find the sweet spot of this tradeoff using only the training data. Our experimental study demonstrates the validity of our assumptions and claims, and shows that our method is competitive with state-of-the-art algorithms.
DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment

The current study investigates DNA methylation as a possible epigenetic regulator of transcription associated with aging and cognitive function. Young and aged male Fischer 344 rats were behaviorally characterized on a set shifting task, and whole genome bisulfite sequencing was employed to profile the DNA methylome of the medial prefrontal cortex (mPFC). DNA methylation was also compared to RNA expression in the mPFC from the same animals. Variability in methylation was mainly observed for CpG sites as opposed to CHG and CHH sites. Gene bodies, specifically introns, contain the highest levels of methylation. During aging, hypermethylation was observed for genes linked to synaptic function and GTPase activity. Furthermore, impaired cognitive flexibility during aging was associated with hypermethylation of genes linked to postsynaptic density, dendrites, the axon terminus, and Ca2+ channels. Finally, comparison with RNA expression confirmed that hypermethylation was correlated with decreased expression of synaptic genes. The results indicate that DNA methylation over the lifespan contributes to synaptic modification observed in brain aging and age-related cognitive impairment.
Differential Allocation by Female Zebrafish (Danio rerio) to Different-Sized Males – An Example in a Fish Species Lacking Parental Care

Organisms allocate resources to reproduction in response to the costs and benefits of current and future reproductive opportunities. According to the differential allocation hypothesis, females allocate more resources to high-quality males. We tested whether a fish species lacking parental care (zebrafish, Danio rerio) expresses male size-dependent differential allocation in monogamous spawning trials. In addition, we tested whether reproductive allocation by females is affected by previous experience of different-quality males, potentially indicating plasticity in mate choice. To that end, females were conditioned to large, small or random-sized males (controls) for 14 days to manipulate females' expectations of the future mate quality. Females showed a clear preference for large males in terms of spawning probability and clutch size independent of the conditioning treatment. However, when females experienced variation in male size (random-sized conditioning treatment) they discriminated less against small males compared to females conditioned to large and small males. This might suggest that differential allocation and size-dependent sexual selection is of less relevance in nature than revealed in the present laboratory study.
Smart systems related to polypeptide sequences

Increasing interest for the application of polypeptide-based smart systems in the biomedical field has developed due to the advantages given by the peptidic sequence. This is due to characteristics of these systems, which include: biocompatibility, potential control of degradation, capability to provide a rich repertoire of biologically specific interactions, feasibility to self-assemble, possibility to combine different functionalities, and capability to give an environmentally responsive behavior. Recently, applications concerning the development of these systems are receiving greater attention since a targeted and programmable release of drugs (e.g. anti-cancer agents) can be achieved. Block copolymers are discussed due to their capability to render differently assembled architectures. Hybrid systems based on silica nanoparticles are also discussed. In both cases, the selected systems must be able to undergo fast changes in properties like solubility, shape, and dissociation or swelling capabilities. This review is structured in different chapters which explain the most recent advances on smart systems depending on the stimuli to which they are sensitive. Amphiphilic block copolymers based on polyanionic or polycationic peptides are, for example, typically employed for obtaining pH-responsive systems. Elastin-like polypeptides are usually used as thermoresponsive polymers, but performance can be increased by using techniques which utilize layer-by-layer electrostatic self-assembly. This approach offers a great potential to create multilayered systems, including nanocapsules, with different functionality. Recent strategies developed to get redox-, magnetic-, ultrasound-, enzyme-, light- and electric-responsive systems are extensively discussed. Finally, some indications concerning the possibilities of multi-responsive systems are discussed.
Tuberculosis and lung damage: from epidemiology to pathophysiology

A past history of pulmonary tuberculosis (TB) is a risk factor for long-term respiratory impairment. Post-TB lung dysfunction often goes unrecognised, despite its relatively high prevalence and its association with reduced quality of life. Importantly, specific host and pathogen factors causing lung impairment remain unclear. Host immune responses probably play a dominant role in lung damage, as excessive inflammation and elevated expression of lung matrix-degrading proteases are common during TB. Variability in host genes that modulate these immune responses may determine the severity of lung impairment, but this hypothesis remains largely untested. In this review, we provide an overview of the epidemiological literature on post-TB lung impairment and link it to data on the pathogenesis of lung injury from the perspective of dysregulated immune responses and immunogenetics. Host factors driving lung injury in TB likely contribute to variable patterns of pulmonary impairment after TB http://ow.ly/a3of30hBsxB
Effect of EDTA on the bioavailability to rats of fortification iron used in Egyptian balady bread

The effectiveness of EDTA compounds on iron fortificants for potential use in Egyptian balady bread was tested in sixty SpragueDawley weanling male rats by the haemoglobin regeneration efficiency (HRE) method. To confirm HRE-derived findings, eight groups of ten animals were repleted with a modified American Institute of Nutrition (1977; AIN) 76A diet, fortified with ferric phosphate, electrolytic Fe, carbonyl Fe or ferrous sulphate, with and without ascorbic acid. Results without ascorbic acid were comparable to findings of a human study by Forbes et al. (1989). Bioavailability of EDTA-enhanced fortificants, FeSO4 + Na2EDTA and NaFe(III)EDTA, was compared with that of FeSO4 in six groups of ten animals repleted with a ground Egyptian bread meal or a casein-based AIN diet fortified with one of the three compounds. Addition of either EDTA compound significantly increased bioavailability of Fe in Egyptian balady bread. When present in the less inhibitory casein meal, however, FeSO4 + Na2EDTA fortification was significantly less effective than NaFe(1II)EDTA or the reference FeSO4. Results indicate that NaFe(I1I)EDTA may be the fortificant of choice in a mixed diet. Further study of EDTA- enhanced Fe fortificants is needed.
Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification

Patient interactions with health care providers result in entries to electronic health records (EHRs). EHRs were built for clinical and billing purposes but contain many data points about an individual. Mining these records provides opportunities to extract electronic phenotypes, which can be paired with genetic data to identify genes underlying common human diseases. This task remains challenging: high quality phenotyping is costly and requires physician review; many fields in the records are sparsely filled; and our definitions of diseases are continuing to improve over time. Here we develop and evaluate a semi-supervised learning method for EHR phenotype extraction using denoising autoencoders for phenotype stratification. By combining denoising autoencoders with random forests we find classification improvements across multiple simulation models and improved survival prediction in ALS clinical trial data. This is particularly evident in cases where only a small number of patients have high quality phenotypes, a common scenario in EHR-based research. Denoising autoencoders perform dimensionality reduction enabling visualization and clustering for the discovery of new subtypes of disease. This method represents a promising approach to clarify disease subtypes and improve genotype-phenotype association studies that leverage EHRs. GRAPHICAL ABSTRACT HIGHLIGHTS Denoising autoencoders (DAs) can model electronic health records. Semi-supervised learning with DAs improves ALS patient survival predictions. DAs improve patient cluster visualization through dimensionality reduction.
Textual Emotion Processing From Event Analysis

Textual emotion recognition has gained a lot of attention recent years; it is however less developed due to the complexity nature of emotion. In this paper, we start with the discussion of a number of fundamental yet unresolved issues concerning emotion, which includes its definition, representation and technology. We then propose an alternative solution for emotion recognition taking into account of emotion causes. Two pilot experiments are done to justify our proposal. The first experiment explores the impact of emotion recognition. It shows that the context contains rich and crucial information that effectively help emotion recognition. The other experiment examines emotion cause events in the context. We find that most emotions are expressed with the presence of causes. The experiments prove that emotion cause serves as an important cue for emotion recognition. We suggest that the combination of both emotion study and event analysis would be a fruitful direction for deep emotion processing.
ANN based prognostication of the PV panel output power under various environmental conditions

The modules of the photovoltaic (PV) generation system convert solar energy into direct current (dc) electricity. Many complex factors, such as temperature and dust, influence PV arrays operation, making it difficult to ensure the optimal utilization of the solar energy. Achieving maximum power output under all possible system operation conditions is an important target. This paper proposes the possibility of developing a reliable relationship between the PV system power generation and efficiency, and various environmental factors such as solar irradiance, temperature, dust, and wind, using artificial neural network (ANN). The study is considering different prediction horizons to identify the influence of climate variability on power output and efficiency of the PV modules and to maximize the system usability. The proposed system does not require any physical definitions of the modules in order to predict power output under varying weather conditions. Experimental implementation is conducted to demonstrate the effectiveness of the proposed system.
Incidence and Risk Factors of Stroke or Systemic Embolism in Patients With Atrial Fibrillation and Heart Failure　- The Fushimi AF Registry.

BACKGROUND Heart failure (HF) is a heterogeneous syndrome, but the effect of the type and severity of HF on the incidence of stroke or systemic embolism (SE) in atrial fibrillation (AF) patients is unclear.Methods and Results:The Fushimi AF Registry is a community-based prospective survey of AF patients in Fushimi-ku, Kyoto, Japan. Follow-up data were available for 3,749 patients. We defined pre-existing HF as having one of the following: prior hospitalization for HF, presence of HF symptoms (NYHA ≥2), or reduced ejection fraction (<40%). At baseline, 1,008 (26.9%) patients had pre-existing HF. On multivariate analysis, the incidence of stroke/SE was not associated with pre-existing HF (hazard ratio (HR), 1.24; 95% confidence interval (CI), 0.92-1.64) or each criterion for the definition of pre-existing HF, but was associated with high B-type natriuretic peptide (BNP) or N-terminal proBNP levels (above the median of the pre-existing HF group) at baseline (HR, 1.65; 95% CI, 1.06-2.53). Stroke/SE was markedly increased in the initial 30-day period following hospital admission for HF (HR, 12.0; 95% CI, 4.59-31.98). CONCLUSIONS The effect of HF on the incidence of stroke/SE may depend on the stage or severity of HF in patients with AF. The incidence of stroke/SE was markedly increased in the 30 days after admission for HF, but compensated 'stable' HF did not appear to confer an independent risk.
Semantic Supersenses for English Possessives

We adapt an approach to annotating the semantics of adpositions to also include English possessives, showing that the supersense inventory of Schneider et al. (2017) works for the genitive ’s clitic and possessive pronouns as well as prepositional of . By comprehensively annotating such possessives in an English corpus of web reviews, we demonstrate that the existing supersense categories are readily applicable to possessives. Our corpus will facilitate empirical study of the semantics of the genitive alternation and the development of semantic disambiguation systems.
MECHANOSENSITIVE ION CHANNELS IN SKELETAL MUSCLE: A LINK IN THE MEMBRANE PATHOLOGY OF MUSCULAR DYSTROPHY

1 Mechanosensitive (MS) channels are expressed abundantly in skeletal muscle at all stages of development. In recordings from membrane patches, MS channels are constitutively active at the resting potential. The channels are selective for cations and have a large single‐channel conductance (approximately 25 pS in physiological saline) and a high Ca2+ permeability (relative permeability of Ca2+ to K+ (PCa/PK) = 7). 2 Mechanosensitive channel activity recorded from the surface of myotubes from dystrophic mdx mice was substantially greater than the activity recorded from wild‐type myotubes. Increased channel activity in the mutant results from the induction in a subpopulation of channels of a novel MS gating mode characterized by markedly prolonged channel openings and inactivation in response to membrane stretch. 3 Membrane stretch or a strong depolarization causes an irreversible switch to the stretch‐inactivated gating mode in mdx myotubes. A stretch‐induced shift in MS channel gating mode may contribute to stretch‐induced elevations in [Ca2+]i during the early stages of disease pathogenesis. 4 Abnormalities of MS channel behaviour are also detected in recordings from patches on flexor digitorum brevis fibres acutely isolated from mdx mice. Mechanosensitive channel opening probability is higher in mdx fibres at all developmental stages. In addition, channel numbers are persistently elevated during postnatal development, failing to undergo a normal process of downregulation during the first 3 postnatal weeks. 5 Two distinct mechanisms may contribute to elevations of [Ca2+]i in dystrophin‐deficient skeletal muscle: (i) a membrane stress‐dependent switch of MS channels into to a prolonged opening mode; and (ii) a loss of developmental downregulation leading to persistent MS channel expression during postnatal muscle development.
Humanized Exposures of a β-Lactam-β-Lactamase Inhibitor, Tazobactam, versus Non-β-Lactam-β-Lactamase Inhibitor, Avibactam, with or without Colistin, against Acinetobacter baumannii in Murine Thigh and Lung Infection Models

β-lactam-β-lactamase inhibitors (BLIs) have previously demonstrated antimicrobial activity against Acinetobacter baumannii (AB). Colistin retains the highest susceptibility rate against A. baumannii, and has demonstrated synergy with other antimicrobials, including β-lactam-BLIs. Therefore, we assessed the potential individual activity and synergistic combinations in vivo against carbapenem-susceptible (CS) and multidrug-resistant (MDR) A. baumannii isolates in neutropenic thigh and lung infection models. In vitro, colistin and tazobactam MICs were 1 and 16 µg/mL against AB 25–49 (CS) and 1 and 128 µg/mL against AB 5075 (MDR) respectively. In the lung model, tazobactam alone and in combination with colistin achieved a 1-log reduction in CFU, while colistin alone was not active against AB 25–49. No activity was observed against AB 5075. In the thigh model, tazobactam with and without colistin was bacteriostatic against AB 25–49 but did not demonstrate any activity against AB 5075. Avibactam and colistin alone and in combination were not active against either isolate. No synergy was observed; however, we found tazobactam activity against A. baumannii. This activity was not observed for the non-β-lactam-BLI, avibactam. This suggests that binding to penicillin-binding proteins of the β-lactam molecule is required for tazobactam activity against A. baumannii. These data point to an added role of β-lactam-BLIs beyond their primary purpose of β-lactamase inhibition in the treatment of MDR A. baumannii infections by enhancing the activity of peptide antibiotics, a property that is not shared by the novel non-β-lactam-BLIs. Future studies are needed to define tazobactam and colistin activity in an A. baumannii infection model.
Robust hand tracking with on-line and off-line learning

Hand tracking is becoming more and more popular in the field of human-computer interaction (HCI). A lot of studies in this area have made good progress. However, robust hand tracking is still difficult in long-term. On-line learning technology has great potential in terms of tracking for its strong adaptive learning ability. To address the problem we combined an on-line learning technology called on-line boosting with an off-line trained detector to track the hand. The contributions of this paper are: 1) we propose a learning method with an off-line model to solve the drift of on-line learning; 2) we build a framework for hand tracking based on the learning method. The experiments show that compared with other three methods, the proposed tracker is more robust in the strain case.
Sub-Category Optimization for Multi-view Multi-pose Object Detection

Object category detection with large appearance variation is a fundamental problem in computer vision. The appearance of object categories can change due to intra-class variability, viewpoint, and illumination. For object categories with large appearance change a sub-categorization based approach is necessary. This paper proposes a sub-category optimization approach that automatically divides an object category into an appropriate number of sub-categories based on appearance variation. Instead of using a predefined intra-category sub-categorization based on domain knowledge or validation datasets, we divide the sample space by unsupervised clustering based on discriminative image features. Then the clustering performance is verified using a sub-category discriminant analysis. Based on the clustering performance of the unsupervised approach and sub-category discriminant analysis results we determine an optimal number of sub-categories per object category. Extensive experimental results are shown using two standard and the authors' own databases. The comparison results show that our approach outperforms the state-of-the-art methods.
Vocal repertoire of free‐ranging black howler monkeys’ (Alouatta pigra): Call types, contexts, and sex‐related contributions

Alouatta species utter the most powerful primate vocalizations in the Neotropics and are well‐known for their loud and long‐lasting male howling bouts. However, the diversity of acoustic structures used in these howling bouts, as well as in non‐howling contexts, and the relative contribution of the different group members to the entire vocal repertoire, needed to be explored further. This report provides the first detailed description of the vocal repertoire of black howler monkeys (Alouatta pigra), focusing on acoustic structures and contexts of emission of both loud and soft calls as well as on the contribution rate of males and females to the different call types. Three free‐ranging social groups of black howler monkeys living in Palenque National Park, Mexico were monitored. We identified twelve acoustically discriminable call types, eight described previously and four described here for the first time. A few call types were systematically emitted either isolated or during howling bouts, but most of them could be heard in both calling contexts. Three call types were emitted only by females and two only by males. Adult males’ call rates (for the seven shared call types) were higher than those of females but only when considering calls emitted within howling bouts. Our contextual analysis enabled us to divide call types into potential functional categories, according to their degree of contribution, to intra‐group versus inter‐group interactions and to neutral‐positive versus negative situations. We then discussed how socio‐ecological factors, notably sex differences in social behaviors, may explain the variability found in the vocal repertoire of this species and compared our findings with the literature on other primate species.
Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

ABSTRACT Cyclic di-GMP (c-di-GMP) synthetases and hydrolases (GGDEF, EAL, and HD-GYP domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. In contrast, identification of c-di-GMP receptors remains a difficult task, and the current list of experimentally characterized c-di-GMP-binding proteins is likely incomplete. Several classes of c-di-GMP-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and for several potential c-di-GMP receptors, the binding sites remain to be determined. We present here a comparative structural analysis of c-di-GMP-protein complexes that aims to discern the common themes in the binding mechanisms that allow c-di-GMP receptors to bind it with (sub)micromolar affinities despite the 1,000-fold excess of GTP. The available structures show that most receptors use their Arg and Asp/Glu residues to bind c-di-GMP monomers, dimers, or tetramers with stacked guanine bases. The only exception is the EAL domains that bind c-di-GMP monomers in an extended conformation. We show that in c-di-GMP-binding signature motifs, Arg residues bind to the O-6 and N-7 atoms at the Hoogsteen edge of the guanine base, while Asp/Glu residues bind the N-1 and N-2 atoms at its Watson-Crick edge. In addition, Arg residues participate in stacking interactions with the guanine bases of c-di-GMP and the aromatic rings of Tyr and Phe residues. This may account for the presence of Arg residues in the active sites of every receptor protein that binds stacked c-di-GMP. We also discuss the implications of these structural data for the improved understanding of the c-di-GMP signaling mechanisms.