Miracle-dz/UniFAR-FTUs huggingface dataset:
Feature selection for chemical compound extraction using wrapper approach with Naive Bayes classifier

Biomedical Entity extraction is the process of identifying biomedical instances such as disorders, viruses, proteins, genes and others. One of these instances is the chemical compound which caught many researchers' attentions regarding the challenging task of extracting them. In fact, most of the studies that have been proposed for chemical compounds extraction have relied on supervised machine learning techniques regarding its ability to adopt a statistical model rather than handcrafted rules. However, the key characteristic of the use of supervised machine learning techniques lies on the utilized features. There is a wide range of features that have been used in the previous studies for the process of extracting chemical compounds. Hence, the need of accommodating a feature selection task in order to determine the best combination of features is becoming imperative. Therefore, this paper aims to apply a combination of Naïve Bayes classification method with the Wrapper Subset Selection approach to identify the best features. Results showed that the proposed combination has the ability to identify the best combination of features which consists of Capitalization, Punctuation, Prefix and Part-Of-Speech Tagging by achieving 0.72 of f-measure. Such result has been compared to the state of the art and it demonstrated competitive performance.
The Importance of Tree Size and Fecundity for Wind Dispersal of Big-Leaf Mahogany

Seed dispersal by wind is a critical yet poorly understood process in tropical forest trees. How tree size and fecundity affect this process at the population level remains largely unknown because of insufficient replication across adults. We measured seed dispersal by the endangered neotropical timber species big-leaf mahogany (Swietenia macrophylla King, Meliaceae) in the Brazilian Amazon at 25 relatively isolated trees using multiple 1-m wide belt transects extended 100 m downwind. Tree diameter and fecundity correlated positively with increased seed shadow extent; but in combination large, high fecundity trees contributed disproportionately to longer-distance dispersal events (>60 m). Among three empirical models fitted to seed density vs. distance in one dimension, the Student-t (2Dt) generally fit best (compared to the negative exponential and inverse power). When seedfall downwind was modelled in two dimensions using a normalised sample, it peaked furthest downwind (c. 25 m) for large, high-fecundity trees; with the inverse Gaussian and Weibull functions providing comparable fits that were slightly better than the lognormal. Although most seeds fell within 30 m of parent trees, relatively few juveniles were found within this distance, resulting in juvenile-to-seed ratios peaking at c. 35–45 m. Using the 2Dt model fits to predict seed densities downwind, coupled with known fecundity data for 2000–2009, we evaluated potential Swietenia regeneration near adults (≤30 m dispersal) and beyond 30 m. Mean seed arrival into canopy gaps >30 m downwind was more than 3× greater for large, high fecundity trees than small, high-fecundity trees. Tree seed production did not necessarily scale up proportionately with diameter, and was not consistent across years, and this resulting intraspecific variation can have important consequences for local patterns of dispersal in forests. Our results have important implications for management and conservation of big-leaf mahogany populations, and may apply to other threatened wind-dispersed Meliaceae trees.
Brucella abortus Invasion of Osteocytes Modulates Connexin 43 and Integrin Expression and Induces Osteoclastogenesis via Receptor Activator of NF-κB Ligand and Tumor Necrosis Factor Alpha Secretion

ABSTRACT Osteoarticular brucellosis is the most common localization of human active disease. Osteocytes are the most abundant cells of bone. They secrete factors that regulate the differentiation of both osteoblasts and osteoclasts during bone remodeling. The aim of this study is to determine if Brucella abortus infection modifies osteocyte function. Our results indicate that B. abortus infection induced matrix metalloproteinase 2 (MMP-2), receptor activator for NF-κB ligand (RANKL), proinflammatory cytokines, and keratinocyte chemoattractant (KC) secretion by osteocytes. In addition, supernatants from B. abortus-infected osteocytes induced bone marrow-derived monocytes (BMM) to undergo osteoclastogenesis. Using neutralizing antibodies against tumor necrosis factor alpha (TNF-α) or osteoprotegerin (OPG), RANKL's decoy receptor, we determined that TNF-α and RANKL are involved in osteoclastogenesis induced by supernatants from B. abortus-infected osteocytes. Connexin 43 (Cx43) and the integrins E11/gp38, integrin-α, integrin-β, and CD44 are involved in cell-cell interactions necessary for osteocyte survival. B. abortus infection inhibited the expression of Cx43 but did not modify the expression of integrins. Yet the expression of both Cx43 and integrins was inhibited by supernatants from B. abortus-infected macrophages. B. abortus infection was not capable of inducing osteocyte apoptosis. However, supernatants from B. abortus-infected macrophages induced osteocyte apoptosis in a dose-dependent manner. Taken together, our results indicate that B. abortus infection could alter osteocyte function, contributing to bone damage.
Crack Detection Methods For Lead-free Solder Joints

This report describes an investigation into the suitability of a number of techniques used to study cracking in lead-free solder joints, and hence their use in assessing joint lifetimes. Cracks were induced into the solder joints of chip resistors on FR4 substrates, and studied using metallographic micro-sectioning, dye penetration, mechanical test and thermal conductivity techniques. The work has shown that those techniques traditionally used to study lead-based solder joints can readily be used for assessing lead-free solder joints The traditional microsectioning method is suitable for locating and imaging the solder joint crack, especially when the section is examined in a SEM. However, it is not very suitable for quantitative analysis of cracks or their detection in small surface mount resistors. Dye penetration techniques allow a better characterisation of cracks in the horizontal plane and can provide a quantitative measure of the cracked surface area. Shear testing is a proven destructive method for evaluating not only the degree of crack propagation and damage to the solder joint, but also the general strength of the joint. The other methods studied (3 and 4-point bend tests, pull test and heat transfer) have severe limitations and are currently unsuitable for studying cracks in the solder joints of electronic assemblies, requiring further development.
Community-acquired Pneumonia with Methicillin-resistant Staphylococcus Aureus in a Patient Admitted to the Intensive Care Unit: A Therapeutic Challenge

Methicillin-resistant Staphylococcus aureus (MRSA) was previously considered a purely nosocomial pathogen. However, community-acquired MRSA has recently emerged as an important cause of severe necrotizing community-acquired pneumonia (CA-MRSA) in previously healthy individuals. This new pathogen exhibits antibiotic resistance and is linked to extended hospital stay and higher mortality. CA-MRSA has presented new therapeutic challenges due to high vancomycin treatment failure and lack of specificity of clinical findings. There is emerging evidence that treatment with linezolid leads to better patient outcomes in patients with CA-MRSA. Through this case, we aim to raise awareness about early institution of therapy for CA-MRSA whenever it is suspected, to improve patient outcomes.
Numerical simulation for in-cloud icing of three-dimensional wind turbine blades

Icing will occur when wind turbines are installed in cold and humid regions. Blade icing will reduce the efficiency of wind turbines. In this paper, a numerical simulation method is proposed for glaze, mixed, and rime ice accretion on three-dimensional wind turbine blades. The air flow field is calculated by the multiple reference frame model and droplet trajectories are obtained using the Eulerian two-phase flow method. In the ice accretion calculation, a three-dimensional icing calculation model is established and a new water flow distribution method based on shear force and centrifugal force is presented. The calculation results of ice shapes are compared with the experimental results and the good agreement proves the validity of the icing numerical simulation method. Based on the calculation results, the influence of centrifugal force on the ice shape is studied. Finally, the droplet impingement characteristics and ice shapes of the wind turbine blade are simulated. The results show that the in-cloud icing of wind turbine blades occurs mainly near the leading edge. The icing thickness is thicker and the icing range is wider with the increase of spanwise length.
Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations

Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, whereby six established genomovars have been described to date. However, little has been done to quantify or characterize this diversity further in a systematic fashion. The objective of this research was to perform phylogenetic analyses of 16S rRNA and housekeeping gene sequences to decipher the genetic diversity of F. columnare. Fifty isolates and/or genomes of F. columnare, originating from diverse years, geographic locations, fish hosts, and representative of the six genomovars were analyzed in this study. A multilocus phylogenetic analysis (MLPA) of the 16S rRNA and six housekeeping genes supported four distinct F. columnare genetic groups. There were associations between genomovar and genetic group, but these relationships were imperfect indicating that genomovar assignment does not accurately reflect F. columnare genetic diversity. To expand the dataset, an additional 90 16S rRNA gene sequences were retrieved from GenBank and a phylogenetic analysis of this larger dataset also supported the establishment of four genetic groups. Examination of isolate historical data indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from specific fish species or families. It is proposed that F. columnare isolates be assigned to the four genetic groups defined in this study rather than genomovar in order to facilitate a standard nomenclature across the scientific community. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries may allow for the development of improved targeted control and treatment measures for columnaris disease.
A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage

The bacterial SOS stress-response pathway is a pro-mutagenic DNA repair system that mediates bacterial survival and adaptation to genotoxic stressors, including antibiotics and UV light. The SOS pathway is composed of a network of genes under the control of the transcriptional repressor, LexA. Activation of the pathway involves linked but distinct events: an initial DNA damage event leads to activation of RecA, which promotes autoproteolysis of LexA, abrogating its repressor function and leading to induction of the SOS gene network. These linked events can each independently contribute to DNA repair and mutagenesis, making it difficult to separate the contributions of the different events to observed phenotypes. We therefore devised a novel synthetic circuit to unlink these events and permit induction of the SOS gene network in the absence of DNA damage or RecA activation via orthogonal cleavage of LexA. Strains engineered with the synthetic SOS circuit demonstrate small-molecule inducible expression of SOS genes as well as the associated resistance to UV light. Exploiting our ability to activate SOS genes independently of upstream events, we further demonstrate that the majority of SOS-mediated mutagenesis on the chromosome does not readily occur with orthogonal pathway induction alone, but instead requires DNA damage. More generally, our approach provides an exemplar for using synthetic circuit design to separate an environmental stressor from its associated stress-response pathway.
Histomorphometry of pancreas development in hybrid chicken (Galus galus) embryo and fetus

The pancreas comprises an important metabolic organ of endocrine and exocrine character that has embryonic origin of rudimentary buds that fuse to form the organ. The present work aims to describe the pancreatic histogenesis of hybrid chick embryos (Gallus gallus). The research was performed in the UFPI, previously approved by the CEUA with protocol no. 040/15. We used 120 fertilized eggs of hybrid chickens kept in an incubator with controlled temperature and humidity. Daily collections of embryos and fetuses were performed from 4 to 21 days of incubation through the anatomical dissection consecutive the euthanasia. The tissues, previously fixed in 10% buffered formaldehyde, were submitted to histological processing and stained with hematoxylin–eosin. Finally, the mounted slides were analyzed in image software to obtain histomorphometric data, which were submitted to statistical analysis. The pancreas of hybrid chicken embryos originates around the fourth day of incubation with the dorsal and ventral pancreatic bud formation, which are composed by epithelial and mesenchymal cells. These cells differ in exocrine and endocrine cells. Around twelve embryonic days occurs the buds fusion and the immature organ formation that will give continue with the ductal system development, vascularization and compartmentalization of the endocrine and exocrine parts. Until 21st day of incubation it is possible to identify undifferentiated tissue forms which suggesting postnatal histogenesis. The description of pancreas histogenesis using histometric data on hybrid chicken embryos contributes to the clarification of embryonic development and reaffirms the premise that chickens serve as an experimental model for embryonic study of mammals.
Non–ST‐Segment–Elevation Myocardial Infarction Among Patients With Chronic Kidney Disease: A Propensity Score–Matched Comparison of Percutaneous Coronary Intervention Versus Conservative Management

Background Chronic kidney disease (CKD) remains an independent predictor of cardiovascular morbidity and mortality. CKD complicates referral for percutaneous coronary intervention (PCI) in non–ST‐segment–elevation myocardial infarction (NSTEMI) patients because of the risk for acute kidney injury and the need for dialysis, with American College of Cardiology/American Heart Association guidelines underscoring the limited data on these patients. Methods and Results Using the National Inpatient Sample to analyze hospitalizations in the United States from 2004 to 2014, we sought to assess PCI utilization and in‐hospital outcomes in NSTEMI admissions with CKD. NSTEMI admissions were identified by International Classification of Diseases, Ninth Edition, Clinical Modification (ICD‐9‐CM) code 410.7. CKD admissions were identified by ICD‐9‐CM code 585. Propensity score–matched cohorts of patients with NSTEMI were matched for age, sex, comorbidities, race, median household income, primary payer status, and hospital characteristics. Of 4 488 795 hospitalizations for NSTEMI, 31% underwent PCI. Overall, 89% of admissions had no CKD. In addition, 32% of NSTEMI admissions with no CKD and 23%, 14%, and 22% with CKD stages 3, 4, and 5 underwent PCI, respectively. Hospitalized NSTEMI patients with CKD stages 4 and 5 had 41% and 20% less likelihood, respectively, of undergoing PCI compared with those with no CKD. Among hospitalized NSTEMI patients with no CKD or CKD stage 3, 4, or 5, PCI‐treated groups had 63%, 57%, 39%, and 59% lower likelihood, respectively, of all‐cause, in‐hospital mortality compared with propensity score–matched medically managed groups. Conclusions PCI use decreased among hospitalized NSTEMI patients as CKD severity increased, and all‐cause, in‐hospital mortality was greater for NSTEMI patients admitted with more severe CKD regardless of treatment strategy.
Development of a Conducting Polymer based Flexible Position Sensor for the Control of Hand Exoskeletons

ii Acknowledgements . iv CHAPTER 1 Introduction . 1 1.1 Exoskeleton Systems . 1 1.1.1 Design and Purpose . 1 1.1.2 Rehabilitation Robotics . 2 1.1.3 Hand Exoskeletons . 5 1.2 The Need for Sensors Development . 6 1.3 Research Motivation . 7 1.4 Sensing Materials . 8 1.4. 1 Smart Materials . 8 1.4. 2 Intrinsically Conducting Polymers . 9 1.5 Research Objectives . 10 1.5. 1 Design of Flexible Strain Sensor . 10 1.5. 2 Development and Optimisation of Fabrication Procedure . 12 1.5. 3 Characterisation of Developed Sensor . 13 1.5. 4 Implementation into a Control System . 13 1.5. 5 Out of Scope . 14 1.6 Thesis Synopsis . 14 CHAPTER 2 Sensor Implications in a Hand Exoskeleton . 16 2.1 Review of Hand Exoskeleton’s Design . 16 2.1.1 Hand Motion . 17 2.1.2 Joint Actuation . 22 2.1.3 Placement of Actuators and Sensors. 25 2.2 Role of Sensors and their Implications . 28 2.3 Review of Existing Position Sensors . 29
Smpd3 Expression in both Chondrocytes and Osteoblasts Is Required for Normal Endochondral Bone Development

ABSTRACT Sphingomyelin phosphodiesterase 3 (SMPD3), a lipid-metabolizing enzyme present in bone and cartilage, has been identified to be a key regulator of skeletal development. A homozygous loss-of-function mutation called fragilitas ossium (fro) in the Smpd3 gene causes poor bone and cartilage mineralization resulting in severe congenital skeletal deformities. Here we show that Smpd3 expression in ATDC5 chondrogenic cells is downregulated by parathyroid hormone-related peptide through transcription factor SOX9. Furthermore, we show that transgenic expression of Smpd3 in the chondrocytes of fro/fro mice corrects the cartilage but not the bone abnormalities. Additionally, we report the generation of Smpd3flox/flox mice for the tissue-specific inactivation of Smpd3 using the Cre-loxP system. We found that the skeletal phenotype in Smpd3flox/flox; Osx-Cre mice, in which the Smpd3 gene is ablated in both late-stage chondrocytes and osteoblasts, closely mimics the skeletal phenotype in fro/fro mice. On the other hand, Smpd3flox/flox; Col2a1-Cre mice, in which the Smpd3 gene is knocked out in chondrocytes only, recapitulate the fro/fro mouse cartilage phenotype. This work demonstrates that Smpd3 expression in both chondrocytes and osteoblasts is required for normal endochondral bone development.
Satellite Telemetry and Long-Range Bat Movements

Background Understanding the long-distance movement of bats has direct relevance to studies of population dynamics, ecology, disease emergence, and conservation. Methodology/Principal Findings We developed and trialed several collar and platform terminal transmitter (PTT) combinations on both free-living and captive fruit bats (Family Pteropodidae: Genus Pteropus). We examined transmitter weight, size, profile and comfort as key determinants of maximized transmitter activity. We then tested the importance of bat-related variables (species size/weight, roosting habitat and behavior) and environmental variables (day-length, rainfall pattern) in determining optimal collar/PTT configuration. We compared battery- and solar-powered PTT performance in various field situations, and found the latter more successful in maintaining voltage on species that roosted higher in the tree canopy, and at lower density, than those that roost more densely and lower in trees. Finally, we trialed transmitter accuracy, and found that actual distance errors and Argos location class error estimates were in broad agreement. Conclusions/Significance We conclude that no single collar or transmitter design is optimal for all bat species, and that species size/weight, species ecology and study objectives are key design considerations. Our study provides a strategy for collar and platform choice that will be applicable to a larger number of bat species as transmitter size and weight continue to decrease in the future.
Neuropathologic Correlates of Hippocampal Atrophy in the Elderly: A Clinical, Pathologic, Postmortem MRI Study

The volume of the hippocampus measured with structural magnetic resonance imaging (MRI) is increasingly used as a biomarker for Alzheimer's disease (AD). However, the neuropathologic basis of structural MRI changes in the hippocampus in the elderly has not been directly assessed. Postmortem MRI of the aging human brain, combined with histopathology, could be an important tool to address this issue. Therefore, this study combined postmortem MRI and histopathology in 100 elderly subjects from the Rush Memory and Aging Project and the Religious Orders Study. First, to validate the information contained in postmortem MRI data, we tested the hypothesis that postmortem hippocampal volume is smaller in subjects with clinically diagnosed Alzheimer's disease compared to subjects with mild or no cognitive impairment, as observed in antemortem imaging studies. Subsequently, the relations of postmortem hippocampal volume to AD pathology, Lewy bodies, amyloid angiopathy, gross infarcts, microscopic infarcts, and hippocampal sclerosis were examined. It was demonstrated that hippocampal volume was smaller in persons with a clinical diagnosis of AD compared to those with no cognitive impairment (P = 2.6×10−7) or mild cognitive impairment (P = 9.6×10−7). Additionally, hippocampal volume was related to multiple cognitive abilities assessed proximate to death, with its strongest association with episodic memory. Among all pathologies investigated, the most significant factors related to lower hippocampal volume were shown to be AD pathology (P = 0.0018) and hippocampal sclerosis (P = 4.2×10−7). Shape analysis allowed for visualization of the hippocampal regions most associated with volume loss for each of these two pathologies. Overall, this investigation confirmed the relation of hippocampal volume measured postmortem to clinical diagnosis of AD and measures of cognition, and concluded that both AD pathology and hippocampal sclerosis affect hippocampal volume in old age, though the impacts of each pathology on the shape of the hippocampus may differ.