Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding information criteria for selection among capture-recapture or ring recovery models

We provide background information to allow a heuristic understanding of two types of criteria used in selecting a model for making inferences from ringing data. The first type of criteria (e.g. AIC, AlCc QAICc and TIC) are estimates of (relative) Kullback-Leibler information or distance and attempt to select a good approximating model for inference, based on the principle of parsimony. The second type of criteria (e.g. BIC, MDL, HQ) are 'dimension consistent' in that they attempt to consistently estimate the dimension of the true model. These latter criteria assume that a true model exists, that it is in the set of candidate models and that the goal of model selection is to find the true model, which in turn requires that the sample size is very large. The Kullback-Leibler based criteria do not assume a true model exists, let alone that it is in the set of models being considered. Based on a review of these criteria, we recommend use of criteria that are based on Kullback-Leibler information in the biolog.
Carrier phase delay altimetry with GPS‐reflection/occultation interferometry from low Earth orbiters

GPS signals reflected off the surface of the Earth can be detected by receivers aboard occulting Low Earth Orbiters (LEOs). In this work, carrier phase interferometry between the reflected and direct occultation signals is performed to infer its relative delay at centimetric error. Our analysis shows that submeter sensitivity on the surface heights can formally be reached with this technique. The potential applications to polar ice altimetry are discussed.
Systematic Reviews of Health Care Interventions: An Essential Component of Health Sciences Graduate Programs

Systematic reviews are an objective, rigorous assessment of both published and unpublished research that enable the reviewer to make recommendations to clinicians, policy-makers, consumers, and researchers. The steps in a systematic review include: (a) developing a research question, (b) developing relevance and validity tools, (c) conducting a thorough literature search of published and unpublished studies, (d) using relevance and validity tools to assess the studies, (e) completing data extraction for each study, (f) synthesizing the findings and, (g) writing the report. The purpose of this paper is to demonstrate the value of providing health science graduate students with the opportunity to learn about the conduct of a systematic review. An example of a thesis utilizing the method of a systematic review is presented.
Extinction of the acoustic startle response in moths endemic to a bat‐free habitat

Most moths use ears solely to detect the echolocation calls of hunting, insectivorous bats and evoke evasive flight manoeuvres. This singularity of purpose predicts that this sensoribehavioural network will regress if the selective force that originally maintained it is removed. We tested this with noctuid moths from the islands of Tahiti and Moorea, sites where bats have never existed and where an earlier study demonstrated that the ears of endemic species resemble those of adventives although partially reduced in sensitivity. To determine if these moths still express the anti‐bat defensive behaviour of acoustic startle response (ASR) we compared the nocturnal flight times of six endemic to six adventive species in the presence and absence of artificial bat echolocation sounds. Whereas all of the adventive species reduced their flight times when exposed to ultrasound, only one of the six endemic species did so. These differences were significant when tested using a phylogenetically based pairwise comparison and when comparing effect sizes. We conclude that the absence of bats in this habitat has caused the neural circuitry that normally controls the ASR behaviour in bat‐exposed moths to become decoupled from the functionally vestigial ears of endemic Tahitian moths.
Projection of Non-peptidergic Afferents to Mouse Tooth Pulp

A large proportion of pulpal nociceptors are known to contain neuropeptides such as CGRP. However, the projection of non-peptidergic nociceptors to tooth pulp is controversial. Recently, the non- peptidergic subset of nociceptors has been implicated in mechanical pain in the skin. Since mechanical irritation of pulpal nociceptors is critical for evoking tooth pain under pathophysiological conditions, we investigated whether the non-peptidergic afferents project to tooth pulp as potential mechanotransducing afferents. For clear visualization of the non-peptidergic afferents, we took advantage of a recently generated knock-in mouse model in which an axonal tracer, farnesylated green fluorescence protein (GFP), is expressed from the locus of a sensory neuron-specific gene, Mrgprd. In the trigeminal ganglia (TG), we demonstrated that GFP is exclusively expressed in afferents binding to isolectin B4 (IB4), a neurochemical marker of non-peptidergic nociceptors, but is rarely co-localized with CGRP. Retrograde labeling of pulpal afferents demonstrated that a low proportion of pulpal afferents was co-localized with GFP. Immunohistochemical detection of the axonal tracer revealed that GFP-positive afferent terminals were densely projected into the tooth pulp. These results provide convincing evidence that non-peptidergic nociceptors are projected into the tooth pulp and suggest a potential role for these afferents in tooth pain.
Toward an Understanding of the Impact of Organizational Climate and Organizational Justice on the Implementation of Enterprise Resource Planning Systems

This research examines the relationship between the organizational factors (such as justice and organizational climate) and behaviors regarding the implementation of enterprise resource planning (ERP) system. Business Process Reengineering (BPR) is emphasized due to its essentiality to ERP success and the symbiotic relationship. There has been much research that has focused on the relationship between justice and business process reengineering, as well as the relationship between BPR and ERP success in separate manners. However, few studies have explored the interrelationships among these constructs. This research helps explain how the organizational climate and organizational justice impacts the likelihood of success of an ERP implementation. While organizational behaviors under involvement are significantly and positively correlated with the success of ERP, justice plays an important mediating role in affecting individual’s attitudes towards organizational changes induced by BPR and ERP implementation.
Analysis of coronary heart disease and prediction of heart attack in coal mining regions using data mining techniques

Heart disease (HD) is a major cause of morbidity and mortality in the modern society. Medical diagnosis is extremely important but complicated task that should be performed accurately and efficiently. This study analyzes the Behavioral Risk Factor Surveillance System, survey to test whether self-reported cardiovascular disease rates are higher in Singareni coal mining regions in Andhra Pradesh state, India, compared to other regions after control for other risks. Dependent variables include self-reported measures of being diagnosed with cardiovascular disease (CVD) or with a specific form of CVD including (1) chest pain (2) stroke and (3) heart attack. Heart care study specifies 15 attributes to predict the morbidity. Beside regular attributes other general attributes BMI (Body Mass Index), physician supply, age, ethnicity, education, income, and others are used for prediction. An automated system for medical diagnosis would enhance medical care and reduce costs. In this paper popular data mining techniques namely, Decision Trees, Naïve Bayes and Neural Network are used for prediction of heart disease.
A pair‐to‐pair amino acids substitution matrix and its applications for protein structure prediction

We present a new structurally derived pair‐to‐pair substitution matrix (P2PMAT). This matrix is constructed from a very large amount of integrated high quality multiple sequence alignments (Blocks) and protein structures. It evaluates the likelihoods of all 160,000 pair‐to‐pair substitutions. P2PMAT matrix implicitly accounts for evolutionary conservation, correlated mutations, and residue–residue contact potentials. The usefulness of the matrix for structural predictions is shown in this article. Predicting protein residue–residue contacts from sequence information alone, by our method (P2PConPred) is particularly accurate in the protein cores, where it performs better than other basic contact prediction methods (increasing accuracy by 25–60%). The method mean accuracy for protein cores is 24% for 59 diverse families and 34% for a subset of proteins shorter than 100 residues. This is above the level that was recently shown to be sufficient to significantly improve ab initio protein structure prediction. We also demonstrate the ability of our approach to identify native structures within large sets of (300–2000) protein decoys. On the basis of evolutionary information alone our method ranks the native structure in the top 0.3% of the decoys in 4/10 of the sets, and in 8/10 of sets the native structure is ranked in the top 10% of the decoys. The method can, thus, be used to assist filtering wrong models, complimenting traditional scoring functions. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The Relationship between Emotional Intelligence and Productive Language Skills.

Emotional intelligence has recently attracted educators' attention around the world. Educators who try to investigate the factors in language learning achievement have decided to pave the way to success through emotional intelligence. The relationship between emotional intelligence and language learning is the major concern of this study. The study is to examine the role of emotional intelligence in second language learning and its effect on productive language skills: speaking and writing. At the end of the academic year, 150 students from different disciplines of the university and studying English as a foreign language in the School of Foreign Languages were asked to complete the Emotional Intelligence Inventory (EQ-i). Collected data were matched with the students’ academic scores in speaking and writing. Predicting foreign language learning success from emotional intelligence variables produced divergent results. When EQ-i variables were compared in groups (successful vs. unsuccessful) who had achieved very different levels of academic success and scores in different skills, foreign language learning was strongly associated with several dimensions of emotional intelligence. All collected data were coded and computerized using the SPSS software and the alpha level for the tests was set at . 05. After calculating each participant’s emotional intelligence scores and their success in speaking and writing skills, their scores were compared to the variables selected for the study and each other. A positive and close relation between EQ and foreign language proficiency can be drawn out according to the results.
Mapping shallow nearshore benthic features in a Caribbean marine-protected area: assessing the efficacy of using different data types (hydroacoustic versus satellite images) and classification techniques

ABSTRACT Various benthic mapping methods exist but financing and technical capacity limit the choice of technology available to developing states to aid with natural resource management. Therefore, we assessed the efficacy of using a single-beam echosounder (SBES), satellite images (GeoEye-1 and WorldView-2) and different image (pixel-based Maximum Likelihood Classifier (MLC), and an object-based image analysis (OBIA)) and hydroacoustic classification and interpolation techniques, to map nearshore benthic features at the Bluefields Bay marine protected area in western Jamaica (13.82 km2 in size). A map with three benthic classes (submerged aquatic vegetation (SAV), bare substrate, and coral reef) produced from a radiometrically corrected, deglinted and water column-corrected WorldView-2 image had a marginally higher accuracy (3%) than that of a map classified from a similarly corrected GeoEye-1 image. However, only one of the two extra WorldView-2 image bands (coastal) was used because the yellow band was completely attenuated at depths ≥3.7 m. The coral reef class was completely misclassified by the MLC and had to be contextually edited. The contextually edited MLC map had a higher overall accuracy (OA) than the OBIA map (86.7% versus 80.4%) and maps that were not contextually edited. But, the OBIA map had a higher OA than a MLC map without edits. Maps produced from the images also had a higher accuracy than the SAV map created from the acoustic data (OAs >80% and kappa >0.67 versus 76.6% and kappa = 0.32). SAV classification was comparable among the classified SBES SAV data points and all the final maps. The total area classified as SAV was marginally larger for satellite maps; however, the total area classified as bare substrate using the images was twice as large. A substrate map with three classes (silt, sand, and coral/hard bottom) produced from the SBES data using a random forest classifier and a Markov chain interpolator had a higher accuracy than a substrate map produced using a fractal dimension classifier and an indicator krig (the default choice) (72.4% versus 53.5%). The coral reef class from the SBES, OBIA, and contextually edited maps had comparable accuracies, but covered a much smaller area in the SBES maps because data points were lost during the interpolation process. The use of images was limited by turbidity levels and cloud cover and it yielded lower benthic detail. Despite these limitations, satellite image classification was the most efficacious method. If greater benthic detail is required, the SBES is more suitable or more effort is required during image classification. Also, the SBES can be operated in areas with turbid waters and greater depths. However, it could not be used in very shallow areas. Also, processing and interpolation of data points can result in a loss of resolution and introduces spatial uncertainty.
Cardiac Autonomic Dysfunction in Brugada Syndrome

Background—Patients with Brugada syndrome present with characteristic ECG abnormalities (atypical right bundle-branch block and ST-segment elevation) and life-threatening ventricular tachyarrhythmias despite structurally normal hearts. Involvement of the autonomic nervous system is suggested by the occurrence of ventricular tachyarrhythmias and sudden death at rest or during sleep and by changes of typical ECG signs under pharmacological modulation of the myocardial autonomic tone. Methods and Results—This study investigated the presynaptic cardiac neuronal reuptake of norepinephrine (uptake 1) in 17 patients with Brugada syndrome and 10 age-matched control subjects with the use of the norepinephrine analogue [123I]m-iodobenzylguanidine (123I-MIBG), single-photon emission CT (SPECT), and quantitative 33-segment bull’s-eye analysis. Regionally reduced 123I-MIBG uptake was present in 8 (47%) of 17 patients with Brugada syndrome but in none of the control subjects. Quantitative analysis showed segmental reduction of 123I-MIBG uptake in the inferior and septal left ventricular wall in patients with Brugada syndrome compared with control subjects (P <0.05). No correlation was found between the findings of 123I-MIBG-SPECT and clinical characteristics of the study patients. Conclusions—The present study demonstrated an abnormal 123I-MIBG uptake in patients with Brugada syndrome, indicating presynaptic sympathetic dysfunction of the heart. These findings may have potential impact on the pathophysiology and arrhythmogenesis in patients with Brugada syndrome. Future quantitative investigations of the presynaptic and postsynaptic sympathetic and parasympathetic branches of the cardiac autonomic nervous system may clarify whether these observations represent a primary adrenergic dysfunction or an imbalance between sympathetic and parasympathetic innervation of the heart.
Polyphonic piano transcription using non-negative Matrix Factorisation with group sparsity

Non-negative Matrix Factorisation (NMF) is a popular tool in musical signal processing. However, problems using this methodology in the context of Automatic Music Transcription (AMT) have been noted resulting in the proposal of supervised and constrained variants of NMF for this purpose. Group sparsity has previously been seen to be effective for AMT when used with stepwise methods. In this paper group sparsity is introduced to supervised NMF decompositions and a dictionary tuning approach to AMT is proposed based upon group sparse NMF using the β-divergence. Experimental results are given showing improved AMT results over the state-of-the-art NMF-based AMT system.
Gene therapy rescues cone structure and function in the 3-month-old rd12 mouse: a model for midcourse RPE65 leber congenital amaurosis.

PURPOSE RPE65 function is necessary in the retinal pigment epithelium (RPE) to generate chromophore for all opsins. Its absence results in vision loss and rapid cone degeneration. Recent Leber congenital amaurosis type 2 (LCA with RPE65 mutations) phase I clinical trials demonstrated restoration of vision on RPE65 gene transfer into RPE cells overlying cones. In the rd12 mouse, a naturally occurring model of RPE65-LCA early cone degeneration was observed; however, some peripheral M-cones remained. A prior study showed that AAV-mediated RPE65 expression can prevent early cone degeneration. The present study was conducted to test whether the remaining cones in older rd12 mice can be rescued. METHODS Subretinal treatment with the scAAV5-smCBA-hRPE65 vector was initiated at postnatal day (P)14 and P90. After 2 months, electroretinograms were recorded, and cone morphology was analyzed by using cone-specific peanut agglutinin and cone opsin-specific antibodies. RESULTS Cone degeneration started centrally and spread ventrally, with cells losing cone-opsin staining before that for the PNA-lectin-positive cone sheath. Gene therapy starting at P14 resulted in almost wild-type M- and S-cone function and morphology. Delaying gene-replacement rescued the remaining M-cones, and most important, more M-cone opsin-positive cells were identified than were present at the onset of gene therapy, suggesting that opsin expression could be reinitiated in cells with cone sheaths. CONCLUSIONS The results support and extend those of the previous study that gene therapy can stop early cone degeneration, and, more important, they provide proof that delayed treatment can restore the function and morphology of the remaining cones. These results have important implications for the ongoing LCA2 clinical trials.
LOCI: fast outlier detection using the local correlation integral

Outlier detection is an integral part of data mining and has attracted much attention recently [M. Breunig et al., (2000)], [W. Jin et al., (2001)], [E. Knorr et al., (2000)]. We propose a new method for evaluating outlierness, which we call the local correlation integral (LOCI). As with the best previous methods, LOCI is highly effective for detecting outliers and groups of outliers (a.k.a. micro-clusters). In addition, it offers the following advantages and novelties: (a) It provides an automatic, data-dictated cutoff to determine whether a point is an outlier-in contrast, previous methods force users to pick cut-offs, without any hints as to what cut-off value is best for a given dataset. (b) It can provide a LOCI plot for each point; this plot summarizes a wealth of information about the data in the vicinity of the point, determining clusters, micro-clusters, their diameters and their inter-cluster distances. None of the existing outlier-detection methods can match this feature, because they output only a single number for each point: its outlierness score, (c) Our LOCI method can be computed as quickly as the best previous methods, (d) Moreover, LOCI leads to a practically linear approximate method, aLOCI (for approximate LOCI), which provides fast highly-accurate outlier detection. To the best of our knowledge, this is the first work to use approximate computations to speed up outlier detection. Experiments on synthetic and real world data sets show that LOCI and aLOCI can automatically detect outliers and micro-clusters, without user-required cut-offs, and that they quickly spot both expected and unexpected outliers.
Two‐component collagen nerve guides support axonal regeneration in the rat peripheral nerve injury model

Progress in material development has enabled the production of nerve guides that increasingly resemble the characteristics of an autologous nerve graft. In the present study, 20 mm adult rat sciatic nerve defects were bridged with the collagen‐based, two‐component nerve guide ‘Neuromaix’, the commercially available NeuraGen® nerve tube or an autologous nerve graft. Neuromaix was able to support structural as well as functional regeneration across this gap. The majority of the axons grew across the scaffold into the distal nerve segment and retrograde tracing confirmed that these axons were of somatosensory and motor origin. Histomorphology revealed that axons regenerating through Neuromaix exhibited reduced myelin sheath thickness, whereas axon diameter and axon density were comparable to those of the autograft. Neuromaix implantation resulted in reinnervation of the gastrocnemius muscle to a level that was not significantly different from that supported by the autograft, as demonstrated by electrophysiology. Our findings show that the use of the Neuromaix scaffold not only allowed axonal regeneration across large nerve gaps, but that the regenerating axons were also able to functionally reinnervate the muscles. These data provide a promising perspective for the first in human application of the materials. Copyright © 2016 John Wiley & Sons, Ltd.
Structural and Functional Restraints on the Occurrence of Single Amino Acid Variations in Human Proteins

Human genetic variation is the incarnation of diverse evolutionary history, which reflects both selectively advantageous and selectively neutral change. In this study, we catalogue structural and functional features of proteins that restrain genetic variation leading to single amino acid substitutions. Our variation dataset is divided into three categories: i) Mendelian disease-related variants, ii) neutral polymorphisms and iii) cancer somatic mutations. We characterize structural environments of the amino acid variants by the following properties: i) side-chain solvent accessibility, ii) main-chain secondary structure, and iii) hydrogen bonds from a side chain to a main chain or other side chains. To address functional restraints, amino acid substitutions in proteins are examined to see whether they are located at functionally important sites involved in protein-protein interactions, protein-ligand interactions or catalytic activity of enzymes. We also measure the likelihood of amino acid substitutions and the degree of residue conservation where variants occur. We show that various types of variants are under different degrees of structural and functional restraints, which affect their occurrence in human proteome.