Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms

When many protein sequences are available for estimating the time of divergence between two species, it is customary to estimate the time for each protein separately and then use the average for all proteins as the final estimate. However, it can be shown that this estimate generally has an upward bias, and that an unbiased estimate is obtained by using distances based on concatenated sequences. We have shown that two concatenation-based distances, i.e., average gamma distance weighted with sequence length (d2) and multiprotein gamma distance (d3), generally give more satisfactory results than other concatenation-based distances. Using these two distance measures for 104 protein sequences, we estimated the time of divergence between mice and rats to be approximately 33 million years ago. Similarly, the time of divergence between humans and rodents was estimated to be approximately 96 million years ago. We also investigated the dependency of time estimates on statistical methods and various assumptions made by using sequence data from eubacteria, protists, plants, fungi, and animals. Our best estimates of the times of divergence between eubacteria and eukaryotes, between protists and other eukaryotes, and between plants, fungi, and animals were 3, 1.7, and 1.3 billion years ago, respectively. However, estimates of ancient divergence times are subject to a substantial amount of error caused by uncertainty of the molecular clock, horizontal gene transfer, errors in sequence alignments, etc.
Fast mining of spatial collocations

Spatial collocation patterns associate the co-existence of non-spatial features in a spatial neighborhood. An example of such a pattern can associate contaminated water reservoirs with certain deceases in their spatial neighborhood. Previous work on discovering collocation patterns converts neighborhoods of feature instances to itemsets and applies mining techniques for transactional data to discover the patterns. We propose a method that combines the discovery of spatial neighborhoods with the mining process. Our technique is an extension of a spatial join algorithm that operates on multiple inputs and counts long pattern instances. As demonstrated by experimentation, it yields significant performance improvements compared to previous approaches.
Chronotypes in the US – Influence of age and sex

An individual’s chronotype reflects how the circadian system embeds itself into the 24-h day with rhythms in physiology, cognition and behavior occurring accordingly earlier or later. In view of an increasing number of people working at unusual times and linked health and safety risks, the wide range in human chronotypes may provide opportunities to allow people to work (and sleep) at times that are in synch with their circadian physiology. We aimed at estimating the distribution of chronotypes in the US population by age and sex. Twelve years (2003–2014) of pooled diary data from the American Time Use Survey were used to calculate chronotype based on mid-point of sleep on weekends (MSFWe, n = 53,689). We observed a near-normal distribution overall and within each age group. The distribution’s mean value is systematically different with age, shifting later during adolescence, showing a peak in ‘lateness’ at ~19 years, and shifting earlier thereafter. Men are typically later chronotypes than women before 40, but earlier types after 40. The greatest differences are observed between 15 and 25 for both sexes, equaling more than 50% of the total chronotype difference across all age groups. The variability in chronotype decreases with age, but is generally higher in males than females. This is the first study to estimate the distribution and prevalence of individual chronotypes in the US population based on a large-scale, nationally representative sample. Our finding that adolescents are on average the latest chronotypes supports delaying school start times to benefit their sleep and circadian alignment. The generally wide range in chronotypes may provide opportunities for tailored work schedules by matching external and internal time, potentially decreasing long- and short-term health and safety risks.
Towards 3D object detection with bimodal deep Boltzmann machines over RGBD imagery

Nowadays, detecting objects in 3D scenes like point clouds has become an emerging challenge with various applications. However, it retains as an open problem due to the deficiency of labeling 3D training data. To deploy an accurate detection algorithm typically resorts to investigating both RGB and depth modalities, which have distinct statistics while correlated with each other. Previous research mainly focus on detecting objects using only one modality, which ignores exploiting the cross-modality cues. In this work, we propose a cross-modality deep learning framework based on deep Boltzmann Machines for 3D Scenes object detection. In particular, we demonstrate that by learning cross-modality feature from RGBD data, it is possible to capture their joint information to reinforce detector trainings in individual modalities. In particular, we slide a 3D detection window in the 3D point cloud to match the exemplar shape, which the lack of training data in 3D domain is conquered via (1) We collect 3D CAD models and 2D positive samples from Internet. (2) adopt pretrained R-CNNs [2] to extract raw feature from both RGB and Depth domains. Experiments on RMRC dataset demonstrate that the bimodal based deep feature learning framework helps 3D scene object detection.
FACTORS AFFECTING SOFTWARE MAINTENANCE PRODUCTIVITY : AN EXPLORATORY STUDY 1

Systems developers and researchers have long been interested in the factors that affect software development productivity. Identification of factors as either aiding or hindering productivity enables management to take steps to encourage the positive influences and to eliminate the negative ones. This research has explored the possibility of developing an estimable model of software development productivity using a frontier estimation method. The approach taken is based upon output metrics for the entire project life-cycle, and includes project quality metrics. A large number of factors potentially affecting software maintenance productivity were included in this initial investigation. The empirical analysis of a pilot data set indicated that high project quality did not necessarily reduce project productivity. Significant factors in explaining positive variations in productivity included project team capability and good system response (turnaround) time. Factors significantly associated with negative variations in productivity included lack of team application experience and high project staff loading. The use of a new structured analysis and design methodology also resulted in lower short term productivity. These preliminary results have suggested a number of new research directions and have prompted the data-site to begin a full scale data collection effort in order to validate a model of software maintenance productivity.
COUPLED QUINTESSENCE AND CMB

We revise the stability of the tracking solutions and briefly review the potentials of quintessence models. We discuss the evolution of linear perturbations for $V(\phi) = V_{0} \exp(\lambda \phi^2/2)$ potential in which the scalar field is non-minimally coupled to cold dark matter. We consider the effects of this coupling on both cosmic microwave background temperature anisotropies and matter perturbations. We find that the phenomenology of this model is consistent with current observations up to the coupling power $n_{c} \leq 0.01$ while adopting the current parameters measured by WMAP, $\Omega_{\phi}^{(0)}=0.76$, $\Omega_{cdm}^{(0)}=0.191$, $\Omega_{b}^{(0)}=0.049$, and $h=0.70$. Upcoming cosmic microwave background observations continuing to focus on resolving the higher peaks may put strong constraints on the strength of the coupling.
Caffeine effect on mortality and oviposition in successive generations of Aedes aegypti.

OBJECTIVE Previous experiments showed that caffeine blocks the development of Aedes aegypti (Diptera, Culicidae) in the larval stage, consequently inhibiting the production of adults. This study aimed at obtaining data suggestive of caffeine resistance by these mosquitoes. METHODS Experiments were carried out in successive generations to assess adult production from eggs laid in previous generation and oviposition rate in every generation using 200 and 500 microg/mL caffeine. Tap water was used as control. Experiments were conducted in the city of São José do Rio Preto, Southeastern Brazil between 2002 and 2005. Statistical tests consisted of exploratory data analysis and smoothing algorithms. RESULTS Increasing reduction in productivity of adults occurred among generations at both caffeine concentrations but the differences were only significant at 200microg/mL caffeine. As for the oviposition rate, there was a decrease in the mean number of eggs per female over generations at both caffeine concentrations. CONCLUSIONS There was no evidence of caffeine resistance over generations. The study results corroborate caffeine as an alternative as an important Ae. Aegypti control agent to avoid resistance.
Accuracy of an electromagnetic measurement device and application to the measurement and description of knee joint motion

Abstract The aims of this study were to analyse the accuracy and sensitivity to metals of an electromagnetic motion measurement device and to use it to provide a description of motion of the human knee joint. A calibrated grid and sine bar were used to measure translational and rotational accuracy, which were found to be ±0.23 per cent of the step size (translation) and ±2.0 per cent of the step size (rotation) within an optimal operational zone of minimal positional error for which the receiver to transmitter separation was between 271 and 723 mm. The presence of multiple receivers was found to have a significant effect on the accuracy only when positioned within 30 mm of one another. Mild steel was found to have a significant detrimental effect when within 150 mm of the transmitter or receiver. A stainless steel bone screw had no effect on the accuracy of the device. A mathematical description of knee joint motion is presented which describes the motion in terms of clinical rotations. The device is a useful tool for measuring joint motion in the operating theatre and laboratory, owing to its accuracy and insensitivity to surgical alloys.
Relation Between Variables of Preadmission, Medical School Performance, and COMLEX–USA Levels 1 and 2 Performance

Abstract The purpose of this study was to investigate the relation between preadmission academic variables, osteopathic medical school performance in the first 2 years, and performance on the Comprehensive Osteopathic Medical Licensing Examination (COMLEX–USA) Levels 1 and 2. The study group comprised 174 students in the class of 2001 of the New York College of Osteopathic Medicine of the New York Institute of Technology, Old Westbury. Preadmission academic variables were the Medical College Admission Test (MCAT) subscores and undergraduate grade point averages (UGPAs). Physical sciences (physical MCAT) and biological sciences MCAT (biological MCAT) subscores were significantly correlated with COMLEX–USA Level 1 performance, and verbal reasoning, physical, and biological MCAT subscores were correlated with Level 2 performance. COMLEX–USA Level 1 performance was correlated with the year 1 grade point average (GPA) (0.78) and the year 2 GPA (0.83). COMLEX–USA Level 2 performance was correlated with the year 1 GPA (0.64) and the year 2 GPA (0.68). Strong correlations existed between all year 1 and most year 2 course grades and COMLEX–USA Level 1 scores. School-specific regression models that were highly predictive of school performance and COMLEX-USA Level 1 performance were developed. COMLEX–USA Level 1 predictive models used preadmission variables combined with the year 1 and year 2 course grades. The year 2 courses' model had a higher predictive value for COMLEX–USA Level 1 performance (R2 = 0.81) than the year 1 courses' model (R2 = 0.77). Significant predictors of COMLEX–USA Level 1 performance in the combined year 1 and 2 courses' model were the pharmacology II, neuropathology, and pulmonary pathology grades, and the verbal and physical MCAT subscores (R2 = 0.820).
Evolutionary Transitions between Sex-Determining Mechanisms : A Review of Theory

The extraordinary diversity of sex-determining mechanisms found in nature is thought to have arisen by the addition, modification or replacement of regulators at the upstream end of the sex-determining pathway. The spread of a novel regulator of sex determination can manifest itself by an evolutionary transition between environmental and genetic sex determination, for example, or between male and female heterogamety. Both kinds of transition have occurred frequently in the course of evolution. In this paper, various evolutionary forces acting on sex-determining mutations that can bias transitions in one direction or the other are reviewed. Furthermore, the adaptive significance of the main modes of sex determination are discussed, and the common principle underlying ultimate explanations for environmental sex determination, genetic sex determination and maternal control over sex determination in the offspring are highlighted. Most of the current theory concentrates on the population-genetic aspects of sex determination transitions, Published online: December 7, 2013 G. Sander van Doorn Theoretical Biology Group, Centre for Ecological and Evolutionary Studies University of Groningen, PO Box 11103 NL–9700 CC Groningen (The Netherlands) E-Mail g.s. van.doorn @ rug.nl © 2013 S. Karger AG, Basel 1661–5425/13/0083–0007$38.00/0
Do Basal Ganglia Amplify Willed Action by Stochastic Resonance? A Model

Basal ganglia are usually attributed a role in facilitating willed action, which is found to be impaired in Parkinson's disease, a pathology of basal ganglia. We hypothesize that basal ganglia possess the machinery to amplify will signals, presumably weak, by stochastic resonance. Recently we proposed a computational model of Parkinsonian reaching, in which the contributions from basal ganglia aid the motor cortex in learning to reach. The model was cast in reinforcement learning framework. We now show that the above basal ganglia computational model has all the ingredients of stochastic resonance process. In the proposed computational model, we consider the problem of moving an arm from a rest position to a target position: the two positions correspond to two extrema of the value function. A single kick (a half-wave of sinusoid, of sufficiently low amplitude) given to the system in resting position, succeeds in taking the system to the target position, with high probability, only at a critical noise level. But for suboptimal noise levels, the model arm's movements resemble Parkinsonian movement symptoms like akinetic rigidity (low noise) and dyskinesias (high noise).
Autophosphorylation of the focal adhesion kinase, pp125FAK, directs SH2-dependent binding of pp60src

The phosphorylation of protein tyrosine kinases (PTKs) on tyrosine residues is a critical regulatory event that modulates catalytic activity and triggers the physical association of PTKs with Src homology 2 (SH2)-containing proteins. The integrin-linked focal adhesion kinase, pp125FAK, exhibits extracellular matrix-dependent phosphorylation on tyrosine and physically associates with two nonreceptor PTKs, pp60src and pp59fyn, via their SH2 domains. Herein, we identify Tyr-397 as the major site of tyrosine phosphorylation on pp125FAK both in vivo and in vitro. Tyrosine 397 is located at the juncture of the N-terminal and catalytic domains, a novel site for PTK autophosphorylation. Mutation of Tyr-397 to a nonphosphorylatable residue dramatically impairs the phosphorylation of pp125FAK on tyrosine in vivo and in vitro. The mutation of Tyr-397 to Phe also inhibits the formation of stable complexes with pp60src in cells expressing Src and FAK397F, suggesting that autophosphorylation of pp125FAK may regulate the association of pp125FAK with Src family kinases in vivo. The identification of Tyr-397 as a major site for FAK autophosphorylation provides one of the first examples of a cellular protein containing a high-affinity binding site for a Src family kinase SH2 domain. This finding has implications for models describing the mechanisms of action of pp125FAK, the regulation of the Src family of PTKs, and signal transduction through the integrins.
The Entrepreneurial Adjunct.

the higher education community is witnessing what I call the "entrepreneurial adjunct phenomenon": a kind of merchandising of the needs, concerns, and activities of faculty with short-term, often part-time, appointments that depend on factors like enrollment, budget, and program changes. These faculty members are called any number of things: adjuncts, part-timers, lecturers, nonregulars, sessionals, and so on. I will call them "contingent faculty" to draw attention to the most important aspect of their employment relationship: its tenuousness.
The Role of Moral Reasoning and Order Effects in Ethical Decision Making Ability: The Case of Novice Vs Experienced Accounting Students

The purpose of this study is two-fold. Using the P-score from the defining issues test as a proxy for ethical decision making ability, this study firstly investigates whether work experience influences the perceptions about prescriptive and deliberative moral reasoning. Secondly, this study investigates the order effects of presentation of dilemmas on ethical decision making ability of novice and experienced accounting students. Moral reasoning can be categorized as prescriptive i.e. what should ideally be done and deliberative i.e. what is actually done. On account of lack of work experience, novice accounting students do not often face scenarios wherein there is a difference between their prescriptive and deliberative reasoning. This study hypothesizes that novice accounting students cannot differentiate between these two types of reasoning but would exhibit order effects while making ethical decisions. 140 graduate accounting students from universities in Denmark respond to an audit specific DIT instrument, measuring prescriptive and deliberative moral reasoning. The results indicate that, accounting students with work experience exhibit different perceptions to deliberative and prescriptive moral reasoning than novices while novice accounting students exhibit order effects. The implication of this study concerns ethics training to accounting students. This study calls for a more practical and hands on approach ethics training, one which teaches students not only to deal with dilemmas ideally but also trains them to handle dilemmas where in the ideal may not always translate into the actual.
Caractéristiques individuelles, pratiques éducatives familiales et performance scolaire au cours préparatoire

L'etude a un double objectif : isoler, decrire et mesurer les comportements educatifs de parents d'ecoliers de 5-6 ans : - Mettre a l'epreuve des faits un modele theorique explicatif de la performance scolaire de C. P. Recapitulant certains determinants familiaux et individuels relatifs a l'enfant. L'echantillon est compose de 81 individus suivis de la grande section maternelle au premier trimestre de C. E. 1. L'exploitation des resultats a ete faite au moyen de l'analyse des pistes causales. Les resultats remettent en cause le concept de "pression" familiale et mettent au jour un reseau particulier de relations entre variables : la perception de soi en tant qu'eleve y occupe une place importante dans le determinisme de la performance scolaire au C. P.
Supervised texture segmentation using DWT and a modified K-NN classifier

We present a texture segmentation scheme based on the discrete wavelet transform (DWT). The DWT is a non-redundant representation which can reduce computational complexity in the processing. The texture segmentation scheme presented here consists of three steps: feature extraction, conditioning, and clustering. For feature conditioning, a number of smoothing windows have been tested. Clustering is performed with a modified k-nearest neighbour clustering algorithm. The proposed scheme consistently achieves error rates of less than 10% with the best average error of 5.62%.
Characteristics and Analysis of Finnish and Swedish Clinical Intensive Care Nursing Narratives

We present a comparative study of Finnish and Swedish free-text nursing narratives from intensive care. Although the two languages are linguistically very dissimilar, our hypothesis is that there are similarities that are important and interesting from a language technology point of view. This may have implications when building tools to support producing and using health care documentation. We perform a comparative qualitative analysis based on structure and content, as well as a comparative quantitative analysis on Finnish and Swedish Intensive Care Unit (ICU) nursing narratives. Our findings are that ICU nursing narratives in Finland and Sweden have many properties in common, but that many of these are challenging when it comes to developing language technology tools.
Continuous variable tangle, monogamy inequality, and entanglement sharing in Gaussian states of continuous variable systems

For continuous-variable (CV) systems, we introduce a measure of entanglement, the CV tangle (contangle), with the purpose of quantifying the distributed (shared) entanglement in multimode, multipartite Gaussian states. This is achieved by a proper convex-roof extension of the squared logarithmic negativity. We prove that the contangle satisfies the Coffman–Kundu–Wootters monogamy inequality in all three-mode Gaussian states, and in all fully symmetric N-mode Gaussian states, for arbitrary N. For three-mode pure states, we prove that the residual entanglement is a genuine tripartite entanglement monotone under Gaussian local operations and classical communication. We show that pure, symmetric three-mode Gaussian states allow a promiscuous entanglement sharing, having both maximum tripartite residual entanglement and maximum couplewise entanglement between any pair of modes. These states are thus simultaneous CV analogues of both the GHZ and the W states of three qubits: in CV systems monogamy does not prevent promiscuity, and the inequivalence between different classes of maximally entangled states, holding for systems of three or more qubits, is removed.
Automatic Weight Generation and Class Predicate Stability in RDF Summary Graphs

In this current study, we use graph localities and neighborhood similarity to enhance the summary graph generation approach for building a summary graph structure for intelligent exploration of semantic data. The key improvements to what we have previously proposed include the addition of a string similarity measure for the literal neighbors, development of a stability measure to evaluate the accuracy of class relations, the addition of auto-generated property weights, and the detection of noise properties.