Miracle-dz/UniFAR-FTUs huggingface dataset:
Theca Interna: The Other Side of Bovine Follicular Atresia1

Abstract Currently, histological classifications of ovarian follicular atresia are almost exclusively based on the morphology of the membrana granulosa without reference to the theca interna. Atresia in the bovine small antral ovarian follicle has been redefined into antral or basal atresia where cell death commences initially within antral or basal regions of the membrana granulosa, respectively. To examine cell death in the theca interna in the two types of atretic follicles, bovine ovaries were collected and processed for immunohistochemistry and light microscopy. Follicles were classified as healthy, antral atretic, or basal atretic. Follicle diameter was recorded and sections stained with lectin from Bandeiraea simplicifolia to identify endothelial cells or with an antibody to cytochrome P450 cholesterol side-chain cleavage to identify steroidogenic cells and combined with TUNEL labeling to identify dead cells. The numerical density of steroidogenic cells within the theca interna was significantly reduced (P < 0.001) in basal atretic follicles in comparison with other follicles. Cell death was greater in both endothelial cells (P < 0.05) and steroidogenic cells (P < 0.01) of the theca interna of basal atretic follicles compared with healthy and antral atretic follicles. Thus, we conclude that the theca interna is susceptible to cell death early in atresia, particularly in basal atretic follicles.
In the Child’s Best Interest: Terminating the Rights of Fathers With Children in Foster Care

The authors conducted a content analysis of appellate court foster care cases in which fathers appealed the termination of their parental rights. Applying the Responsible Fathering framework to organize the contextual issues that impede men from responsibly fathering, the authors sought to learn what factors affect decisions regarding the termination of their parental rights. Multiple risk factors emerged including lack of social support, financial resources, and opportunities. Implications for practitioners include attending to father’s mental health, alcohol and/or substance abuse, issues surrounding incarceration, and the coparental relationship.
Automatic generation of visual-textual web video thumbnail

Thumbnails provide an efficient way to perceive video content and give online viewers instant gratification of making relevance judgements. In this paper, we proposed an automatic approach to generate magazine-cover-like thumbnail using the salient visual and textual metadata extracted from video. Compared with traditional snapshot, the synthesized thumbnail is more informative and attractive, which would be helpful for online video selection.
Analysis of the effects of lifetime learning on population fitness using vose model

Vose's dynamical systems model of the simple genetic algorithm (SGA) is an exact model that uses mathematical operations to capture the dynamical behavior of genetic algorithms. The original model was defined for a simple genetic algorithm. This paper suggests how to extend the model and incorporate two kinds of learning, Darwinian and Lamarckian, into the framework of the Vose model. The extension provides a new theoretical framework to examine the effects of lifetime learning on the fitness of a population. We analyze the asymptotic behavior of different hybrid algorithms on an infinite population vector and compare it to the behavior of the classical genetic algorithm on various population sizes. Our experiments show that Lamarckian-like inheritance - direct transfer of lifetime learning results to offsprings - allows quicker genetic adaptation. However, functions exist where the simple genetic algorithms without learning, as well as Lamarckian evolution, converge to the same local optimum, while genetic search based on Darwinian inheritance converges to the global optimum.
Indoor Scene Recognition Using Local Semantic Concepts

This paper introduces a system for recognizing indoor scene images. The system aims at recognizing the environment illustrated in an image and assigning an appropriate semantic label to it. Developing such systems is one of the most important issues in the field of machine vision and robotics. They are extensively used in object recognition, image and video semantic recognition, motion detection, positioning, and robot direction. The overall algorithm involves three major steps. The first is to extract local information and spatial relationships in the images, modeling the environment based on those pieces of information, and using this model for the semantic sectioning of the image and labeling local areas using graph-based energy minimization algorithm. Results show that this system can perform as well as other object-based and 3D-image features-based environment recognition systems.
Texture analysis of periventricular echogenicity on neonatal cranial ultrasound predicts periventricular leukomalacia.

BACKGROUND White matter periventricular echogenicity detected in neonatal cranial ultrasound (US) scans may be followed by cystic periventricular leukomalacia (PVL) or might resolve. Serial US are therefore needed to clarify the outcome. Texture analysis is a computerized method to analyze images and distinguish findings that are undetectable by the human eye. OBJECTIVE To test whether texture analysis can differentiate echogenicities that resolve from those that develop cystic PVL. MATERIAL AND METHODS Neonates with echogenicities on their initial US scan were studied; texture analysis was performed on the coronal and sagittal sections. Texture parameters were entered into a linear discriminant analysis (LDA) to classify the scans along two axes called most discriminant features (MDF) 1 and 2. RESULTS We studied twenty infants with periventricular echogenicities on initial scans; ten of them later resolved (group A), while the other ten infants developed cystic PVL (group B). The classification accuracy was 66% and 82% for group A and B on sagittal sections, and 75%, and 80% on coronal. In the coronal and sagittal plane respectively, a MDF1 value of 0.98 and 0.24 and an MDF2 value of 0.86 and 0.001 provided the best sensitivity, specificity, positive and negative likelihood ratio. CONCLUSION Texture analysis is a promising objective tool to early identify which cranial echogenicity that will develop into cystic PVL.
Airline Reservations Systems: Lessons from History

This article discusses the evolution of airline reservation systems - from their inception as manually maintained inventories of seat availability, through their description as "anticompetitive weapons" used "unlawfully" to obtain and exercise monopoly power. The evolutionary perspective reveals interdependent industry, company, and technology forces that shaped the pattern of competition. Although many facets of the airline experience are unique to the air transport industry, the authors identify three features with broad implications for the strategic use of information technology. First, large installed processing capacity can be a source of economies of scale and scope. Second, established technical competence is a necessary requirement for gaining competitive advantage. Finally, sustainable advantage need not be the result of extraordinary vision, but the result of consistent exploitation of opportunities revealed during the evolution of adaptable systems.
Algorithmic Meta-Theorems for Graphs of Bounded Vertex Cover

Possibly the most famous algorithmic meta-theorem is Courcelle's theorem, which states that all MSO-expressible graph properties are decidable in linear time for graphs of bounded treewidth. Unfortunately, the running time's dependence on the MSO formula describing the problem is in general a tower of exponentials of unbounded height, and there exist lower bounds proving that this cannot be improved even if we restrict ourselves to deciding FO logic on trees. In this paper we attempt to circumvent these lower bounds by focusing on a subclass of bounded treewidth graphs, the graphs of bounded vertex cover. By using a technique different from the standard decomposition and dynamic programming technique of treewidth we prove that in this case the running time implied by Courcelle's theorem can be improved dramatically, from non-elementary to doubly and singly exponential for MSO and FO logic respectively. Our technique relies on a new graph width measure we introduce, for which we show some additional results that may indicate that it is of independent interest. We also prove lower bound results which show that our upper bounds cannot be improved significantly, under widely believed complexity assumptions. Our work answers an open problem posed by Michael Fellows.
Effects of cardiac resynchronisation therapy in patients with heart failure having a narrow QRS Complex enrolled in PROSPECT

Introduction Current guidelines recommend cardiac resynchronisation therapy (CRT) in patients with severe symptomatic heart failure, depressed left ventricular (LV) systolic function and a wide QRS complex (≥120 ms). However, patients with heart failure having a narrow QRS complex might also benefit from CRT. Design setting patients interventions During the Predictors of Response to Cardiac Resynchronisation Therapy (PROSPECT) trial, 41 patients were enrolled in a ‘narrow’ QRS sub-study. These patients had a QRS complex <130 ms, but documented evidence of mechanical dyssynchrony by any of seven pre-defined echocardiographic measures. Results After 6 months of CRT, 26 (63.4%) patients showed improvement according to the Clinical Composite Score, 4 (9.8%) remained unchanged and 11 (26.8%) worsened. In patients with paired data, the 6-min walking distance increased from 334±118 m to 382±128 m, (p=0.003) and quality-of-life score improved from 44.2±19.7 to 26.8±20.2 (p<0.0001). Furthermore, there was a significant decrease in LV end-systolic diameter (from 59±9 to 55±12 mm, p=0.002) and in LV end-diastolic diameter (from 67±9 to 63±11 mm, p=0.007). Conclusion The results suggest that CRT may have a beneficial effect in heart failure patients with a narrow QRS complex and mechanical dyssynchrony as assessed by echocardiography. The majority of patients improved on clinical symptoms, and there was an evident reduction in LV diameters. Larger studies are needed to clearly define selection criteria for CRT in patients with a narrow QRS complex.
Revisiting crime surveys: emotional responses without emotions? OR Look back at anger

Research exploring the emotional responses to crime experienced by the citizens of several major European and North American countries has suggested that a significant proportion of the residents of these countries 'fear' or feel 'angry' about the possibility of criminal victimization. It has ceased to appear incredible to us that we are regularly finding that between a quarter and two thirds of our citizens are fearful or 'angry about crime' 'all of the time'. The argument put forward in this contribution to the work in this field is that the emotional responses to crime have been exaggerated by the inappropriate use of the survey as a measurement tool. Ethnographic and qualitative data suggest that experiences of 'fear' and 'anger' are less common. Suggestions for improving the ability of the questions used in surveys to accurately capture these emotional responses are advanced.
CIAL at IJCNLP-2017 Task 2: An Ensemble Valence-Arousal Analysis System for Chinese Words and Phrases

Sentiment lexicon is very helpful in dimensional sentiment applications. Because of countless Chinese words, developing a method to predict unseen Chinese words is required. The proposed method can handle both words and phrases by using an ADVWeight List for word prediction, which in turn improves our performance at phrase level. The evaluation results demonstrate that our system is effective in dimensional sentiment analysis for Chinese phrases. The Mean Absolute Error (MAE) and Pearson’s Correlation Coefficient (PCC) for Valence are 0.723 and 0.835, respectively, and those for Arousal are 0.914 and 0.756, respectively.
Error filtering, pair assembly and error correction for next-generation sequencing reads

MOTIVATION Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage is low. RESULTS We demonstrate large reductions in error frequencies, especially for high-error-rate reads, by three independent means: (i) filtering reads according to their expected number of errors, (ii) assembling overlapping read pairs and (iii) for amplicon reads, by exploiting unique sequence abundances to perform error correction. We also show that most published paired read assemblers calculate incorrect posterior quality scores. AVAILABILITY AND IMPLEMENTATION These methods are implemented in the USEARCH package. Binaries are freely available at http://drive5.com/usearch. CONTACT robert@drive5.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Learning user simulations for information state update dialogue systems

This paper describes and compares two methods for simulating user behaviour in spoken dialogue systems. User simulations are important for automatic dialogue strategy learning and the evaluation of competing strategies. Our methods are designed for use with “Information State Update” (ISU)-based dialogue systems. The ﬁrst method is based on supervised learning using linear feature combination and a normalised exponential output function. The user is modelled as a stochastic process which selects user actions ( (cid:2) speech act, task (cid:3) pairs) based on features of the current dialogue state, which encodes the whole history of the dialogue. The second method uses n-grams of (cid:2) speech act, task (cid:3) pairs, restricting the length of the history considered by the order of the n-gram. Both models were trained and evaluated on a subset of the C OMMUNICATOR corpus, to which we added annotations for user actions and Information States. The model based on linear feature combination has a perplexity of 2.08 whereas the best n-gram (4-gram) has a perplexity of 3.58. Each one of the user models ran against a system policy trained on the same corpus with a method similar to the one used for our linear feature combination model. The quality of the simulated dialogues produced was then measured as a function of the ﬁlled slots, conﬁrmed slots, and number of actions performed by the system in each dialogue. In this experiment both the linear feature combination model and the best n-grams (5-gram and 4-gram) produced similar quality simulated dialogues.
Conditional mode regression: Application to functional time series prediction

We consider $\alpha$-mixing observations and deal with the estimation of the conditional mode of a scalar response variable $Y$ given a random variable $X$ taking values in a semi-metric space. We provide a convergence rate in $L^p$ norm of the estimator. A useful and typical application to functional times series prediction is given.
Deep Supervised Discrete Hashing

With the rapid growth of image and video data on the web, hashing has been extensively studied for image or video search in recent years. Benefit from recent advances in deep learning, deep hashing methods have achieved promising results for image retrieval. However, there are some limitations of previous deep hashing methods (e.g., the semantic information is not fully exploited). In this paper, we develop a deep supervised discrete hashing algorithm based on the assumption that the learned binary codes should be ideal for classification. Both the pairwise label information and the classification information are used to learn the hash codes within one stream framework. We constrain the outputs of the last layer to be binary codes directly, which is rarely investigated in deep hashing algorithm. Because of the discrete nature of hash codes, an alternating minimization method is used to optimize the objective function. Experimental results have shown that our method outperforms current state-of-the-art methods on benchmark datasets.
Flow Orientation Analysis for Major Activity Regions Based on Smart Card Transit Data

Analyzing public movement in transportation networks in a city is significant in understanding the life of citizen and making improved city plans for the future. This study focuses on investigating the flow orientation of major activity regions based on smart card transit data. The flow orientation based on the real movements such as transit data can provide the easiest way of understanding public movement in the complicated transportation networks. First, high inflow regions (HIRs) are identified from transit data for morning and evening peak hours. The morning and evening HIRs are used to represent major activity regions for major daytime activities and residential areas, respectively. Second, the directional orientation of flow is then derived through the directional inflow vectors of the HIRs to show the bias in directional orientation and compare flow orientation among major activity regions. Finally, clustering analysis for HIRs is applied to capture the main patterns of flow orientations in the city and visualize the patterns on the map. The proposed methodology was illustrated with smart card transit data of bus and subway transportation networks in Seoul, Korea. Some remarkable patterns in the distribution of movements and orientations were found inside the city. The proposed methodology is useful since it unfolds the complexity and makes it easy to understand the main movement patterns in terms of flow orientation.
The differential facilitatory effects of gesture and visualisation processes on object naming in aphasia

This study investigated the differential facilitation effects of gesture and visualisation processes on object naming in individuals with aphasia. Six participants with word production deficits resulting from varying levels of impairment in the word production system, underwent a series of naming trials. Baseline measures of naming were compared to those obtained following instructions to point, visualise, and produce gesture. The results supported the superiority of iconic gesture as a facilitator of object naming in aphasia. In particular, individuals with phonological access, storage, or encoding difficulties demonstrated significantly enhanced naming abilities with the use of iconic gesture as compared to individuals with a semantic impairment or an apraxia of speech. Pointing, cued articulation, and visualisation processes did not significantly enhance naming skills in these individuals. These results are discussed within the model of lexical gesture and word production proposed by Krauss and Hadar (1999).
Genome-wide expression profiling in Escherichia coli K-12.

We have established high resolution methods for global monitoring of gene expression in Escherichia coli. Hybridization of radiolabeled cDNA to spot blots on nylon membranes was compared to hybridization of fluorescently-labeled cDNA to glass microarrays for efficiency and reproducibility. A complete set of PCR primers was created for all 4290 annotated open reading frames (ORFs) from the complete genome sequence of E.coli K-12 (MG1655). Glass- and nylon-based arrays of PCR products were prepared and used to assess global changes in gene expression. Full-length coding sequences for array printing were generated by two-step PCR amplification. In this study we measured changes in RNA levels after exposure to heat shock and following treatment with isopropyl-beta-D-thiogalactopyranoside (IPTG). Both radioactive and fluorescence-based methods showed comparable results. Treatment with IPTG resulted in high level induction of the lacZYA and melAB operons. Following heat shock treatment 119 genes were shown to have significantly altered expression levels, including 35 previously uncharacterized ORFs and most genes of the heat shock stimulon. Analysis of spot intensities from hybridization to replicate arrays identified sets of genes with signals consistently above background suggesting that at least 25% of genes were expressed at detectable levels during growth in rich media.
Generating Multivariate Normal Data by Using PROC IML

In simulation studies in statistics, there are many situations that we need to generate data from a multivariate normal distribution. By multivariate normal data we mean joint observations of p variables Y1, Y2, . , Yp, in which each individual variable by itself is normally distributed, the variables are mutually correlated, and come from a joint multivariate normal distribution. The procedure for generation of multivariate normal data is similar to the univariate case, that is, we can generate pairs of independent normals and then multiplied that pairs by the Cholesky square root of the desired variancecovariance matrix. One way to do that is to obtain the formula for the Cholesky square root of the variance-covariance matrix, and which is easy for bivariate normal data. However, it becomes complicated when p is large. An alternative method by using PROC IML can be used to accomplish the desired data easily by using matrix computations. Function HALF in PROC IML can be used to obtain the Cholesky square root of the desired variance-covariance matrix.
HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and computationally much cheaper constrained geometrical simulation approach framework rigidity optimized dynamic algorithm (FRODA). Atomic fluctuations obtained by replica-exchange molecular dynamics (REMD) simulations agree quantitatively with those obtained by molecular dynamics (MD) and FRODA simulations for the unbound TAR structure. Regarding the stereochemical quality of the generated conformations, backbone torsion angles and puckering modes of the sugar-phosphate backbone were reproduced equally well by MD and REMD simulations, but further improvement is needed in the case of FRODA simulations. Essential dynamics analysis reveals that all three simulation approaches show a tendency to sample bound conformations when starting from the unbound TAR structure, with MD and REMD simulations being superior with respect to FRODA. These results are consistent with the experimental view that bound TAR RNA conformations are transiently sampled in the free ensemble, following a conformation selection model. The simulation-generated TAR RNA conformations have been successfully used as receptor structures for docking. This finding has important implications for RNA-ligand docking in that docking into an ensemble of simulation-generated RNA structures is shown to be a valuable means to cope with large apo-to-holo conformational transitions of the receptor structure.