Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multistaged Automatic Restoration of Noisy Microscopy Cell Images

Automated cell segmentation for microscopy cell images has recently become an initial step for further image analysis in cell biology. However, microscopy cell images are easily degraded by noise during the readout procedure via optical-electronic imaging systems. Such noise degradations result in low signal-to-noise ratio (SNR) and poor image quality for cell identification. In order to improve SNR for subsequent segmentation and image-based quantitative analysis, the commonly used state-of-art restoration techniques are applied but few of them are suitable for corrupted microscopy cell images. In this paper, we propose a multistaged method based on a novel integration of trend surface analysis, quantile-quantile plot, bootstrapping, and the Gaussian spatial kernel for the restoration of noisy microscopy cell images. We show this multistaged approach achieves higher performance compared with other state-of-art restoration techniques in terms of peak signal-to-noise ratio and structure similarity in synthetic noise experiments. This paper also reports an experiment on real noisy microscopy data which demonstrated the advantages of the proposed restoration method for improving segmentation performance.
Building a Climate for Innovation Through Transformational Leadership and Organizational Culture

Research has called for organizations to be more flexible, adaptive, entrepreneurial, and innovative in meeting the changing demands of today's environment. Appropriate leadership to effect such change is required; however, there has been little empirical analysis of the theoretical relationships among the key components that make up such change strategy, including transformational leadership, organizational culture, and organizational innovation. This study examines these linkages in terms of their relationships with climate for organizational innovation in Australian private sector organizations. Structural equation modeling based on responses to a survey of 1,158 managers explores the relationship between transformational leadership and climate for organizational innovation and the extent to which a competitive, performance-oriented organizational culture mediates this relationship. Strategies for building innovative organizations are discussed.
Modularisation of state-dependent crosscutting concerns using TinySAOP

In aspect-oriented programming (AOP), to specify its intention clearly, a pointcut definition must specify the join point where to adapt a crosscutting functionality, as well as the applicability condition of the crosscutting functionality (if any). Meanwhile, to realise modular abstraction of a crosscutting functionality, an advice must contain the crosscutting functionality only. A state-dependent crosscutting concern is an aspect whose applicability of its advice at a matched join point is state-dependent, and call graph-based AOP approaches are insufficient for a state-dependent crosscutting concern because they do not allow specification of the state-dependent applicability condition in the pointcut definition. Thus, the state-dependent applicability condition has to be embedded inside the aspect's advice, and as a result, the intention of the pointcut definition is not clearly defined and the modularity of the advice is broken. To solve the state-dependent crosscutting concern problem, the paper discusses TinySAOP language that exposes applicability join point and supports in pointcut to allow the applicability condition of a state-dependent crosscutting concern to be clearly specified in the pointcut definition and cleanly separated from the aspect's advice.
[Three-dimensional ultrasound biomicroscopic examinations for haptic differentiation of potentially accommodative intraocular lenses].

PURPOSE The principal ability of potentially accommodative IOLs is based on an axial shift of the IOL optics induced by the ciliary body action in interaction with a reversible change in haptic angulation. The aim of this study was to investigate the accommodative performance of this new IOL generation. METHOD The authors have designed a test device to study IOL performance experimentally. These results were extrapolated to the in vivo situation in patients with accommodative implants. RESULTS The 3D high-resolution presentation of the anterior segment of the eye allows a separation of the IOL haptic elements. In vitro and in the selected in vivo cases a change in haptic angulation <10 degrees in combination with a maximal IOL shift of 0.5 mm was found. CONCLUSIONS The simulation model used in combination with 3D ultrasound biomicroscopy provides information about the potential of accommodative IOL designs. Conclusions corresponding to changes in haptic angulation during accommodation can be drawn and applied to the in vivo situation.
Brain maps, great and small: lessons from comparative studies of primate visual cortical organization

In this paper, we review evidence from comparative studies of primate cortical organization, highlighting recent findings and hypotheses that may help us to understand the rules governing evolutionary changes of the cortical map and the process of formation of areas during development. We argue that clear unequivocal views of cortical areas and their homologies are more likely to emerge for ‘core’ fields, including the primary sensory areas, which are specified early in development by precise molecular identification steps. In primates, the middle temporal area is probably one of these primordial cortical fields. Areas that form at progressively later stages of development correspond to progressively more recent evolutionary events, their development being less firmly anchored in molecular specification. The certainty with which areal boundaries can be delimited, and likely homologies can be assigned, becomes increasingly blurred in parallel with this evolutionary/developmental sequence. For example, while current concepts for the definition of cortical areas have been vindicated in allowing a clarification of the organization of the New World monkey ‘third tier’ visual cortex (the third and dorsomedial areas, V3 and DM), our analyses suggest that more flexible mapping criteria may be needed to unravel the organization of higher-order visual association and polysensory areas.
Susceptibility to tulathromycin in Mannheimia haemolytica isolated from feedlot cattle over a 3-year period

Mannheimia haemolytica isolated from feedlot cattle were tested for tulathromycin resistance. Cattle were sampled over a 3-year period, starting 12 months after approval of tulathromycin for prevention and treatment of bovine respiratory disease. Nasopharyngeal samples from approximately 5,814 cattle were collected when cattle entered feedlots (N = 4) and again from the same cattle after ≥60 days on feed. The antimicrobial use history for each animal was recorded. Mannheimia haemolytica was isolated from 796 (13.7%) entry samples and 1,038 (20.6%) ≥ 60 days samples. Of the cattle positive for M. haemolytica, 18.5, 2.9, and 2.4% were administered therapeutic concentrations of tulathromycin, tilmicosin, or tylosin tartrate, respectively. In addition, 13.2% were administered subtherapeutic concentrations of tylosin phosphate in feed. In years one and two, no tulathromycin-resistant M. haemolytica were detected, whereas five isolates (0.4%) were resistant in year three. These resistant isolates were collected from three cattle originating from a single pen, were all serotype 1, and were genetically related (≥89% similarity) according to pulsed-field gel electrophoreses patterns. The five tulathromycin-resistant isolates were multi-drug resistant also exhibiting resistance to oxytetracycline, tilmicosin, ampicillin, or penicillin. The macrolide resistance genes erm(42), erm(A), erm(B), erm(F), erm(X) and msr(E)-mph(E), were not detected in the tulathromycin-resistant M. haemolytica. This study showed that tulathromycin resistance in M. haemolytica from a general population of feedlot cattle in western Canada was low and did not change over a 3-year period after tulathromycin was approved for use in cattle.
An information theoretic approach to sentiment polarity classification

Sentiment classification is a task of classifying documents according to their overall sentiment inclination. It is very important and popular in many web applications, such as credibility analysis of news sites on the Web, recommendation system and mining online discussion. Vector space model is widely applied on modeling documents in supervised sentiment classification, in which the feature presentation (including features type and weight function) is crucial for classification accuracy. The traditional feature presentation methods of text categorization do not perform well in sentiment classification, because the expressing manners of sentiment are more subtle. We analyze the relationships of terms with sentiment labels based on information theory, and propose a method by applying information theoretic approach on sentiment classification of documents. In this paper, we adopt mutual information on quantifying the sentiment polarities of terms in a document firstly. Then the terms are weighted in vector space based on both sentiment scores and contribution to the document. We perform extensive experiments with SVM on the sets of multiple product reviews, and the experimental results show our approach is more effective than the traditional ones.
Multivariate Texture Measured by Local Binary Pattern for Multispectral Image Classification

Local Binary Pattern is a new texture measure which is theoretically simply but powerful. When used in remote sensing multi-channel image processing, the multivariate version of LBP operator should be considered. In this paper, a multivariate LBP operator was proposed to calculate multivariate texture for multi-spectral remote sensing image. Both single-band texture and multivariate texture were employed in the classification process. Segmented Minimum Noise Fraction transform was conducted before classification to reduce features. Experiment shows that compared to spectral classification, the classification accuracy can be significantly improved when the proposed classification scheme was used.
Item and order information in subject-performed tasks and experimenter-performed tasks.

This study investigated the enactment effect from the perspective of the item-order hypothesis (e.g., M. Serra & J. S. Nairne, 1993). The authors assumed that in subject-performed tasks (SPTs), item encoding is improved but order encoding is disrupted compared with experimenter-performed tasks (EPTs), that order encoding of EPTs is only better in pure lists, and that the item--order hypothesis is confined to short lists. Item information was tested in recognition memory tests, order information in order reconstruction tasks, and both item and order information in free-recall tests. The results of 5 experiments using short (8 items) and long lists (24 items) in a design with list type (pure, mixed) and encoding condition (EPT, SPT) as factors supported the hypotheses.
Going from where to why—interpretable prediction of protein subcellular localization

Motivation: Protein subcellular localization is pivotal in understanding a protein's function. Computational prediction of subcellular localization has become a viable alternative to experimental approaches. While current machine learning-based methods yield good prediction accuracy, most of them suffer from two key problems: lack of interpretability and dealing with multiple locations. Results: We present YLoc, a novel method for predicting protein subcellular localization that addresses these issues. Due to its simple architecture, YLoc can identify the relevant features of a protein sequence contributing to its subcellular localization, e.g. localization signals or motifs relevant to protein sorting. We present several example applications where YLoc identifies the sequence features responsible for protein localization, and thus reveals not only to which location a protein is transported to, but also why it is transported there. YLoc also provides a confidence estimate for the prediction. Thus, the user can decide what level of error is acceptable for a prediction. Due to a probabilistic approach and the use of several thousands of dual-targeted proteins, YLoc is able to predict multiple locations per protein. YLoc was benchmarked using several independent datasets for protein subcellular localization and performs on par with other state-of-the-art predictors. Disregarding low-confidence predictions, YLoc can achieve prediction accuracies of over 90%. Moreover, we show that YLoc is able to reliably predict multiple locations and outperforms the best predictors in this area. Availability: www.multiloc. org/YLoc Contact: briese@informatik.uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online.
Linguistic variable elimination for a heart failure dataset

Patients with heart failure often suffer disabling symptoms. In addition to these symptoms, half of all patients diagnosed with heart failure die within four years. The prevalence of heart failure is currently about 2%-3% of the adult population and it is expected to grow. It is interesting to predict if a patient with heart failure dies soon so that life-threatening situations and costs are minimized. In this paper, a data mining method for discovering fuzzy rules with different truth level thresholds in linguistic variable elimination for prediction of death on the basis of data available in hospitals is presented. Cognitive uncertainties are taken into consideration through the use of fuzzy sets, membership functions and membership degrees. The accuracy of the prediction of the death for a patient with heart failure and the interpretability of fuzzy rules are discussed. Our study shows, in comparison to other data mining methods, that it is useful for this type of prediction.
Tropism of Avian Influenza A (H5N1) Virus to Mesenchymal Stem Cells and CD34+ Hematopoietic Stem Cells

The presence of abnormal hematologic findings such as lymphopenia, thrombocytopenia, and pancytopenia were diagnosed in severe cases of avian influenza A H5N1. Whether direct viral dissemination to bone marrow (BM) cells causes this phenomenon remains elusive. We explore the susceptibility of the two stem cell types; hematopoietic stem cells (HSCs) and mesenchymal stromal cells (MSCs) isolated from human BM cells or cord blood, to infection with avian H5N1 viruses. For the first time, we demonstrated that the H5N1 virus could productively infect and induce cell death in both human stem cell types. In contrast, these activities were not observed upon human influenza virus infection. We also determined whether infection affects the immunomodulatory function of MSCs. We noted a consequent dysregulation of MSC-mediated immune modulation as observed by high cytokine and chemokine production in H5N1 infected MSCs and monocytes cocultures. These findings provide a better understanding of H5N1 pathogenesis in terms of broad tissue tropism and systemic spread.
Cell Adhesion and Fertilization: Steps in Oocyte Transport, Sperm-Zona Pellucida Interactions, and Sperm-Egg Fusion1

Abstract Fertilization in mammals requires the successful completion of many steps, starting with the transport of gametes in the reproductive tract and ending with sperm-egg membrane fusion. In this minireview, we focus on three adhesion steps in this multistep process. The first is oocyte “pick-up,” in which the degree of adhesion between the extracellular matrix of the cumulus cells and oviductal epithelial cells controls the successful pick-up of the oocyte-cumulus complex and its subsequent transfer into the oviduct. The second part of this review is concerned with the interaction between the sperm and the zona pellucida of the egg. Evidence is discussed that a plasma membrane form of galactosyltransferase on the surface of mouse sperm binds to ZP3 in the zona pellucida and initiates an acrosome reaction. Additional evidence raises the possibility that initial sperm binding to the zona pellucida is independent of ZP3. Last, we address the relationship between sperm adhesion to the egg plasma membrane and membrane fusion, especially the role of ADAM family proteins on the sperm surface and egg integrins.
ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes in various cellular responses or functions. A fundamental challenge is to chart the molecular pathways that underlie these systems. ANAT is an interactive software tool, implemented as a Cytoscape plug-in, for elucidating functional networks of proteins. It encompasses a number of network inference algorithms and provides access to networks of physical associations in several organisms. In contrast to existing software tools, ANAT can be used to infer subnetworks that connect hundreds of proteins to each other or to a given set of “anchor” proteins, a fundamental step in reconstructing cellular subnetworks. The interactive component of ANAT provides an array of tools for evaluating and exploring the resulting subnetwork models and for iteratively refining them. We demonstrate the utility of ANAT by studying the crosstalk between the autophagic and apoptotic cell death modules in humans, using a network of physical interactions. Relative to published software tools, ANAT is more accurate and provides more features for comprehensive network analysis. The latest version of the software is available at http://www.cs. tau.ac. il/~bnet/ANAT_SI.
JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.
Cognitive debiasing 1: origins of bias and theory of debiasing

Numerous studies have shown that diagnostic failure depends upon a variety of factors. Psychological factors are fundamental in influencing the cognitive performance of the decision maker. In this first of two papers, we discuss the basics of reasoning and the Dual Process Theory (DPT) of decision making. The general properties of the DPT model, as it applies to diagnostic reasoning, are reviewed. A variety of cognitive and affective biases are known to compromise the decision-making process. They mostly appear to originate in the fast intuitive processes of Type 1 that dominate (or drive) decision making. Type 1 processes work well most of the time but they may open the door for biases. Removing or at least mitigating these biases would appear to be an important goal. We will also review the origins of biases. The consensus is that there are two major sources: innate, hard-wired biases that developed in our evolutionary past, and acquired biases established in the course of development and within our working environments. Both are associated with abbreviated decision making in the form of heuristics. Other work suggests that ambient and contextual factors may create high risk situations that dispose decision makers to particular biases. Fatigue, sleep deprivation and cognitive overload appear to be important determinants. The theoretical basis of several approaches towards debiasing is then discussed. All share a common feature that involves a deliberate decoupling from Type 1 intuitive processing and moving to Type 2 analytical processing so that eventually unexamined intuitive judgments can be submitted to verification. This decoupling step appears to be the critical feature of cognitive and affective debiasing.
Evidence of Microbial Translocation Associated with Perturbations in T Cell and Antigen-Presenting Cell Homeostasis in Hookworm Infections

Background Microbial translocation (MT) is the process by which microbes or microbial products translocate from the intestine to the systemic circulation. MT is a common cause of systemic immune activation in HIV infection and is associated with reduced frequencies of CD4+ T cells; no data exist, however, on the role of MT in intestinal helminth infections. Methods We measured the plasma levels of MT markers, acute-phase proteins, and pro- and anti - inflammatory cytokines in individuals with or without hookworm infections. We also estimated the absolute counts of CD4+ and CD8+ T cells as well as the frequencies of memory T cell and dendritic cell subsets. Finally, we also measured the levels of all of these parameters in a subset of individuals following treatment of hookworm infection. Results Our data suggest that hookworm infection is characterized by increased levels of markers associated with MT but not acute-phase proteins nor pro-inflammatory cytokines. Hookworm infections were also associated with increased levels of the anti – inflammatory cytokine – IL-10, which was positively correlated with levels of lipopolysaccharide (LPS). In addition, MT was associated with decreased numbers of CD8+ T cells and diminished frequencies of particular dendritic cell subsets. Antihelmintic treatment of hookworm infection resulted in reversal of some of the hematologic and microbiologic alterations. Conclusions Our data provide compelling evidence for MT in a human intestinal helminth infection and its association with perturbations in the T cell and antigen-presenting cell compartments of the immune system. Our data also reveal that at least one dominant counter-regulatory mechanism i.e. increased IL-10 production might potentially protect against systemic immune activation in hookworm infections.
Ultra-low power 90nm 6T SRAM cell for wireless sensor network applications

This paper presents a comparative study of leakage reduction techniques applied to a 90 nm 6T SRAM to find an optimal design for ultra-low power wireless sensor applications. A 4-Kb SRAM implemented with the proposed techniques has a leakage as low as 26.5 nA in the idle mode, a 189times improvement over a memory without applying such techniques