Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteolytic Processing Is Not Essential for Multiple Functions of the Escherichia coli Autotransporter Adhesin Involved in Diffuse Adherence (AIDA-I)

ABSTRACT The Escherichia coli adhesin involved in diffuse adherence (AIDA-I), like many other autotransporter proteins, is released in the periplasm as a proprotein undergoing proteolytic processing after its translocation across the outer membrane. The proprotein is cleaved into a membrane-embedded fragment, AIDAc, and an extracellular fragment, the mature AIDA-I adhesin. The latter remains noncovalently associated with the outer membrane and can be released by heat treatment. The mechanism of cleavage of the proprotein and its role in the functionality of AIDA-I are not understood. Here, we show that cleavage is independent of the amount of AIDA-I in the outer membrane, suggesting an intramolecular autoproteolytic mechanism or a cleavage mediated by an unknown protease. We show that the two fragments, mature AIDA-I and AIDAc, can be cosolubilized and copurified in a folded and active conformation. We observed that the release by heat treatment results from the unfolding of AIDA-I and that the interaction of AIDA-I with AIDAc seems to be disturbed only by denaturation. We constructed an uncleavable point mutant of AIDA-I, where a serine of the cleavage site was changed into a leucine, and showed that adhesion, autoaggregation, and biofilm formation mediated by the mutant are indistinguishable from the wild-type levels. Lastly, we show that both proteins can mediate the invasion of cultured epithelial cells. Taken together, our experiments suggest that the proteolytic processing of AIDA-I plays a minor role in the functionality of this protein.
Correction for Chen et al., Bindarit, an Inhibitor of Monocyte Chemotactic Protein Synthesis, Protects against Bone Loss Induced by Chikungunya Virus Infection

Weiqiang Chen, Suan-Sin Foo, Adam Taylor, Aleksei Lulla, Andres Merits, Linda Hueston, Mark R. Forwood, Nicole C. Walsh, Natalie A. Sims, Lara J. Herrero, Suresh Mahalingam Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia; Institute of Technology, University of Tartu, Tartu, Estonia; Arbovirus Emerging Diseases Unit, Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Westmead, NSW, Australia; School of Medical Science and Griffith Health Institute, Griffith University, Gold Coast, QLD, Australia; St. Vincent’s Institute of Medical Research and Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Melbourne, VIC, Australia
Scientific Collaboration Network Evolution Model Based on Motif Emerging

Based on the evolvement characteristic of the author collaboration in the scientific thesis, a motif emerging model of the scientific cooperation network is presented. It is validated by the theoretic analysis and computer simulation that the degree distribution of the network nodes is a power law and this network is a scale-free network. In order to make sure the validity of the network model, we gather the articles in Journal of Information Science, and construct a author collaboration network. By analyzing the data of the network, the demonstration results are consistent with that of the model.
Exposing Computationally-Challenged Byzantine Impostors

Internet protocols permit a single machine to masquerade as many, allowing an adversary to appear to control more nodes than it actually does. The possibility of suchSybil attackshas been taken to mean that distributed algorithms that tolerate only a fixed fract ion of faulty nodes are not useful in peer-to-peer systems unless identities can be verified externally. The pr esent work argues against this assumption, by presenting practical algorithms for the distributed com puting problem ofByzantine agreement that defend against Sybil attacks by using moderately hard puzzl es as a pricing scheme for identities. Though our algorithms do not prevent Sybil attacks entirely, they s olve Byzantine agreement (and some useful variants) when the limited fraction of nodes that can fail is replaced by a limited fraction of the total computational power. These results suggest that Byzantine agr ement and similar tools from the distributed computing literature are likely to help solve the p roblem of adversarial behavior by components of peer-to-peer systems.
Malaria's deadly grip: cytoadhesion of Plasmodium falciparum‐infected erythrocytes

Cytoadhesion of Plasmodium falciparum‐infected erythrocytes to host microvasculature is a key virulence determinant. Parasite binding is mediated by a large family of clonally variant adhesion proteins, termed P. falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by var genes and expressed at the infected erythrocyte surface. Although PfEMP1 proteins have extensively diverged under opposing selection pressure to maintain ligand binding while avoiding antibody‐mediated detection, recent work has revealed they can be classified into different groups based on chromosome location and domain composition. This grouping reflects functional specialization of PfEMP1 proteins for different human host and microvascular binding niches and appears to be maintained by gene recombination hierarchies. Inone extreme, a specific PfEMP1 variant is associated with placental binding and malaria during pregnancy, while other PfEMP1 subtypes appear to be specialized for infection of malaria naïve hosts. Here, we discuss recent findings on the origins and evolution of the var gene family, the structure–function of PfEMP1 proteins, and a distinct subset of PfEMP1 variants that have been associated with severe childhood malaria.
Analysis of the Robustness of Network-Based Disease-Gene Prioritization Methods Reveals Redundancy in the Human Interactome and Functional Diversity of Disease-Genes

Complex biological systems usually pose a trade-off between robustness and fragility where a small number of perturbations can substantially disrupt the system. Although biological systems are robust against changes in many external and internal conditions, even a single mutation can perturb the system substantially, giving rise to a pathophenotype. Recent advances in identifying and analyzing the sequential variations beneath human disorders help to comprehend a systemic view of the mechanisms underlying various disease phenotypes. Network-based disease-gene prioritization methods rank the relevance of genes in a disease under the hypothesis that genes whose proteins interact with each other tend to exhibit similar phenotypes. In this study, we have tested the robustness of several network-based disease-gene prioritization methods with respect to the perturbations of the system using various disease phenotypes from the Online Mendelian Inheritance in Man database. These perturbations have been introduced either in the protein-protein interaction network or in the set of known disease-gene associations. As the network-based disease-gene prioritization methods are based on the connectivity between known disease-gene associations, we have further used these methods to categorize the pathophenotypes with respect to the recoverability of hidden disease-genes. Our results have suggested that, in general, disease-genes are connected through multiple paths in the human interactome. Moreover, even when these paths are disturbed, network-based prioritization can reveal hidden disease-gene associations in some pathophenotypes such as breast cancer, cardiomyopathy, diabetes, leukemia, parkinson disease and obesity to a greater extend compared to the rest of the pathophenotypes tested in this study. Gene Ontology (GO) analysis highlighted the role of functional diversity for such diseases.
Comparative Assessment of Supervised Classifiers for Land Use–Land Cover Classification in a Tropical Region Using Time-Series PALSAR Mosaic Data

Numerous classification algorithms have been proposed to create accurate classification maps using optical remote sensing data. However, few comparative studies evaluate the performance of classification algorithms with focus on tropical forests due to cloud effects. Advances in synthetic aperture radar (SAR) techniques and spatial resolution, mapping, and comparison of classification algorithms are possible. This research investigated the accuracy and processing speeds of five supervised classifiers, including Naïve Bayes, AdaBoost, multi-layer perceptron, random forest (RF), and support vector machine, for land use-land cover (LULC) classification in a tropical region using time-series Advanced Land Observing Satellite-phased array type L-band SAR (ALOS-PALSAR) 25-m mosaic data. The study area is located in central Sumatra, Indonesia, where abundant forest-related carbon stocks exist. This investigation was intended to aid the implementation of a classification algorithm for the automatic creation of LULC classification maps. We perform object-based and pixel-based analyses to investigate the ability of the classifiers and their accuracies, respectively. RF had the best classification accuracy and processing speed in which the accuracies for 10 classes and 2 classes were 64.07% and 90.22% for pixel-based and 82.94% and 86.23% for object-based evaluations, respectively. These results indicate that RF is a useful classifier for the analysis of PALSAR mosaic data and that the automatic creation of highly accurate classification maps is possible by using time-series data. The outcome of this research will be valuable resources for biodiversity and global-warming mitigation efforts in the region.
The control of septum formation in fission yeast.

If cell division is to produce two daughter cells that are viable, faithful copies of the parent cell, the landmark events of the cell division cycle, S phase, mitosis, and cytokinesis, must be executed in the correct order and with high fidelity. Though considerable advances have been made toward understanding the mechanisms that control the onset of S phase and mitosis, regulation of the events that occur at the end of the cell cycle, such as the reorganization of the cytoskeleton and the initiation of cell separation or cytokinesis, are less well understood. The fission yeast Schizosaccharomyces pombe provides a simple eukaryotic model for the study of cytokinesis. S. pombe cells are rod shaped, grow mainly by elongation at their ends, and divide by binary fission after forming a centrally placed division septum. Study of S. pombe mutants has begun to shed light on how septum formation and cytokinesis are regulated both spatially and temporally, to achieve proper co-ordination with mitosis. Some of the genes defined by these mutants have been functionally conserved through eukaryotic evolution, suggesting that aspects of this control will be common to all eukaryotic cells.
Spatial distribution of tuberculosis in a municipality in the interior of São Paulo, 2008-2013 1

ABSTRACT Objective: to describe the epidemiological clinical profile of tuberculosis and analyze the spatial distribution of cases in a municipality in the state of São Paulo. Method: descriptive and ecological study of cases of tuberculosis through the records in an information system. Descriptive statistics were used to calculate central tendency (mean) and chi-square test, with Yates correction or Fisher exact test, when necessary. The Kernel technique was also used to calculate the occurrence densities of tuberculosis cases, using a radius of 1000 meters. Type I error was set at 5%. Results: 299 cases of tuberculosis were identified, with 290 (96.98%) being geocoded. The majority of these were male (n = 212; 70.91%), median age 40 years, and the pulmonary clinical form was predominant (n = 244, 81.60%). The distribution occurred in a non-random manner, observing important areas of the municipality with a higher density of cases of the disease. Conclusion: the study evidenced an epidemiological profile of tuberculosis cases similar to those in the literature; however, their distribution does not occur in a random manner, pointing to specific population groups that require greater management and planning of health services for the control of tuberculosis.
The mesentery in Crohn's disease: friend or foe?

Purpose of review This article assesses the role of the mesentery in Crohn's disease. Recent findings The mesentery is centrally positioned both anatomically and physiologically. Overlapping mesenteric and submucosal mesenchymal contributions are important in the pathobiology of Crohn's disease. Mesenteric contributions explain the topographic distribution of Crohn's disease in general and mucosal disease in particular. Operative strategies that are mesenteric based (i.e. mesocolic excision) may reduce rates of postoperative recurrence. Summary The net effect of mesenteric events in Crohn's disease is pathologic. This can be targeted by operative means. Video abstract http://links.lww. com/COG/A18.
The Cdk1 and Ime2 Protein Kinases Trigger Exit from Meiotic Prophase in Saccharomyces cerevisiae by Inhibiting the Sum1 Transcriptional Repressor

ABSTRACT The induction of middle meiotic promoters is a key regulatory event in the life cycle of Saccharomyces cerevisiae that controls exit from prophase, meiosis, and spore formation. The Sum1 repressor and Ndt80 activator proteins control middle promoters by binding to overlapping DNA elements. NDT80 is controlled by a tightly regulated middle meiotic promoter through a positive autoregulatory loop and is repressed in vegetative cells by Sum1. It has previously been shown that the meiosis-specific kinase Ime2 promotes the removal of Sum1 from DNA. Here, we show that Sum1 is also regulated by the cyclin-dependent kinase, Cdk1. While sum1 phosphosite mutants that are insensitive to Cdk1 or Ime2 complete meiosis and form spores, a mutant that is insensitive to both Ime2 and Cdk1 (sum1-ci) blocks meiotic development in prophase with an ndt80Δ-like phenotype. Ectopic expression of NDT80 or mutation of a Sum1-binding element in the NDT80 promoter bypasses the sum1-ci block. Hst1 is a NAD+-dependent histone deacetylase that is linked to Sum1 by the Rfm1 tethering factor. Deletion of HST1 or RFM1 also bypasses the sum1-ci block. These results demonstrate that Sum1 functions as a key meiotic brake through the NDT80 promoter and that Cdk1 and Ime2 trigger exit from meiotic prophase by inhibiting the Sum1 transcriptional repression complex.
Strain sensing fabric integrated with carbon nanotube yarn for wearable applications

Textiles, as a desired platform for wearable smart technology, can be integrated with smart elements in the hierarchical levels of the fabric structure. In this study, a new way to make strain sensing fabric was developed by embedding a single strain sensing carbon nanotube (CNT)-based yarn into the woven structure. To overcome the abrasion during insertion, the yarn was coated with poly(vinyl alcohol) (PVA) to achieve higher mechanical performance. The gauge factor of the yarn was improved from 0.91 to 1.64. The sensing properties of CNT/PVA yarn integrated strain sensing fabric showed a gauge factor of over 1.1, a degree of linearity of more than 97% and good stability and repeatability during cyclic loading. Fabric with different integrated yarn lengths, patterns and output connections has also been investigated. The results showed that the yarn length and bend over section had a great influence on the strain sensing properties of the fabric. Furthermore, the fabric strain sensor exhibited a quick and precise response to the finger motion detection, demonstrating potential in wearable electronics.
Review of the potential use of blood neuro-biomarkers in the diagnosis of mild traumatic brain injury

Head injury is a common presenting complaint amongst emergency department patients. To date, there has been no widespread utilization of neuro-biomarkers to aid the diagnosis of traumatic brain injury. This review article explores which neuro-biomarkers could be used in the emergency department in aiding the clinical diagnosis of mild traumatic brain injury. Based on the available evidence, the most promising neuro-biomarkers appear to be Glial fibrillary acidic protein (GFAP) and Ubiquitin C-Terminal Hydrolase Isozyme L1 (UCH-L1) as these show significant rises in peripheral blood levels shortly after injury and these have been demonstrated to correlate with long-term clinical outcomes. Treatment strategies for minor traumatic brain injury in the emergency department setting are not well developed. The introduction of blood neuro-biomarkers could reduce unnecessary radiation exposure and provide an opportunity to improve the care of this patient group.
Statin Use Is Associated with Bladder Pain Syndrome/Interstitial Cystitis: A Population-Based Case-Control Study

Introduction: Statin may induce epithelial dysfunction of the bladder urothelium. Epithelial dysfunction was proposed as one of the major potential etiologies for bladder pain syndrome/interstitial cystitis (BPS/IC). In this study, we examined the association between statin use and BPS/IC using a population-based study. Subjects and Methods: This case-control study used the Taiwan Longitudinal Health Insurance Database. In total, 815 female subjects with BPS/IC and 4075 randomly selected female controls were included. We used a conditional logistic regression to compute the odds ratio (OR) for having previously used statins between cases and controls. Results: A conditional logistic regression analysis showed that the OR of prior statin users for cases was 1.52 (95% confidence interval (CI): 1.19-1.94) compared to controls after adjusting for diabetes, hypertension, coronary heart disease, obesity, chronic pelvic pain, irritable bowel syndrome, fibromyalgia, chronic fatigue syndrome, depression, panic disorder, migraines, sicca syndrome, allergies, endometriosis, and asthma. Furthermore, adjusted ORs of regular and irregular statin use for cases were 1.58 (95% CI: 1.20-2.08) and 1.53 (95% CI: 1.02-2.31), respectively, compared to controls. Conclusion: We concluded that there was an association between statin use and BPS/IC.
Research Process Support with Organizational Flow in e-Science

To utilize an e-Science application service which is built on a grid computing environment efficiently, it is vital to develop technologies for integrating each e- Science application service into a workflow and to execute the workflow in a cooperative environment. In this paper, the required workflow in e-Science is analyzed using a conceptual scenario and categorized into three types of workflows: simulations, experiments, and collaborative work. Additionally, the workflow of the aerospace research community, an e-Science environment is shown. The necessary applications and functionalities for the required workflow are then proposed.
Visualization of intracerebral arteries by synchrotron radiation microangiography.

BACKGROUND AND PURPOSE Small cerebral vessels are a major site for vascular pathology leading to cerebral infarction and hemorrhage. However, such small cerebral vessels are difficult to visualize by using conventional methods. The goal of our study was the development of methodology allowing visualization of small cerebral arteries in rodents, suitable for experimental models. MATERIALS AND METHODS Using barium sulfate as a contrast material, we obtained microangiographic images of physiologic and pathologic changes consequent to cerebral infarction in mouse brain by monochromatic synchrotron radiation (SR). To achieve high-resolution and high-contrast images, we used a new x-ray camera with a pixel size of 4.5 microm, and we set the energy level at 37.5 keV, just above the K absorption of barium. RESULTS Small intracerebral arteries ( approximately 30 microm in diameter) were clearly visualized, as well as the cortical branches (50-70 microm in diameter) at the brain surface. The limit of detection appeared to be vessels approximately 10 microm in diameter. Compared with the noninfarcted side, the number of intracerebral arteries was dramatically decreased in the middle cerebral artery area affected by stroke. CONCLUSIONS These results indicate the potential of SR for evaluating pathologic changes in small cerebral arteries and for monitoring the impact of pro- and antiangiogenic therapeutic strategies.
High-Mannose Glycans are Elevated during Breast Cancer Progression*

Alteration in glycosylation has been observed in cancer. However, monitoring glycosylation changes during breast cancer progression is difficult in humans. In this study, we used a well-characterized transplantable breast tumor mouse model, the mouse mammary tumor virus-polyoma middle T antigen, to observe early changes in glycosylation. We have previously used the said mouse model to look at O-linked glycosylation changes with breast cancer. In this glycan biomarker discovery study, we examined N-linked glycan variations during breast cancer progression of the mouse model but this time doubling the number of mice and blood draw points. N-glycans from total mouse serum glycoproteins were profiled using matrix-assisted laser desorption/ionization Fourier transform-ion cyclotron resonance mass spectrometry at the onset, progression, and removal of mammary tumors. We observed four N-linked glycans, m/z 1339.480 (Hex3HexNAc), 1485.530 (Hex3HexNAc4Fuc), 1809.639 (Hex5HexNAc4Fuc), and 1905.630 (Man9), change in intensity in the cancer group but not in the control group. In a separate study, N-glycans from total human serum glycoproteins of breast cancer patients and controls were also profiled. Analysis of human sera using an internal standard showed the alteration of the low-abundant high-mannose glycans, m/z 1419.475, 1581.528, 1743.581, 1905.634 (Man6–9), in breast cancer patients. A key observation was the elevation of a high-mannose type glycan containing nine mannoses, Man9, m/z 1905.630 in both mouse and human sera in the presence of breast cancer, suggesting an incompletion of the glycosylation process that normally trims back Man9 to produce complex and hybrid type oligosaccharides.
Radiation Constrained Fair Wireless Charging

Recently wireless power transfer technology (WPT attracts considerable attention, its incurred electromagnetic radiatio (EMR), however, is largely overlooked by most existing literatures. In this paper, we first propose and study the radiation constrained fair wireless charging problem, i.e., maximizing the minimum utility of devices by adjusting the power of wireless chargers with no EMR intensity at any location in the field exceeding a given threshold Rt. To address this problem, we first adopt an area discretization method to transform it fro nonlinear to linear. Then, we propose two algorithms to deal with the reformulated problem. One is called Primal-Dual algorithm, which is semi-distributed and uses lagrangian dual and subgradient methods to solve the problem iteratively. The other is called area division algorithm. It is not only fully distributed and scalable with network size, but also provably achieves an approximation ratio of (1&#8722;&#949;). We conducted extensive simulations and built a field test-bed to verify our theoretical findings. Our simulations show that the approximation ratio of the area division algorithm holds; the Primal-Dual and area division algorithms can have comparable and over 90.9% performance of the optimal results, respectively; and both of the algorithms outperform a baseline algorithm by more than 37%.