Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the indirect effect of Wolbachia on the infection dynamics of horizontally transmitted viruses

Intracellular bacteria of the genus Wolbachia are widely distributed in arthropods. There is growing empirical evidence that Wolbachia directly interacts with viruses and other parasites inside the arthropod host, sometimes resulting in low or no pathogen replication. Previous theoretical studies showed that this direct effect of Wolbachia can result in a reduced virus prevalence (within the population), suggesting that Wolbachia could be used in the biological control of vector-borne diseases (e.g., dengue fever). However, Wolbachia might also indirectly affect virus dynamics because Wolbachia-induced reproductive phenotypes (cytoplasmic incompatibility or male killing) increase the larval mortality of hosts and thus alter the age structure of populations. We investigated this indirect effect using mathematical models with overlapping generations, and found the results to depend strongly on the host's life history. In general, the indirect effect can result in two different outcomes: (1) reduced virus prevalence and virus invasion ability, and (2) increased virus prevalence and virus invasion ability. The former occurs for host species with larval competition and undercompensation, the latter for hosts with either adult competition or larval competition and overcompensation. These findings suggest that the effect of Wolbachia on a specific virus is sensitive to the host's life history. We discuss the results with respect to biocontrol programs using Wolbachia.
Do Mossy Fibers Release GABA?

Purpose: Mossy fibers are the sole excitatory projection from dentate gyrus granule cells to the hippocampus, forming part of the trisynaptic hippocampal circuit. They undergo signficiant plasticity during epileptogenesis and have been implicated in seizure generation. Mossy fibers are a highly unusual projection in the mammalian brain; in addition to glutamate, they release adenosine, dynorphin, zinc, and possibly other peptides. Mossy fiber terminals also show intense immunoreactivity for the inhibitory neurotrasnmitter γ‐aminobutyric acid (GABA), and immunoreactivity for GAD67. The purpose of this review is to present physiologic evidence of GABA release by mossy fibers and its modulation by epileptic activity.
Clustering Microarray Data based on Density and Shared Nearest Neighbor Measure

Microarray technology is being used to study several genes at a time generating huge amounts of data. Managing and extracting useful information from such data is a big challenge for the bioinformatics community. Clustering is an important data mining technique that has been proved to be useful for the analysis and understanding of such data. Clustering is used to automatically identify similar groups of objects based on a given measure. In microarray data, the genes that exhibit similar expression profiles are co-expressed and will be grouped into a single cluster. In this paper, we propose a new clustering algorithm based on density and shared nearest neighbor measure to identify clusters of genes exhibiting similar expression profiles. In our algorithm, we used an efficient bitwise vertical data structure called P-tree to decompose the microarray data into separate bit vectors. Pearson’s correlation coefficient is used as the similarity measure to identify the core points of the clusters by calculating the density of the genes. Also in our algorithm, there is no need to specify the number of clusters ahead. The clusters in the data set are identified automatically based on the core genes. We experimentally show that our algorithm is fast and scalable when applied on Iyer’s microarray data set for cluster analysis.
Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes

Abstract Using an independent fosmid cloning approach and comprehensive transcriptome analysis to complement data from the Selaginella moellendorffii genome project, we determined the complete mitochondrial genome structure of this spikemoss. Numerous recombination events mediated mainly via long sequence repeats extending up to 7kbp result in a complex mtDNA network structure. Peculiar features associated with the repeat sequences are more than 80 different microsatellite sites (predominantly trinucleotide motifs). The S. moellendorffii mtDNA encodes a plant-typical core set of a twin-arginine translocase (tatC), 17 respiratory chain subunits, and 2 rRNAs but lacks atp4 and any tRNA genes. As a further novelty among plant chondromes, the nad4L gene is encoded within an intron of the nad1 gene. A total of 37 introns occupying the 20 mitochondrial genes (four of which are disrupted into trans-splicing arrangements including two novel instances of trans-splicing introns) make the S. moellendorffii chondrome the intron-richest and gene-poorest plant mtDNA known. Our parallel transcriptome analyses demonstrates functional splicing of all 37 introns and reveals a new record amount of plant organelle RNA editing with a total of 2,139 sites in mRNAs and 13 sites in the two rRNAs, all of which are exclusively of the C-to-U type.
Image-Based Monitoring of Jellyfish Using Deep Learning Architecture

Jellyfish blooms have caused great damage to the fishery industry. In efforts to solve this problem, various systems to remove jellyfish have been proposed. This letter presents preliminary results of applying an image-based jellyfish distribution recognition algorithm to increase the efficiency of an existing jellyfish removal system. By using a convolutional neural network and dedicated image processing techniques, the experimental results show reasonable performance for real-world application.
Activation of Sphingosine Kinase by Tumor Necrosis Factor-α Inhibits Apoptosis in Human Endothelial Cells*

Human umbilical vein endothelial cells (HUVEC), like most normal cells, are resistant to tumor necrosis factor-α (TNF)-induced apoptosis in spite of TNF activating sphingomyelinase and generating ceramide, a known inducer of apoptosis. Here we report that TNF activates another key enzyme, sphingosine kinase (SphK), in the sphingomyelin metabolic pathway resulting in production of sphingosine-1-phosphate (S1P) and that S1P is a potent antagonist of TNF-mediated apoptosis. The TNF-induced SphK activation is independent of sphingomyelinase and ceramidase activities, suggesting that TNF affects this enzyme directly other than through a mass effect on sphingomyelin degradation. In contrast to normal HUVEC, in a spontaneously transformed endothelial cell line (C11) TNF stimulation failed to activate SphK and induced apoptosis as characterized by morphological and biochemical criteria. Addition of exogenous S1P or increasing endogenous S1P by phorbol ester markedly protected C11 cell line from TNF-induced apoptosis. Conversely,N,N-dimethylsphingosine, an inhibitor of SphK, profoundly sensitized normal HUVEC to killing by TNF. Thus, we demonstrate that the activation of SphK by TNF is an important signaling for protection from the apoptotic effect of TNF in endothelial cells.
Backstepping adaptive variable structure excitation controller for multi-machine power system

The integrated control of the power system should combine kinds of different control methods to gain the expected performances due to the very complex uncertain nonlinear power system. The combination of backstepping adaptive control and variable structure control has some complementary when handling the uncertainty in nonlinear system. The backstepping adaptive variable structure excitation controller is proposed by combining variable structure control, adaptive control and backstepping control for the multi-machine power system with the uncertain parameters. Simulations of two areas with four generators show this excitation controller can rapidly stabilize the multi-machine power system after disturbance. This excitation controller guarantees the transient stability of multi-machine power system and has a better performance than PSS controller.
Changes in regional brain glucose metabolism measured with F-18-FDG-PET in essential tremor

Background There is growing evidence that essential tremor (ET) is a multiple-system disorder. Previous PET studies in ET typically have measured brain oxygen consumption and cerebral blood flow. Purpose To compare ET patients with control subjects to investigate any regional change in cerebral glucose metabolism through statistical parametric mapping (SPM) analysis of F-18-fluorodeoxyglucose positron emission tomography (F-18-FDG-PET). Material and Methods We studied 17 patients with ET (17 men; mean age, 67.3 ± 4.8 years) and age-sex matched normal subjects. All subjects underwent FDG-PET imaging, and evaluated severity of tremor symptoms was measured as score on the Fahn-Tolosa-Marin rating scale (FTM). We also evaluated detailed the medical history and neurological examinations in all patients. Results The mean age of tremor onset was 57.6 ± 12.9 years and the mean FTM score was 15.1 ± 4.9. Brain FDG-PET analysis demonstrated hypometabolism in the medial frontal lobe, medial temporal lobe, and the precuneus of parietal lobe. However, there was no significant difference of glucose metabolism in the cerebellum. Conclusion We propose that motor symptom of ET are caused by electrophysiological disturbances within cortical–cerebellar networks, rather than degenerative process of cerebellum, because the metabolism of the cerebellum was normal at rest. Furthermore, the abnormal glucose metabolism in the cerebral regions that do not mainly participate in motor function suggest that these regions may play a role as early markers of non-motor manifestations.
Strange Fruit Indeed: Interrogating Contemporary Textbook Representations of Racial Violence toward African Americans

Background/Context Recent racial incidents on college and high school campuses throughout the United States have catalyzed a growing conversation around issues of race and racism. These conversations exist alongside ongoing concerns about the lack of attention given to race and racism in the official school curriculum. Given that the field of education is generally located as a space to interrogate why these difficult issues of race in schools and society still persist, this study illustrates how contemporary official school knowledge addresses historical and contemporary issues of race and racism. To do this, we examine how historic acts of racial violence directed toward African Americans are rendered in K–12 school textbooks. Using the theoretical lenses of critical race theory and cultural memory, we explicate how historic acts of racial violence toward African Americans receives minimal and/or distorted attention in most K–12 texts. Purpose/Objective/Research Question/Focus of Study We examined the knowledge constructed about racial violence and African Americans in the United States. Using the theoretical lenses of critical race theory and cultural memory, we show how the topic of historic acts of racial violence toward African Americans receives minimal and/or distorted attention in most K–12 texts. The purpose of this study is to illustrate that although accounts of racial violence that historically have been excluded from textbooks are now being included, this inclusion matters little if it is presented in a manner that disavows material implications of racial violence on sustained White privilege and entrenched African American inequities. Research Design The findings from this study come from a textbook analysis of 19 recent U.S. history social studies textbooks adopted by the state of Texas. Drawing from the tradition of recent critical textbook studies, this study used a literary analysis methodology. Findings/Results In this study, we found that although narratives of racial violence were present throughout the texts, they often rendered acts of violence as the immorality of single actors or “bad men doing bad things. ” Additionally, these presentations portray violence as disconnected from the institutional and structural ties that supported and benefited from such acts. Conclusions/Recommendations The findings from this study illustrate the limited historical and sociocultural knowledge about race and racism provided to teachers and students through K–12 social studies textbooks. These findings have direct implications for how teachers and students conceptualize and grapple with real issues of race and racism in schools and society. We suggest that the knowledge contained in school texts must go beyond simply representing acts of racism, situating such acts of racism within the discursive and material realities that have shaped the lives of African Americans in the United States.
Adjacent-MBU-Tolerant SEC-DED-TAEC-yAED Codes for Embedded SRAMs

As technology scaling increases embedded static random access memory bit-cell density, the number of soft errors due to radiation-induced multiple-bit upsets (MBUs) also increases. Traditionally, these errors have been addressed using a simple error correction code (ECC) combined with word interleaving. With continued scaling, however, errors beyond this setup begin to emerge. Although more powerful ECCs exist, they come at an increased overhead in terms of area and latency. Additionally, interleaving adds complexity to the system and may not always be feasible for the given architecture. In this brief, a set of double adjacent error correction (DAEC) codes is modified to provide triple adjacent error correction for a cost of zero additional check-bits over the code's DAEC equivalent, yielding a 2.25× reduction in bit-level soft error rate for a 22-nm MBU error channel model. MATLAB simulation and HDL synthesis results are included for standard 16- and 32-data-bit memory word sizes and compared against existing codes.
An experiment in authorship attribution

This paper reports an experiment in authorship attribution that reveals considerable authorial structure in texts written by authors with very similar background and training, with genre and topic being strictly controlled for. We interpret our results as supporting the hypothesis that authors have ’ textual fingerprints’, at least for texts produced by authors who are not consciously changing their style of writing across texts. What this study has also taught us is that discriminant analysis is a more appropriate technique to use than principal components analysis when predicting the authorship of an unknown (held-out) text on the basis of known (training) texts of which the authorial provenance is available. Finally, standard discriminant analysis can be enhanced considerably by using an entropy-based weighting scheme of the kind used in latent semantic analysis (Landauer et al., 1998).
Seasonality of Coliform Bacteria Detection Rates in New Jersey Domestic Wells

It is important that indicators of fecal pollution are reliable. Coliform bacteria are a commonly used indicator of fecal pollution. As other investigators have reported elsewhere, we observed a seasonal pattern of coliform bacteria detections in domestic wells in New Jersey. Examination of a statewide database of 10 years of water quality data from 93,447 samples, from 78,207 wells, generated during real estate transactions, revealed that coliform bacteria were detected in a higher proportion of wells during warm weather months. Further examination of the seasonal pattern of other data, including well water pH, precipitation, ground and surface water temperatures, surface water coliform bacteria concentrations, and vegetation, resulted in the hypothesis that these bacteria may be derived from nonfecal (or environmentally adapted) as well as fecal sources. We provide evidence that the coliform seasonality may be the result of seasonal changes in groundwater extraction volumes (and to a lesser extent precipitation), and temperature‐driven changes in the concentration of surface or near‐surface coliform sources. Nonfecal coliform sources may not indicate the presence of fecal wastes and hence the potential presence of pathogens, or do so in an inconsistent fashion. Additional research is needed to identify the sources of the coliforms detected in groundwater.
Pesticide Residues and Bees – A Risk Assessment

Bees are essential pollinators of many plants in natural ecosystems and agricultural crops alike. In recent years the decline and disappearance of bee species in the wild and the collapse of honey bee colonies have concerned ecologists and apiculturalists, who search for causes and solutions to this problem. Whilst biological factors such as viral diseases, mite and parasite infections are undoubtedly involved, it is also evident that pesticides applied to agricultural crops have a negative impact on bees. Most risk assessments have focused on direct acute exposure of bees to agrochemicals from spray drift. However, the large number of pesticide residues found in pollen and honey demand a thorough evaluation of all residual compounds so as to identify those of highest risk to bees. Using data from recent residue surveys and toxicity of pesticides to honey and bumble bees, a comprehensive evaluation of risks under current exposure conditions is presented here. Standard risk assessments are complemented with new approaches that take into account time-cumulative effects over time, especially with dietary exposures. Whilst overall risks appear to be low, our analysis indicates that residues of pyrethroid and neonicotinoid insecticides pose the highest risk by contact exposure of bees with contaminated pollen. However, the synergism of ergosterol inhibiting fungicides with those two classes of insecticides results in much higher risks in spite of the low prevalence of their combined residues. Risks by ingestion of contaminated pollen and honey are of some concern for systemic insecticides, particularly imidacloprid and thiamethoxam, chlorpyrifos and the mixtures of cyhalothrin and ergosterol inhibiting fungicides. More attention should be paid to specific residue mixtures that may result in synergistic toxicity to bees.
Privacy in a mobile environment

Future mobile network operators will provide users with all the information and services they want. Using a mobile phone for services is strongly dependent on personalization to provide the user with a comfortable experience. Hence many of these services (e.g. location, electronic wallet) will handle sensitive user data. This article presents a technique with which the network operator supports user needs for personal information privacy against third parties like Internet service providers. We propose a new and user-friendly method for handling privacy. The method is based on a privacy receipt mechanism for all personal data that the user agrees to be transferred to third parties. The role of the network operator in our scenario is that of consumer privacy protector, since the operators already store and process many sensitive user data and must comply with data protection legislation.
Kernelizing Spatially Consistent Visual Matches for Fine-Grained Classification

This paper introduces a new image representation relying on the spatial pooling of geometrically consistent visual matches. We therefore introduce a new match kernel based on the inverse rank of the shared nearest neighbors combined with local geometric constraints. To avoid overfitting and reduce processing costs, the dimensionality of the resulting over-complete representation is further reduced by hierarchically pooling the raw consistent matches according to their spatial position in the training images. The final image representation is obtained by concatenating the resulting feature vectors at several resolutions. Learning from these representations using a logistic regression classifier is shown to provide excellent fine-grained classification performances outperforming the results reported in the literature on several classification tasks.
The FACE Trial: Letrozole or Anastrozole as Initial Adjuvant Therapy?

The adjuvant Femara versus Anastrozole Clinical Evaluation (FACE) trial compares upfront therapy letrozole 2.5 mg with anastrozole 1 mg daily for up to 5 years in postmenopausal, hormone receptor-positive, node-positive breast cancer patients. This phase III b open label, randomized, multicenter study will include 4000. patients from up to 250 international sites. Patients will be stratified by degree of lymph node involvement and HER-2 status. Any efficacy and safety difference of the two drugs will be reported. Primary objective is DFS, secondary objectives are safety, OS, time to distant metastases, time to contralateral breast cancer and breast cancer specific survival.
GREATER HAPPINESS FOR A GREATER NUMBER Is that possible? If so, how?

INTRODUCTION Positive psychology is the scientific study of optimal human functioning (Sheldon et. all. 2000). Happiness is not the same as optimal functioning but is a closely related phenomenon. Happiness is a major manifestation of optimal functioning, since we are hard-wired to feel good when functioning well (e.g. Balcombe 2006). Happiness is also a determinant of optimal functioning, since happiness “broadens” our behavioral repertoire and “builds” resources (Fredrickson 2004). Consequently, happiness is a major topic in positive psychology. Much research in positive psychology aims at understanding why some people are happier than others and tries to find ways for making people happier. As such, the science of positive psychology links up with the ideology that we should foster human happiness. The idea of a moral obligation to advance human happiness is a fruit of the European “Enlightenment,” an intellectual movement that took position against religious views that had dominated thinking in the Middle Ages. One of the contested views was that happiness can be found only in the afterlife and that earthly life serves as an entrance test to Heaven. Enlightened opinion was rather that happiness is possible on Earth and that we should not renounce it. Another contested view was that the basis of morality is in divine revelation, and in particular in the 10 Commandments. Enlightened thinkers came to see morality more as a matter of human agreement and discussed the intellectual foundations for social contracts. Much of this thought was voiced by Jeremy Bentham (1789) in his famous book On Morals and Legislation, in which he argued that the good and bad of actions should be judged by their effects on human happiness. In this view, the best thing to do is what results in the “greatest happiness, for the greatest number. ” This moral creed is called “the greatest happiness principle. ”
Lean Software Development

Lean software development is the application of the principles of the Toyota product development system to software development. Toyota has been extremely successful developing complex new vehicles, which include a vast amount of embedded software, in a very short time and always on time. This tutorial examines the underlying engineering principles Toyota uses to develop vehicles and shows how they can be applied to software development. When correctly applied, lean software development results in high quality software that is developed quickly and at the lowest possible cost. Moreover, the success of many of the practices of Agile Software Development can be explained by understanding the principles of Lean Software development.
Intron Size Correlates Positively With Recombination Rate in Caenorhabditis elegans

A negative correlation between intron size and recombination rate has been reported for the Drosophila melanogaster and human genomes. Population-genetic models suggest that this pattern could be caused by an interaction between recombination rate and the efficacy of natural selection. To test this idea, we examined variation in intron size and recombination rate across the genome of the nematode Caenorhabditis elegans. Interestingly, we found that intron size correlated positively with recombination rate in this species.