Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemic Style Reliable Subgroup Multicast for Mutual Anonymity

Epidemic Style Reliable Subgroup Multicast for Mutual Anonymity by Neelesh P. Bansod Advisor Dr. Jean Mayo Multicasting is an important tool for various applications requiring group communication. An emerging application is the use of multicasting to provide anonymous communication over dynamic peer-to-peer (P2P) networks. However multicast based anonymity protocols incur the high overhead associated with reliable multicasting. Epidemic protocols are an emerging class of protocols that provide low-cost reliable group communication in dynamic networks. Prior work in epidemic protocols has focused primarily on providing reliable group multicasting, in which all group members receive every multicast message. In this work we first design an epidemic protocol to provide subgroup multicasting. In subgroup multicasting, different subgroups of members are interested in different messages sent to the multicast group. The varying interests of group members and overlap between subgroups, make it virtually impossible to model each subgroup as an independent multicast group. We then use our subgroup multicast protocol to design a system for reliable mutually anonymous communication over dynamic P2P networks. The subgroup multicast protocol is evaluated via simulations in the context of the anonymity protocol. Results from simulations and security analysis indicate that the use of epidemic style subgroup multicast enables mutually anonymous communication over dynamic P2P networks while maintaining predictable latencies, high reliability, and low communication overhead.
Exploring the Role of CCR6/CCL20 Axis in B Cell Migration into the CNS during EAE

B cells have been implicated in the pathogenesis of multiple sclerosis (MS) but how they migrate into the central nervous system (CNS) is poorly understood. Previous work demonstrated the use of chemokine CCL20 signaling through CCR6, in driving B cell migration during various states of inflammation. Using a transwell assay, we determined that CCR6 expressing B cells are responsive to CCL20 in a dose-dependent manner. During experimental autoimmune encephalomyelitis (EAE), CCR6 expression is upregulated on CNS-infiltrated B cells and there is increased serum concentration of CCL20. However, lack of CCR6 expression on B cells did not affect their ability to migrate into the CNS nor did it affect the severity of disease in a B cell independent model of EAE. Our data therefore suggest that the CCR6/CCL20 axis is not the main driver of B cell migration into the CNS during EAE.
A NEW APPROACH TO MODELING CONDITION-BASED MAINTENANCE FOR STOCHASTICALLY DETERIORATING SYSTEMS

This paper develops the degradation and maintenance modeling technique for repairable systems subject to deterioration due to aging and damage caused by operating environment factors. This provides a relaxed and generalized approach to modeling condition-based maintenance. The approach can deal with both the maintenance scheduling problem and failures preventing the system functioning further. Controlled by a virtual age process and a general class of process called Piecewise-Stochastic (Damage) process (PSP), the proportional intensity model (PIM) is used to describe the system state. The state of the system is monitored at periodic times and maintenance actions are carried out in response to the system state revealed at inspection times. Assuming a threshold-type policy, the approach aims at minimizing the long-run average cost per unit time subject to maintenance parameters; the inspection interval and preventive replacement threshold. To this end, given some assumptions, expressions for the expected c.
Embryological studies on seed development in reciprocal crosses between Lolium perenne and Festuca pratensis

Following reciprocal interspecific hybridisation between Lolium perenne and Festuca pratensis pronounced differences in endosperm growth rate and behaviour were obtained not only in reciprocal crosses, but also between different genotypic combinations of the two species. Where, in crosses, L. perenne was used as the female parent, it was found that in comparison with the parental controls, cell formation in the endosperm occurred precociously and further division was markedly retarded. In F. pratensis by L. perenne hybrids, on the other hand, cell formation was suppressed completely and although the growth of the endosperm was not inhibited, extreme mitotic abnormalities appeared which eventually resulted in the complete disintegration of the tissue. Quantitative observations have further shown that early endosperm growth rate differs with genotype and that in hybrid seeds the rate of growth agrees very closely with that of the maternal controls. Moreover, in crosses of L. perenne x F. pratensis, initial rate of endosperm development determines the amount of endosperm formed before cell formation and, in consequence, is crucial in determining whether a particular cross will give rise to viable seeds or not.
Multiscale Conditional Random Fields for Machine Vision

We develop a single joint model which can classify images and label super-pixels, based on tree-structured conditional random fields (CRFs) derived from a hierarchical image segmentation, extending previous work by Reynolds and Murphy, and Plath and Toussaint. We show how to train this model in a weakly-supervised fashion, in which some of the images only have captions specifying which objects are present; this information is propagated down the tree and thus provides weakly labeled data at the leaves, which can be used to improve the performance of the super-pixel classifiers. After training, information can be propagated from the super-pixels up to the root-level image classifier (although this does not seem to help in practice compared to just using root-level features). We compare two kinds of tree: the standard one with pairwise potentials, and one based on noisy-or potentials, which better matches the semantics of the recursive partitioning used to create the tree. However, we do not find any significant difference between the two.
Analyzing the effects of Ca 2+ dynamics on mitochondrial function in health and disease

Mitochondria plays a crucial role in cells by maintaining energy metabolism and directing cell death mechanisms by buffering calcium (Ca) from cytosol. Therefore, the Ca overload of mitochondria due to the upregulated cytosolic Ca, observed in many neurological disorders is hypothesized to be a key pathway leading to mitochondrial dysfunction and cell death. In particular, Ca homeostasis disruptions due to Alzheimer′s disease (AD)-causing presenilins (PS1/PS2) and oligomeric forms of β-amyloid peptides Aβ commonly found in AD patients are presumed to cause detrimental effects on the mitochondria and its ability to function properly. We begin by showing that Familial Alzheimer′s disease (FAD)-causing PS mutants affect intracellular Ca ([Ca]i) homeostasis by enhancing the gating of inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) Ca 2+ channels on the endoplasmic reticulum (ER), leading to exaggerated Ca release into the cytoplasm. Using experimental IP3R-mediated Ca 2+ release data in conjunction with a computational model of mitochondrial bioenergetics, we explore how the differences in mitochondrial Ca uptake in control cells and cells expressing FADcausing PS mutants affect key variables such as ATP, reactive oxygen species (ROS), NADH, and mitochondrial Ca ([Ca]m). We find that as a result of exaggerated [Ca ]i in FADcausing mutant PS-expressing cells, the rate of oxygen consumption increases dramatically and overcomes the Ca dependent enzymes that stimulate NADH production. This leads to decreased rates of proton pumping due to diminished membrane potential (4Ψm) along with less ATP and enhanced ROS production. These results show that through Ca signaling disruption, mutant PS leads to mitochondrial dysfunction and potentially cell death.
First observations of hermaphroditism in the patellid limpet Patella piperata Gould, 1846

Abstract Hermaphroditism is thought to be an advantageous strategy common in marine molluscs that exhibit simultaneous, sequential or alternating hermaphroditism. Several species of patellid limpets have previously been shown to be protandrous hermaphrodites. The present study aimed to confirm whether this phenomenon occurs in Patella piperata. Transitional forms of simultaneous protandrous hermaphroditism were found in intermediate size classes of P. piperata, in Madeira (North-eastern Atlantic). Sequential hermaphroditism was confirmed after histological analysis. The overall sex-ratio was biased towards females but approached similar proportions in the larger size classes. Analysis of size at sex change showed that at a shell length of 36 mm 50% of the population probably have changed sex. The results reported confirm the occurrence of sequential hermaphroditism. These findings are of utmost importance to the understanding of the reproductive biology of this species with direct effect on management and conservation of this traditionally harvested limpet.
Bilateral Filtering for Image Processing Based on Pulse Coupled Neural Networks

Abstract To effectively remove Gaussian noise in images, a novel bilateral filtering algorithm based on improved pulse coupled neural networks (PCNN) is introduced. Firstly, smooth restraining factor and adaptive linking strength are adopted. They are combined with the synchronous fire of similar neuron in improved PCNN from the aspect of the characteristics of image Gaussian noise. Secondly, the noisy image is processed by using PCNN pre-de-noise iteration. The extreme value noise is removed and the time matrix that can reflect image spatial–temporal information is also formed. Finally, the time matrix is operated in bilateral filtering which is given adaptive improvement and de-noise application. The results of experiments show that the novel algorithm can effectively remove noise in smooth region in the case of good preserving image edges and details; the de-noised images have good subjective vision effects and objective quality. Meanwhile, this algorithm presents high signal-to-noise ratio, strong capability to reduce any and has good adaptability.
Fungal systematics and evolution : FUSE 4

Eight new species presented are Calostoma areolatum collected in Wuyishan National Park (China), Crinipellis bidens from Hubei Province (China), Lactifluus sainii from Himalayan India, Inocybe elata from Yunnan (China), Inocybe himalayensis from Pakistan. Specimens previously identified as Massalongia carnosa represent a new species, namely M. patagonica restricted to southern South America. Saprolegnia maragheica is a new oomycete species of fresh water in Maraghe (Iran). Uncispora wuzhishanensis is a new aquatic hyphomycete species. A type specimen of Raddetes turkestanicus was studied and based on this the new combination Conocybe turkestanica, is proposed. Argyranthemum frutescens is a new host for Alternaria alternata and Syzygium cumini for Phyllosticta capitalensis in India. Crepidotus ehrendorferi is confirmed for Hungary and Pluteus leucoborealis for Central Europe, and for the phytogeographical region of Carpaticum. Pseudopithomyces palmicola is shown to occur on grapevine and it is validated by adding a unique identifier. Terfezia fanfani is reported first from Algeria.
Unbiased Assessment of H-STS cells as high-fidelity models for gastro-enteropancreatic neuroendocrine tumor drug mechanism of action analysis

Quantitative metrics to objectively assess the fidelity of cancer models, such as cell lines, organoids, or patient-derived xenografts (PDXs), remain elusive, with histological criteria or the presence of specific mutations often used as driving principles. We show that molecular criteria, based on the regulatory proteins responsible for maintaining transcriptional cell state and its regulatory network, are effective in identifying models that can recapitulate drug mechanism of action and drug sensitivity, independent of histological consideration.
Longitudinal, Multiparametric MRI Assessment of repetitive mild TBI in rats

Repetitive mild traumatic brain injury (mTBI) has long term health effects and may result in the development of neurodegenerative or neuropsychiatric disorders. Histology shows axonal and dendritic beading, synaptic atrophy, vasodilation and gliosis occuring within hours/days post-mTBI. However, current neuroimaging techniques are unable to detect the early effects of repetitive mTBI. Consequently, mTBI brain scans are normal appearing and inconclusive. Hence, neuroimaging markers capable of detecting subtle microstructural and functional alterations are needed. We present results from longitudinal, multiparametric magnetic resonance imaging (MRI) assessment of repetitive mTBI in rats. We employ advanced in-vivo diffusion MRI (dMRI) to probe brain microstructural alterations, perfusion MRI to assess cerebral blood flow (CBF), close to the injury site, and proton MR spectroscopy to assess metabolic alterations in the ipsilateral cerebral cortex. High resolution anatomical scans were also acquired. In agreement with clinical observations, anatomical scans of rats were normal appearing even after repeated mTBI. Throughout, significance is regarded as p<0.05 post false discovery rate correction. dMRI revealed significant microstructural remodelling in ipsilateral hippocampus (reduced radial kurtosis), may be due to axonal/dendritic beading, demyelination, synaptic atrophy and edema. Consistent with prior reports of reduced cell/fiber density in mTBI, we find significantly increased mean diffusivity in ipsilateral corpus callosum. We also find significantly decreased glutathione (GSH) and increased total Choline (tCho) following second and third mTBI (vs baseline), also reported in clinical mTBI cohorts. Reduced GSH suggests oxidative stress and increase in tCho indicate cell damage/repair. CBF did not change significantly, however, high variability in CBF following the second and third mTBI suggest increased variability in CBF likely due to tissue hypoxia and oxidative stress. Oxidative stress may affect capillary blood flow by disturbing pericyte capillary contraction. Around 40% of pericytes retract after mTBI causing pericyte depletion and white matter dysfunction as suggested by dMRI findings. Multiparametric MRI detects meaningful mTBI-induced alterations otherwise undetectable with conventional MRI. Similar strategies may provide useful information to aid diagnosis of human mTBI.
Complex indirect effects of epiphytic bromeliads on the invertebrate food webs of their support tree

Ecosystem engineers are species that affect others through the provision of habitat rather than consumptive resources. The extent to which ecosystem engineers can indirectly affect entire food webs, however, is poorly understood. Epiphytic tank bromeliads (Bromeliaceae) are ecosystem engineers that are common throughout the Neotropics, and are associated with a variety of predatory arthropods. Here, we examine if bromeliads, by increasing predator densities, indirectly benefit their support tree through reduction in herbivorous insects and leaf damage. We observed and manipulated bromeliad densities in Costa Rican orange orchards, and measured impacts on leaf damage and arboreal and bromeliad invertebrate communities in two different seasons. Our results show that bromeliads are associated with predatory and herbivorous invertebrates but not leaf damage. Bromeliads were correlated with increased densities of their associated predators, especially ants and hunting spiders, but we could not confirm a causal link. Associations with bromeliads changed over time, with seasonal shifts interfering with responses to our manipulations. Bromeliads had a reduced association with predators in the dry season. Moreover, a null association between bromeliads and herbivorous invertebrates in the dry season unexpectedly became positive in the wet season. In summary, we have only limited evidence that bromeliads indirectly promote the top‐down control of arboreal herbivores; instead, our manipulations suggest that bromeliads increase herbivore densities in the wet season. This research suggests that although bromeliads may act as ecosystem engineers, indirectly influencing the invertebrate food web on support trees, their effects are trophically complex and seasonally dependent.
Terasaki spiral ramps and intracellular diffusion

The sheet-like endoplasmic reticulum (ER) of eukaryotic cells has been found to be riddled with spiral dislocations, known as ‘Terasaki ramps’, in the vicinity of which the doubled bilayer membranes which make up ER sheets can be approximately modeled by helicoids. Here we analyze diffusion on a surface with locally helicoidal topological dislocations, and use the results to argue that the Terasaki ramps facilitate a highly efficient transport of water-soluble molecules both within the lumen of the endoplasmic reticulum, and in the adjacent cytoplasmic space.
Microbiological and physicochemical properties of smoked ricotta cheese during refrigeration and temperature abuse storage

In the last years changes occurred in the production process of ricotta mustia, a traditional smoked, salted and sometimes ripened ricotta cheese, produced in Sardinia. Fresher, slightly smoked and with reduced salt content products, were introduced into the market to meet changes in consumer’s preferences for milder products. The present study of durability was conducted on an innovative fresh and smoked industrial product, also characterized by the small size and the packaging in modified atmosphere. A durability test to assess the evolution of microbiological and physicochemical profile of the product stored at refrigeration (4°C) and mild abuse (7°C) temperatures was carried out. A total of 126 ricotta samples smoked for either 1, 2, or 3 h were analyzed at intervals during shelflife for the determination of aerobic mesophilic counts, Enterobacteriaceae, yeast, moulds, L. monocytogenes, Pseudomonas spp. and B. cereus. Intrinsic properties, physic-chemical and headspace gas composition were also analyzed. Average and standard deviation were respectively 6,06±0,22 for pH, 0,982±0,05 for aW, 74,67%±1,81% for moisture, 10,25%±1,35% for fat, 10,92%±0,46% for protein and 1,70%±0,42% for salt content. Total bacterial count ranged between 3.88±0.48 log cfu/g at T0 and 3.25±1.02 at T45. L. monocytogenes, Pseudomonas spp. and E. coli were always below the detection limit. Enterobacteriaceae prevalence (percentage) was 3.17% (2.62±0.42 lg10 cfu/g) and was limited to samples stored longer than 30 days while B. cereus was recovered in 5.55% (2.36±0.35 lg10 cfu/g) of the samples and was never observed in samples after 45 days of refrigerated storage. The durability study is preliminary to challenge test to assess the shelf-life of this product in compliance with the requirements of Regulation (EC) 2073/2005.
Wnt signalling drives context-dependent differentiation or proliferation in neuroblastoma

Neuroblastoma is one of the commonest and deadliest solid tumours of childhood, and is thought to result from disrupted differentiation of the developing sympathoadrenergic lineage of the neural crest. Neuroblastoma exhibits intra-and intertumoural heterogeneity, with high risk tumours characterised by poor differentiation, which can be attributable to MYCN-mediated repression of genes involved in neuronal differentiation. MYCN is known to co-operate with oncogenic signalling pathways such as Alk, Akt and MEK/ERK signalling, and, together with c-MYC has been shown to be activated by Wnt signalling in various tissues. However, our previous work demonstrated that Wnt3a/Rspo2 treatment of some neuroblastoma cell lines can, paradoxically, decrease c-MYC and MYCN proteins. This prompted us to define the neuroblastoma-specific Wnt3a/Rspo2-driven transcriptome using RNA sequencing, and characterise the accompanying changes in cell biology. Here we report the identification of ninety Wnt target genes, and show that Wnt signalling is upstream of numerous transcription factors and signalling pathways in neuroblastoma. Using live-cell imaging, we show that Wnt signalling can drive differentiation of SK-N-BE(2)-C and SH-SY5Y cell-lines, but, conversely, proliferation of SK-N-AS cells. We show that cell-lines that differentiate show induction of pro-differentiation BMP4 and EPAS1 proteins, which is not apparent in the SK-N-AS cells. In contrast, SK-N-AS cells show increased CCND1, phosphorylated RB and E2F1 in response to Wnt3a/Rspo2, consistent with their proliferative response, and these proteins are not increased in differentiating lines. By meta-analysis of the expression of our 90 genes in primary tumour gene expression databases, we demonstrate discrete expression patterns of our Wnt genes in patient cohorts with different prognosis. Furthermore our analysis reveals interconnectivity within subsets of our Wnt genes, with one subset comprised of novel putative drivers of neuronal differentiation repressed by MYCN. Assessment of β-catenin immunohistochemistry shows high levels of β-catenin in tumours with better differentiation, further supporting a role for canonical Wnt signalling in neuroblastoma differentiation.
USE OF GLIRICIDIA-ENRICHED LIQUID ORGANIC FERTILIZER FOR PRODUCTION OF CAISIM (Brassica juncea L.)

Green biomass is one of major nutrient source and determines the quality of liquid organic fertilizer (LOF), including Gliricidia sepium (Jacq.) Kunth ex Walp. An experiment was conducted to study the effects of Gliricidia-enriched LOF on growth and yields of caisim, arranged in randomized complete design with three replicates. Treatments consisted of six LOF concentrations, 0%, 20%, 40%, 60%, 80% and 100%. Results indicated that concentration of gliricidia-LOF significantly influenced leaf greenness and shoot fresh weight, but not root to shoot ratio and shoot water content. Concentrations of gliricidia-LOF increased leaf greenness and shoot fresh weight of caisim. The optimum concentration was 70.85% to produce weight of 73 grams caisim per plant. Root to shoot ratio was not significantly different. Although treatments did not affect shoot water content, all caisim water content was on average above 90 %.
Long‐term variation in environmental conditions influences host–parasite fitness

Abstract Long‐term data on host and parasite fitness are important for predicting how host–parasite interactions will be altered in an era of global change. Here, we use data collected from 1997 to 2013 to explore effects of changing environmental conditions on bird–blowfly interactions in northern New Mexico. The objectives of this study were to examine what climate variables influence blowfly prevalence and intensity and to determine whether blowflies and climate variables affect bird fledging success. We examined how temperature, precipitation, and drought affect two parasitic blowflies and their hosts, Western Bluebirds (Sialia mexicana) and Ash‐throated Flycatchers (Myiarchus cinerascens). We found that blowfly prevalence did not change over time. Blowfly intensity increased over time in bluebird nests, but not in flycatcher nests. More blowflies result in slightly higher fledging success in bluebirds, but not flycatchers. There was a significant interaction between blowflies and precipitation on bluebird fledging success. For flycatchers, there was a significant interaction between blowflies and temperature and between blowflies and drought severity on fledging success. Given that the southwest is projected to be hotter and have more frequent and prolonged droughts, we predict that flycatchers may be negatively impacted by blowflies if these trends continue. Future work should focus on investigating the role of both blowflies and climate on fledging success. Climate patterns may negatively impact host fitness through altered parasite pressure.