Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiome composition of Pisaster ochraceous sea stars affected by sea star wasting disease

The largest epidemic of sea star wasting disease is affecting over 20 different species of sea stars in the west coast of the United States. The etiology of sea star wasting disease is currently unknown. Given the important role an organism’s bacterial community plays in health and disease, we sought to compare the composition of the microbiome of sick and healthy Pisaster ochraceous​ sea stars. Because tissue types often differ in their microbiomes, we also compared body wall, tube feet, ampullae, stomach, pyloric caeca, gonad, and cross section tissues. To do this, we used 16s amplicon sequencing to classify the bacterial communities and compare across disease state and tissue type. We found some degree of overlap in the microbiome of sick and healthy tissues, with ​Tenacibaculum​ as the most common genera of higher differential abundance. We also found clustering by tissue type, and stomach and body wall tissue particularly differed from other tissues in their bacterial composition. Introduction The relatively recent development of molecular sequencing technologies has allowed biologists to further understand the interdependent relationship between host animals and their bacterial communities, changing our outlook on the role of pathogens in disease. Traditionally, it has been thought that a single pathogen infects a host and causes disease (Lloyd and Pespeni 2018, McFall-Ngai et al. 2013). This is changing in favor of the view that a combination of multiple microorganisms may lead to illness, and that this “polymicrobial” etiology may be more common than previously thought. To name a few examples in humans, acute necrotizing ulcerative gingivitis, lyme disease, and a variety of respiratory diseases are all thought to be polymicrobial (Brogden 2002). Polymicrobial diseases are also common in animals, for example Black Band disease in Corals and bovine respiratory disease (Brogden 2002, Sato 2016). Additionally, certain illnesses could be caused by the disruption of the homeostasis of an organism’s microbial community, known as “dysbiosis. ” This is common in conditions that affect the gut, such as inflammatory bowel disease and Chron’s disease, as intestinal bacteria play an important role in digestion (Tamboli et al. 2004, Joossens et al. 2011). This study aims to
In Vitro Cytotoxicity and Cell Viability Assays: Principles, Advantages, and Disadvantages

Cytotoxicity is one of the most important indicators for biological evaluation in vitro studies. In vitro, chemicals such as drugs and pesticides have different cytotoxicity mechanisms such as destruction of cell membranes, prevention of protein synthesis, irreversible binding to receptors etc. In order to determine the cell death caused by these damages, there is a need for cheap, reliable and reproducible short-term cytotoxicity and cell viability assays. Cytotoxicity and cell viability assays are based on various cell functions. A broad spectrum of cytotoxicity assays is currently used in the fields of toxicology and pharmacology. There are different classifications for these assays: (i) dye exclusion assays; (ii) colorimetric assays; (iii) fluorometric assays; and (iv) luminometric assays. Choosing the appropriate method among these assays is important for obtaining accurate and reliable results. When selecting the cytotoxicity and cell viability assays to be used in the study, different parameters have to be considered such as the availability in the laboratory where the study is to be performed, test compounds, detection mechanism, specificity, and sensitivity. In this chapter, information will be given about in vitro cytotoxicity and viability assays, these assays will be classified and their advantages and disadvantages will be emphasized. The aim of this chapter is to guide the researcher interested in this subject to select the appropriate assay for their study.
Avaliando a Detecção e o Tratamento de Flash Crowds Utilizando o SimGrid

Este artigo propoe uma simulacao, onde recursos da nuvem podem ser contratados dinamicamente com a finalidade de mitigar os efeitos dos eventos de flash crowds. Esta simulacao foi desenvolvida atraves da integracao do simulador SimGrid com solucoes ja existentes na literatura para a deteccao e tratamento de flash crowds. Os testes iniciais foram satisfatorios e promissores. Futuramente, pretende-se realizar mais testes com cenarios maiores.
Temporal evolution of beta bursts in the parkinsonian cortico-basal ganglia network

Prevalence and temporal dynamics of transient oscillations in the beta frequency band (15-35 Hz), referred to as beta bursts, are correlated with motor performance and tactile perception. Disturbance of these activities is a candidate mechanism for motor impairment in Parkinson’s disease (PD), where the excessively long bursts correlate with symptom severity and are reduced by pharmacological and surgical treatments. To date, characterization of beta bursts in PD has been limited to the local field potentials in the subthalamic nucleus (STN) and cortical EEG. Here, we describe the changes that take place in spiking activity across the cortico-basal ganglia circuit, providing a unique insight into the network dynamics of these transient oscillations. Firstly, we demonstrate that rhythmic subthalamic spiking activity emerges at a fixed phase relationship with respect to cortical beta bursts in PD patients. Using multichannel recordings of ensembles of neurons in the 6-OHDA rat model of PD, we then dissect the beta burst dynamics across the sensorimotor cortex and several basal ganglia structures: striatum (Str), globus pallidus externus (GPe) and STN. Each subcortical structure exhibits enhanced rhythmic activity in the beta band locked to the onset of cortical beta bursts and longer cortical bursts lead to stronger subcortical rhythmicity. Crucially, enhanced subcortical rhythmic activity emerges at a fixed phase relationship with respect to the motor cortex, comparable to the relationship observed in PD patients. Striatal beta bursts terminate prior to the recruitment of those in the STN and GPe, suggesting that while they could play an important role in establishing synchrony in the beta band, they do not extensively contribute to its maintenance in other basal ganglia structures. Critically, changes in cortico-subcortical phase coupling precede the onset of a cortical beta burst, supporting the hypothesis that phase alignment across the cortico-basal ganglia network could recruit these structures into synchronous network oscillations. We provide a powerful approach that not only examines pathophysiology of PD across the motor circuit, but also offer insights that could aid in the design of novel neuromodulation strategies to manipulate the state of the motor system before pathological activities emerge.
IN VITRO MICROTUBERIZATION OF POTATO: EFFECT OF EXPLANT DENSITY, SOURCE, AND GENOTYPE

This study was conducted to examine explant density and source on production of in vitro potato microtubers, as well as survey of different newly-introduced potato cultivars for their microtuberization capacity at the Plant Tissue Culture Facility of the Department of Horticulture, Suez Canal University between 2014 until 2016. Results indicated that as culture density from single node explants increased, microtuber number and yield/petri dish were also increased. However, at the lowest density (10 explants/petri dish), the % tuberization and the average microtuber weight increased significantly over the higher densities (20, 25 and 30 explants/petri dish). Potato microtuber production from plantlets grown in vitroon microtuberization induction medium (liquid over solid media) was also studied using 5, 10 and 15 plantlets per jar.Results showed that microtuber number and yield/jar increased gradually with increasing plantlet density. However, on per plantlet basis, microtuber number increased at the lowest density. Microtuber yield/jar increased significantly at the highest density (1099 mg/jar) compared to 563.6 mg/jar at the lowest density. Average microtuber weight was also affected by culture density and genotype. At the lowest density, microtubers were significantly heavier than at the high density, and the cv. 'Safrane' recorded the highest weight per microtuber. Regarding the effect of explant source on microtuber production, results indicated that the use of single node explants derived from the top of the plantlet produced more microtubers than those taken from the basal part, or 3 node segments. Explant source also affected microtuber yield/dish. Single nodes from the top produced the highest yield compared to 3-nodes segment from the top (205 vs. 104.8 mg). The highest mean microtuber fresh weight was obtained from the culture of 3-node layered segment from the plantlet base, while single nodes from the top recorded lower microtuber fresh weight. The highest microtuber fresh weight was recorded in cv 'Universa' (114.3 mg) using single nodes from the plantlet base. Differences among the tested potato cultivars in microtuber production were detected.
An experiment on attention ability based on electroencephalogram (EEG) in different PMV Conditions

Occupants’ attention ability in seven PMV conditions is measured by means of electroencephalogram (EEG) and verbal voting. This can show us occupants’ attention state change by time and environmental condition. To achieve the objective of this study, seven healthy male students’ EEG was measured in seven PMV conditions each. Their EEG was measured in each condition for 65 minutes. EEG was measured on Fp1 and Fp2, and sorted out according to the frequency using power spectral analysis. The following results were achieved. First, in scope of moderate temperature environment, a higher level of attention was shown in relatively lower temperatures than in higher temperatures. Second, higher level of attention was shown in higher temperature in extreme condition compared to extremely cold temperature. Third, the occupants’ attention ability, measured by EEG varied with time and was found to be different than the occupants’ perceived attention from a verbal vote.
Elastic constants of B-HMX and tantalum, equations of state of supercritical fluids and fluid mixtures and thermal transport determinations

Ultrasonic sound speed measurements via Impulsive Stimulated Light Scattering (ISLS) were made in single crystals of b-HMX and tantalum over an extended range of temperatures. Elastic constants are consequently determined for b-HMX. Sound speeds are calculated for tantalum, from known elastic constants, and compare favorably with the results presented here. ISLS time-domain fits of tantalum records allowed for thermal diffusion determinations and, correspondingly, thermal conductivity. Measurements of the speed of sound and of the thermal diffusivities of fluid oxygen up to pressures of 13 GPa and at several temperatures are presented. Between 0.1 and 13 GPa the fluid's density increases by a factor of three. Thermal diffusivities rise slowly over this range, and are substantially smaller than those previously measured for the solid b-phase. Additional sound speed measurements were made along the 250 C isotherm in a 1:1 molar ratio mixture of liquid oxygen and nitrogen. These experiments demonstrate the versatility and potential application of a new laboratory within the U. S. DOD and DOE complex. 1
From space to time: Spatial inhomogeneities lead to the emergence of spatio-temporal activity sequences in spiking neuronal networks

Spatio-temporal sequences of neuronal activity are observed in many brain regions in a variety of tasks and are thought to form the basis of any meaningful behavior. Mechanisms by which a neuronal network can generate spatio-temporal activity sequences have remained obscure. Existing models are biologically untenable because they require manual embedding of a feedforward network within a random network or supervised learning to train the connectivity of a network to generate sequences. Here, we propose a biologically plausible, generative rule to create spatio-temporal activity sequences in a network model of spiking neurons with distance dependent connectivity. We show that the emergence of spatio-temporal activity sequences requires: (1) individual neurons preferentially project a small fraction of their axons in a specific direction, and (2) the preferential projection direction of neighboring neurons is similar. Thus, an anisotropic but correlated connectivity of neuron groups suffices to generate spatio-temporal activity sequences in an otherwise random neuronal network model.
HYDROGEOPHYSICAL DELINEATION OF PROLIFIC GROUNDWATER AQUIFER AROUND STUDENTS’ HOSTELS IN FUPRE CAMPUS, NIGERIA

Electrical Resistivity survey was conducted around Students’ Hostels, FUPRE to delineate prolific aquifer for potable water to serve the teeming population of staff and students. Five vertical electrical soundings (VES) using Schlumberger electrode configuration with a maximum current electrode spread of 300m were employed for data acquisition. WINRESIST software was employed to execute the iteration and inversion processes of computing resistivities, depths and thicknesses of the various layers and the curve types. Results indicate that the area is characterized by 4 distinct geoelectric layers inferred differently at the VES locations. Two potential groundwater aquifer zones are delineated. The unconfined shallow aquifer zones found at VES 1, 3, 4 and 5 locations have shallow overburden depth ranging between 3.7-19.3m and coarse-grained sand columns with thicknesses ranging between 2.8-17.7m while the confined deep aquifer zone found at VES 2 location coincides with deep overburden layer at a depth of 42.6m and coarse-grained sand column with appreciable thickness of 19.1m. These results suggest that boreholes for sustainable groundwater supply around the Students’ Hostels should be sited at VES 2 location and screened at a depth ≥40.0m. However, aquifers at VES 1, 3, 4 and 5 have potentials for groundwater but are vulnerable to contamination. It is recommenced that electrical resistivity survey and hydrogeological surveys should be conducted at all times and locations in FUPRE to delineate the appropriate aquifer before any borehole(s) are drilled for potable groundwater supply to avoid possible contamination.
GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner

There has been much effort to prioritize genomic variants with respect to their impact on “function”. However, function is often not precisely defined: Sometimes, it is the disease association of a variant; other times, it reflects a molecular effect on transcription or epigenetics. Here we coupled multiple genomic predictors to build GRAM, a generalized model, to predict a well-defined experimental target: the expression-modulating effect of a non-coding variant in a cell-specific manner. As a first step, we performed feature engineering: using a LASSO regularized linear model, we found transcription factor (TF) binding most predictive, especially for TFs that are hubs in the regulatory network; in contrast, evolutionary conservation, a popular feature in many other functional-impact predictors, has almost no contribution. Moreover, TF binding inferred from in vitro SELEX is as effective as that from in vivo ChIP-Seq. Second, we implemented GRAM integrating SELEX features and expression profiles. The program combines a universal regulatory score for a variant in a non-coding element with a modifier score reflecting the particular cell type. We benchmarked GRAM on a large-scale MPRA dataset in the GM12878 cell line, achieving a ROC score of ~0.73; performance on the K562 cell line was similar. Finally, we evaluated the performance of GRAM on targeted regions using luciferase assays in MCF7 and K562 cell lines. We noted that changing the insertion position of the construct relative to the reporter gene gives very different results, highlighting the importance of carefully defining the functional target the model is predicting. Author Summary Noncoding variants lie outside of protein-coding regions, and are found to have disease associations. However, knowledge on the molecular effect of these non-coding variants in a cell-specific context is very limited. Also, different output between multiple experiment platforms may introduce extra complexity in analyzing the molecular function of these variants. We developed GRAM, a generalized model to predict molecular effect of non-coding variants in multiple cell types for different experimental platforms. We first selected the most informative cell-independent SELEX transcription factor binding score on the variant locus as features and then combine cell-specific gene expression profile to build a multi-step prediction model. GRAM has been successfully tested on both MPRA and Luciferase assay, and on three different cell lines: GM12878, K562 and MCF7, shows high performance.
Prevalence of Depression among Epileptic Patients and its Association with Drug Therapy: A Systematic Review and Meta-Analysis

Background Despite the high prevalence of epilepsy in sub-Saharan Africa and the established relationship between depression and epilepsy, the extent of comorbid epilepsy and depression in the region is still poorly understood. This systematic review and meta-analysis aims to address this gap in the literature by determining the pooled prevalence of depression among epileptic patients in sub-Saharan Africa. Methods A systematic desk review and electronic web-based search of PubMed, Google Scholar, EMBASE, PsycINFO and the World Health Organization’s Hinari portal (which includes the SCOPUS, African Index Medicus, and African Journals Online databases) identified peer-reviewed research studies and doctoral dissertations on the prevalence of depression among patients with epilepsy using pre-defined quality and inclusion criteria. Relevant data were extracted and descriptive summaries of the studies presented in tabular form. The I2 test was used to assess heterogeneity across studies. A random effects model was used to estimate the pooled prevalence of comorbidity at a 95% confidence interval (CI). Funnel plot asymmetry and Egger’s tests were used to check for publication bias. The final effect size was determined by applying a trim and fill analysis in a random-effects model. Results Our search identified 167 studies, of which 16 articles were eligible for inclusion the final analysis. The pooled estimate of prevalence of depression among patients with epilepsy was 32.71 (95% CI: 25.50 - 39.91). Regional sub-group analysis found that the pooled prevalence in East Africa was 34.52 (95% CI: 23.53 - 45.51) and 29.69 (95% CI: 22.7 - 36.68) in Southern and West Africa. The odds of depression among epileptic patients receiving polytherapy were 2.65 higher than in those receiving monotherapy (95% CI: 1.49 - 4.71, I2=79.1%, p < 0.05). Conclusion Our findings indicate high comorbidity in sub-Saharan Africa and suggests that it may be more prevalent there than elsewhere. Comorbidity is statistically associated with polytherapy. Given the high levels of epilepsy in the region, more attention should be paid to incorporating depression screening and treatment into existing epilepsy programs and to revising treatment guidelines on comorbid depression to reduce polytherapy.
Self-disclosure in Marriage

: Marriage is an emotional bond between two individuals who share physical and emotional intimacy and sharing responsibility. Everyone wants to have a harmonious marriage, but there will be a problem that usually occurs in their relationships. Communication occurs in couples is very important for the welfare and harmony of marriage. One of the most important forms of communication is self-disclosure. Self-disclosure is the process of making oneself known by others by verbally expressing thoughts, attitudes, feelings, beliefs and past experiences to a partner. This study aimed to determine the differences in self-disclosure in long-distance married couples and couples who live together using quantitative methods with incidental sampling techniques. This study consisted of 100 samples (25 long-distance married couples and 25 married couples living together). The data were collected using the Marital Self-Disclosure Questionnaire (MSDQ) scale which showed the reliability of coefficient value (α) = 0.907. The results of the Mann-Whitney test analysis (U = 600) and also showed that the significance value (p) = 0,000 (p < 0.05). Based on these results it can be concluded that there are differences in self-disclosure in long-distance married couples and couples who live together. The self-disclosure in long-distance married couples is less than the couples who live together.
Biofilm formation by Vibrio parahaemolyticus on different surfaces and its resistance to sodium hypochlorite

ABSTRACT: Vibrio parahaemolyticus is an important pathogen for both fish industry and consumers. It forms biofilm which makes it difficult to eliminate this microorganism using sanitizers. This study aimed to assess biofilm formation on different surfaces and effect of biofilm on resistance to sanitizers. Eight isolates of biofilm-forming V. parahaemolyticus were tested for the ability to form biofilms on a number of surfaces including high density polyethylene, stainless steel, glass, exoskeleton of Farfantepenaeus paulensis (Pink Shrimp), and operculum of Micropogonias furnieri (Whitemouth Croaker). Efficiency of sanitizer sodium hypochlorite against the bacteria was evaluated in the biofilms formed on the surface of the materials used; out the eight strains analyzed four formed biofilm on different surfaces. The present study shows that there are variations between surfaces in terms of biofilm formation, with more than one bacterial strain being able to form biofilm on the surface of the operculum of M. furnieri and on high density polyethylene as well. One isolate formed biofilm on glass, and one isolate formed biofilm on stainless steel. Sanitizers reduced biofilm formation on all surfaces. Based on our findings, we concluded that V. parahaemolyticus isolates have different ability to form biofilm on different surfaces. No isolates formed biofilm on shrimp shells. Results of this study also showed that sodium hypochlorite eat a concentration of 20 parts per million (20ppm) of Cl2, albeit not able to eliminate bacteria reported in biofilms, is still capable of reducing bacterial populations.
Design and optimization of Surface Plasmon Resonance (SPR) biosensors

En terme de performance, le biocapteur ideal doit avoir tres grande sensibilite, basse limite de detection et temps d’analyse qui est extremement court. Les biocapteurs sans marquage a base de resonance de plasmons de surface (biocapteurs SPR) possedent naturellement le temps d’analyse le plus court parmi different types de biocapteurs. Leur limite de detection n’est cependant pas la plus impressionnante. Il y a donc un besoin pour augmenter considerablement la sensibilite intrinseque des biocapteurs SPR afin de permettre de plus basses limites de detection. Quelques approches pour exalter la sensibilite optique des biocapteurs SPR dans la configuration « traditionnel » de Krestchmann telles que film SPR bimetallique, plasmons a longues portees et detection dans l’infrarouge proche sont examinees dans ce travail. Des configurations « non traditionnelles » comme guides optiques planaires avec couplage par reseau et structures sub-longueur d’ondes ont ete aussi theoriquement etudiees. Nouvelle strategie de fonctionnalisation de surface a base de graphene qui augmente la sensibilite de reconnaissance biomoleculaire et peut etre appliquee a quasiment toute structure SPR a ete egalement demontree.