Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of molecular tools based on CRISPR/Cas9 system for epigenetic modulation of gene expression

Repurposing of platforms for targeted genome engineering, zinc finger nucleases (ZFNs), transcription activator-like nucleases (TALENs) and especially CRISPR/Cas9 system, has enabled targeted manipulation of epigenetic marks and new insights into epigenetic regulatory mechanisms. In this work, I have fused the catalytic domain of human TET1 (Ten-Eleven Translocation 1) protein Cterminally to the catalytically inactive Cas9 (dCas9) from Streptococcus pyogenes to create the dCas9- TET1 molecular tool. I have also tested the activity of N-terminal fusion of TET1-dCas9. The TET1 protein is a methylcytosine dioxygenase involved in active demethylation of 5-methylctosines to 5- hydroxymethylcytosines. In context of gene expression, methylated CpG dinucleotides within gene promoters are usually associated with gene silencing, and unmethylated CpGs with active gene transcription. Constructed molecular tools were successfully used for targeted CpG demethylation in promoter regions of two candidate genes, MGAT3 and LAMB1. I also showed that following demethylation the MGAT3 gene changed expression level. I have compared MGAT3 gene activation rates achieved following demetlylation using dCas9-TET1 with a more conservative approach of VPR-dCas9 mediated direct activation. For this approach, I used an N-terminal fusion of VPR activation domain and dCas9 from Staphylococcus aureus (dSaCas9).
Pretreatment with the Micro-alga, Spirulina Platensis Ameliorates Cyclophosphamide -Induced Hematological, Liver and Kidney Toxicities in Male Mice.

Cyclophosphamide (CTX) is used for the treatment of tumors however, it has several side effects which led to failure of the liver functions and significant reduction in the white blood cells total number (W.B.Cs). Spirulina platensis extract (S. platensis) has been found to restore the count of W.B. Cs to normal level with antioxidant properties. The aim of this study is to determine the prophylactic effect of Spirulina extract on CTX-induced hematological, liver and kidney toxicities. Thirty-two male albino mice were divided into four groups (8 mice/group). The first group (G1) was served as a control, the second group (G2) had injected i.p with 200 mg /kg CTX and the third group (G3) had orally treated with S. platensis extract (1000 mg /kg b.w.) for two weeks every day. Group four (G4) had treated orally with 1000 mg/kg of S. platensis extract, and then injected with 200 mg /kg CTX once. Three days after CTX injection, mice were sacrificed and blood samples were collected for complete blood count analysis and biochemical liver and kidney parameters. Liver and kidney tissues were harvested for histological examinations. The results showed that the injection of CTX reduced the total W.B. Cs number and did not affect the red blood cells and hemoglobin or hematocrit levels. Treatment with 1000 mg/kg S. platensis prior CTX treatment for two weeks did not lead to a restoration of W.B. Cs. However, the pre-treatment with S. platensis (1000 mg/kg/body weight) ameliorated the hepatic and renal dysfunctions and decreases the hepatic and renal histological changes which induced by CTX. In summary, the treatment with S. platensis for two weeks before CTX-injection led to a significant protection on both of the liver and kidney organs in mice.
Latitudinal and seasonal plasticity in American bison
 Bison bison
 diets

Lee J. HECKER* Department of Renewable Resources, University of Alberta, Edmonton, Alberta, T6G 2H1, Canada and Royal Alberta Museum, Edmonton, Alberta, T5J 0G2, Canada. Email: lhecker@ualberta.ca Sean C. P. COOGAN Department of Renewable Resources, University of Alberta, Edmonton, Alberta, T6G 2H1, Canada. Email: scoogan@ualberta.ca Scott E. NIELSEN Department of Renewable Resources, University of Alberta, Edmonton, Alberta, T6G 2H1, Canada. Email: scottn@ualberta.ca Mark A. EDWARDS Department of Renewable Resources, University of Alberta, Edmonton, Alberta, T6G 2H1, Canada and Royal Alberta Museum, Edmonton, Alberta, T5J 0G2, Canada. Email: mark.edwards@gov.ab. ca
A Multiple Agencies and Counties Partnership: Improving Parental Substance Use and Services Delivery Outcomes through a Network Development And Collaboration

Cross-sector collaboration has been defined as connecting or sharing information, resources, activities, and capabilities by organizations in two or more areas to achieve together an outcome that could not be achieved by organizations in one area separately (Bryson, Crosby, & Stone, 2006). To collaborate, agencies may need to consider questions, such as why to collaborate; what theory or theories will guide the collaboration; what are characteristics of effective networks; what governing structure will be used; how to evaluate the effectiveness of the collaboration network; and what are the benefits and challenges of collaboration. Because families are not being provided services within expected timeframes and because of a significant increase in foster care placements—which was largely driven by parental substance use—there is a need for collaboration among service providers in Central Virginia. A Multiple Agencies and Counties Partnership (MACP) was formed to address these problems. The purpose of this article is to present a case study of the development and accomplishments of MACP in Central Virginia and to relate the development and accomplishments of MACP to each of the aforementioned considerations, which may provide generalized lessons that other agencies may consider when collaborating. Keywords: collaboration, substance use, community, lessons learned
CNN-BASED FRAMEWORK FOR DCASE 2020 TASK 1B CHALLENGE Technical Report

This technical report presents a low-complexity CNN-based deep learning framework for acoustic scene classiﬁcation. Particularly, the proposed architecture constitute of two main steps front-end feature extraction and back-end network. Firstly, spectrogram representation is approached as front-end feature extraction in this framework. Next, the spectrograms extracted are fed into a CNN-based architecture for classiﬁcation. Obtained experimental results conducted over the DCASE 2020 Task 1B dataset improve DCASE baseline by 7.2%.
Earthquake source properties from analysis of dynamic ruptures and far-field seismic waves in a damage-breakage model

We present results on earthquake source properties using simulations of dynamic rupture and radiated seismic waves in a continuum damage-breakage rheological model. The source properties are derived by (1) calculation of source parameters directly from the simulated ruptures and (2) observational processing of the far-field radiated waves. The seismic potency, moment, damage-related source term, rupture velocity and effective rigidity are estimated directly from the simulated sources, while the radiation pattern, dominant frequency, directivity, rupture velocity and seismic potency are calculated through analysis of the radiated waves. The potencies calculated directly from the sources are used to validate those estimated by wave analysis. The effective rigidity at the rupture zone during failure is about four times smaller than that of the intact surrounding rocks. Rupture velocity can be estimated by far-field measurements for sources with unidirectional ruptures with prominent rupture directivity. The dominant frequencies for P and S waves $f_d^S/f_d^P$ reflect clearly the rupture duration and have a ratio in the range 0.87–1.12. Seismic potencies obtained through processing the P or S waves have an overall ±15 per cent difference from the source reference values. The calculated values of the coefficient ${\rm{\kappa }}$, relating rupture length to corner or dominant frequency, have strong dependency on the source geometry. Using a strain-rate dependent ${\rm{\kappa }}$, we obtain much weaker dependencies of strain-drop on the dominant frequencies, $\Delta {\rm{\varepsilon }} \propto {( {{f_d}} )^{3/4}}$, than the classical cube-dependency between stress drop and corner frequency, and corresponding weak dependency of average slip on dominant frequency, ${\rm{\bar{D}}} \propto {( {{f_d}} )^{1/2}}$. The obtained analysis procedure and relations can be used to reduce the uncertainty of source properties derived from far-field seismic waves.
Glyphosate-Based Herbicide Toxicophenomics in Marine Diatoms: Impacts on Primary Production and Physiological Fitness

Glyphosate is the main active component of the commercial formulation Roundup®, the most widely used chemical herbicide worldwide. However, its potential high toxicity to the environment and throughout trophic webs has come under increasing scrutiny. The present study aims to investigate the application of bio-optical techniques and their correlation to physiological and biochemical processes, including primary productivity, oxidative stress, energy balance, and alterations in pigment and lipid composition in Phaeodactylum tricornutum, a representative species of marine diatoms, using the case study of its response to the herbicide glyphosate-based Roundup® formulation, at environmentally relevant concentrations. Cultures were exposed to the herbicide formulation representing effective glyphosate concentrations of 0, 10, 50, 100, 250, and 500 μg L−1. Results showed that high concentrations decreased cell density; furthermore, the inhibition of photosynthetic activity was not only caused by the impairment of electron transport in the thylakoids, but also by a decrease of antioxidant capacity and increased lipid peroxidation. Nevertheless, concentrations of one of the plastidial marker fatty acids had a positive correlation with the highest concentration as well as an increase in total protein. Cell energy allocation also increased with concentration, relative to control and the lowest concentration, although culture growth was inhibited. Pigment composition and fatty acid profiles proved to be efficient biomarkers for the highest glyphosate-based herbicide concentrations, while bio-optical data separated controls from intermediate concentrations and high concentrations.
Catalytic Ozonation and Membrane Contactors—A Review Concerning Fouling Occurrence and Pollutant Removal

Membrane filtration has been widely used in water and wastewater treatment. However, this process is not very effective for the removal of refractory organic compounds (e.g., of pharmaceutical origin). Coupling membrane filtration with ozonation (or other Advanced Oxidation Methods) can enhance the degradation of these compounds and, subsequently, the incidence of membrane fouling (i.e., the major problem of membrane uses) would be also limited. Ozonation is an efficient oxidative process, although ozone is considered to be a rather selective oxidant agent and sometimes it presents quite low mineralization rates. An improvement of this advanced oxidation process is catalytic ozonation, which can decrease the by-product formation via the acceleration of hydroxyl radicals production. The hydroxyl radicals are unselective oxidative species, presenting high reaction constants with organic compounds. An efficient way to couple membrane filtration with catalytic ozonation is the deposition of an appropriate solid catalyst onto the membrane surface. However, it must be noted that only metal oxides have been used as catalysts in this process, while the membrane material can be of either polymeric or ceramic origin. The relevant studies regarding the application of polymeric membranes are rather scarce, because only a few polymeric materials can be ozone-resistant and the deposition of metal oxides on their surface presents several difficulties (e.g., affinity etc.). The respective literature about catalytic membrane ozonation is quite limited; however, some studies have been performed concerning membrane fouling and the degradation of micropollutants, which will be presented in this review. From the relevant results it seems that this hybrid process can be an efficient technology both for the reduction of fouling occurrence as well as of enhancement of micropollutant removal, when compared to the application of single filtration or ozonation.
Chemical and Phytochemical Analyses of Extracts from the Leaves of Acalypha wilkesiana, “an Herbal Plant used for the Treatment of Various Skin Disorders”

Abstract Acalypha wilkesiana is a tropical herb used for the treatment of skin disorders. Phytochemical studies carried out on the pulverized dried leaves of the plant revealed the presence of alkaloids, cardiac glycosides, anthraquinones, saponins, flavonoids and tannins. The crude 50% methanol extract obtained from the dried leaves was sequentially partitioned into three fractions. Thin layer chromatography of the fractions revealed three (3) components each in hexane fraction; ethyl acetate fraction and butanol fraction of the plant extract. Column chromatography of the fractions was carried out. The infrared analyses of the components revealed the presence of alkenes, hydroxyl group, conjugate carbonyls, esters in the hexane fraction components. Those from the ethyl acetate and butanol fractions contained aliphatic amides or amines with carbonyl and esters attached in the two fractions. Essential oil was extracted from the dried leaves using hydro-distillation method. GC-MS analysis of the essential oil revealed the presence of major compounds which included: n-Hexadecanoic acid 4-Hexen-2-one-3-methyl, Pyrrole and 6-Benzamido-4-benzoyl-1,2,4-triazine-3,5. The presence of the functional groups inferred from IR and GC-MS analyses with the antimicrobial potential of the essential oil may support the use of the plant in the management of skin infections, gastrointestinal disorders and other ailments.
Role of VTC4 in Stress Response and Regulation of Inorganic Polyphosphate Levels in Yeast

Inorganic polyphosphate (polyP) is an important factor of stress tolerance in microbial cells. In yeast, the major enzyme of polyP biosynthesis is Vtc4, a subunit of the vacuole transporter chaperone (VTC) complex. In this study, we demonstrated that Vtc4 knockout in Saccharomyces cerevisiae not only decreased polyP content but also caused shifts in the composition of the intracellular polyP pool and changed the stress tolerance profile. In the mutant S. cerevisiae, the level of short-chain acid-soluble polyPs was decreased nearly 10-fold, whereas that of longer acid-insoluble polyPs was decreased only 2-fold, suggesting the existence of other enzymes compensating the production of long-chain polyPs. The Δvtc4 mutant showed inhibition of Mg-dependent phosphate uptake and decreased resistance to alkaline stress but increased tolerance to oxidation and heavy metal ions, especially Mn. Quantitative PCR revealed the upregulation of the DDR2 gene implicated in multiple stress responses and downregulation of PHO84 encoding a phosphate and Mn transporter, which could account for the effects on phosphate uptake and Mn-related stress response in the Δvtc4 mutant. Our study indicates that short-chain polyPs, plays an important role in the regulation of stress response in yeast.
Effect of Alum-treated Groundnut (Arachis hypogea) Shell Meal on Blood Chemistry and Carcass Characteristics of Broiler Chickens

Effect of alum-treated groundnut (Arachis hypogea) shell (ATGNS) meal was studied on the blood chemistry and carcass characteristics of broiler chickens. Two hundred and forty (240) day-old broiler chicks of Anak strain were used for the study in a completely randomized design for eight weeks. The chicks were allotted into six groups of forty chicks each and further divided into four replicates of ten chicks each.Groundnut shell (GNS) was processed by soaking it in water containing alum in ratio 1kg of groundnut shell: 15 litre of water: 600g of alum for three, four, five and six days. Wheat offal was included at 10% in T1 as positive control, 4% wheat offal and 6% untreated groundnut shell (GNS) in T2 as negative control, and 4% wheat offal with 6% treated GNS in treatments 3, 4, 5 and 6 at three days, four day, five days and six days of processing respectively. Results on haematological parameters were not significantly (p>0.05) different except mean corpuscular volume (MCV) and mean corpuscular haemoglobin (MCH). Birds in T5 performed better than others in mean corpuscular volume (MCV) and mean corpuscular haemoglobin (MCH) with highestvalues of 123.83% and 41.93pg respectively, while birds in T3 had the lowest values of 115.28% and 39.05pg in the two parameters respectively. There were significant (p 0.05) differences in serum biochemical studies. Birds fed treatment 1 (T1) had the highest values of 3.95 and 2.72g/dl in total protein and globulin respectively, while the lowest values 2.55 and 0.97g/dl were obtained from birds in T6 respectively. Cut-up parts showed significant (p 0.05) different, were better (p<0.05) than those on untreated groundnut shell meal (T2). Birds in T6 had the highest values (2.95, 4.60 and 12.53%) in head, neck and thigh respectively. The highest weight (18.02%) of back was recorded in T1. Birds in T4 had the highest values of 19.60 and 4.20% in breast muscle and shank respectively, while those in T3 recorded the lowest (14.65%) in breast muscle, and those in T2 had the lowest (3.56%) in shank. The results in conclusion, showed that alum-treated groundnut shell(ATGNS) could replace wheat offal at 6% level of inclusion by improving carcass yield as well as maintainingblood profile of broiler chickens. Keywords: Groundnut shell, alum, blood chemistry, carcass, broiler
Comparison of three diagnostic methods for Salmonella enterica serovars detection in chicken rinse

ABSTRACT: Salmonella detection is a key point in food safety testing, because of the frequent association of this pathogen with food poisoning in humans. The standard bacteriological tests currently used for Salmonella-detection are time-consuming; therefore, there is a need to develop alternative methods to accelerate the detection. In order to accelerate Salmonella diagnosis, we used the immunomagnetic separation assay associated with bacteriophage P22 for the rapid detection of the following Salmonella serovars in chicken rinses of drumsticks, artificially contaminated with 5, 10, and 100 CFU/25mL of bacteria: Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg), Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) and Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). The efficiency of the technique, represented by the time required for detection of positive and negative samples, was compared with that of the standard diagnostic tests used for this pathogen, the bacteriological assay and the polymerase chain reaction (PCR)-based test. This study confirmed the ability of the bacteriophage-associated immunomagnetic separation assay to identify 99.6% of Salmonella-positive samples of the three serovars tested. In contrast, the bacteriological assay and PCR-based test detected 95.1% and 98.5% of the Salmonella-positive samples respectively.
Non-Linguistic Challenges Faced by Malaysian Students in Enhancing Speaking Skills

One important skill that second language learners find difficult to acquire is speaking skills. Despite learning English language in both primary and secondary school, students face challenges to speak the language confidently. The purpose of this study was to in investigate the non-linguistic challenges faced by Malaysian students in enhancing speaking skills. This quantitative study used a questionnaire consisting 20 items based on five Likert scales. The purposive sampling of form three students, and data were collected from 13 females and 17 males. The data were analysed through SPSS software that suggest most students experience speaking skill is difficult, anxiousness, lack of confidence, shyness and afraid of making mistakes while speaking. The findings could help teachers to understand students’ non-linguistics challenges in speaking skills and adapt various techniques to encourage students to speak in English language. It is suggested more studies need to be done to addressspea- king competency of students in Malaysian schools.
Neuroimaging supports the representational nature of the earliest human engravings

The earliest human graphic productions dating to the Lower and Middle Palaeolithic are associated with anatomically modern and archaic hominins. These productions, which consist of abstract patterns engraved on a variety of media, may have been used as symbols, and their emergence is thought to be associated with the evolution of the properties of the visual cortex. To test this hypothesis, we used functional magnetic resonance imaging to compare brain activations triggered by the perception of engraved patterns dating between 540,000 and 30,000 years before the present with those elicited by the perception of scenes, objects, symbol-like characters, and written words. The perception of the engravings bilaterally activated regions in the ventral route in a pattern similar to that produced by the perception of objects, suggesting that these graphic productions are processed as organized visual representations in the brain. Moreover, the perception of the engravings led to a leftward activation of the visual word form area. These results support the hypothesis that in contrast to random doodles, the earliest abstract graphic productions had a representational purpose for modern and archaic hominins.
Challenging a Global Land Surface Model in a Local Socio-Environmental System

Land surface models (LSMs) predict how terrestrial fluxes of carbon, water, and energy change with abiotic drivers to inform the other components of Earth system models. Here, we focus on a single human-dominated watershed in southwestern Michigan, USA. We compare multiple processes in a commonly used LSM, the Community Land Model (CLM), to observational data at the single grid cell scale. For model inputs, we show correlations (Pearson’s R) ranging from 0.46 to 0.81 for annual temperature and precipitation, but a substantial mismatch between land cover distributions and their changes over time, with CLM correctly representing total agricultural area, but assuming large areas of natural grasslands where forests grow in reality. For CLM processes (outputs), seasonal changes in leaf area index (LAI; phenology) do not track satellite estimates well, and peak LAI in CLM is nearly double the satellite record (5.1 versus 2.8). Estimates of greenness and productivity, however, are more similar between CLM and observations. Summer soil moisture tracks in timing but not magnitude. Land surface reflectance (albedo) shows significant positive correlations in the winter, but not in the summer. Looking forward, key areas for model improvement include land cover distribution estimates, phenology algorithms, summertime radiative transfer modelling, and plant stress responses.
Identifying sensor species to predict critical transitions in complex ecosystems

Ecosystems provide key services needed for human well-being, such as purifying air and regulating our health, many of which are disrupted when these ecosystems undergo a critical transition to undesired states. Detecting early-warning signals of these critical transitions remains challenging for complex ecosystems with a large number of species. Here we built a mathematical formalism to identify minimal sets of “sensor species” from which we can determine the state of a whole ecosystem, allowing us to predict a critical transition in an ecosystem by monitoring a minimal subset of its species. We rigorously prove that minimal sets of sensor species can be generically identified knowing only the structure of the ecological network underlying the ecosystem, regardless of its population dynamics. We numerically validated our formalism to predict critical transitions in large complex ecosystems, and then we applied it to experimental data of a critical transition in a lake food-web. Our results contribute to better monitoring complex ecosystems, especially those with poorly known population dynamics such as host-associated microbial communities.