Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Magnet-based Nanofection in Embryonic Stem Cell Research

Embryonic stem (ES) cells are derived from the epiblast of the inner cell mass (ICM) of a blastocyst. These are pluripotent cells and can give rise to all derivatives of the three primary germ layers ectoderm, endoderm, and mesoderm. ES cells require specific signals for specific lineage of differentiation if injected directly into another body, ES cells will differentiate into many different types of cells, causing a teratoma (Wu et al., 2007). The techniques for culturing mouse embryonic stem (ES) cells from the inner cell mass of the preimplantation blastocyst were first done in 1981 (Martin, 1981), and versions of these standard procedures are used today in laboratories throughout the world. The first successful derivation of human ES (hES) cells was reported by Thomson et al. (Thomson et al., 1998). They isolated and plated the cells onto mitotically inactivated MEF (mouse embryonic fibroblast) cells. In 2000, Reubinoff et al. confirmed that hES cells could be efficiently derived from surplus embryos and possess the differentiation potential under in vitro conditions. Since then, there has been rapid progress made and numerous studies have described the derivation of new hES cell lines including methods of growing both undifferentiated hES cells and their differentiated progeny. In last 6 years, there has been exponential increase in methods to improve culture conditions, differentiation patterns to produce human cells for transplantation and drug testing (Trounson, 2006, Gepstein, 2002) and genetic manipulation (Draper et al., 2004, Zwaka and Thomson, 2003). Generating cultures of mouse or human ES cells that remain in a proliferating and undifferentiated state is multistep process. Typically, the inner cell mass of a preimplantation blastocyst is removed from the trophectoderm that surrounds it and cultured in the small plastic culture dishes containing growth medium supplemented with fetal calf serum. The culture dishes are sometimes coated with a "feeder" layer of nondividing cells, which are often MEF cells that have been chemically inactivated so they will not divide. Mouse ES cells can be grown in vitro without feeder layers if the cytokine leukemia inhibitory factor (LIF) is added to the culture medium, but human ES cells do not respond to LIF. The process of generating an embryonic stem cell line is somewhat difficult, so lines are not produced every time from the preimplantation-stage embryo maintained in a culture dish. However, if the plated cells survive, divide and multiply enough to crowd the dish, they are removed, and plated into several fresh culture dishes. The process of re-plating or
Forest malaria vectors in northwest Thailand and a trial of control with pyrethroid-treated bednets.

In forest and forest fringe settings of northwest Thailand, Anopheles minimus A was found to be the primary vector while An. dirus s. /. , An. sawadwongporni and An. maculatus s.s. are secondary vectors of malaria. The sites of transmission were investigated entomologically; parallel epidemiological investigations were made by another team. Malaria transmission in the villages in terms of the number of cases was as or more important than in the farm huts or in the forest, although the daily risk of infection was greater in forest activities. In a cage tunnel, lambdacyhalothrin on netting significantly reduced feeding success and killed mosquitoes which attempted to bite on a human arm through the treated nets. The aerial toxicity of the insecticide is apparently due to the spread of insecticide into the air as dust rather than as vapour. The biting rate of mosquitoes on humans close to a treated net was significantly reduced. The entomological impact of treated nets was evaluated in both long-term (two years) and short-term (48 days) studies in five and four communities, respectively. The results in the long-term evaluation showed that treated nets had very little effect on the densities and parous rates of An. minimus A, An. sawadwongporni and An. maculatus s.s. populations. However, the evaluation was carried out with a high washing rate, low coverage of re-impregnation and variations in climatic factors. In the short-term evaluation with intensive mosquito sampling, no mass effect on An. minimus A was observed. The exophagy, zoophily and early evening biting behaviours are probably the main factors reducing the effectiveness of treated nets. It is concluded that treated nets may provide improved personal protection especially among mobile populations but have little benefit in reducing mosquito population vectorial capacity of these species. There was cross-reactivity between the sporozoite monoclonal antibodies employed in the enzyme-linked immunosorbent assay and unknown factor(s) in blood of cows, buffaloes and pigs. This presumably caused false positive results when testing blood-fed zoophilic mosquitoes. Membrane feeding experiments showed that several zoophilic species are susceptible to both Plasmodium falciparum and P. vivax, except for a few species that are refractory to the former.
Blending Quantitative, Qualitative, Geospatial, and Temporal Data: Progressing Towards the Next Generation of Human Social Analytics

—Human social analytics in the next generation will need to embrace more multifaceted representations of human behavior with more complex models. Such models will need to integrate data of disparate forms, using disparate units of measure, collected from disparate sources, at disparate scales. Next generation social scientists will also face issues related to developing methods and tools to help facilitate the collection, processing, analyzing, and visualizing of such multifaceted social data. This paper illustrates these challenges by reporting on the development of a complex model of societal well-being (an inherently qualitative construct) which blends large scale quantitative, geospatial, and temporally referenced data of disparate forms, units, sources, and scales. We then demonstrate tools and methods intended to facilitate the progression towards next generational social analytics at large scales. We conclude by discussing several open questions with regards to social analytics, including those related to ethics and privacy concerns.
Mass production of Beauveria bassiana and its potentiality on rice hispa

Both resorcinol and phloroglucinol inhibited growth of D. oryzae [Cochliobolus miyabeanus] at 10 mM. The mode of action of these phenols was studied on hexokinase, malate dehydrogenase, succinate dehydrogenase and fumarase of C. miyabeanus.
Toxicity and signaling mechanisms underlying interactions of Stachybotrys chartarum toxins with lung macrophages

Stachybotrys chartarum (SC) is a mycotoxin-producing indoor mold, growing on humidified cellulose-based materials in water-damaged buildings. For the past two decades, SC has been linked to indoor mold-related health problems in residents and office personnel. SC produces highly toxic mycotoxins including several macrocyclic trichothecenes. Submicron sized trichothecene-containing air aerosols have been detected in moldy indoor environments. SC trichothecenes have been tested positive in the serum of workers exposed to moldy working environments. Experimentally, purified SC trichothecene or crude SC toxin extract and SC spores haven been shown to induce extensive cytotoxicity in various cultured cell lines or lung tissue toxicity in animal models (mice and rats). The inhaled toxin-containing aerosols pass nasal cavity and deposit in the deeper alveolar where resident macrophages could interact via phagocytosis and induction of host response. To study the toxicity of SC trichothecenes to alveolar macrophages, we used the murine alveolar macrophage cell line MH-S and the methanol extracted toxin-mixture from the SC spores. SC toxin-treated MH-S cells showed apoptosis (including DNA ladder fragmentation, activation of Caspase 3/7, and sub-G1 peak in flow cytometry analysis), DNA damage (comet assay and micronuclei formation assay), and activation of stress-inducible MAPK and DNA-damage responsive p53 signaling pathways (Chapter II). To study the underlying mechanism of interaction of alveolar macrophage cells with SC toxin, genome-wide transcriptional changes were evaluated in SC toxin-treated MH-S cell line using gene expression microarray and qRT-PCR (Chapter III). The results implied that SC toxin regulated various genes involved in multiple cellular processes (cell growth, proliferation and i ii death, inflammatory/immune response, genotoxic stress and oxidative stress) and signal transduction pathways (MAPK-, NF-kB-, TNF-, and p53-mediated signaling), indicating that SC toxin activated cascades of cellular signaling events leading to apoptosis. Several trcichothecene mycotoxins including both simple (T-2 toxin and DON) and macrocyclic (satratoxin G) types are known to bind to ribosome and inhibit protein synthesis. Since ribosomal proteins have also been reported to be involved in extra-ribosomal functions including cell cycle progression, cell proliferation, turmorigenesis, and apoptosis, we hypothesized that ribosomal component proteins might play a critical role in SC toxin (trichothecene)-induced toxicity in alveolar macrophage. In order to test this, we used yeast mat-a haploid yeast gene knockout library as a tool. The library was screened using both the SC toxin mixture and pure macrocyclic trichothecenes (Verrucarin A and Roridin A). The results revealed multiple ribosome-related genes and DNA damage/repair genes which could mediate SC toxin-induced toxicity, and could function as transducers in SC toxin-induced apoptosis signaling events (Chapter IV).
Diversidade de Mucorales em duas áreas de brejo de altitude de Pernambuco

The Mucorales order mostly comprises fungi saprobes commonly isolated from soil and herbivore dung, belonging to the phylum Mucoromycota and subphylum Mucoromycotina. In Brazil, specimens of this order were recorded in soils of Caatinga, Atlantic Forest and Cerrado, with a few records in soil from upland rainforest. Therefore, the present study aimed to know the diversity, frequency of occurrence, relative abundance and richness of these fungi in soils from upland rainforest areas located in the Agreste of Pernambuco. Six collections were made in the upland rainforest of Serra de Bonito and Sítio da Palmeira, located in Bonito and Camocim de São Félix municipalities, respectively. Overall, 72 soil samples were analyzed. For the isolation of Mucorales specimens, five milligrams of soil were added to a wheat germ agar medium in Petri dishes, in triplicate. The specimens were identified by observing its macroscopic and microscopic characteristics according to the specific bibliography. Sequencing of ITS and LSU regions of the rDNA was performed for the genetic identification of a newly isolated species. Thirty-eight species of Mucorales (4.32 x 10 CFU.g of soil) distributed in nine genus were isolated from soils from the upland rainforest areas: Absidia, Actinomucor, Backusella, Cunninghamella, Gongronella, Lichtheimia, Mucor, Rhizopus and Syncephalastrum. Among the isolates, C. bertholletiae showed the higher number of CFU.g soil, followed by Absidia sp. 3 and R. stolonifer. Absidia sp. 3, C. bertholletiae and R. stolonifer were more frequent and abundant in the inventoried soils. The composition of Mucorales between soils from the two upland rainforest areas was different, although significant variations between the diversity and richness of these fungi in these areas were not observed. Mucor pernambucoensis is a new species, whereas Absidia (sp. 1, sp. 2, sp. 3 and sp. 4), Actinomucor sp. , Backusella (sp. 1 and sp. 2), Cunninghamella (sp. 1 and sp. 2), Gongronella (sp. 1 and sp. 2), Mucor (sp. 1 and sp. 2), Rhizopus (sp. 1 and sp. 2) and Syncephalastrum sp. are likely new species.
Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria

A comprehensive biological understanding of nitrite-oxidizing bacteria (NOB) will be important to improve the functional stability of wastewater treatment systems and to reduce detrimental effects of nitrification in agriculture. The first part of this chapter provides an overview of the phylogenetic diversity and distribution of NOB in the environment and in engineered systems. Subsequently, the chapter focuses on the ecophysiology and ecological niche differentiation of the genera Nitrobacter and Nitrospira. The third part of this chapter addresses most recent insights into the biology of Nitrospira, which are based on the first sequenced genome from this genus. Future research should clarify whether Nitrobacter strains indeed are ecophysiologically different and how their diversity influences ecosystem functioning. The chapter also provides an overview of selected metabolic characteristics of ‘’Candidatus Nitrospira defluvii’’ as derived from the genomic data. Nevertheless, the microbial genome could be sequenced by using an environmental genomics approach that had been developed for sequencing an uncultured anaerobic ammonium-oxidizing bacterium. Although the phylogeny, might be blurred by past lateral gene transfer events, it is tempting to speculate that the aerobic nitrite-oxidizing system of Nitrospira was derived from an anaerobic protein complex and that the ancestor of Nitrospira was adapted to life under hypoxic conditions. The distant relationship between the NxrA forms of Nitrospira and those of Nitrobacter and Nitrococcus suggests that the use of nitrite as an energy source was invented more than once in the course of bacterial evolution.
Sampling-Based Accuracy Testing of Posterior Estimators for General Inference

Parameter inference, i.e. inferring the posterior distribution of the parameters of a statistical model given some data, is a central problem to many scientific disciplines. Generative models can be used as an alternative to Markov Chain Monte Carlo methods for conducting posterior inference, both in likelihood-based and simulation-based problems. However, assessing the accuracy of posteriors encoded in generative models is not straightforward. In this paper, we introduce `Tests of Accuracy with Random Points' (TARP) coverage testing as a method to estimate coverage probabilities of generative posterior estimators. Our method differs from previously-existing coverage-based methods, which require posterior evaluations. We prove that our approach is necessary and sufficient to show that a posterior estimator is accurate. We demonstrate the method on a variety of synthetic examples, and show that TARP can be used to test the results of posterior inference analyses in high-dimensional spaces. We also show that our method can detect inaccurate inferences in cases where existing methods fail.
The group process of bullying: Developmental, methodological, and social-cognitive perspectives

In this dissertation, peer victimization was placed in the context of the group process of bullying by examining six bullying participant roles. Part 1 focuses specifically on children’s experiences of peer victimization. Part 2 focuses on all six bullying participant roles (bully, victim, assistant, reinforcer, defender, and outsider). In both parts, I am covering three themes: measurement, development, and social cognitions. First, understanding a developmental phenomenon implies that we are able to measure it. Different methods have been used to measure youths’ involvement in peer victimization and the bullying participant roles. The first goal of this dissertation was to address the measurement of peer victimization and the participant roles by examining the concordance between different methods. Second, children’s social experiences in early childhood form the basis for their social and emotional functioning later in childhood and adolescence. Despite the importance of early childhood functioning, little is known about the development of peer victimization and its socio-emotional adjustment from early life on. In addition, youths’ motives to be involved in bullying may change over time and the power imbalance associated with bullying plays a more prominent role in adolescence than in childhood. It is unknown whether these changes are reflected in the social profiles of the participant roles in adolescence, as most studies on the participant roles have focused on middle childhood and early adolescence. Therefore, the second goal of this dissertation was to provide a developmental perspective on socio-emotional adjustment associated with peer victimization and the bullying participant roles. Third, I am addressing why children behave in certain ways in bullying situations. The mechanisms underlying children’s behaviors in bullying situations may be found in their social cognitions. Therefore, the third goal of this dissertation was to address the social cognitions of victims and the bullying participant roles.
Effects of Diphenylether Herbicides on Reactions of Mitochondria and Chloroplasts

Effects of three diphenylether herbicides [2,4-dichlorophenyl-p-nitrophenyl ether (nitrofen); 2,4,6-trichlorophenyl-4′-nitrophenyl ether (hereinafter referred to as MC-1478); and 2,4′-dinitro-4-trifluoromethyl-diphenylether (hereinafter referred to as C-6989)] were measured on phosphorylation and electron transport in spinach (Spinacia oleracea L.) chloroplasts, and mung bean (Phaseolus aureus L., var. Jumbo) and white potato tuber (Solarium tuberosum L.) mitochondria. All of the diphenylethers acted primarily as inhibitors of chloroplast noncyclic electron transport, and the coupled photophosphorylation. The compounds ranked in the following decreasing order of inhibitory effectiveness: MC-1478 ≥ C-6989 >> nitrofen. A site of action close to light reaction II was suggested. At high molar concentrations, marginal interference with cyclic electron transport or phosphorylation was obtained. In mitochondria, MC-1478 and nitrofen acted primarily as electron transport inhibitors with malate, NADH, and succinate as substrates. MC-1478 was a slightly stronger inhibitor than nitrofen. Only slight stimulation of ADP-limited oxygen uptake was obtained during the oxidation of NADH and succinate; whereas, strong inhibition of oxygen uptake was obtained with malate. C-6989 also weakly stimulated ADP-limited oxygen uptake with NADH and succinate but differed from the two chlorinated diphenylethers in that electron transport was not inhibited when ADP was present in excess. Interference with ATP generation could be one of the mechanisms through which the phytotoxicity of diphenylether herbicides is expressed.
Structural and biochemical study of the proteins AmiC, NlpD and FtsW involved in the bacterial cell division

Cell division in the Gram negative bacterium Escherichia coli is a highly coordinated mechanism involving various physiological functions such as chromosome segregation, cell envelope invagination, peptidoglycan synthesis at the division site and separation of the daughter cells. All these functions require a high level of spatio-temporal regulation in order to preserve the physical integrity of the cell. At least 20 proteins required for a proper cell division are recruited to the division site to form a supramolecular complex called the divisome. This thesis work focused on three major components of the E. coli division machinery: the N-acetylmuramyl L-alanine amidase AmiC, the LytM factor NlpD and the lipid II flippase FtsW. These proteins are recruited at midcell at a late stage of cell division. FtsW is an integral membrane protein crucial for the translocation of the peptidoglycan precursor from the cytoplasm to the periplasm where it will be processed to produce septal peptidoglycan. AmiC acts as a septal peptidoglycan hydrolase that allow the separation of the daughter cells. This enzyme has been shown to be activated by the LytM factor NlpD. The crystal structure of AmiC from E. coli presented in this work confirms the presence of an inhibitory helix in the active site. The AmiC variant lacking this helix exhibits by itself an activity comparable to that of the wild type AmiC activated by NlpD. Furthermore, the direct interaction between AmiC and NlpD has been detected by microscale thermophoresis with an apparent Kd of about 13 μM. The crystal structure of AmiC also reveals the β-sandwich fold of the AMIN domain, responsible for the septal targeting of AmiC to the division site. The two symmetrical four-stranded β-sheets exhibit highly conserved motifs on the two outer faces. Along with the peptidoglycan binding capacity of the AMIN domain, results obtained so far suggest that the AMIN domain could be involved in the recognition of a specific peptidoglycan architecture or a composition different than the lateral peptidoglycan. Production screenings of FtsW from different strains were realized and FstW from E. coli was purified. This challenging project will require additional efforts to obtain sufficient amount of protein for structural investigation. Information gathered in this work confirms the high level of regulation of the hydrolytic activity at the septum and gives a structural basis for a more precise molecular characterization of the division site targeting. Disruption or over-activation of these regulation mechanisms could represent a new strategy in the development of antibacterial compounds.
ESTIMATION OF NUMBER OF ROOT-NODULE BACTERIA BY A NODULATION-DILUTION FREQUENCY METHOD : ECOLOGICAL STUDIES OF RHIZOBIUM IN SOILS (PART 1)

Abstract Rhizobia spend most of their life in the soil outside the host plants. Soil conditions, therefore, may exert influence on the survival and variation of rhizobia so as to contribute to the nitrogen fixation of the legumes. The knowledge on the ecology of Rhizobium in soils may expected to give basis for the success of seed inoculation and establishment of effective strains in the field. In addition, it will render service for the study of the ecological soil microbiology, for example, ecology of pathogens of soil-borne plant diseases.
Cryptic diversity in forest shrews of the genus Myosorex from southern Africa, with the description of a new species and comments on Myosorex tenuis

Forest or mouse shrews (Myosorex) represent a small but important radiation of African shrews generally adapted to montane and/or temperate conditions. The status of populations from Zimbabwe, Mozambique, and the north of South Africa has long been unclear because of the variability of traits that have traditionally been ‘diagnostic’ for the currently recognized South African taxa. We report molecular (mitochondrial DNA and nuclear DNA), craniometric, and morphological data from newly collected series of Myosorex from Zimbabwe (East Highlands), Mozambique (Mount Gorogonsa, Gorongosa National Park), and the Limpopo Province of South Africa (Soutpansberg Range) in the context of the available museum collections from southern and eastern Africa and published DNA sequences. Molecular data demonstrate close genetic similarity between populations from Mozambique and Zimbabwe, and this well-supported clade (herein described as a new species, Myosorex meesteri sp. nov.) is the sister group of all South African taxa, except for Myosorex longicaudatus Meester & Dippenaar, 1978. Populations of Myosorex in Limpopo Province (herein tentatively assigned to Myosorex cf. tenuis) are cladistically distinct from both Myosorex varius (Smuts, 1832) and Myosorex cafer (Sundevall, 1846), and diverged from M. varius at approximately the same time (2.7 Mya) as M. cafer and Myosorex sclateri Thomas & Schwann, 1905 diverged (2.4 Mya). Morphometric data are mostly discordant with the molecular data. For example, clearly distinct molecular clades overlap considerably in craniometric variables. On the other hand, extreme size differentiation occurs between genetically closely related populations in the Soutpansberg Range, which coincides with the bissection of the mountain range by the dry Sand River Valley, indicating the potential for strong intraspecific phenotypic divergence in these shrews. © 2013 The Linnean Society of London