Miracle-dz/UniFAR-FTUs huggingface dataset:
Scanning Near-Field Fluorescence Microscopy Applied to ESEM

A scanning near-field fluorescence microscopy for in situ test is demonstrated in this letter. The scanning near-field fluorescence microscopy can be applied to commercial environmental scanning electron microscopy (ESEM) without changing the ESEM performance. The designed scanning near-field fluorescence microscopy combines the advantage of the ESEM and scanning near-field optical microscopy (SNOM). The CdSe/ZnS quantum dot samples are prepared to verify system performance. The system offers fluorescence image and topography image simultaneously with a high depth and high resolution, thus permitting further ingredient and functional research. The topography image spatial resolution and the fluorescence image spatial resolution are below 130 nm and 115 nm, respectively, with a tip aperture of ~100 nm. The image range reaches $300\,\,\times \,\,300\,\,\mu \text{m}$ by virtue of the micromanipulators and image stitching technology.
E-Readiness for ICT Implementation of the Higher Education Institutions in the Indonesian

ZEN Framework is a tool used to measure the readiness of the use of Information and Communication Technologies (ICT) both external and internal readiness measurements of Higher Education Institutions (HEI). E-readiness is an essential element in the advancement of ICT in higher education. ICT plays a role to the process of organizing and managing the management of higher education institutions such as to support operational and administrative activities, to assist the decision making process, to support communication activities and interactions among stakeholders, to enable the optimization of processes and resources, and to establish strategic partnerships with external parties. The role of ICT is highly strategic so ICT is no longer just a supporting tool, but as an integral part and can not be separated from HEI business itself. This study is a preliminary study which attempt to correlate one of the E-readiness frameworks with Indonesia’s national framework of ZEN for ICT adoption in HEI. The result shows that the ZEN Framework and the E-readiness are related to each other. The E-readiness model has three success factors of the use of ICT correlated with the ZEN Framework attribute as an attribute used for readiness assessment. From the correlation process, added a new factor, named Service Quality so that the E-readiness model has four factors, i.e., People, Process, Technology, and Service Quality.
Molecular Characterization of Endophytic Fungal Colonizers of Plant Roots: A Comparison between the Aggressive Invasives Vincetoxicum rossicum, Alliaria petiolata, and Local Native Plant Species

Soil fungi play an important role in regulating plant communities as well as above and below ground ecosystem-level processes; conversely, plant communities may also affect the structure and functionality of these root-associating fungi. Alteration of these fungal communities due to non-native plant invasion has the potential to disrupt biogeochemical cycling, soil structure, and plant growth. Both beneficial symbionts such as arbuscular mycorrhizal fungi (AMF) as well as the total fungal community are potentially altered by aggressive invasive plant species in such a way as to disrupt existing native endophytic fungal communities in the soil post invasion. This disruption could provide a pathway for invasion and suggests the importance of investigating plant-fungal associations in invaded ranges. I used molecular techniques to characterize the fungal communities colonizing Vincetoxicum rossicum or Dog-strangling vine (DSV) and Alliaria petiolata or garlic mustard, both European natives
Acute Toxicity, Phytochemistry and Anti-diarrheal Effects of Celtis integrifolia Lam. Aqueous Leaf Extract in Wistar Albino Rats

Celtis integrifolia Lam. plants also known as hackberries or nettle trees are widely spread in warm temperate region of African, Latin America and Asia. The aqueous leaf extract of Celtis integrifolia was obtained by soxhlet extraction using distilled water as a solvent. The aqueous leaf extract was then evaluated for its acute toxicity, phytochemical compounds and anti-diarrheal potential using standard protocol. The results showed that the LD50 of aqueous leaf extract of Celtis integrifolia was greater than 3000 mg/kg following up and down procedure, an indication of low toxicity. The phytochemical analysis of the leaf extract indicates the presence of saponins, reducing sugar, tannins, flavonoids, carbohydrate and cardiac glycoside. The leave extract significantly (p<0.01) Original Research Article Mahre et al.; BJPR, 14(5): 1-7, 2016; Article no.BJPR. 31222 2 reduced the number of unformed faeces in castor oil induced diarrhea in rats. It also significantly (p<0.01; 0.001) reduced the gastrointestinal transit of activated charcoal. Therefore, the aqueous leaf extract of Celtis integrifolia is relatively safe and possesses an anti-diarrheal activity.
Within-host evolution of HIV-1: Novel pathways of virus escape from cellular and humoral immunity

Longitudinal HIV-1 single genome sequencing (SGS), which permits unambiguous genetic characterization of circulating viral strains without introduction of PCR error, can be used to identify sites in the viral genome that are under selective pressure. Following transmission, the earliest sites under positive selection often fall in cytotoxic T lymphocyte (CTL) epitopes. During escape from CTL immune pressure, viral sequences typically exhibit nonsynonymous mutations within the span of the cognate T cell epitope. I applied SGS to study sequence evolution in the HIV-1 5’ leader sequence, which is thought to be translationally silent. I observed mutational patterns consistent with CTL escape and demonstrated that the HIV-1 5’ leader expresses T cell antigens from non-canonical one-off AUG codons (e.g. CUG). While these non-canonical start codons can be mutated during CTL escape, a reverse transcriptase overextension error periodically restores a one-off AUG within the 5’ leader. As infection ensues, sites under selection within the gene encoding the viral envelope glycoprotein (Env) often fall within autologous neutralizing antibody epitopes. In a subset of individuals, the strain-specific neutralizing antibody response develops into a broadly crossreactive neutralizing antibody (bnAb) response. To understand what factors influence bnAb ontogeny, I used SGS to study Env evolution both during natural infection and immunotherapy. I found viral diversification in bnAb contact residues and divergence of the virus population into multiple persistent lineages to precede bnAb development. Taken together, these data demonstrate that longitudinal HIV-1 SGS can be used to discover novel aspects of virus biology and host-pathogen interactions. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Beatrice H. Hahn Subject Categories Microbiology This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2406 WITHIN-HOST EVOLUTION OF HIV-1: NOVEL PATHWAYS OF VIRUS ESCAPE FROM CELLULAR AND HUMORAL IMMUNITY Edward F. Kreider A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2016 Supervisor of Dissertation ________________________ Dr. Beatrice H. Hahn, MD Professor, Departments of Medicine and Microbiology Graduate Group Chairperson ________________________ Dr. Daniel S. Kessler, PhD Associate Professor of Cell and Developmental Biology Dissertation Committee James A. Hoxie, MD (Chair), Professor, Department of Medicine Robert W. Doms, MD, PhD, Professor, Department of Pathology and Laboratory Medicine Scott E. Hensley, PhD, Associate Professor, The Wistar Institute Rahul M. Kohli, MD, PhD, Assistant Professor, Department of Medicine
Role of microRNA in early life placental programming of insulin resistance and metabolic health.

Intrauterine growth restriction (IUGR) is associated with insulin resistance and diabetes, particularly later in adult life. Placental restriction is a common cause of IUGR, this condition induces insulin resistance and/ or insulin deficiency and consequently, impaired glucose tolerance in offspring, in the sheep and rat. Reduced expression of insulin signalling genes and that of their key metabolic targets in insulin sensitive tissues and of some molecular determinants of pancreatic β-cell insulin secretion and mass, contributes to impaired insulin action in offspring, in experimental and human IUGR. However, the underlying molecular mechanisms whereby IUGR alters the molecular profile of insulin sensitive and secreting tissues in later life are largely unknown. The studies described in this thesis examine the potential role of microRNAs (miRNAs) in the developmental programming of impaired insulin action in IUGR offspring. MiRNAs are short single-stranded RNAs (22 nucleotide in length), which are able to reduce the translation and/or abundance of mRNA and protein of targets. Each miRNA is predicted to regulate the abundance of many targets in co-ordinated networks to modify function, providing a potentially powerful pathway for developmental programming to influence later phenotype. Here, IUGR was induced by restricting placental growth and development surgically in sheep (pre-conception removal of most implantation sites) or in the rat (ligation of uterine blood vessels in late gestation). In each species, the effect of placental restriction and IUGR on miRNA expression and expression of key predicted targets, including that of insulin signalling and key metabolic genes in the insulin sensitive tissues: liver, skeletal muscle and adipose (perirenal in sheep and omental in rat), in adult offspring were characterised. The effect of placental restriction on pancreatic miRNA expression in adult offspring was also determined in the sheep. Placental restriction and IUGR mostly increased miRNA expression in insulin sensitive tissues of the adult sheep and in a sex specific manner, suggesting the potential for increased repression of the translation or abundance of their molecular targets and related functions. The liver, followed by skeletal muscle and adipose tissue, showed the greatest susceptibility in terms of numbers of miRNAs with altered expression following placental restriction. In males, placental restriction increased hepatic expression of eight miRNAs by ~1.5-3.5-fold, with differential expression of four independently confirmed by qPCR (hsa-miR-1, hsa-miR-21, hsa-miR-142-3p and hsa-miR-144). Each of these four miRNAs was predicted to target molecules involved in insulin signalling, metabolism and hepatic disease. The latter included p85α, Pparα, Igf1, Foxo3 and Acox1, all exhibiting reduced hepatic expression (~2.3-4.0 fold) following placental restriction in males, with the abundance of hsa-miR-1, hsa-miR-142-3p and hsa-miR-144 correlating negatively with Acox1 expression. Thus, placental restriction…
Ecologie van Fluiters Phylloscopus sibilatrix in Nederlandse bossen

tallen op de broedplaatsen van jaar op jaar, het veelal geclusterde voorkomen, die ogenschijnlijk eeuwig zingende mannetjes, dat prachtige reikhalzen in de boomtoppen, wat zit daar allemaal achter? De sterke aantalsschommelingen zijn al heel lang bekend (Bijlsma et al. 2001, van der Weele 2004, Wesołowski et al. 2009). Dat geldt ook voor de veelwijverij waar Fluiters – soms aan doen (Svärdson 1947). Toch wordt er in Nederland geen aandacht aan polygynie besteed tijdens inventarisaties, afgezien van de wat cryptische opmerking dat de zangactiviteit sterk kan verschillen naar individu (Hustings et al. 1985). Dat verschil heeft echter niets van doen met individuele variatie in gedrag, maar alles met de status van de zanger binnen de populatie (gepaard of niet), tijd van de dag (‘s middags zingende Fluiters zijn vaak ongepaard) en seizoen (vroeg in het seizoen verlaten gepaarde mannetjes hun territorium vaker om op een andere plek te gaan zingen dan laat in het seizoen) (Temrin & Stenius 1994).
Growth and reproductive traits of F1-generation transgenic goats for human granulocyte-colony stimulating factor

To ensure that animal welfare requirements and phenotypic characteristics of the newly produced transgenic lines are not compromised, an evaluation of all individuals is necessary. This can be inferred by the analysis of the growth and reproduction parameters. The present study was designed to determine the impact of the insertion of human granulocyte-colony stimulating factor (hG-CSF) transgene on growth and reproductive characteristics in first-generation (F1) goats from two transgenic lines. Bodyweight (BW) development (BW at birth, mean BW gain before weaning, BW at weaning, mean BW gain after weaning, BW at puberty), as well as reproductive parameters (age at puberty, ejaculate volume, concentration, total sperm per ejaculate, massal motility, progressive individual motility, major and minor defects) were similar (P > 0.05) between transgenic (T) and non-transgenic (NT) goats. Significant (P < 0.05) differences in mean (±s.d.) white blood cell count were observed between T and NT in first day of life (174.6 ± 14.7 × 103 and 15.0 ± 4.0 × 103 cells/µL), and during (66.8 ± 21.1 × 103 and 17.0 ± 4.6 × 103 cells/µL) and after (36.6 ± 4.0 × 103 and 15.5 ± 2.2 × 103 cells/µL) suckling, even though hG-CSF has not been detected in blood serum in any analysis. Although other cell counts were occasionally higher in T animals, differential counts showed that this difference was mainly due to an increased number of neutrophils, which represents 84.6%, 67.2% and 56.8% of total white blood cell count respectively, in the three time periods. Kidney and liver biochemical analyses indicated that all goats were healthy. Thus, it is possible to assume that all animals are normal and had no deleterious effects on either growth or reproductive parameters by the presence of transgene or as a consequence of leukocyte profile alteration.
Combination of in-situ diffraction experiments and acoustic emission testing to understand the compression behaviour of Mg-Y-Zn alloys containing LPSO phase under different loading conditions

Combination of in-situ diffraction experiments and acoustic emission testing to understand the compression behaviour of Mg-Y-Zn alloys containing LPSO phase under different loading conditions. G. Garcésa,*, K. Máthisb, J. Medinaa, K. Horváthb, D. Drozdenkob, E. Oñorbec, P. Dobroňb, P. Péreza, M. Klausd, P. Adevaa aDepartment of Physical Metallurgy, CENIM-CSIC, Avenida Gregorio del Amo 8, E-28040 Madrid, Spain bDepartment of Physics of Materials, Faculty of Mathematics and Physics, Charles University, KeKarlovu 5, 121 16 Praha 2, Czech Republic cDepartment of technology. Division of materials of energy interest, CIEMAT. Avenida Complutense, 40, 28040 Madrid, Spain dHelmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany. *corresponding author. Tel +34-91-553-8900; fax: +34-91-534-7425; E-mail address: ggarces@cenim.csic. es Abstract The effect of the orientation of the non-recrystallized grains (non-DRX) and the LPSO phase on plasticity in extruded Mg97Y2Zn1 alloy with a bimodal grain structure have been studied in-situ using the combination of synchrotron diffraction and acoustic emission techniques during compression tests. The adaptive sequential k-means (ASK) procedure was applied to analyze the acoustic emission signal. This method can successful separate the signal for each possible deformation systems. Combining both techniques the deformation mechanisms that take place during the compression tests under different loading directions have been distinguish. Independently of the loading direction, the beginning of the macroscopic plasticity is always controlled by the activation of basal slip system in the DRX grains. However, highly oriented non-DRX grains and LPSO phase have a strong influence over the compressive deformation of the MgY2Zn1 alloy. The basal planes in the non-DRX grains were oriented parallel to the
DIVERSITY OF PLANTS USED FOR PLAITED CRAFTS BY THE DAYAK IBAN-DÉSA IN KABUPATEN SINTANG, KALIMANTAN BARAT, INDONESIA

DEWI, A. P., ARIYANTI N. S. & WALUJO, E. B. 2016. Diversity of plants used for plaited crafts by the Dayak Iban-Desa in Kabupaten Sintang, Kalimantan Barat. Reinwardtia 15(2): 67 – 79. — Many plants are used for making plaited crafts such as basketry and woven mats by the Dayak Iban-Desa, a sub-tribe of the Dayak in Kalimantan Barat, Indonesia. The Dayak Iban-Desa gather the craft materials mostly from the plants in the forest. However, the habitats of these plants are being threatened by deforestation. The diversity of plants used for crafts is here documented. This study recorded the scientific names of plant species used for the craft plaiting, and observed abundance of plants used for craft. Information about the plants used were gathered using non-structural interview and focus group discussion (FGD) with the informants and participants. The abundance of plaited plants was observed in 46 plots of 10 × 10 m2 plots by participative ecological method. Nineteen plants species were used as plaited material, belonging to four families: Arecaceae, Poaceae, Pandanaceae and Zingiberaceae. Two species of rattan (Calamus sp. and Plectocomiopsis wrayi Becc.) have the highest Index Cultural Significance (ICS) value. Those species were considered as the most valuable plant materials because of the quality of fiber, intensity on harvesting, and the resulting quality of plaited craft products. However, the demand for high quality products is not always supported by the availability of plant materials in the forest. Therefore, the cultural significance of plants (the ICS values) and their availability should be considered when determining the conservation strategy for each of these species.
Depth and physical properties of soil in a forest and a rubber plantation in Peninsular Malaysia

NOGUCHI, S. , BAHARUDDIN, K. , ZULKIFLI, Y. , TSUBOYAMA, Y. & TANI, M. 2003. Depth and physical properties of soil in a forest and a rubber plantation in Peninsular Malaysia. Soil depth and soil physical properties were investigated in a tropical rain forest and a rubber plantation in Peninsular Malaysia. For the forested site, thickness of surface soil layer (A and B horizons) and total soil depth ranged from 52 to 160 cm and from 118 to 640 cm respectively. The corresponding values for riser bank in the rubber plantation ranged from 42 to 121 cm and from 106 to 162 cm respectively. Total soil depth at the terrace bench in the rubber plantation was shallower (mean: 119 cm) than at the riser bank. The saturated hydraulic conductivity (Ks) in the forested site and plantation site ranged from 6.40 x 10 to 7.51 x 10m sand from 1.79 x 10 to 5.68 x 10 m s respectively. The Ks values decreased with increasing soil depth at both sites. The average Ks values in the forested site were larger (10cm: 1466 mm h, 80 cm: 169 mm h) than the prevailing rainfall intensity in this region. Although the average Ks values at the riser bank in the rubber plantation were similar to those in the forested site, the average Ks values
Checklist of the Heleomyzidae, Neriidae and Oestridae (Insecta, Diptera) in the State of Mato Grosso do Sul, Brazil

We provide a checklist of fl ies of the families Heleomyzidae, Neriidae and Oestridae in the State of Mato Grosso do Sul, Brazil. Heleomyzida are represented in Brazil by 13 species, and only Neorhinotora aristalis (Fischer) is recorded to the state of Mato Grosso do Sul. The two reported species of Neriidae, Longina abdominalis Wiedemann and Nerius pilifer Fabricius, are among the 15 species now known in Brazil. The Oestridae family is represented by two species distributed in two genera: Dermatobia hominis (Linnaeus Jr.) and Cuterebra rufiventris Macquart.
Deciphering the Role of LRH-1 in Liver Intermediary Metabolism and Cancer

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer death worldwide. Gaining insight into the molecular pathways involved in the development of HCC is hence a prerequisite to design and develop novel and effective therapeutic strategies. Metabolic reprogramming is a universal feature of tumor cells and is characterized by increased glycolysis and diminished oxidative phosphorylation, a phenomenon known as the Warburg effect. More recently, it has become evident that tumor cells heavily rely on gluta-mine metabolism to compensate for the Warburg effect and to replenish the tricarboxylic acid (TCA) cycle. However, the molecular mechanisms by which glutamine supports tumor cell metabolism remain largely unexplored. In this thesis, I have established the role of the nuclear receptor LRH-1 as a key regulator in the process of hepatic tumorigenesis. I observed that LRH-1 promotes DEN-induced hepatocellular carcinogenesis (HCC). I demonstrated that LRH-1 facilitates the production of NADPH from glutamine by favoring a non-canonical glutamine pathway that optimizes reductive biosynthesis. Importantly, chronic and acute disrup-tion of LRH-1 also impaired glutamine-induced anaplerosis and I±-KG availability, ultimately leading to im-paired mTORC1 signaling to block cell proliferation. Moreover, LRH-1 also coordinates glutamine-dependent asparagine synthesis to protect tumor cell from apoptosis induced by glutamine depletion itself. As a result, gain-of-function of LRH-1 sustained aspar-agine homeostasis upon glutamine-deprivation to promote cell survival. Collectively, these studies unveiled an unexpected role of LRH-1 in cancer intermediary metabolism, and warranted further studies on pharma-cological inhibition of LRH-1 to interfere with hepatocellular carcinogenesis.
Construction and validation of Escherichia coli mutants to improve the curcumin production by an engineered strain

vii Resumo. ix Scientific Output . xi List of Figures . xv List of Tables . xvii Abbreviations . xix Scope . xxi 1. State-of-the-art . 1 1.1 Curcuminoids . 1 1.1.1 Curcuminoids relevance and therapeutic use . 1 1.1.2 Cancer and bacterial therapies . 2 1.1. 3 Biosynthetic pathway of curcuminoids in Curcuma longa . 4 1.2 Heterologous production of curcumin . 6 1.2. 1 Possible hosts – advantages and drawbacks . 7 1.2. 2 Curcumin production in Escherichia coli . 9 1.2. 3 Optimization of curcumin production . 12 2. Objectives. 17 3. Materials and Methods . 19 3.1 Strains and plasmids . 19 3.2 Chemicals and culture media . 19 3.3 Preparation of electrocompetent cells and transformation step . 21 3.4 Preparation of chemical competent cells and transformation step . 21 3.5 Optimization of curcumin production in E. coli using an artificial biosynthetic pathway . 22 3.5. 1 Curcumin production . 22 3.5. 2 Curcumin extraction and samples preparation . 24 3.5. 3 Substrate and product quantification by HPLC . 24 3.6 Curcumin toxicity assay . 25 3.7 Gene deletion in E. coli . 26
Quantitative Risk Assessment of Vibrio parahaemolyticus in Mytilus edulis in China

The objective of this study was to conduct Vibrio parahaemolyticus risk assessment associated with the consumption of Mytilus edulis among the people of Zhejiang Province, China. It was based on the quantitative risk assessment framework developed by the Codex Alimentarius Commission. In order to calculate the quantitative risk assessment, the data generated in this study as well as data gathered from other reports were taken into account. The exposure assessment of Vp was conducted with estimation of its density in Mytilus edulis by using Monte Carlo simulation and considering cooking and consumption modes. The Matlab software package, version 7.10. 0.499 (R2010a) in combination with Microsoft-Excel was used to run the Monte Carlo simulations. We found that the probability of illness for people eating Mytilus edulis per meal was 8.4×10, which means the incidence rate of illness/10,000,000 population/year is 8.4 if each person eats 10 meals of Mytilus edulis in summer.