Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-scale population structure of two anemones (Stichodactyla gigantea and Heteractis magnifica) in Kimbe Bay, Papua New Guinea

Fine-scale population structure of two anemones (Stichodactyla gigantea and Heteractis magnifica) in Kimbe Bay, Papua New Guinea. Anemonefish are one of the main groups that have been used over the last decade to empirically measure larval dispersal and connectivity in coral reef populations. A few species of anemones are integral to the life history of these fish, as well as other obligate symbionts, yet the biology and population structure of these anemones remains poorly understood. The aim of this study was to measure the genetic structure of these anemones within and between two reefs in order to assess their reproductive mode and dispersal potential. To do this, we sampled almost exhaustively two anemones species (Stichodactyla gigantea and Heteractis magnifica) at two small islands in Kimbe Bay (Papua New Guinea) separated by approximately 25 km. Both the host anemones and the anemonefish are heavily targeted for the aquarium trade, in addition to the populations being affected by bleaching pressures (Hill and Scott 2012; Hobbs et al. 2013; SaenzAgudelo et al. 2011; Thomas et al. 2014), therefore understanding their biology is crucial for better management strategies. Panels of microsatellite markers were developed for each species using next generation sequencing tools. Clonality analyses confirm six pairs of identical genotypes for S. gigantea (n=350) and zero for H. magnifica (n=128), indicating presence/absence of asexual reproduction in this region. S. gigantea showed low structure between islands (FST= 0.003, p-value= 0.000), however, even if the majority of the individuals were unrelated (r~0), 81 families that shared 50% of their genetic material formed from two to four members were found. Out of these families,
HIV-1 R5 Tropism: Determinants, Macrophages, and Dendritic Cells: A Dissertation

Around thirty years ago HIV-1 was identified, and from that point the known epidemic has grown to over 30 million infected individuals. Early on in the course of HIV-1 research, viruses were classified as either syncytia inducing, CXCR4-using, T-cell tropic or non-syncytia inducing, CCR5-using, macrophage tropic. Since that time, several groups have shown that this is an oversimplification. There is a great deal of diversity amongst CCR5-using HIV-1 variants. There remains a great deal to be discovered regarding HIV-1 CCR5-tropism and how this affects other aspects of HIV-1 infection. The CD4 binding site (CD4bs) on the HIV-1 envelope plays a major role in determining the capacity of R5 viruses to infect primary macrophages. Thus, envelope determinants within or proximal to the CD4bs have been shown to control the use of low CD4 levels on macrophages for infection. These residues affect the affinity for CD4 either directly or indirectly by altering the exposure of CD4 contact residues. In this thesis, a single amino acid determinant is described in the V1 loop that also modulates macrophage tropism. I identified an E153G substitution that conferred high levels of macrophage infectivity for several heterologous R5 envelopes, while the reciprocal G153E substitution abrogated infection. Shifts in macrophage tropism were associated with dramatic shifts in sensitivity to the V3 loop monoclonal antibody (MAb), 447-52D and soluble CD4, as well as more modest changes in sensitivity to the CD4bs MAb, b12. These observations are consistent with an altered conformation or exposure of the V3 loop that enables the envelope to use low CD4 levels for infection. The modest shifts in b12 sensitivity suggest that residue 153 impacts on the exposure of the CD4bs. However, the more intense shifts in sCD4 sensitivity suggest additional mechanisms that likely include an increased ability of the envelope to undergo conformational changes following binding to suboptimal levels of cell surface CD4. In summary, a conserved determinant in the V1 loop modulates the V3 loop to prime low CD4 use and macrophage infection. In addition to determinants, this thesis seeks to evaluate the roles of macrophage tropic and non-macrophage tropic envelopes during the course of infection. Non-macrophage tropic virus predominates in immune tissue throughout infection, even in individuals suffering from HIV-associated dementia (HAD) who are known to carry many macrophage tropic viruses. There must be some advantage for these non-macrophage tropic viruses allowing them to persist in immune tissue throughout the disease. This thesis demonstrates that there is no advantage for these viruses to directly infect CD4+ T-cells, nor is there an advantage for them to be preferentially transmitted by dendritic cells to CD4+ T-cells. Given that transmitted/founder (T/F) viruses may preferentially interact with α4β7, and T/F viruses are non-macrophage tropic, I tested whether non-mac viruses could utilize α4β7 to their advantage. These experiments show that…
Functional analysis of ATP binding cassette (ABC) transporters in Caenorhabditis Elegans

This thesis deals with functional analysis of ABC transporter genes in Caenorhabditis elegans. ABC transporters constitute one of the largest gene families in C. elegans. Sixty ABC genes have been identified and classified into eight different subfamilies. Fifty-seven orthologous pairs can be found between C. elegans and C. briggsae. As an initial step toward understanding the functions of the ABC genes, I generated transgenic animals containing prornoter::GFP/DsRed fusion constructs for the whole family in order to address when and where these genes are turned on in vivo. I observed frequent expression of ABC genes in intestine, pharynx and excretory cell, especially for those in subfamilies B and C. Sixteen of the 60 ABC genes are tandemly duplicated genes, forming two 4-gene and four 2-gene clusters. Interestingly, the majority of the promoters from the same clusters drive temporally andfor spatially differential expressions, suggesting active function of these duplicated genes in different tissues or stages rather than their being inactivated, as is typical for duplicated genes. Currently 18 single ABC gene mutants have been created. All of them are wild type under normal laboratory conditions. I used one of the ABC genes, pgp-12, an excretory cell-expressing gene, to characterize its transcriptional regulation. A 10 base pair (bp) cis-element, Ex-1 and its binding protein C26C6.5a, were isolated. C26C6.5a is also expressed in the excretory cell and binds Ex-l in vitro. RNAi analysis revealed that the C26C6.5a protein functions as a trans-activator for excretory cell specific expression. The only member of subfamily E is the ABCE gene that has been annotated as an RNase L inhibitor. This annotation is unlikely to be correct because of the lack of the inhibitor gene in C. elegans. Functional analysis of the gene reveals that it is essential for life, possibly involved in transcription and translation, and may function as a nucleocytoplasrnic transporter. RNAi data implies that the protein functions in both germline and vulvae. I woul;ili&e to dedicate this thesir to my daughter, Sarah F. zhao, w h o has 6een the comfort of her mamma a n d the joy of herfather.
Nomenclatural changes and new species in Platypodidae and Scolytidae (Coleoptera), Part II.

— New names are presented to replace junior homonyms as follows in Platypodidae: Platypus acuticornifer for Platypus acuticornis Schedl, 1975 (nee Schedl, 1973), Platypus tuberculifer for Platypus bituberciilatus Schedl, 1975 (nee Nunberg, 1967), Platypus obliquus for Platypus obliquesectus Schedl, 1975 (nee Schedl, 1973); and in Scolytidae: Amphicranus electus for Amphicranus elegantulus Schedl, 1978 (nee Schedl, 1963), Araptus crassulus for Araptus crassus Wood (nee Schedl, 1966), Corthycyclon tardulus for Corthycyclon tardus Schedl, 1976 (nee Wood, 1974), Corthylus brunnescens for Corthylus brunneus Wood, December 1974 (nee Schedl, November 1974), Monarthrum denticulatum for Monarthrum { = Pterocyclon) dentatttm Eggers, 1941 (nee Eggers, 1935), Monarthrum peruvianum for Monarthrum peruanum Schedl, 1978 (nee Schedl, 1950), Scolytodes exitnius for Scolytodes grandis Schedl, 1978 (nee Schedl, 1962), Scolytodes minutus for Scolytodes { = Hexacolus) minutissimus Schedl, 1978 (nee Schedl, 1952). New synonymy is proposed in Platypodidae for Genyocerus albipennis Motschulsky (=^Diacavus irregularis Browne). The emendation in Scolytidae of Cnemonyx vismiacolens is presented to correct the lapsis calami Cnemonyx visimiacolens Wood, 1979. The following species of Scolytidae are named as new to science: Chramesus atkinsoni, Liparthrum thevetiae, Microborus mexicanus, Phloeocleptus ardis, Phloeocleptus atkinsoni, Phloecleptus cristatus, Phloeocleptus spicatus, Pseudothysanoes perseae (Mexico), Scolytodes anceps, Scolytodes pusillimus, Scolytodes tardus, Scolytodes vesculus (Colombia), Scolytodes ficicolens, Scolytodes naevius (Venezuela). While updating my taxonomic files of bark and ambrosia beetles, I found several homonyms that require new names and a few other taxonomic and nomenclatural errors that require correction. These are summarized in the above abstract. In addition, 14 species of Scolytidae are described as new to science. These are presented in alphabetical order and represent the genera Chramesus (1), Liparthrum (1), Microborus (1), Phloeocleptus (4), Pseudothysanoes (1), and Scolytodes (6) and are from the following countries: Mexico (8), Colombia (4), and Venezuela (2). New Names in Platypodidae Platypus acuticornifer, n. n. Platypus acuticornis Schedl, 1975, Reichenbachia 15:223 (Holotype, male; Luth. Miss. Sawmill, Porotop, Papua; Schedl Coll.). Preoccupied The name Platypus acuticornis Schedl, 1975, is preoccupied by Schedl, 1973 (Papua New Guinea Agric. J. 24:77), and must be replaced. The new name acuticornifer is proposed as a replacement. Platypus bituberculifer, n. n. Platypus bituberculatus Schedl, 1975, Reichenbachia 15:224 (Holotype, male; Wau, Morobe Distr., New Guinea; Schedl Coll.). Preoccupied The name Platypus bituberculatus Schedl, 1975, is preoccupied by Nunberg, 1967 (Rev. Zool. Bot. Afr. 76:325), and must be replaced. The new name bituberculifer is proposed as a
Comparison of genomes of African swine fever virus isolates from Cameroon, other african countries and Europe

Une comparaison des cartes de restriction enzymatique des genomes d'isolats de virus de la peste porcine africaine (ppa) provenant du Cameroun, d'autres pays africains et d'Europe a montre que les souches du Cameroun et d'Europe etaient apparentees, a l'exception du virus Lisbon/57 dont la region terminale gauche du genome etait plus longue. Par ailleurs, les genomes d'isolats d'Angola, de la Republique democratique du Congo (Rdc) et du Senegal etaient semblables a ceux du Cameroun et de l'Europe. Cependant, ceux d'Angola et du Katanga, en Rdc, avaient une longue region terminale gauche semblable a celle du Lisbon/57. Les souches d'Afrique de l'Est et du Sud-Est etaient genetiquement differentes de celles du Cameroun et d'Europe et differaient aussi entre elles. La comparaison des cartes de restriction obtenues par digestion de virus du Cameroun et d'Europe avec l'enzyme BamH1 a montre des differences de la taille du fragment BamHI-L qui est localise au milieu du genome, alors qu'en comparant les isolats provenant du Cameroun, d'Afrique de l'Ouest et du Sud-Ouest les differences observees etaient situees au centre et aux extremites du genome. Malgre ces petites variantes entre les genomes d'isolats de virus de la ppa provenant du Cameroun, d'Europe, d'Afrique de l'Ouest et du Sud-Ouest, on peut considerer qu'ils appartiennent au meme groupe etant donne la grande ressemblance entre les cartes de restriction enzymatique de leurs genomes. Les resultats de cette etude ont egalement montre que les foyers recurrents de la ppa chez les populations porcines domestiques du Cameroun pouvaient etre dus a la reintroduction de souches apparentees du virus a partir des zones infectees situees hors du pays.
Two-minute miniprep method for plasmid DNA isolation.

: An extremely rapid method, INSTA-PREP, has been developed to prepare plasmid DNA from 1 to 3 mL miniprep Escherichia coli bacterial cultures. Direct extraction of plasmid DNA from E. coli bacterial cells is achieved by a two-phase solution consisting of phenol-chloroform-isoamyl alcohol and water or buffer with efficient separation of the phases by centrifugation in the presence of the INSTA-PREP gel barrier material. Processing time, from E. coli culture to usable plasmid DNA, is two minutes or less per sample. Supercoiled plasmid DNA yields ranged from 3 to 10 micrograms per mL of culture depending on plasmid copy number. Plasmid DNAs prepared by INSTA-PREP were analyzed and are suitable for use in molecular biology procedures including restriction digestion, ligation with T4 DNA ligase, bacterial transformation, PCR, cultured cell transfection and T7 DNA polymerase or thermostable DNA polymerase-mediated dideoxynucleotide sequencing.
Culture medium, BAP and NAA on in vitro multiplication of Eucalyptus globulus Labill clone.

Given the lack of studies involving the micropropagation of Eucalyptus globulus with purpose of rejuvenation, the present study aimed to evaluate the in vitro multiplication of axillary buds of E. globulus under the interaction of different culture media (WPM, JADS and MS) and BAP (0; 0.50 and 1.0 mg L-1) and NAA (0; 0.050 and 0.100 mg L-1) concentrations. After 84 days, we evaluated the number of buds per explant. The results showed that in vitro multiplication of E. globulus buds is a process highly regulated by media composition and concentration of the plant growth regulator. In general, the best results, as the proliferation of axillaries buds, were obtained in WPM culture media supplemented with 0.7 mg L-1 BAP and 0.05 mg L-1 NAA. In addition, there were variations among genotypes.
LPS induces GROa chemokine production via NF-jB in oral fibroblasts

Objective and design Chemotaxis of neutrophils from blood to the inflammation process plays an important role in development of periodontal inflammation. The novel chemokine GROa, also named CXCL1, is a strong chemoattractant for neutrophils. Data on production and regulation of GROa by oral fibroblasts have not previously been presented. Materials and methods GROa mRNA and protein levels were determined in human periodontal ligament cells and mouse gingival fibroblasts by quantitative real-time PCR and ELISA. Results We disclose that both human periodontal ligament cells and mouse gingival fibroblasts produce GROa in response to LPS stimulation. Stimulation with LPS for 24 h increased both mRNA for GROa and GROa protein. The steroid hormone estrogen had no effect on LPS-induced GROa mRNA expression. Treatment with the glucocorticoid dexamethasone attenuated LPS-induced GROa production, and the NF-jB blocker MG 132 fully prevented LPS-induced GROa. Conclusions Oral fibroblasts respond to LPS stimulation by increasing GROa production via the transcription factor NF-jB, suggesting that this mechanism may be involved in development of periodontal inflammation.
PERPEST Version 1.0, manual and technical description; a model that predicts the ecological risks of pesticides in freshwater ecosystems

This report is a technical description and a user-manual of the PERPEST model, able to Predicts the Ecological Risks of PESTicides in freshwater ecosystems. This system predicts the effects of a particular concentration of a pesticide on various (community) endpoints, based on empirical data extracted from the literature. The method that it uses solves new problems (e.g., what is the effect of pesticide A? ) by using past experience (e.g., published microcosm experiments). The database containing the `past experience` has been constructed by performing a review of freshwater model ecosystem studies evaluating the effects of pesticides. The PERPEST model searches for situations in the database which resemble the question case, based on relevant (toxicity) characteristics of the compound.The model is described in the scientific paper written by Van den Brink et al. (2002) and available via the enclosed CD-ROM and the website www.perpest. alterra.nl.
Assessing the role of Hsp70 in prion propagation in Saccharomyces cerevisiae

The term Prion (Proteinaceous infectious) was first described by Stanley Prusiner in 1982. Prions are infectious proteins and are responsible for many neurodegenerative diseases, collectively termed as transmissible spongioform encephalopathies, including; BSE, vBSE, scrapie and CJD. Prions are also present in fungi. There have been a number of prion proteins discovered in the yeast Saccharomyces cerevisiae. Probably the most studied of these is the [PSI+], which is the prion form of the protein Sup35, which is required for the release of nascent polypeptide chains from the ribosome during translation termination. Studies indicate that the de novo formation and propagation of yeast prions require the function of protein chaperones and co-chaperones. The heat shock proteins (HSP) such as Hsp40, Hsp70 and Hsp104, are essential for prion propagation in yeast. Hsp70 is a highly conserved protein composed of an N-terminal ATPase domain, a peptide-binding domain (PBD) and a C-terminal domain. In this study we describe a genetic screen that identifies an array of mutants within different domains of the major cytosolic Hsp70 chaperones of yeast, Ssa1-4 which impair the propagation of [PSI+]. A majority of isolated mutants are located within the ATPase domain and have no significant affect on Hsp70 function. The PBD mutant Ssa1F475S, which impairs [PSI+] propagation also appears to make Ssa1 non-functional and may implicate Ssa1 in an array of cellular functions. We also highlight differences between the Hsp70 cytosolic Ssa family members with respect to prion propagation and Hsp70 function.
Daily-life training and monitoring methodologies for chronic obstructive pulmonary disease patients

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
THE TECHNIQUE FOR ORDER OF PREFERENCE BY SIMILARITY TO IDEAL SOLUTION (TOPSIS) UNTUK PENENTUAN PENERIMA BEASISWA

TOPSIS menggunakan prinsip bahwa alternatif yang terpilih harus mempunyai jarak terdekat dari solusi ideal positif dan jarak terpanjang (terjauh) dari solusi ideal negatif dari sudut pandang geometris dengan menggunakan jarak euclidean (jarak antara dua titik) untuk menentukan kedekatan relatif dari suatu alternatif dengan solusi optimal. Pada makalah ini dijelaskan tentang menggunakan TOPSIS untuk menentukan penerima beasiswa.
Formation of Threonine Aldolase by Bacteria and Yeasts

Threonine aldolase was found to be formed in various strains of bacteria and yeasts when they were grown in media containing l-threonine as a sole source of carbon. As the other sources of carbon, d, l-allothreonine, l-serine and glycine were effective but glucose and sucrose were inert for the formation of the enzyme.The maximal formation of the enzyme was observed in the initial of stationary phase of growth and, thereafter, the enzyme disappeared with the consumption of l-threonine. It seems that the enzyme is adaptive in nature and that it is responsible for the growth in threonine as the carbon source.
Strategies for the expansion and directed differentiation of stem cells

Alternative Sources of Adult Stem Cells: Human Amniotic Membrane, by S. Wolbank, M. van Griensven, R. Grillari-Voglauer, and A. Peterbauer-Scherb Mesenchymal Stromal Cells Derived from Human Umbilical Cord Tissues: Primitive Cells with Potential for Clinical and Tissue Engineering Applications, by P. Moretti, T. Hatlapatka, D. Marten, A. Lavrentieva, I. Majore, R. Hass and C. Kasper Isolation, Characterization, Differentiation, and Application of Adipose-Derived Stem Cells, by J. W. Kuhbier, B. Weyand, C. Radtke, P. M. Vogt, C. Kasper and K. Reimers Induced Pluripotent Stem Cells: Characteristics and Perspectives, by T. Cantz and U. Martin Induced Pluripotent Stem Cell Technology in Regenerative Medicine and Biology, by D. Pei, J. Xu, Q. Zhuang, H. -F. Tse and M. A. Esteban Production Process for Stem Cell Based Therapeutic Implants: Expansion of the Production Cell Line and Cultivation of Encapsulated Cells, by C. Weber, S. Pohl, R. Poertner, P. Pino-Grace, D. Freimark, C. Wallrapp, P. Geigle and P. Czermak Cartilage Engineering from Mesenchymal Stem Cells, by C. Goepfert, A. Slobodianski, A.F. Schilling, P. Adamietz and R. Poertner Outgrowth Endothelial Cells: Sources, Characteristics and Potential Applications in Tissue Engineering and Regenerative Medicine, by S. Fuchs, E. Dohle, M. Kolbe, C. J. Kirkpatrick Basic Science and Clinical Application of Stem Cells in Veterinary Medicine, by I. Ribitsch, J. Burk, U. Delling, C. Geissler, C. Gittel, H. Julke, W. Brehm Bone Marrow Stem Cells in Clinical 4 Application: Harnessing Paracrine Roles 5 and Niche Mechanisms 6, by R. M. El Backly, R. Cancedda Clinical Application of Stem Cells 4 in the Cardiovascular System 5, C. Stamm, K. Klose, Y. -H. Choi
Web Based Screening for Depression in the Workplace

Aims: The aim of this study was to examine an effective screening method of depressive disorders in the workplace. Methodology: Employees with a managerial career track of a large size company completed a web-based psychological assessment using the Patient Health Questionnaire depression scale (PHQ-9) and the Generalized Anxiety Disorder Scale (GAD-7) at the first screening. After three months, employees who had a PHQ-9 score of 10 or greater were further re-assessed using the PHQ-9 and GAD-7 at the second screening. They were then interviewed using the Mini International Neuropsychiatric Interview (MINI) to determine a clinical diagnosis of depressive disorders. Moreover, analysis of the validity of the PHQ-9 categorical algorithm and the cut-off score of PHQ-9 ≥ 10 were conducted. Results: Of the 402 participants, 350 employees completed the depression and anxiety scales. Though 20 subjects had a score of 10 points or more on the PHQ-9 score at the first screening, Original Research Article Isoda et al.; BJMMR, 15(6): 1-10, 2016; Article no.BJMMR. 25311 2 and nine of them maintained a score of 10 points or more at the second screening. While nine subjects were diagnosed with a major depressive syndrome by the PHQ-9 categorical algorithm at the first screening, only three of them remained with a major depressive syndrome at the second screening. Conclusion: Considering the spontaneous remission rate of depression, it seems reasonable to conduct double web-based screening for major depressive disorders in the workplace.