Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of methods for stable isotope ratio (δ13C, δ15N, δ2H, δ18O) measurements of feathers

Natural variations in the stable isotope ratios of bioelements in bird feathers are being increasingly used by animal ecologists to investigate different aspects of bird life. However, to ensure reliability of the data, a critical and very delicate aspect is the preparatory phase (cleaning, drying and subsampling) and the proper analysis, mainly in relation to δ2H and δ18O, respectively, for the presence of exchangeable Hs and of nitrogen and sulphur in keratin. With respect to determination of the isotope ratios of C, N, O and H, in this work, we compare the cleaning mixture most commonly used in the literature (chloroform : methanol 2 : 1) with diethylether : methanol 2 : 1, which avoids the use of the carcinogenic solvent chloroform. We also compared oven‐drying with air‐drying of samples, as well as subsampling of feathers by cutting with surgical scissors or cryogenic pulverization. Finally, we investigated whether stable isotope ratios varied along the vane and between the rachis and vane. The different methods compared in the three preparatory stages showed no differences performance‐wise and can therefore be used interchangeably. Variability in stable isotope ratios can be considerable, both along the vane and between rachis and vane, which is because their compositions register changes in diet, area and climate. However, in this specific study, when the parts of the feather closest to the calamus were removed, the delta values were clearly more homogeneous. Finally, we demonstrate that a casein with a known δ2H value, although probably differing from keratin in the number of exchangeable Hs, can be used to normalize the δ2H values of feathers, although only in the range of values close to that of the reference material. In determining δ18O, the use of a longer gas chromatography‐GC column, its frequent change and the use of a linear equation built with matrix match equivalent reference materials seems to reduce the drift of GC column performance due to the presence of nitrogen and the accumulation of sulphur.
Riboswitches : le cas des atténuateurs de la transcription du type terminateur/antiterminateur chez les bactéries

It is essential for each organism to have the possibility to regulate its functions to allow its survival and improve its capacity to reproduce in different environments. With the information available, it is apparent that most organisms dedicate an important piece of their genetic material to regulating functions. We could think that certain regulating mechanisms have most likely persisted over time because they fulfilled their roles. The first prokaryotes studies indicated that there are few regulating mechanisms that take control over genes, but it has been proven that a variety of these mechanisms are used in the regulation of genes and operons. In particular, the bacterial operons involved in the biosynthesis of amino acids, tRNA synthetase, the degradation of amino acids, the ribosomal proteins and RNA ribosomal could be controlled by transcription attenuation. This mechanism of regulation differs from others for the creation of two different structures of the mRNA where one of these structures represses the gene in 3’ and the other one allows the transcription/translation to continue. In this work, I’m interested in the mechanism of transcription attenuation in prokaryotes where no molecule appears to act as a regulatory factor. In particular, I’m interested in the regulation of bacterial operons. The principal goal of this work is to present a new method for detecting riboswitches that combines the traditional research of these elements with the structural research by incorporating the study of mRNA folding.
DETERMINAN TINGKAT PENGUNGKAPAN LAPORAN KEUANGAN PEMERINTAH DAERAH (Studi Kasus pada LKPD Kabupaten/Kota di Provinsi Jawa Tengah Tahun Anggaran 2014-2016)

ABSTRAK Penelitian ini bertujuan untuk menguji pengaruh pendapatan asli daerah, jumlah satuan kerja perangkat daerah, ukuran pemerintah daerah, rasio kemandirian, umur pemerintah daerah, ukuran legislatif, dan intergovernmental revenue terhadap tingkat pengungkapan LKPD Kabupaten/ Kota di Provinsi Jawa Tengah. Populasi penelitian ini adalah Kabupaten/ Kota di Provinsi Jawa Tengah selama tahun anggaran 2014- 2016 yang telah di audit oleh BPK. Sampel yang digunakan sebanyak 105 laporan keuangan pemerintah daerah adalah semua populasi dijadikan sampel. Metode analisis data dalam penelitian ini menggunakan analisis regresi linear berganda dengan program SPSS 19. Hasil penelitian menunjukkan bahwa pendapatan asli daerah berpengaruh positif signifikan terhadap tingkat pengungkapan LKPD. Rasio kemandirian dan jumlah satuan kerja perangkat daerah berpengaruh negatif signifikan terhadap tingkat pengungkapan LKPD. Sedangkan ukuran pemerintah daerah, umur pemerintah daerah, ukuran legislatif dan intergovernmental revenue tidak berpengaruh terhadap tingkat pengungkapan LKPD. Kata kunci : Tingkat Pengungkapan LKPD, Pendapatan Asli Daerah, Ukuran Pemerintah Daerah, Rasio Kemandirian, Umur Pemerintah Daerah, Ukuran Legislatif, dan Intergovernmental Revenue.
LATERAL PLATE VARIATION IN GALICIAN STICKLEBACK POPULATIONS IN THE RIVERS MIÑO AND LIMIA, NW SPAIN

We examined lateral plate variation in populations of stickleback, Gasterosteus aculeatus, from the rivers Mino and Limia in Galicia (Northwest Spain), by analysing morphs, number of lateral plates, and position of the plates. In order to test for sexual dimorphism, the means and variances of plates were compared in males and females of some populations. No significant differences were found between sexes, therefore all remaining populations were analysed without controlling for sex. As stickleback populations in Galicia have an annual life span, the populations from the river Mino were divided in two age groups to compare lateral plate number. Analysis of each group revealed significant differences among populations, in accordance with the large amount of variation found in populations from other regions. Analysis of samples collected from the same place and at the same time of year, but in different years, indicated that there was little year to year variation. This suggests that populations are well adapted to their habitat, or that environmental conditions did not change significantly during the period of sampling. Finally, we propose a new method for the evaluation of scute variation analysis of the position of lateral plates. Cluster analysis of our data clearly differentiated populations from the rivers Mino and Limia.
253 Bovine oocyte cyclin B1 MRNA undergoes cytoplasmicpolyadenylation before the beginning of in vitro maturation

Maternal oocyte Cyclin B1 mRNA is known to be stored in the cytoplasm with a short poly(A) tail and be translationally dormant at GV stage. During maturation, Cyclin B1 poly(A) tail is elongated by a process called cytoplasmic polyadenylation and driven by A/U-rich cis-acting elements in its 3′ untranslated region (UTR) known as cytoplasmic polyadenylation elements (CPEs). The objective of this study was to elucidate whether GV-stage bovine oocytes possess a stockpile of Cyclin B1 mRNA stored with a short a poly(A) tail that is elongated during maturation by CPE regulation. The mRNA poly(A) tail length was measured by Rapid Amplification of cDNA Ends Polyadenylation test (Race-PAT) on oocytes (n = 100) at the GV stage and 3, 5, 8, 10, 15, 20, and 25 h of in vitro maturation. The mRNA poly(A) tail length was also measured in triplicate (n = 20) on cold oocytes in GV (all manipulations on ice), warm oocytes in GV (ovaries transported in warm saline and manipulations on ice) and warm + 2 h 30 min oocytes in GV (oocytes left for an additional 2 h and 30 min at room temperature). To assess for variation in mRNA quantity, Cyclin B1 mRNA level was quantified by real-time PCR (Lightcycler, Roche, Indianapolis, IN, USA) in cold, warm or warm + 2 h 30 min GV oocytes (n = 20). The data were treated as factorial design, using treatment and type of RT as factors, and analysed by ANOVA (SAS Inst., Cary, NC, USA). Differences between means were checked using Tukey’s test. Oocyte Cyclin B1 transcript show two different 3′ UTRs. These transcripts had the same ORF but different 3′ UTR lengths because of an alternative nuclear polyadenylation element AAUAAA (NPE). The longest form (Cyclin B1L) that possessed a putative CPE (UUUUAAUAAA) fused to the last NPE was studied. In warm GV oocytes, Cyclin B1L had a long poly(A) tail of 100 adenosine residues, and this length did not change during in vitro maturation. Interestingly, we found that Cyclin B1L showed an expected short poly(A) tail when the ovaries and the oocytes were transported and manipulated on ice. We showed that Cyclin B1L mRNA is cytoplasmically polyadenylated (addition of 75 adenosine residues) between the time of collection and the end of manipulation. This lengthening is most probably sufficient to promote translation. There was no significant difference between the Cyclin B1 mRNA quantity of cold oocytes or warm oocytes when the oligo used for the reverse transcription was either dt or decamers. Therefore, we believe that the increase in poly(A) tail length is not the result of Cyclin B1L mRNA degradation in cold oocytes or de novo transcription in warm oocytes. We report for the first time that Cyclin B1L cytoplasmic polyadenylation is carried out well before the beginning of in vitro maturation in bovine oocytes when ovaries are transported from the slaughterhouse in warm saline. Studying the real early mechanisms leading to resumption of meiosis in bovine oocytes is complicated by Cyclin B1 polyadenylation occurring prior to in vitro maturation. (Supported by NSERC.)
ONe WD+He star systems as the progenitors of IMBPs

Abstract Previous theoretical studies can only explain part of the observed intermediate-mass binary pulsars (IMBPs) with short orbital periods. Note that an ONe white dwarf (WD) accreting mass from a He star may experience the accretion-induced collapse process and eventually form IMBPs, known as the ONe WD+He star scenario. By investigating the evolution of a large number of ONe WD+He star binaries, we found that the ONe WD+He star scenario can form IMBPs including pulsars with 5 – 340 ms spin periods, and the orbital periods range from 0.04 to 900 d. Compared with the observed IMBPs, this scenario can cover almost all of the IMBPs with short orbital periods. Thus, we suggest that the ONe WD+He star channel is responsible for the formation of IMBPs with short orbital periods.
Assessment of Introduction Pathway for Novel Avian Influenza Virus into North America by Wild Birds from Eurasia

A critical question surrounding emergence of novel strains of avian influenza viruses (AIV) is the ability for wild migratory birds to translocate a complete (unreassorted whole genome) AIV intercontinentally. Virus translocation via migratory birds is suspected in outbreaks of highly pathogenic strain A(H5N1) in Asia, Africa, and Europe. As a result, the potential intercontinental translocation of newly emerging AIV (e.g. A(H7N9) from Eurasia to North America via migratory movements of birds) remains a concern. An estimated 1.48 to 2.91 million aquatic birds, principally Anseriformes (ducks, geese, and swans) and Charadriiformes (gulls, terns, and shorebirds) move annually between Eurasia and North America. AIV prevalence in Alaskan waterfowl populations shared between Eurasia and North America has been reported to range from <0.1 to 32.2 percent. Here we present an assessment to address the likelihood of whole (unreassorted) genome translocation of Eurasian strain AIV into North America. The scope of this assessment was limited specifically to assess the weight of evidence to support the movement of an unreassorted AIV intercontinentally by migratory aquatic birds. We reviewed high impact scientific publications to assess the evidence related to intercontinental movement of avian influenzas by aquatic birds, specifically between Eurasia and North America. In addition, we reviewed the available information for bird populations and movements (migratory and other) between North America and all other continents. We then identified common factors described across the publications related to the pathway of introduction of a novel AIV intercontinentally into North America. In our assessment of the scientific published literature, there appear to be at least four factors that may contribute to the potential for introduction of a specific AIV intercontinentally into North America by wild birds. These factors, in aggregate, may provide a framework for evaluating the likelihood of new forms of AIV from Eurasia to be introduced through aquatic birds and become established in North America.
ESTUDIO DE POTENCIA DE PRUEBAS DE NORMALIDAD USANDO DISTRIBUCIONES DESCONOCIDAS CON DISTINTOS NIVELES DE NO NORMALIDAD

La mayoría de pruebas de hipótesis paramétricas están sujetas al cumplimiento de normalidad. Debido a la gran variedad de opciones para contrastar este supuesto, se considera como mejor alternativa el test que presente una mayor potencia. Investigaciones preliminares estiman este valor a partir de muestras provenientes de distribuciones no normales conocidas pero cuyo alejamiento o contaminación respecto a la normalidad se desconoce. En el presente estudio seleccionamos siete pruebas que además de ser las más comunes parecen ser las mejores. Mediante un proceso de simulación, estimamos la potencia de cada una de ellas usando muestras provenientes de distribuciones desconocidas, pero con un alejamiento medible de la normalidad. Parece ser que el test de Shapiro – Wilk es la mejor opción, su potencia es muy elevada, pero solo para muestras no normales grandes y alejamientos fuertes. Para distribuciones con alejamientos débiles y muestras pequeñas parece ser que ninguna de las pruebas tradicionales en estudio es buena. Se discute un posible mal planteamiento de estos test y su incidencia en los resultados obtenidos. Finalmente se introduce la posibilidad de incluir pruebas basadas en el enfoque de equivalencia, las cuales quizás podrían resultar mejores que las pruebas estudiadas.
CONTROLLED MILK FAT DEPRESSION AS A MANAGEMENT TOOL TO IMPROVE ENERGY BALANCE IN LACTATING DAIRY CATTLE

Research conducted for this dissertation had three goals; 1) determine if CLA can induce milk fat depression immediately postpartum, 2) determine if CLA can alter energy availability, 3) determine the mechanism behind the mammary gland’s decreased sensitivity to CLA immediately postpartum. The first study provides strong evidence indicating CLA can decrease milk fat synthesis immediately postpartum, but the dose required is approximately 3x greater than in established lactation. This trial also provided evidence that CLA can alter energy status, as CLA decreased days to EBAL nadir by nearly 5 days. This is relevant as recovery of EBAL from its lowest point provides an important signal for initiating ovarian activity and days to nadir is highly correlated with days to first ovulation. Study two was designed to determine if CLA induced milk fat depression could improve energy status during heat stress. Rumen-inert CLA reduced milk fat synthesis, and was able to improve energy availability, but did not increase milk yield or yield of other milk components. Although production was unchanged in this study, the study did provide further evidence that rumeninert CLA can alter energy availability. Study three utilized intravenous infusion of CLA in cows in mid and early lactation to determine the mechanism for the mammary gland’s decreased sensitivity in early lactation. It is postulated that increased fatty acid oxidation and subsequent enhanced levels of circulating NEFA present during the transition period competitively prevent adequate CLA uptake by the mammary gland. In the current study, trans-10, cis-12 CLA
INHIBITION OF NON-PRIMATE LENTIVIRUSES BY APOBEC3 CYTIDINE DEAMINASE

APOBEC3 (apolipoprotein B mRNA editing catalytic polypeptide 3 [A3]) proteins are an element of the intrinsic immunity of modern mammalia against retroviruses. The evolution of the A3 genes is characterized by an adaptive selection and a taxon-specific expansion and/or extinction. All A3 genes consist either of one zinc (Z)-coordinating domain (Z1, Z2 or Z3) or two Z-domains (Z2-Z1, Z2-Z2, Z2-Z3). While humans carry seven A3 genes, Equus caballus carries six and Felis catus four A3 genes. The genome of Equus caballus carries two Z1, two Z2-Z2, one Z2 and one Z3 A3 gene. Some of the equine A3 are able to restrict the Equine infectious anaemia virus (EIAV). Equine macrophages, which are the natural target cells for EIAV, express only a limited repertoire of the A3 genes. In addition, the transcriptional level of the anti-EIAV A3 mRNAs was significantly lower in macrophages than in equine peripheral blood mononuclear cells. Equine A3 proteins hyper-mutated EIAV genomes supporting their predicted function. In contrast to all other extant lentiviruses, EIAV does not encode a vif gene. Other EIAV-specific genes as dUTPase and S2, whose relevance for the viral replication in previous studies was only insufficiently characterized, did not influence the inhibitory effect of the equine A3 proteins. Thus, EIAV does not have an antagonist against its species-own A3 proteins. These findings indicate that lentiviral replication can occur independent from a vif gene, which likely developed later in the evolution of the lentiviruses. Felis catus and of other Felidae encode A3 genes of the type Z2 and Z3. Beside one-domain molecules, also two-domain encoding read-through transcripts with two Vif interaction sites were detectable, that restricted different feline retroviruses. FIV (Feline immunodeficiency virus) encodes a Vif protein that counteracts the inhibitory effect of the feline A3 proteins. Despite a high genetic diversity in felid A3 genes, no strong resistance could be shown against the neutralizing activity of Vif of the domestic cat FIV. Non-feline A3 proteins restricted FIV independently of Vif, which proves that the interaction between A3 and Vif proteins is species-specific and thus limits interspecies virus transmission. Species-specificity was also demonstrated for the interaction of feline A3 and the Vif protein of HIV-1. Feline cells that expressed human entry receptors were permissive for the transduction with a HIV-1 reporter virus but the virus was not able to spread in these cells. HIV replication in feline cells is strongly inhibited by the feline A3 proteins. In order to overcome this restriction, the vif gene of HIV-1 was replaced by vifFIV. This chimeric HIV-1 showed spreading replication in feline cells expressing human receptors. Altogether, these findings implicate the importance of a novel animal model for HIV-1 based on Felis catus.
Hawaii's Ferns and Fern Allies

Hawai'i's Ferns and Fern Allies is the first comprehensive survey of Hawai'i's ferns to be published in more than 100 years. The book covers endemic, indigenous, and naturalized ferns and fern allies (including rare and endangered taxa), providing dichotomous keys, basionyms and synonyms, technical descriptions and distributions, a glossary, and statistical information. The author addresses unresolved taxonomic problems and offers suggestions for future research. He includes information from Hawaiian folklore and mythology, describes uses of ferns by native Hawaiians, and updates Hawaiian common names. More than 100 line drawings illustrate all 222 species, varieties, and forms, and some hybrids. The volume is based on extensive field-work, studies of herbarium collections worldwide, and consultations with preridologists, local ecologists, and collectors. It provides the much-needed scientific basis for a new, worldwide appreciation of Hawaiian ferns and fern allies and for major efforts to protect and conserve them. This well-researched and highly readable book will be enthusiastically received by amateur and professional naturalists, fern enthusiasts, and professional botanists.
Development of an intra- and intergenotypic HCV cell culture method to phenotype and assess antiviral susceptibilities and resistance development of HCV NS3 protease genes from HCV genotypes 1-6

The development of specific antiviral drugs directly target ing the hepatitis C virus (HCV) is clinically important, as the current standard inter feron/ribavirin combination treatment is only partially effective, expensive and o ften associated with severe side effects. Inhibitors of the NS3 protease (PI) therefore represent a promising alternative or additional therapy. To date, the development and in vitro evaluation of PIs is restricted to the genotype 1/2 based replicon and the genoty pe 2a full length viral cell culture system. However, proteases of the different HCV geno types vary substantially in their amino acid sequence and secondary structure and req uire separate evaluation of their efficacy before they go into clinical trials. To address this issue, a panel of intraand intergenotypic r ecombinants based on the recombinant infectious clone Jc1 (pFK JFH1/J6/C-846) was deve loped in this work. The viability of these recombinants was assessed in the Huh7.5 c ell culture system, where replicating viruses were detected by HCV-NS5A immunostaini ng. Intergenotypic recombinants containing genotype 1a, 1b, 3a, 4a and 6a derived proteases were replication defective, whereas the recombinant with genotype 5a derived protease replicated efficiently after acquiring cell culture adaptive mut ations. The replacement of not only the NS3 protease gene region, but also its cofactor N S4A, allowed the generation of replication competent intraand intergenotypi c recombinants for all 6 major genotypes. Replacing the NS3 protease of the recombinant s with that of patientderived proteases also generated replicating recombinant s, greatly expanding the panel of intergenotypic recombinants available for phenotyping and PI evaluation. However, intraand intergenotypic recombinants showed subst antial differences in their replication kinetics, which may be influenced by naturally o ccurring polymorphism between genotypes and the differential requirement of adap tive/attenuating cell culture mutations. Genotype 1a recombinants replicated very p oorly, which may be due to incompatibilities between the type 1a NS3/4A protease an d the type 2a backbone.
Performance Analysis of Synchronous Generator: A Case Study in Steam Power Plant at PT POMI Paiton Unit 7 Probolinggo, East Java, Indonesia

This paper presents performance analysis of synchronous generator: a case study in steam power plant PT POMI Paiton unit 7 Probolinggo, East Java, Indonesia. The steam power plant is the most powerful in Indonesia. The dominance of this type of power plant can be seen from statistical data that until the end of 2018 there were 48.43% of steam power plants out of the total installed capacity of national plants. Generators used in steam power plants are generally of the synchronous generator type, which in its operation always experiences dynamics from time to time as the load changes in electricity. In this study, an analysis of the performance of synchronous generators has been carried out concerning changes in electricity load. Synchronous generator performance analysis includes output voltage, active power, reactive power, power factor, and generator efficiency. The steam power plant in this study is the largest capacity power plant in Indonesia, thus providing an important role in the supply of electric power. Based on the results of the study, it has been shown that although the load dynamics that experience changes are very dynamic, the generator performance still has good performance.