Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence of Multiple Euchromatic B Microchromosomes in Moenkhausia sanctaefilomenae (Pisces, Characidae) from the Upper Paraná River Basin, Brazil

Moenkhausia sanctaefilomenae is a small freshwater characid fish that shows a conserved karyotype with respect to the standard genome, but also carries B microchromosomes. In the present study, one population of M. sanctaefilomenae from the Upper Paraná River basin was cytogenetically characterized, with emphasis on the analysis of B chromosomes. The M. sanctaefilomenae individuals showed a karyotype consisting of 2n=50 chromosomes with eight metacentrics, 36 submetacentrics, and six subtelocentrics, and a FN value of 100 in both sexes. In addition to the basic karyotype, all male and female individuals presented a variation from zero to eight B microchromosomes in mitotic metaphases. A secondary constriction was evident in the terminal region of the short arm of the subtelocentric pair 24, which corresponds to the Ag-NORs location. Analysis of the constitutive heterochromatin patterns by C-banding showed heterochromatic blocks in the centromeric and pericentromeric regions in most of the chromosomes. However, the B chromosomes were faintly stained with C-banding, similar to euchromatin in the A chromosomes. Aspects regarding the differences in the number and C-banding pattern of B chromosomes are discussed.
Bilateral Involvement of Juvenile Temporal Arteritis Associated with Kimura Disease

Received:April 10, 2017, Revised:May 13, 2017, Accepted:May 29, 2017 Corresponding to:Young Mo Kang, Division of Rheumatology, Department of Internal Medicine, Kyungpook National University Hospital, 130 Dongdeok-ro, Jung-gu, Daegu 41944, Korea. E-mail:ymkang@knu.ac. kr Copyright c 2018 by The Korean College of Rheumatology. All rights reserved. This is a Open Access article, which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. Case Report pISSN: 2093-940X, eISSN: 2233-4718 Journal of Rheumatic Diseases Vol. 25, No. 1, January, 2018 https://doi.org/10.4078/jrd.2018. 25.1. 65
Production performance of HyCole, New Zealand White Rabbits and its reciprocal

New Zealand White rabbits (NZW) has been known as broiler rabbit that has been well adapted in Indonesia. HyCole rabbits were imported from France that were selected for high reproduction and growth rate. This study was aimed to evaluate the productivity of HyCole and New Zealand White rabbits and their reciprocal as the basis to develop broiler rabbit which adaptive to tropical climate. Forty heads of doe (P B P B ) and 17 heads of buck (P A P A ) of HyCole rabbit, and 30 heads of doe and 6 heads of buck of New Zealand White rabbits (NN) were used. The ration was given according to IRIAP standard ration (18 % CP, 2500 kcal ME/kg and 14 % CF). The diet was provided in the morning and the evening, and drinking water was provided ad libitum. Reproductive performance of does (litter size at birth, litter size at wean, mortality and weekly does body weight) and the kit’s growth performance (weekly body weight from weaning until the age of 20 weeks) were evaluated. Data were analyzed using the SAS program (SAS 2001). Rabbits growth data were periodically analyzed by Gompertz model (Blasco & Gomez 1993). HyCole rabbit which was bred in Indonesia had production performance better than NZW rabbit and P A N crossbred (HyCole bucks x NZW does) had the potential to be bred as superior rabbit adaptive to tropical climate because they had hybrid vigor of the number of litter size at birth and kit’s growth rate.
Landscape complexity promotes hoverflies across different types of semi‐natural habitats in farmland

1. Semi-natural habitats (SNH) provide essential resources for many organisms in ag ricultural landscapes and can increase biodiversity at the local and landscape scale. For the management of ecosystem services, it is crucial to understand how local characteristics of SNH and the surrounding landscape complexity affect beneficial species. 2. We investigated this for hoverflies (Diptera: Syrphidae)—an important functional group providing both pest control and pollination services—in a total of 138 SNH within 35 agricultural landscapes in Switzerland and Germany. SNH differed in type (woody, herbaceous), shape (areal, linear) and availability of food resources (floral resources and aphids). They were located along a gradient of landscape complexity (1%–75% SNH in a 1 km radius). 3. In total, 9,030 hoverflies belonging to 89 species were collected. In both countries, hoverfly community composition was mainly driven by SNH type and SNH shape, in addition to landscape complexity in Switzerland. Species richness of hoverflies increased with additional SNH at the landscape scale. However, the ubiquitous and dominant aphidophagous species Episyrphus balteatus was indifferent to landscape composition. hoverflies (and many other non- bee insects) are generally understud ied (Rader et al., 2016). With regard to ecological intensification and agri- environmental schemes (AES), a better knowledge of how local and landscape characteristics of SNH drive the abundance, diversity and community composition of hoverflies is essential to optimize the effectiveness of measures and to support management decisions of farmers and other stakeholders. In a highly replicated field study, we therefore investigated hov erflies in different SNH in agricultural landscapes in Central Europe (Switzerland and Germany). By analysing two different countries, we are able to evaluate the role of regional adapted management. In par -ticular, we analysed the effects of different SNH types (woody or her -baceous) and shapes (linear or areal), and their habitat characteristics as well as landscape complexity on two functional groups of hoverflies (aphidophagous and non- aphidophagous). We addressed the follow ing research questions: (1) How do local SNH characteristics (i.e. type, shape and food resource availability) drive hoverfly community com position, abundance and species richness? (2) How does SNH amount at the landscape scale affect hoverfly community composition, spe cies richness and abundance and how does it interact with local SNH effects? (3) How do drivers of abundance and species richness of aphidophagous hoverflies differ from those of non- aphidophagous hoverflies and what is the relative importance of drivers across these functional hoverfly groups? Thereby, we were especially interested how local SNH characteristics interact with the landscape complexity. consider differences in habitat characteristics.
Serotypes and antimicrobial resistance profiles of Salmonella isolated from fresh beef processing and chilled fresh beef samples produced and marketed in the metropolitan region of Cuiabá, in the State of Mato Grosso, Brazil

Salmonella spp. in food products of animal origin can cause foodborne infections, and when antimicrobial-resistant strains are present, can evolve to severe disease. This study aims to determine the occurrence of Salmonella and identify the serotypes present in the beef production chain of the metropolitan region of Cuiaba, State of Mato Grosso, Brazil, and evaluate their antimicrobial resistance profile. The presence of Salmonella was determined by the ISO-6579:2002 method and evaluation of resistance to 17 antibiotics was performed by the CSLI 2014 method. The following samples were analyzed: (1) environmental samples: corral swab, bleeding, skinning and deboning knives, ribbon saw, boning bench; (2) animal samples: anal swab, internal and external carcass sponge, organ pool, boning shavings and by-products in the slaughterhouse; and (3) ground meat samples from retail sales from 10 butcher shops and permanent fair stalls. Salmonella was present in ten of the 182 samples (5.5%), five of which were Salmonella Panama detected in the corral, boning tables, meat from the butcher's shop and permanent market. These strains were sensitive to all antibiotics characteristics and similar to Salmonella enterica rough, and being isolated from the ribbon saw used in the production chain. However, Salmonella Anatum and Salmonella Infantis isolated from carcasses, bone meal and viscera presented resistance to sulfonamides, trimethoprim, sulfametazol/ trimethoprim and nitrofurantoin in relation to the use of antibiotics in animal production and the selective pressure of multiresistant Salmonella spp. in products derived from these animals.
Study of Resistant Starch (RS) Content in Peas during Maturation

Total starch (TS), amylose and resistant starch (RS) were determined in the sets of smooth pea and wrinkled pea varieties in the years 2006–2008. Starch content of smooth peas varied in the range 53.61–57.23%. Average amylose content was 27.8%. Resistant starch content varied from 2.07% to 6.31%. Content of starch at wrinkled pea varied from 26.57% to 32.55%. Average amylose content was 76.82% of total starch. Content of total starch increases continually during seed development. The dependence of total starch on determined dry mass in harvested sample can be defined by equation y = 1.2427 × –6.5611, by determination coefficient R2 = 0.8936 and highly significant correlation coefficient r = 0.945. Total starch content in dry seed reached final average value 29.56%. In garden pea, the level of maturity (by tenderometric measurement) and dry matter were determined. Resistant starch content of 11 garden pea cultivars was studied in three different terms of technological harvest.
Compositional Shifts in Ammonia-Oxidizing Microorganism Communities of Eight Geographically Different Paddy Soils —Biogeographical Distribution of Ammonia-Oxidizing Microorganisms

Soil nitrification is mediated by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which occupy different specialized ecological niches. However, little is known about the diversification of AOA and AOB communities in a large geographical scale. Here, eight paddy soils collected from different geographic regions in China were selected to investigate the spatial distribution of AOA and AOB, and their potential nitrification activity (PNA). The result showed that the abundance of AOA was predominant over AOB, indicating that the rice fields favor the growth of AOA. PNA highly varied from 0.43 to 3.57 μg NOX-N·g·dry·soil·h-1, and was positively related with soil NH3 content, the abundance of AOA community, and negatively related with the diversity of AOB community (P amoA genes revealed remarkable differences in the compositions of AOA and AOB community. Phylogenetic analyses of amoA genes showed that Nitrosospiracluster-3-like and Nitrosomonas cluster 7-like AOB extensively dominated the AOB communities, and 54d9-like AOA within the soil group 1.1b predominated in AOA communities in paddy soils. Redundancy analysis suggested that the spatial variations of AOA community structure were influenced by soil TN content (P < 0.01), while no significant correlation between AOB community structure and soil properties was found. Findings highlight that ammonia oxidizers exhibit spatial variations in complex paddy fields due to the joint influence of soil variables associated with N availability.
Virus-host interactions in the early stages of the Equine Hepacivirus (EqHV) lifecycle

EqHV is the most closely related virus to HCV, and is proposed to have diverged from HCV within the last 1000 years. Studying viruses which share a close evolutionary relationship, yet differ greatly in their ability to cause disease, provides a unique opportunity to facilitate comparative analysis of both replication strategies and pathogenic mechanisms. It has previously been demonstrated that, like HCV, the EqHV 5’UTR functioned as an IRES. Here we set out to undertake a more detailed structural and functional analysis of the 5’UTR. A mutational analysis of the structural features of the EqHV 5′UTR was undertaken to investigate their roles in its function as an IRES. A complementary study utilising 2’ hydroxyl acylation and analysis by primer extension (SHAPE), to experimentally confirm the predicted structure of the EqHV 5’UTR in order to reveal how this related to function, was also conducted. This combined approach revealed that miR122 mediated enhancement of translation was dependent on a seed site located directly upstream of stem-loop (SL) II and that SLI was not required for EqHV IRES mediated translation. SLIII was absolutely essential, as was SLIIId and the conserved GGG motif. An essential role for SLIIIb was demonstrated for translation from an EqHV sub-genomic replicon. SHAPE experiments revealed that the conserved GGG motif was essential for EqHV 5′UTR:40S ribosomal subunit interactions, and that a GTC sequence in the apical loop of SLIIIb mediated an interaction with eIF3. This study also set out to establish an EqHV sub-genomic replicon capable of replicating in vitro in mammalian cells; however, this could not be achieved. When taken with published data it is possible to conclude that current EqHV isolates are not able to replicate in currently available cell culture systems and it is likely that new isolates, or cell lines, will be required to achieve in vitro replication.
Notes on the geographical distribution range of Sedum mucizonia (Ortega) Raym.-Hamet (Crassulaceae), a miniature, annual succulent, in continental Portugal

Summary: In continental Portugal, Sedum mucizonia (Ortega) Raym. -Hamet (Crassulaceae), a miniature, annual succulent, is known to occur especially in southern and central-western coastal areas, as well as along the central- and southeastern border between Portugal and Spain. Current records indicate that its northwestern-most limit in central Portugal is in the Parque Natural das Serras de Aire e Candeeiros, in the province of Estremadura. With at least 35% of the Crassulaceae species known from Portugal having been recorded from this region, it is established as a significant present-day centre of diversity for the family in the country. In addition to a distribution map for S. mucizonia in central continental Portugal, illustrations of the species are provided for the various locations from which the species has been collected in that part of the country. We also establish beyond doubt the location of the type locality of S. mucizonia, which is at San Sebastian, near Puertollano in the province of Ciudad Real, in Spain.
Antimicrobial resistance prevalence of Aeromonas hydrophila isolates from motile Aeromonas septicemia disease

Fish suffer, from bacteria, fungi, virus and parasites or by physical ailments. Gurami (Osphronemus gouramy), nila (Oreochromis niloticus), carp (Cyprinus carpio), catfish (Clarias sp.) were the most reported infections caused by Aeromonas are bacterial hemorrhagic septicemia or Motile Aeromonas Septicemia (MAS). Antibiotics are drugs of natural or synthetic origin that have the capacity to kill or to inhibit the growth of micro-organisms included MAS. However, the use of antibiotics in the long term can cause negative impacts, among others, feared the occurrence of bacterial resistance in certain antibiotics. The results showed five of isolates were sensitive to antibiotics of chloramphenicol, gentamycin, oxytetracycline, cefradoxil and nalidixic acid but resistant to vancomycin colistin sulphate, rifampisin, cephalosporin and novobiocin.
Statistical Methods For Whole Transcriptome Sequencing: From Bulk Tissue To Single Cells

RNA-Sequencing (RNA-Seq) has enabled detailed unbiased profiling of whole transcriptomes with incredible throughput. Recent technological breakthroughs have pushed back the frontiers of RNA expression measurement to single-cell level (scRNA-Seq). With both bulk and single-cell RNA-Seq analyses, modeling of the noise structure embedded in the data is crucial for drawing correct inference. In this dissertation, I developed a series of statistical methods to account for the technical variations specific in RNA-Seq experiments in the context of isoformor genelevel differential expression analyses. In the first part of my dissertation, I developed MetaDiff (https://github.com/jiach/MetaDiff), a random-effects meta-regression model, that allows the incorporation of uncertainty in isoform expression estimation in isoform differential expression analysis. This framework was further extended to detect splicing quantitative trait loci with RNASeq data. In the second part of my dissertation, I developed TASC (Toolkit for Analysis of Single-Cell data; https://github.com/scrna-seq/TASC), a hierarchical mixture model, to explicitly adjust for cell-to-cell technical differences in scRNA-Seq analysis using an empirical Bayes approach. This framework can be adapted to perform differential gene expression analysis. In the third part of my dissertation, I developed, TASC-B, a method extended from TASC to model transcriptional burstinginduced zero-inflation. This model can identify and test for the difference in the level of transcriptional bursting. Compared to existing methods, these new tools that I developed have been shown to better control the false discovery rate in situations where technical noise cannot be ignored. They also display superior power in both our simulation studies and real world applications. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Epidemiology & Biostatistics First Advisor Mingyao Li Second Advisor Hongzhe Li
The Use of Biodegradable Mulches in Pie Pumpkin Crop Production in Two Diverse Climates

The use of plastic biodegradable mulch (BDM) in many vegetable crops such as tomato ( Solanum lycopersicum L.), broccoli ( Brassica oleracea L. var. italica), and pepper ( Capsicum annuum L.) has been proven to be of equal beneﬁt as polyethylene (PE) mulch. However, there are limited research ﬁndings on the performance of BDM with a large fruited cropsuchaspumpkin( Cucurbitapepo L.)wherethefruitcanrestdirectlyonthemulchforan extended period. To investigate whether heavy fruit might cause the mulch to degrade more quickly than expected, thereby, inﬂuencing weed control, fruit yield, and fruit quality including mulch adhesion on fruit, we carried out a ﬁeld experiment in 2015 and 2016 at two locations in the United States with distinctive climates, Mount Vernon, WA and Knoxville, TN. Three plastic mulches marketed as biodegradable (BioAgri, Organix, and Naturecycle), one fully biodegradable paper mulch (WeedGuardPlus),
Governance explains variation in national responses to the biodiversity crisis

SUMMARY Growing concern about the biodiversity crisis has led to a proliferation of conservation responses, but with wide variation between countries in the levels of engagement and investment. Much of this variation is inevitably attributed to differences between nations in wealth. However, the relationship between environmentalism and wealth is complex and it is increasingly apparent that other factors are also involved. We review hypotheses that have been developed to explain variation in broad environmentalism and show that many of the factors that explain such variation in individuals, such as wealth, age and experience, also explain differences between nation states. We then assess the extent to which these factors explain variation between nation states in responses to and investment in the more specific area of biodiversity conservation. Unexpectedly, quality of governance explained substantially more variation in public and state investment in biodiversity conservation than did direct measures of wealth. The results inform assessments of where conservation investments might most profitably be directed in the future and suggest that metrics relating to governance might be of considerable use in conservation planning.
Determining Bioindicators for Coastal Tidal Marsh Health Using the Food Web of Larvae of the Greenhead Horse Fly (Tabanus nigrovittatus)

vi Chapter 1. Literature review . 1 1.1 Wetlands, Coastal Wetlands and Salt Marshes . 1 1.2 Importance of Wetlands, Coastal Wetlands and the Salt Marshes of Louisiana . 1 1.3 Vulnerability of Coastal Wetlands globally and within the United States with special emphasis on the Salt Marshes of Louisiana . 2 1.4 Oil spills – a major anthropogenic stressor of Coastal Wetlands . 2 1.5 Impacts and restoration efforts of damaged Coastal Wetlands within the United States with special emphasis on the Salt Marshes of Louisiana . 3 1.6 Impacts and restoration effects after oil spills on marine and coastal ecosystems . 4 1.7 Deepwater Horizon Oil Spill – A wake up call for urgent assessment methods . 5 1.7. 1. Distribution of oil . 5 1.7. 2. PAH assessment . 5 1.7. 3 Impact of the spill . 6 1.8 Need for assessment tools for marsh health and role of bioindicators . 9 1.9 Environmental monitoring using invertebrate bioindicators with special emphasis on insects and food webs . 10 1.10 Food webs for understanding ecosystem dynamics . 12 1.11 Deciphering food webs. 13 1.12 Current methods for environmental monitoring. 14 1.13 DNA metabarcoding and Next generation sequencing . 15 Chapter 2. Introduction . 18 2.1 Objectives of the study . 24
Food foraging in adult parasitoid Cotesia rubecula : how sugar sources contribute to survival and reproduction / by Gitta Siekmann.

Examines sugar foraging in the field by adult female parasitoid wasp, Cotesia rubecula (Hymenoptera, Braconidae), to determine its effect on fecundity and lifespan. In the field, the area in which wasps search for sugar is likely to depend on the degree of association of hosts with nectar or honeydew, supporting the hypothesis that sugar encounters in the field happen opportunistically during host foraging activities. The survival gained by sugar feeding my often be severely limited by quality and quantity of sugary food and extrinsic mortality factors such as adverse weather conditions and predation, so the need for food must be studied in relation to a species' adaptation to its environment. Concentrations of sugar sources may distract wasps from host-foraging when the density of hosts is low. This has implications for flower propagation in agro-ecosystems with a view to supporting natural enemies of insect pests.
Winter Activity of Bats in Mediterranean Peri-Urban Deciduous Forests

Although the Vespertilionid bats typically hibernate during the winter to minimize energy expenditure in the cold months, in the temperate regions torpor breaks can be rather frequent. The aim of our study was to conduct a preliminary characterisation of the winter bat activity patterns in Mediterranean peri-urban deciduous forests of North Portugal. Echolocation calls were recorded between November and February, and bat activity was regularly detected on warm evenings, with sun set temperatures above 4.6°C during the night sampling, mostly in November (89.9%), only rarely in December (3.7%) and February (6.4%) and without activity detected in January. The most commonly recorded species were Pipistrellus pygmaeus, P. pipistrellus, and P. kuhlii. Socialization activity was mostly concentrated in November (96.8%), only with rare records in February (3.2%) and absent in December and January. Regarding the best fitting average model, obtained by the Multi-Model Inference (MMI) method to explaining the variation of bat passes, the main positive influencing factors are related with the night period of the monitoring process and temperature, and the negative influence with the precipitation recorded in the last 48 hours before surveys. The MMI results for the variation of social calls revealed as significant positive influences the humidity, temperature and wind speed and as negative influence the precipitation recorded in the last 48 hours before surveys. We outline our study as a promising baseline to the studies of winter bat activity, demonstrating how the present and past weather conditions can play a major role in bat torpor breaks. Therefore, for conservation purposes, further winter acoustic research efforts should be consider mandatory for full understanding the bat activity patterns facing the potential impacts of global climatic changes expected to occur in the Mediterranean region.