Miracle-dz/UniFAR-FTUs huggingface dataset:
Current nature reserve management in China and effective conservation of threatened pheasant species

Protected areas, such as nature reserves, are essential for effective conservation of threatened species through protection and management of populations and habitats. Habitat evaluation is a key method that has been frequently used to assess the effectiveness of protected areas. Previous research has mainly focused on species conservation related to changes in land cover and habitat fragmentation while few studies have examined changes in microhabitat structure. Using a multi-scale habitat change analysis (i.e. regional, macro- and microhabitat) in a temporal framework, we assessed the effectiveness of current nature reserve management for the habitat protection of the Reeves's pheasant Syrmaticus reevesii, a vulnerable, forest-dwelling species. We measured land use/land cover changes inside and outside the Dongzhai National Nature Reserve (DNNR), in 2002 and 2013 corresponding to the times at and after the establishment of the DNNR. We also compared differences in habitat fragmentation patterns and microhabitat structure and composition between the two periods. Results show that the forest coverage has slightly increased both inside and outside DNNR, and habitat fragmentation metrics have not changed substantially since the establishment of DNNR. Significant differences were detected in microhabitat structure and composition between 2002 and 2013. After more than 10 years of no disturbance, canopy cover and density of the shrub layer increased, while herbaceous plant height declined. The observed changes reduced resource availability resulting in increased foraging time for pheasants and increased predation rates. This suggests that current nature reserve management systems may have negative impacts on the conservation of the Reeves's pheasant. We propose that the Regulations of Nature Reserves in China should be revised to account for the habitat requirements of different threatened species with varied life history traits.
Chemical composition and structural characterization of contrasting colors of soybean seed coats Composição química e caracterização estrutural de tegumentos de sementes de soja com cores contrastantes

Seed coats provide protection to seeds and present differential traits between soybean genotypes. The aim of this study was to determine the chemical composition and analyze the internal coat structure of soybean genotypes with contrasting seed coat color, as well as to evaluate the rate of water absorption by seeds. Four genotypes were tested: two genotypes with black seed coat (IAC and TP lines) and two genotypes with yellow seed coat (BMX Potencia RR and CD 202 cultivars). The seeds of the four genotypes were grown during the 2012/0213 crop season, in a greenhouse at the Embrapa Clima Temperado - Estacao Experimental Terras Baixas. After the harvest, the seeds were stored in controlled conditions for five months. After this period, concentration of phenolic compounds, antioxidant potential, anthocyanins, carotenoids, and lignin in seed coats were determined at the Universidade Federal de Pelotas. Internal coat structure was examined on anatomical slides and documented with image capturing software using a microscope at the Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sao Paulo. Finally, water absorption of contrasting seeds was evaluated at 42 hours of imbibition. Experimental design was completely randomized with five replicates. Data were subjected to analysis of variance and the means were compared by Tukey’s test, at 5% probability level. Coat structure was characterized by the image analysis. Imbibition data were subjected to regression analysis. The concentration of phenolic compounds, antioxidant potential, anthocyanins, carotenoids, and lignin are higher in black coated genotypes. Their palisade layer and hourglass cells are thicker and the former are more lignified in black seed coats compared to yellow seed coats. The water gain by the seeds is dependent on the conditions in which the seeds were formed and varied between genotypes, independent of coat coloration and lignin concentration.
Combined Application of Different Species of Trichoderma and Pseudomonas fluorescens on the Cellulolytic Enzymes of Fusarium oxysporum for the Control of Fusarium wilt Disease in Arachis hypogea. L

Fusarium oxysporum causes Fusarium wilt of crop plants leads to considerable yield loss. The study was conducted to determine the beneficial effects of combining Trichoderma species and Pseudomonas fluorescens i.e Trichodema viride+ Pseudomonas fluorescens (Tv+Pf) (1+2%), Trichoderma harzianum+Pseudomonas fluorescens (Th+Pf) (1.5+2%), Trichoderma viride +Trichoderma harzianum (Tv+Th) (1+1.5%) on the activity of cellulolytic enzymes of Fusarium oxysporum to control Fusarium wilt of Arachis hypogaea. L wilt in vitro. The activity of 1,4 -β – Endoglucanase, 1,4 -β – Exoglucanase, Cellobiases produced by Fusarium oxysporum (Control) was higher. Maximum inhibition of Cellulolytic enzymes was shown by culture filtrate of Trichoderma viride + Pseudomonas fluorescens (Tv+Pf) (1+2%), followed by Trichoderma harzianum + Pseudomonas fluorescens, (Th +Pf) (1.5+2%) and Trichoderma viride + Trichoderma harzianum (Tv+Th) (1+1.5%). However, disease suppression of Fusarium wilt of Arachis hypogaea. L by the compatible combination of Trichodema viride + Pseudomonas fluorescens (1+2%) was considerably better as compared to other two strains. At the same time the other two combinations resulted in enhanced disease suppression as compared to single strains. This indicates that the potential benefits of using combination treatments to suppress Fusarium wilt. The study suggests the significance of interactive effects of Trichoderma and Pseudomonas in biocontrol of wilt disease.
Characterization of B-Cells Epitopes on HPV Capsid Proteins

Human Papillomavirus (HPV) are considered as the major etiologic cause for a variety of benign and malignant epithelial lesions. The so-called high risk-HPV types are related to cervical cancer, while low-risk types are associated with benign mucosal lesions only. HPV types 16 and 18 are the most frequently found types in cervical cancers. Antibodies to HPV major capsid protein, L1, can develop in response to natural HPV infection as well as after vaccination. In contrast, antibodies to early, non-structural proteins, mainly E6 and E7 which are consistently expressed in HPVtransformed cells, have been found to be strongly associated with invasive carcinoma. Virus-like particles (VLP) which mimic morphologically and immunologically the native virions have been used so far as standard serological antigens. This PhD thesis had two main objectives, first to characterize the bacterially expressed, affinity-purified glutathione S-transferase fusion proteins (GST) as alternative antigens for serology in terms of displayed epitope repertoire, using a panel of 92 VLP-specific monoclonal antibodies (mAb) generated against 9 mucosal alpha papillomavirus types. The second objective was to analyze in details the natural as well as HPV vaccine-induced immune response in patients with cervical intraepithelial neoplasias (CIN II/III). Additionally, an antibody blocking assay based on Maltose binding protein (MBP)-fusions was established to analyze the typespecificity of HPV antibodies. It is shown here that GST-L1 fusion proteins display a broad variety of epitopes and thus are well suited for detection of human HPV antibodies. Cross-reactivity is associated with linear as well as conformational epitopes and can be intra- and/or interspecies specific and follows the phylogenetic relationships only loosely. Neutralizing epitopes are always conformational and mostly, but not always typespecific. The established MBP-16L1 allowed blocking the binding of mono-specific as well as cross-reactive antibodies to GST-16L1 but not that of specific antibodies to other HPV types. Vaccination of patients with cervical intraepithelial neoplasias with HPV16L1/E7 chimeric VLP induced strong 16L1 specific and weaker 16E7 specific responses as well as L1 neutralizing antibodies. The response was positively correlated with vaccine dose the immune status before vaccination. Vaccination-induced crossreactivity to both L1 and E7 was across species and the cross-reactive sera were non cross-neutralizing for distantly related HPV. Chimeric VLP vaccination also induced antibody responses to other HPV16 early proteins suggesting that these proteins were released from the lesions in response to vaccination. In conclusion, bacterially expressed GST fusion proteins are good candidates to be used as antigens in HPV serology and are also useful tools to define and characterize the complex patterns of conformational and linear cross-reactive epitopes.
DISEASES DIVERSITY FOR FLAX GENETIC RESOURCES IN LATVIA

Flax ( Linum usitatissimum L) yield of stem and seeds and them quality is influenced by a number of harmful diseases but investigation about pathogens in recent years have not been done in Latvia. Each stage of development of disease is important in the pathogen life cycle and requires certain condition. Goal of this study have identify possibilities of the pathogens and were assess disease severity depending on the genotypes on flax in variable environmental conditions. The resistance to the diseases for 24 flax genotypes and standard variety ‘Vega 2’ were evaluated. The field trials have been carried out over the period from 2015 to 2016 at the Research Centre of Priekuli, part of Vilani in Latgale. Disease progress was measured every week , and for each treatment, severity of diseases index and the area under the disease progressive curve (AUDPC) were calculated. The flow cytometry method for detection of flax pathogens was developed. The Fusarium avenaveum was dominating disease and statically significant in both vegetation periods. In 2015 were identified statically significant (p<0.001) highest AUDPC the casual agents powdery mildew ( Oidium lini ) and of stem break and browning caused by Polyspora lini but in 2016 anthracnose ( Colletotrichum lini ), pasmo ( Septoria linicola ) and fusarium wilt caused by fungus Fusarium oxysporum f. sp. lini . The resistance of Colletotrichum lini, Fusarium oxysporum f. sp. lini, Septoria linicola and Oidium lini have flax variety of ‘Rezekne’ in both years.
Relationship between HLA and T cell responses to Ebola virus

6 Zusammenfassung . 7 Introduction . 8 Ebola Virus . 8 Molecular characterization of EBOV . 8 Historical overview of Ebola virus disease (EVD) outbreaks . 9 Ebola virus disease . 10 Animal reservoir . 11 Human to human transmission . 12 Animal models . 13 Immune response . 14 EBOV portals of entry . 15 Innate antiviral immune response . 15 EBOV infects macrophages and dendritic cells . 16 EBOV inhibits the IFN-I response . 18 Adaptive antiviral immune response . 18 The immunological synapse . 19 T cell response . 21 EBOV affects the adaptive antiviral immune response . 23 B cell response . 24 B cell response during EVD . 24 Immune memory . 25 Immunogenetics . 25 Aim of this thesis . 27 Results . 28 Publication I: Ebola Virus Disease Is Characterized by Poor Activation and Reduced Levels of Circulating CD16 Monocytes (Lüdtke, Ruibal, Becker-Ziaja et al., 2016) . 28 Publication II: Unique human immune signature of Ebola virus disease in Guinea (Ruibal, Oestereich, Lüdtke, Becker-Ziaja et al., 2016) . 42 Publication III: Immunogenetics of Ebola virus disease (manuscript in preparation) . 61 Discussion . 80 Materials and methods . 92 Patients and samples . 92 Flow cytometry . 92 In silico peptide analysis and dextramer design . 94 Isolation of DNA . 95 HLA genotyping and count of allele frequency . 95 TCR amplification, amplicon purification and library construction . 96 Sequencing of TCR library pool . 99 Bioinformatical analysis of MiSeq sequencing results . 99 Statistical analysis . 100 References . 101 List of abbreviations . 112 Curriculum vitae . 115 Publications overview . 116 Acknowledgments . 119 Versicherung an Eides Statt . 121
Pathogenesis of systemic sclerosis: recent insights of molecular and cellular mechanisms and therapeutic opportunities

Systemic sclerosis (SSc) is a complex disease characterized by early microvascular abnormalities, immune dysregulation and chronic inflammation, and subsequent fibrosis of the skin and internal organs. Excessive fibrosis, distinguishing hallmark of SSc, is the end result of a complex series of interlinked vascular injury and immune activation, and represents a maladaptive repair process. Activated vascular, epithelial, and immune cells generate pro-fibrotic cytokines, chemokines, growth factors, lipid mediators, autoantibodies, and reactive oxygen species. These paracrine and autocrine cues in turn induce activation, differentiation, and survival of mesenchymal cells, ensuing tissue fibrosis through increased collagen synthesis, matrix deposition, tissue rigidity and remodeling, and vascular rarefaction. This review features recent insights of the pathogenic process of SSc, highlighting three major characteristics of SSc, microvasculopathy, excessive fibrosis, and immune dysregulation, and sheds new light on the understanding of molecular and cellular mechanisms contributing to the pathogenesis of SSc and providing novel avenues for targeted therapies.
Abundance and stability of populations of chewing lice (Phthiraptera: Amblycera and Ischnocera) infesting two species of woodpeckers (Aves: Piciformes: Picidae)

Abstract The annual abundance of chewing lice (Phthiraptera) was recorded from 1996 to 2015 in Manitoba, Canada, on two species of woodpeckers (Piciformes: Picidae). Yellow-bellied sapsuckers (Sphyrapicus varius (Linnaeus)) were infested with Menacanthus pici (Denny) (Amblycera: Menoponidae) and Penenirmus auritus (Scopoli) (Ischnocera: Philopteridae); northern flickers (Colaptes auratus (Linnaeus)) were also infested with M. pici, as well as two other Ischnocera, Penenirmus jungens (Kellogg) and Picicola porisma Dalgleish. The mean annual abundance varied from nine to 51 lice per bird for the four species, with prevalence, mean intensity, sex ratio, and nymphs per female also varying among louse species. Menacanthus pici populations on both hosts were unstable: abundance rose over two decades because of increasing prevalence, whereas the abundance of the other three louse species fluctuated around a mean. Population variability was similar for the lice on both hosts, with the metric, PV, ranging from 0.41 to 0.51 on a 0–1 scale, once the effect of the trend in abundance for M. pici had been removed. Although the population dynamics for species of lice on these two woodpeckers were distinct, inter-specific differences in population stability were less pronounced than observed in the few other species of bird lice studied in this way.
Review of the leaf-litter skinks (Scincidae: Panaspis) from the Gulf of Guinea Oceanic Islands, with the description of a new species

ABSTRACT Leaf-litter skinks of the genus Panaspis are currently represented in the oceanic islands of the Gulf of Guinea by two species, Panaspis africana and P. annobonensis. Here we describe a third species, Panaspis thomensis sp. nov., endemic to São Tomé Island. Data from previous studies and a new phylogenetic analysis using the mitochondrial 16S gene shows that the new species is genetically divergent and reciprocally monophyletic with respect to P. africana. Morphological data (scalation and morphometry) identify consistent, yet subtle, phenotypic differences between the two island populations. We also confirm that P. annobonensis represents a valid species, sister to the species pair P. africana + P. thomensis sp. nov., based on both molecular and morphological evidence. This description raises the number of known Panaspis species in the Gulf of Guinea oceanic islands to three, with consequences for the interpretation of local endemicity. ZooBank—Panaspis thomensis: lsid: zoobank.org:act:A1E69D28-CF4C-4070-BBCC-91E39C21DBA6
Vocal individuality of large-tailed nightjar (Caprimulgus macrurus) in Peninsular Malaysia

Abstract All four nightjar species resident in Peninsular Malaysia are vocally distinct, yet they remain little studied. Conventional field methods based on visual cues to study diurnal species may be impractical for nightjars. Alternatively, aural survey can potentially be applied on nightjars provided that individuality in their vocalisations can be proven. Our study aimed to determine the vocal individuality of the common, large-tailed nightjar (Caprimulgus macrurus) in oil palm smallholdings and an isolated forest patch located in Selangor, Peninsular Malaysia. From the call recordings obtained from 22 individuals, results of the Kruskal-Wallis analysis revealed significant differences in all the nine vocal parameters (call length, interquartile range bandwidth, low, high, average, centre and peak frequencies as well as first and third quartile frequencies) measured among individual nightjars (p < 0.001) regardless of study sites. Discriminant Function Analysis showed that more than 94.5% of original grouped cases were correctly classified. This implied that the majority of vocalizations can be assigned to individual birds based on the parameters measured. This study demonstrated the occurrence of vocal individuality in the large-tailed nightjar and such a finding pertaining to distinct vocalisations at the individual level will compensate for the limited access to visual cues in field surveys, as with the case for all nocturnal birds.
The Effects of Gonadal Hormones on Hippocampal Neuroplasticity

THE EFFECTS OF GONADAL HORMONES ON HIPPOCAMPAL NEUROPLASTICITY Sarah Atwi Advisor: University of Guelph, 2014 Professor Neil MacLusky The relationship between gonadal hormones and hippocampal neuroplasticity remains controversial. This thesis explores the effects of estradiol on dendritic spine density (DSD) in CA1 and CA3 of the hippocampus in intact female rats. Results showed a mixed-mode response to higher estradiol: CA1 DSD significantly increased in the apical dendritic tree, but not in CA3. Despite evidence that CA3 synaptic characteristics are dependent on BDNF and estradiol interactions, other mechanisms maybe involved. This thesis also addresses the connection between androgen and BDNF-dependent mechanisms on hippocampal neuroplasticity in male mice. Gonadectomy led to atrophy of CA3 neurons but did not alter BDNF transcript or protein expression. Interestingly, surgerized groups expressed greater proBDNF 8-12 days, not 27-30 days following surgery, and atrophy in CA3 neurons compared to un-surgerized groups. It is likely that surgical stress might have played a role in the neuromorphological changes observed. This is key to understanding hippocampaldependent cognitive dysfunction.
Anti-dsDNA antibody up-regulates interleukin 6, but not cyclo- oxygenase, gene expression in glomerular mesangial cells: a marker of immune-mediated renal damage?

Objective and Design: To determine whether anti- double stranded DNA antibody (anti-dsDNA) can affect the synthesis of eicosanoids and cytokines in rat glomerular mesangial cells (RMC). Materials or Subjects: Glomerular mesangial cells were iso- lated and subcultured from Sprague-Dawley rats. Monoclo- nal anti-dsDNA (12B3 clone) was derived from autoimmune MRL-lpr/lpr mouse by hybridoma technology. Methods: The mRNA expression of cyclo-oxygenase type 1 (COX-1), type 2 (COX-2), Th1 (IL-2 and IFN-g)/Th2 (IL-4 and IL-10) and proinflammatory (IL-6 and TNF-a) and anti- inflammatory (TGF-b) cytokines of RMC ± anti-dsDNA was detected by RT-PCR. The PGE2 production by RMC ± anti- dsDNA was measured by ELISA. The statistical significance was assessed by non-parametric Wilcoxon signed rank test. Results: We found RMC spontaneously expressed COX-1, but not COX-2. The incubation of RMC with anti-dsDNA (50 ng/ml) did not affect COX expression and PGE2 produc- tion by RMC. RMC also spontaneously expressed IL-6, TNF-a and TGF-b mRNA. However, only IL-6 was up-regu- lated by anti-dsDNA. Conclusions: Increased IL-6 expression in RMC may be- come a marker of anti-dsDNA-mediated immune damage of mesangial cells.
Forecasting the mortality rates of Indonesian population by using neural network

A model that can represent a problem is required in conducting a forecasting. One of the models that has been acknowledged by the actuary community in forecasting mortality rate is the Lee-Certer model. Lee Carter model supported by Neural Network will be used to calculate mortality forecasting in Indonesia. The type of Neural Network used is feedforward neural network aligned with backpropagation algorithm in python programming language. And the final result of this study is mortality rate in forecasting Indonesia for the next few years
Cladistics, classification and identification of the brachycercine mayflies (Insecta: Ephemeroptera: Caenidae)

The mayfly subfamily Brachycercinae (Pannota: Caenidae) is redefined and shown to be an apotypic, monophyletic group based on numerous synapomorphies, including, for example in the larvae, the presence of ocellar tubercles, an anterior row of long setae on the larval head capsule, a patch of long setae posterior to the base of the glossae, a broad prosternum, and the absence of toothlike claw denticles. Over 100 morphological characters of larvae, adults, and eggs discovered to be useful for phylogenetic analysis and diagnoses are detailed and illustrated. Thirty-eight species are recognized among the genera Brachycercus Curtis, Caenoculis Soldan, Cercobrachys Soldan, Insulibrachys Soldan, Sparbarus, n. gen., Oriobrachys, n. gen., Latineosus, n. gen., Susperatus, n. gen., and Alloretochus, n. gen., by adopting a strictly phylogenetic classification, including a first tribal classification within the subfamily. Brachycercus ojibwe, n. sp. , Cercobrachys fox, n. sp. , C. lilliei, n. sp. , C. pomeiok, n. sp. , C. winnebago, n. sp. , Latineosus cayo, n. sp. , L. cibola, n. sp. , Oriobrachys mahakam, n. sp. , Sparbarus choctaw, n. sp. , S. coushatta, n. sp. , S. miccosukee, n. sp. , and Susperatus tonkawa, n. sp. are newly described. The Nearctic Brachycercus articus Soldan, n. syn. , and B. edmundsi Soldan, n. syn. , are shown to be equivalent to B. harrisella Curtis, proving the latter to be a widespread Holarctic species. Sparbarus capnicus (Zhou, Sun and McCafferty), n. comb. , S. corniger (Kluge), n. comb. , S. europaeus (Kluge), n. comb. , S. gilliesi (Soldan and Landa), n. comb. , S. japonicus (Gose), n. comb. , S. kabyliensis (Soldan), n. comb. , S. lacustris (Needham), n. comb. , S. maculatus (Berner), n. comb. , S. nasutus (Soldan), n. comb. , S. tubulatus (Tshernova), n. comb. , Susperatus prudens (McDunnough), n. comb. , and S. tuberculatus (Soldan), n. comb. , are transferred from Brachycercus. Alloretochus peruanicus (Soldan), n. comb. , and Latineosus colombianus (Soldan), n. comb. , are transferred from Cercobrachys. Caenis dangi (Soldan), n. comb. , is transferred from Caenoculis and Brachycercinae to Caeninae, and provisionally placed in Caenis Stephens. Sparbarus flavus (Traver), n. comb. , is transferred from Brachycercus and considered to be a nomen dubium. Nomenclatural history, new or revised descriptions as appropriate, diagnoses, illustrations, and keys are provided for known stage of species. Origins and evolutionary relationships of the Brachycercinae are hypothesized based on cladistic results. Brachycercinae is considered to have originated from a Caenis-like ancestor. The genera Cae- WORLD BRACHYCERCINAE noculis and Insulibrachys represent more ancestral lineages, whereas the genera Sparbarus, n. gen., Brachycercus, Oriobrachys, n. gen., Latineosus, n. gen., Susperatus, n. gen., Alloretochus, n. gen., and Cercobrachys appear more derived. Cercobrachys pomeiok and other closely related species are most apotypic in terms of numbers of accumulated apomorphies.