Miracle-dz/UniFAR-FTUs huggingface dataset:
Mold Allergomics: Comparative and Machine Learning Approaches

Fungi are one of the major organisms that cause allergic disease in human. A number of proteins from fungi have been found to be allergenic or possess immunostimulatory properties. Identifying and characterizing allergens from fungal genomes will help facilitate our understanding of the mechanism underlying hostpathogen interactions in allergic diseases. Currently, there is a lack of tools that allow us to rapidly and accurately predict allergens from whole genomes. In the context of whole genome annotation, allergens are rare compared to non-allergens and thus the data is considered highly skewed. In order to achieve a confident set of predicted allergens from a genome, false positive rates must be lowered. Current allergen prediction tools often produce many false positives when applied to large-scale data set such as whole genomes, and thus lower the precision. Moreover, the most accurate tools are relatively slow because they use sequence alignment to construct feature vectors for allergen classifiers. This dissertation presents computational approaches in characterizing the allergen repertoire in fungal genomes as part of the whole genome studies of Alternaria, an important allergenic/opportunistic human pathogenic fungus and necrotrophic plant parasite. In these studies, the genomes of multiple Alternaria species were characterized for the first time. Functional elements (e.g. genes, proteins) were first identified and annotated from these genomes using computational tools. Protein annotation and comparative genomics approaches revealed the link between Alternaria genotypes and its prolific saprophytic lifestyle that provides at least a partial explanation for the development of pathological relationships between Alternaria and humans. A machine learning based tool (Allerdictor) was developed to address the neglected problem of allergen prediction in highly skewed large-scale data sets. Allerdictor exhibited high precision over high recall at fast speed and thus it is a more practical tool for large-scale allergen annotation compared with existing tools. Allerdictor was then used together with a comparative genomics approach to survey the allergen repertoire of known allergenic fungi. We predicted a number of mold allergens that have not been experimentally characterized. These predicted allergens are potential candidates for further experimental and clinical validation. Our approaches will not only facilitate the study of allergens in the increasing number of sequenced fungal genomes but also will be useful for allergen annotation in other species and rapid prescreening of synthesized sequences for potential allergens.
Ion exchange membranes as an indicator of soil mineral nitrogen availability and nitrogen uptake by arugula (Eruca sativa L.) in soils amended with green manure

Abstract Green manure crops are a common N fertilizer source in organic agriculture. Producers need guidance on when to incorporate the green manure for efficient N uptake by the following crop. The objective of this study was to describe the temporal dynamics of soil mineral N following green manure plough-down and N available to arugula (Eruca sativa L. sp.) also known as salad rocket, a fast-growing leafy herb used in salads. Green manure was a mixture of field pea (Pisum sativum L.) cv. CDC Meadow and oat (Avena sativa L. sp.) grown on fields with sandy loam and sandy clay loam soils at an organic vegetable farm in southwestern Quebec, Canada. Ion exchange membranes (IEMs) were used to monitor the ammonium (IEM––N) and nitrate (IEM––N) released following green manure plough-down. The IEM––N concentration was positively correlated with rainfall (r = 0.57 to 0.95, p < 0.05) and was greater from 2 to 5 weeks after green manure plough-down than in soils without green manure. Arugula N uptake and IEM––N were positively correlated in sandy clay loam (r = 0.86, p < 0.01) and sandy loam (r = 0.71, p < 0.05) soils. IEM––N concentrations were found to be sensitive to weather, green manure decomposition and arugula growth, and could be a tool to monitor soil mineral N available for short-season vegetable crops.
Role of GAL3ST1 in Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy characterized by inactivation of the von Hippel-Lindau tumour suppressor gene, the protein product of which mediates degradation of the transcription factor hypoxia-inducible factor (HIF). GAL3ST1 is a sulfotransferase which catalyzes the production of sulfatide, a plasma membrane sulfolipid previously implicated in metastasis. We observed GAL3ST1 overexpression in primary ccRCC tumours relative to matched-normal tissue and subsequently asked if GAL3ST1 was a HIF-responsive gene that facilitates ccRCC metastasis. GAL3ST1 expression was suppressed in ccRCC cells by stable reconstitution of wild-type VHL and also siRNA-mediated knockdown of HIF1alpha and HIF2alpha. Dual luciferase assays and chromatin immunoprecipitation revealed a hypoxia-response element in the GAL3ST1 5’-UTR that appeared to be crucial for HIF-mediated upregulation. Finally, stable knockdown of GAL3ST1 significantly impeded ccRCC cell invasion through an in vitro basement membrane mimic. These results suggest GAL3ST1 is a HIF-responsive gene that promotes tumour cell invasion. %%%%MAST
Comparative and Functional Morphology of Wing Coupling Structures in Trichoptera: Integripalpia

Trichoptera and several other insect orders have evolved functional diptery while retaining four wings (morphological tetraptery), which results from the interaction of specialized structures that unite the wings. In this contribution, the comparative and functional morphology of the forewing-hindwing coupling apparatuses and related structures in the suborder Integripalpia are presented. The components of the wing coupling apparatuses have varied and complex morphologies and interaction modes, that result in partial to complete wing coupling. Wing coupling has evolved repeatedly within the infraorders Brevitentoria and Plenitentoria, and the morphologies of the wing coupling apparatuses are synapomorphies for several families. Phylogenetic trends are discussed that relate to the evolution of functional diptery, such as the diminution of forewing jugal lobes and hindwing prehumeral setae, reinforcement of wing veins, changes in vein topology and elaboration of wing surface features. A novel at-rest forewing-forewing coupling apparatus that has also evolved repeatedly is described and related to the evolution of wing coupling.
Molecular Appraisal of the Host-Range K1L Gene of Buffalopox Virus Isolates from an Outbreak (2010) in Maharashtra

The buffalopox virus (BPXV) has emerged as an occupational zoonotic disease in the country. Host-range genes play a critical role in the host tropism of poxviruses as in the case of vaccinia viruses (VACV). Among hostrange genes, the K1L gene is required for viral replication by antagonising host-imposed interferon resistance. This study was undertaken for genetic characterisation of this VACV homologue host-range gene of BPXV isolates from buffaloes (BPXV/buffalo/Jalgaon/2010) and humans (BPXV/human/Jalgaon/2010) from an outbreak (2010) in Maharashtra. Furthermore, we also analysed the phylogenetic relationship of BPXVs with other Orthopoxviruses (OPXVs) to determine the nature of this gene within the genus. Sequence analysis revealed ORFs of 855 bp. Current isolates shared maximum homology (~99%) at both nt and aa levels with VACV. There was no sequence variation in this gene with respect to buffalo and human isolates of BPXV; however, a significant point mutation (D249N) was observed in the BPXV isolates as compared with VACV and other VACV-like viruses. Phylogenetic analysis revealed clustering of BPXV isolates with VACVs along with the vaccine strains. The close homology between BPXV and VACV suggests their similar roles in viral pathogenesis.This analysis could provide an avenue for discovering critical innate antiviral responses for the development of vaccine and antiviral agents required in the context of reduction of cohort immunity against poxviruses in the human population. This is the first report of genetic analysis of the K1L gene of the buffalopox virus.
Ecology and population structure of the hyperbenthic copepod Mesaiokeras hurei Kršinić, 2003 (Calanoida: Mesaiokeratidae) from an isolated marine lake (Mljet island, Southern Adriatic Sea, Croatia)

The monogeneric family Mesaiokeratidae (Copepoda: Calanoida) is exclusively bentho-pelagic and comprises nine small hyperbenthic species. Previous knowledge of these species has been limited to the description of their morphology and habitat. We provide new information about the ecology of Mesaiokeras hurei Krsinic, 2003, one of the small-size species of the family and found only in an isolated marine lake on the southern Adriatic island of Mljet (Croatia). Genetic markers were used to investigate its phylogenetic relationships with other copepods. The abundance of M. hurei abundance was highly variable over the years and seasons sampled. Densities were higher in spring and autumn. It was particularly abundant in 2011, averaging 629 ± 800 individuals/m3, and with a maximum of 1971 individuals m−3 in November, but averaged 74 ± 71 individuals/m3 and 66 ± 71 individuals/m3 in 2001 and 2008, respectively. Specimens were found in a range of temperatures, from 10.5°C to 18.3°C, but a majority of individuals (67%) was found in the 12-14°C layer. In addition to temperature, oxygen was a significant predictor ( p < 0 . 001 ) of the vertical micro-distribution of M. hurei. The DNA barcode sequence for the species is reported here for the first time. Analysis of the nuclear small subunit rRNA gene fragment (18S) showed a genetic similarity with representatives of the superfamily Clausocalanoidea.
Survival of Pathogenic Bacteria on Pork Loins as Influenced by Hot Processing and Packaging.

The impact of hot and cold processing on the survival and/or growth of Salmonella , Listeria monocytogenes , pathogenic Yersinia enterocolitica , Aeromonas hydrophila , and Campylobacter spp. On inoculated pork loins was studied. Loin pieces were inoculated with pathogen-containing feces, then vacuum packaged directly after hot boning (hot packaging), vacuum packaged after chilling for 1 d, or left unpackaged. Pathogen numbers were assayed after storage at 1 + 1°C for 0, 1, 2, 5, and 9 d. Campylobacter numbers decreased during the storage period, but the organisms could still be recovered after 9 d storage. A lower Campylobacter survival rate was observed on unpackaged pork loin pieces. The other pathogens were less affected by packaging treatment. Numbers of L. monocytogenes increased by approximately 1-log10 CFU/cm2. Survival and growth of A. hydrophila during refrigerated storage varied between trials. In Experiment 1, numbers increased by ca. 2-log10 CFU/cm2, while levels were stable or decreased slightly in Experiment 2. Salmonella levels decreased during storage, with the greatest survival observed on hot-packaged pork. Despite the fact that pork loins were inoculated with ca. 102 CFU pathogenic Y. enterocolitica per cm2, the organism was recovered only sporadically during the storage period. This may be due to competition with the natural microflora. Existing procedures are often inadequate for recovering small numbers of pathogenic Y. enterocolitica in the presence of large numbers of competing flora. Until recovery procedures are improved, the effect of packaging treatment on pathogenic Y. enterocolitica cannot be determined.
New combinations arising from a new classification of non-African Restionaceae

Briggs, Barbara G. and Johnson, L.A. S. (Royal Botanic Gardens, Mrs Macquaries Road, Sydney, NSW 2000, Australia) 1998. New combinations arising from a new classification of non-African Restionaceae. Telopea 8(1): 21–33. New combinations are made in accord with a new, broadly based classification of extraAfrican Restionaceae. These involve 39 Australian species, of which two extend to New Guinea and the Aru Islands, and one species in each of south-east Asia, New Zealand and Chile. The name Baloskion Raf. is adopted for eight eastern Australian species excluded from Restio Rottb. and Desmocladus Nees is adopted for a group of Western Australian species mostly transferred from Loxocarya R. Br. The previously monotypic genera Meeboldina Suesseng. and Sporadanthus F. Muell. are enlarged. Most other changes involve newly described genera. Four combinations replace illegitimate epithets, two new combinations are made at subspecific rank, and lectotypes are selected for 18 taxa.
Biochemical Investigation on Antioxidative and Antinutritional Characters of Yellow Seeded Brassica Genotypes for Quality Assessment

Yellow seeded Brassica is one of the most important oilseed crop cultivated in many parts of the world. The oil is consumed predominantly as edible oil and the defatted meal cake is utilized as animal/poultry feed. In the present study, intact seeds and defatted meal of 12 yellow-seeded Brassica genotypes evaluated for the presence of anti-oxidative and anti-nutritive factors. The maximum phenolic, orthodihydroxy phenols, flavonoid contents observed for Bio 39(16.946 mg/g), Bio 30(2.38 mg/g) and Bio 39(8.282 mg/g) repectively. The crude fibre, phytic acid and glucosinolate contents were found to be minimum in Bio 21 (6.95%), Bio 2 (3.632%) and Bio 38 (54.324 μmole/g) respectively. Vitamin C content was maximum in Bio 36 and Bio 3. The α-tocopherol content was observed to be maximum Bio 2 (61.875 mg/100g). The total antioxidant activity varied from 5.95 mg AAE/g in Bio 28 to 14.395 mg AAE/g in Bio 39. The DPPH radical scavenging activity was observed to be maximum in Bio 30 and reducing power was found to be maximum in Bio 21(0.867 ± 0.023). The present findings may be utilized for determining the quality status to ascertain their potential for development of better cultivar.
The functional significance of multiple Pax7 isoforms

The Pax7 gene is critical for specification of both neurons in the mid-brain and skeletal muscle satellite cells. Several alternate transcripts are transcribed from the single gene. Previous studies have shown that the resultant alternate Pax7 isoforms differ in the structure of their paired domain (a DNAbinding domain that influences target gene selection), yet the functional significance of each isoform for specification of neurogenic and myogenic cell types remains unknown. Although previous studies have identified the presence of multiple alternate Pax7 transcripts in both neurogenic and myogenic cell lines, more research is necessary to understand the functional significance of the alternate Pax7 isoform that each transcript encodes. The aim of this research was to investigate DNA-binding differences of each Pax7 isoform to reveal it's specific contribution to embryonic development. A chromatin immunoprecipitation technique which purifies genomic fragments bound by individual Pax7 isoforms was employed, for the purpose of determining DNA-binding differences. Understanding the functional specificity of each Pax7 transcript i's important as these transcripts are possible candidates for future stem cell/ gene therapy approaches aimed at developing novel treatments for Neurodegenerative diseases and Duchene Muscular Dystrophy.
An Original Theory or New Hypothesis of the Universe

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Recognition of the pyrimidine-tract of the pre-mRNA by U2AF and a novel splicing factor PUF60

The genetic information required for encoding functional protein molecules is interrupted in eukaryotes by non-coding sequences. These non-coding sequences, called introns, must be removed from the transcribed RNA molecule by the spliceosome before the genetic information, encoded in exons, can be used by the cell. The process of removing introns and joining exons is called splicing. The splice site sequences are recognized multiple times during splicing of the intron, presumably as a mechanism to ensure high fidelity splicing. Recognition of the intron by the spliceosome requires the interaction of many protein and snRNP components. The first intron recognition events are the recognition of the 5' splice site sequence by U 1 snRNP, recognition of the branch sequence by SF1/BBP, and recognition of the pyrimidine-tract sequence by U2AF. The 5' splice site and the branch sequence are subsequently recognized by U5 and U6 snRNPs and by U2 snRNP, respectively. The PUF splicing activity was identified as a second pyrimidinetract binding factor that is required for efficient splicing in vitro. The PUF activity is required for efficient formation of the stable, ATP-independent U2 snRNP:pre-mRNA complex, An . U2AF is not required for splicing under certain conditions. However, the PUF activity is required for splicing even in the absence of U2AF. The PUF activity is composed of the previously described splicing factor p54 and the novel protein PUF60. PUF60 binds specifically to pyrimidine-tract RNA, is conserved between vertebrates and the invertebrate Drosophila, and forms SDS-resistant dimers. The SDS-resistant dimerization of PUF60 is mediated by the C-terminal domain, the PUMP domain. Several other proteins containing PUMP-domain homologies have been identified. Among these PUMP-domain homologies is the domain of the small subunit of U2AF which is required for the stable proteinprotein interaction between the small subunit of U2AF and the large subunit of U2AF. The PUMP domain may generally mediate protein-protein interactions. Thesis Supervisor: Phillip A. Sharp Title: Salvador E. Luria Professor of Biology and Head, Department of Biology
Regulation of SCF Ubiquitin Ligases by Jab1/Csn5 and the Cop9 Signalosome

SCF ubiquitin ligases regulate the ubiquitin-dependent proteolysis of a myriad of substrate proteins, including p27, Cyclin E, and IkBa. To further gain insight into SCF regulation and function, we purified SCF from mammalian cells and found the Cop9 Signalosome associated with SCF. Interestingly, deletion of the CSN in S. pombe resulted in the hypermodification of Cul1 with Nedd8 in vivo. Furthermore, we found that the CSN can promote the removal of Nedd8 from Cul1 in vitro, suggesting CSN regulates SCF through deneddylation. To investigate the basis of CSN-dependent deneddylation activity, we analyzed the CSN and the 26S proteasome for conserved sequences that could be representative of a catalytic motif. We identified the JAMM motif in Csn5 and Rpn11 of the proteasome. Mutations in JAMM eliminated CSN-dependent deneddylating activity. Moreover, mutations in JAMM reduce the restrictive temperature of several SCF temperature sensitive mutants, suggesting that CSN acts positively on SCF activity. Finally, a JAMM mutant failed to rescue Csn5D defects in drosophila. To investigate the biological effect due to loss of deneddylating activity, we constructed a stable cell line that expresses an inducible siRNA sequence toward CSN5. We found that knock-down of Csn5 results in a dramatic decrease in F-box protein levels. Moreover, this loss correlates with F-box protein substrate accumulation and hyperneddylation of Cul1. We propose an autocatalytic mechanism for the turnover of F-box proteins that is dependent upon the deneddylating activity of CSN.
Lymphomatous Variant of Adult T-cell Leukemia/Lymphoma

Sir, A 70-year-old male presented with chief complaints of asymptomatic raised skin lesions on the face, trunk, and upper extremities of 1-month duration. Skin lesions increased in number and size rapidly. No history of weight loss or loss of appetite was noted. No history of blood transfusion or travel abroad was also found. On examination, there were multiple discrete erythematous dome-shaped papules and nodules of sizes varying from 0.2 to 2 cm with shiny surface distributed on the face, trunk, and extremities [Figure 1]. Multiple, firm, mobile, nontender, enlarged lymph nodes 2 cm x 2 cm were found bilaterally at cervical, axillary and inguinal regions. Systemic examination was non-contributory. Clinical possibilities of B-cell lymphoma and mycosis fungoides (MF) were considered.
Multivariate data analysis

Chapter 1: Introduction Chapter 2: Examining Your Data Chapter 3: Factor Analysis Chapter 4: Regression Chapter 5: Multiple Discriminant Analysis Chapter 6: Manova Chapter 7: Conjoint Analysis Chapter 8: Cluster Analysis Chapter 9: MDS Chapter 10: Structural Equation Modeling: An Introduction Chapter 11: SEM: Confirmatory Factor Analysis Chapter 12: SEM: Testing A Structural Model
New Genera and New Species of the Tribe Elicini (Hemiptera: Fulgoroidea: Tropiduchidae) with Key to Tropiduchid Genera Known from Madagascar

Abstract. The family Tropiduchidae Stål in Madagascar according to distribution and relationships of genera is discussed. A key to all tropiduchid genera as well as the checklist of species known from Madagascar are proposed. Two new genera of the tribe Elicini Melichar, Bolitropis gen. nov. with 6 new species (B. irwini sp. nov., B. montanus sp. nov., B. olsufievi sp. nov., B. imperator sp. nov., B. strobilus sp. nov., B. synavei sp. nov.) and Bambomada gen. nov. with a single new species B. flava sp. nov. are described.