Miracle-dz/UniFAR-FTUs huggingface dataset:
GenBank

GenBank® (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.
Elucidation of the Multi-Faceted Roles of the SIN (Septation Initiation Network); Understanding How the SIN Promotes Cytokinesis and Inhibits Interphase Growth in the Fission Yeast Schizosaccharomyces pombe: A Dissertation

Cytokinesis is the cytoplasmic division of one cell into two independent daughter cells. Precise regulation of cytokinesis during cell cycle is essential for healthy and rapid multiplication of any organism. Schizosaccharomyces pombe has emerged as an excellent model system to study eukaryotic cell division regulation. This rod shaped organism grows by bipolar elongation in interphase when its actin cytoskeleton is concentrated at the cell ends (poles). However, growth stops in mitosis and the actin cytoskeleton is rearranged to facilitate assembly of the contractile actomyosin ring at the cell middle. Although several studies have focused on the separate processes of growth and division, it was unclear how cells regulate the cytoskeletal remodeling during the transition between the different stages of the cell cycle. The Septation Initiation Network (SIN) is a signaling cascade essential for fission yeast cytokinesis (Balasubramanian et al., 1998; Mishra et al., 2004) and the MOR (morphogenesis) signaling pathway is essential for interphase bipolar growth (Kanai et al, 2005). Interestingly, inactivation of the SIN not only failed to maintain the cytokinetic apparatus at the cell middle but also caused the redistribution of the cytoskeletal elements like actin to the cell ends that led to bipolar cell elongation similar to cells in interphase (Mishra et al., 2004). These results suggested that SIN signaling inhibits interphase bipolar growth, but it was not clear if the SIN had a direct role in inhibition of interphase growth during mitosis and this question was the major focus of this thesis. The results presented in Chapter II show a novel cross-pathway interaction between the SIN and the MOR in the fission yeast. Our results in Chapter III suggest that some of the MOR pathway components might be important for coordination between nuclear and cytoplasmic divisions in mitosis, revealing novel roles of the pathway. In a separate study (Chapter IV) we sought to identify additional regulators of the SIN and cytokinesis through a suppressor screen and found that the nucleolar rDNA transcription machinery inhibits cytokinesis in fission yeast.
Manipulation of pyrophosphate fructose 6-phosphate 1-phosphotransferase activity in sugarcane

Despite the apparent ubiquity of pyrophosphate: fructose 6-phosphate 1phosphotransferase (PFP) in plants no clear physiological role has emerged for it. Transgenic plants with upor down-regulated PFP activity showed only small changes in the levels of metabolites directly associated with it but no significant, stable phenotypic changes. In sugarcane PFP activity is inversely correlated to sucrose content in maturing internodal tissues, suggesting a more prominent role for it in carbohydrate partitioning in these tissues. In this review I will therefore first give an overview of the molecular, kinetic and regulatory characteristics of plant PFPs, which could help elucidate its apparent role in sucrose metabolism and then I will discuss these potential roles with specific reference to the sucrose accumulation phenotype in sugarcane. Finally, I present two hypotheses that might explain PFP’s role in sucrose accumulation in sugarcane. INTRODUCTION Sugar metabolism has been studied extensively in sugarcane in an attempt to elucidate the molecular basis of the sucrose storing phenotype (Batta et al. 1995, Moore 1995, Botha et al. 1996, Moore and Maretzki 1996, Lingle 1999, Moore 2005, Rae et al. 2005 and the references in these). In doing so, many of the enzyme reactions involved in sucrose metabolism in sugarcane sink tissues (Figure 1) have been characterised. These include sucrose phosphate synthase (SPS, Grof et al. 1998, Botha and Black 2000), sucrose phosphatase (Gutierrez-Miceli et al. 2002), sucrose synthase (SuSy, Lingle and ∗ To be submitted to Plant Physiology and Biochemistry
Summer Ecology of Indiana Bats in Ohio

The Indiana bat (Myotis sodalis) is a tree roosting species found throughout the eastern United States that is federally listed as endangered by the U.S. Fish and Wildlife Service. A more detailed understanding of summer roosting and foraging habitat for Indiana bats is needed for effective conservation and management. The objectives of this research included identifying and describing aspects of the summer ecology of this species, especially selection of tree roosts and foraging habitat in the Big Darby Creek area in Ohio. During the 2008–2010 seasons, the authors captured 55 Indiana bats and radiotracked 51 individuals. They tracked bats to 56 roost trees 474 times (bat roost days). Roosts were largely clustered in riparian woodland habitat along the Big Darby Creek. Roost trees were of 11 different species but two of the trees could not be identified. Eight of the trees were alive, two were declining, and the rest were dead or in a greater stage of decay. Roost trees were found relatively close to water, and tended to be dead or decaying, have a high percentage of loose bark, and be of a dominant canopy class, when compared to other available trees. The authors calculated 33 home ranges. Average home range size was 210.5 ± 130.6 SD ha (0.84 ± 0.52 SD mi²) for fixed kernel and 374.2 ± 359.6 SD ha (1.49 ± 1.44 SD mi²) for minimum convex polygon. Bats selected woodland and water habitats, and avoided cropland at multiple spatial scales. Although most foraging flights occurred within the riparian corridor, bats also moved outside the corridor to upland areas.
Investigating Functional Motifs within the N- Terminal Domain of Novel Actin Binding Proteins NET1A and NET2A

The NET proteins are a novel family of actin binding proteins that all share a homologous n-terminal actin binding domain (ABD). The aims of this project were to probe potential functional domains within this ABD by creating mutants of NET1A and NET2A as representative family members. Mutants were designed with the aim of disrupting f-actin binding. To identify possible sites for mutation, the ABDs of the NET family were analysed to look for residues that were homologous to all members except NET3B, which has been shown not to bind actin. Once potential residues were identified, point mutants were designed and cloned alongside an ABD deleted construct. The clones were then expressed in a dominant negative approach using transient expression techniques. Infiltrations of NET1A mutants into Nicotiana benthamiana leaves showed changes in the localisation and behaviour of the protein relative to wild type. These included a potential association between NET1A and the ER, identification of a potential single residue in the ABD that contacts f-actin and whose mutation reduces NET1A’s f-actin affinity and the disruption to the association between both the ER and f-actin, and the plasma membrane. Results from these infiltrations have led to the development of a model that suggests potential functions for discrete domains within NET1A. This model will be useful for directing future experiments that aim to identify proteins that NET family interact with and perhaps identify common functions for these novel actin binding proteins.
Symposium on toxicologic pathology of the upper respiratory system. September 14-16, 1988, Durham, North Carolina.

Background: Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies. Results: This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals. Conclusion: These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity. Published: 28 August 2007 BMC Evolutionary Biology 2007, 7:146 doi:10.1186/1471-2148-7-146 Received: 7 November 2006 Accepted: 28 August 2007 This article is available from: http://www.biomedcentral. com/1471-2148/7/146 © 2007 Barthélémy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A chytridiomycosis epidemic and a severe dry season precede the disappearance of Atelopus species from the Venezuelan Andes

Chytridiomycosis has been identified as one of the major forces driving global amphibian declines. Between 1988 and 1994, five Atelopus species endemic to the Venezuelan Andes disappeared. We examined histological samples of Andean Atelopus species available in Venezuelan museum collections for the presence of the chytrid fungus Batrachochytrium dendrobatidis. When infection was detected, sympatric species were examined to investigate the occurrence of the pathogen and how widespread it was. Infection with B. dendrobatidis is reported for the first time in Atelopus carbonerensis, A. mucubajiensis and A. sorianoi, Mannophryne cordilleriana and an undescribed Leptodactylus species. The spatio-temporal patterns of prevalence of this pathogen in Atelopus individuals, with all infections concentrated in one year but spread over distant locations, suggest that synchronized epidemic outbreaks occurred in populations of these Atelopus species in the years prior to their disappearances. Local climate data indicate that one of the most severe dry seasons recorded in the region since 1970 coincided with these epidemic events. The climatic-linked epidemic hypothesis seems a plausible explanation for the coincidence between the observed amphibian declines, the chytridiomycosis outbreaks,and the droughts recorded in that area.
Antioxidant capacities of seven flavonoid compounds isolated from pulp of acai fruit (Euterpe oleracea)

The pulp of açai fruit (Euterpe oleracea Mart.) has been demonstrated to exhibit extremely high antioxidant capacity. Seven major flavonoids were isolated from freeze‐dried acai pulp by various chromatographic methods. Their structures were elucidated as orientin (1), homoorientin (2), vitexin (3), luteolin(4), chrysoeriol (5), quercetin (6), and dihydrokaempferol (7) by NMR, MS and compared to authentic standards. Antioxidant capacities of these flavonoids were evaluated by the following assays: oxygen radical absorbance capacity (ORAC); cell‐based antioxidant protection in erythrocyte (CAP‐e); ROS formation in polymorphonuclear granulocytes (ROS PMN). ORAC values varied widely (1,423.6 – 14,817.4 μmol TE/g) among the seven compounds based on numbers and positions of hydroxyl groups and/or substitute groups. The ORAC values of aglycones were generally higher than that of glycosides. CAP‐e results indicated that three compounds (4, 6, 7) could enter the cytosol and significantly reduce oxidative damage within living cells. ROS PMN assay showed four compounds (2, 3, 7, 6) had exceptional anti‐inflammatory properties in reducing ROS formation in PMN cells, even when high amounts of ROS were produced upon hydrogen peroxide administration. Supported by MonaVie LLC.
A Concept Map of Information Systems Research Approaches

This paper presents a simple concept map of the wide and diverse spectrum of information system (IS) research approaches, focusing on helping researchers in having an overview of what these approaches are, what they are grounded on and what methods are available for them. It considers research philosophy, methodology, and method. It should help researchers, especially those getting started in IS research, in getting acquainted with the approaches and in justifying their choices coherently
Discovery and evaluation of novel antimicrobial agents against nosocomial pathogens

[Abstract]: High risks and costs are associated with infections caused by antibiotic-resistant organisms. The continued development of antibiotic resistance in pathogenic organisms means that in order to maintain our current standards in health care and disease treatment, new antibiotics need to be sourced. Such was the ultimate goal of this project. Endophytic fungi, due to their broad diversity, unique habitats and ease of acquisition, have been shown to be an important source of bioactive natural products, including novel antibiotics. Thus, the effort of this project was concentrated on the isolation of endophytic fungi associated predominantly with native plants, and the evaluation of the secondary metabolites they produced. Tissues were harvested from 61 individual plant hosts representing 15 plant species. Tissue segments were prepared and incubated on two different media formulations. As fungal growths became apparent, they were subcultured in order to obtain pure fungal isolates. A total of 133 fungal cultures were progressively isolated, covering over 100 fungal species. Ultimately, 77 of these isolates were screened for antimicrobial activity against a panel of 7 bacterial strains. Three isolates subsequently demonstrated repeatable antimicrobial action. They were identified as Schizophyllum commune, a species of Penicillium and Sporormiella isomera, and their bioactivity further evaluated. During the course of the project, activity originally detected in the S. isomera became indiscernable. The Penicillium species demonstrated some activity, being able to inhibit the growth of Staphylococcus aureus at a dilution of 1:2. It was also found to be mildly toxic to murine fibroblast L929 cells at a dilution factor of between 1:16 and 1:32, depending on the cytotoxicity assay used. Of the three isolates S. commune possessed the highest level of activity. A 1:256 dilution inhibited the growth of staphylococci, including an MRSA strain. A 1:32 dilution was bactericidal against E. coli. However, while it demonstrated useful antimicrobial activity, its toxicity would prevent its immediate development as such – a dilution factor of 1:1024, the highest dilution tested in the cytotoxicity assay, was capable of killing over 50% of L929 cells. Further analysis of this isolate’s products may reveal multiple products, with varying levels of activity and toxicity, novel modes of action, or novel structures. Separation of the active products could allow for further investigations, and if combinatorial chemistry is utilised, their structures may be manipulated in order to reduce the levels of toxicity. As long as bacteria continue to develop resistance to the antibiotics we use to treat their infections, we will need to source new antibiotics. The continued isolation, screening and evaluation of endophytic fungi and their secondary metabolites can only be of benefit to all higher life forms on Earth.
Spatiotemporal organization of exocytosis emerges during neuronal shape change

developed computer-vision software and statistical tools to uncover spatiotemporal aspects of exocytosis. Vesicle fusion behavior differed between vesicle types, cell types, developmental stages, and extracellular environments. Experiment-based mathematical calculations indicated that VAMP2-mediated vesicle fusion supplied excess material for the plasma membrane expansion that occurred early in neuronal morphogenesis, which was balanced by clathrin-mediated endocytosis. Spatial statistics uncovered distinct spatiotemporal regulation of exocytosis in the soma and neurites of developing neurons that was modulated by developmental stage, exposure to the guidance cue netrin-1
The Retropancreatic Fusion Fascia Oriented Splenic Hilar Lymphadenectomy Versus Laparoscopic Approach In D2 Total Gastrectomy

Background The retropancreatic fusion fascia is recognized as the anatomical landmark during retropancreatic mobilization. However, its role in D2 total gastrectomy for proximal advanced gastric cancer (PAGC) remains unexplored. This study aimed to develop the retropancreatic fusion fascia-oriented ex vivo approach for splenic hilar lymphadenectomy (RP-SL) to avoid difficulty in using the total laparoscopic approach (TL-SL). Material/Methods The data for patients with PAGC who underwent D2 total gastrectomy were retrieved from our clinical database and electronic medical records (December 2016 to December 2018), with a 1:1 match ratio for balance of the 2 groups. Results In sum, 84 matched patients were included in the study. There were 2360 retrieved lymph nodes (LNs), with an average of 28.10. Sixteen patients were confirmed with positive splenic hilar lymphadenectomy, and the mean harvested lymph nodes (LNs) were significantly increased in the RP-SL group compared to the TL-SL group (3.07 vs. 2.29, P<0.001), decreased operative time (193.21 min vs. 247.74 min, P<0.001), and less blood loss (96.90 mL vs. 185.24 mL, P=0.001) in the RP-SL group. Postoperative hospital stay (6.55 days vs. 7.26 days), rate of morbidity (9.50% vs. 11.91%), and overall costs (¥65255.64 vs. ¥64419.91) were comparable between the groups (P>0.05). Conclusions The landmark at the conjunction between the superior mesenteric vessels and the inferior pancreatic margin made it feasible to identify the retropancreatic areolar. The RP-SL approach was safe and efficient for splenic hilar lymphadenectomy.
Cytoarchitecture of the Locust Olfactory System

The insect mushroom body (MB) receives and processes olfactory information. The MB is a highly conserved structure found in all but a few insect species, and has been shown to be a relevant area in learning and memory of olfactory information. The functional properties of the intrinsic cells of the MB -- the Kenyon cells (KCs) -- have been extensively studied, and their integrative properties are starting to be understood, particularly in locust. To help decipher its role in odor processing, this thesis presents an in-depth study of the architecture of the locust MB, using a variety of anatomical techniques and original software. Four divisions in the MB's input area, the calyx, are defined and described, as well as a division in one of its output regions, the beta lobe. KCs are characterized based on their morphologies and extents within the calyx divisions and the beta lobe. MB input cells - the projection neurons - are described in relation to their own input area, the antennal lobe, as well as their output to MB calyx divisions. Two classes of cells downstream from the KCs are also defined anatomically and related to immunochemistry on neurotransmitters. A specific area within the brain - the lateral horn lobe - to which projection neurons and extrinsic cells project, is also defined. Similarities of these structures to other insect orders are discussed.
PERIO-ESTHETICS: AN OVERVIEW

Dr. Pradip Giri Associate Professor, Department of Periodontics Department of Periodontics Dr R Ahmed Dental College & Hospital, Kolkata. Contact no.: 9830223821, e-mail: pradipgiri1960@gmail.com CORRESPONDING AUTHOR Esthetic dentistry has seen an evolution in last few decades with the improvement in materials, techniques and conceptual understanding. In terms of clinical evaluation and management in esthetic smile designing, the role of periodontics has seen an uprise over the years. This has helped in achieving not only esthetic but also biologic and functional precision in esthetic dental treatment. Periodontal treatment rendering to better esthetics comprises the establishment of health of the tissue along with a physiologic form and functionality. A variety of esthetic periodontal procedures have been developed which include correction of defects like gingival recession, osseous defects with or without formation of black triangles. Furthermore, correction of the relationship of the teeth and gingiva in frame of the lips has ensured more predictable and esthetic results in conjunction with restorative procedures. Hence, a precise implementation of these procedures in the esthetic management of the dentition is mandatory for better clinical outcomes. This article aims at emphasizing on the factors involved in esthetic evaluation and treatment goals of esthetic periodontal procedures
Feeding style of adolescent mothers and complementary feeding practice of their infants

Objective To evaluate feeding styles of adolescent mothers and complementary feeding practices of their infants. Methods A cross-sectional study comparing a group of dyads of 50 adolescent mothers (ages 15 to 19) with 62 adult mothers (ages 24 to 44) and their infants (9 to 24 months) was performed. All mothers and infants were assisted by three basic health family units in the city of Recife, Brazil. Data were collected through a structured interview on socioeconomic conditions, maternal styles of feeding the child, and evaluation of infant feeding practices. The food styles were classified as responsive, authoritative, and passive, according to the adapted form of
A Phylogenetic Analysis of the Social Wasp Genus Brachygastra Perty, 1833, and Description of a New Species (Hymenoptera: Vespidae: Epiponini)

ABSTRACT Phylogenetic relationships among the species of the genus Brachygastra Perty, 1883, are analyzed based on characters of female morphology, male genitalia, and nest architecture. Analysis of the data matrix with equal weights results in one tree, which is also obtained under implied weighting. A new species is described and an identification key is presented. The males of B. borellii and B. scutellaris are described.