1,721,009 research outputs found
A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization
No full textA novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits
Full text linkThe enrichment of targeted regions within complex next generation sequencing libraries commonly uses biotinylated baits to capture the desired sequences. This method results in high read coverage over the targets and their flanking regions. Oxford Nanopore Technologies recently released an USB3.0-interfaced sequencer, the MinION. To date no particular method for enriching MinION libraries has been standardized. Here, using biotinylated PCR-generated baits in a novel approach, we describe a simple and efficient way for multiplexed enrichment of MinION libraries, overcoming technical limitations related with the chemistry of the sequencing-adapters and the length of the DNA fragments. Using Phage Lambda and Escherichia coli as models we selectively enrich for specific targets, significantly increasing the corresponding read-coverage, eliminating unwanted regions. We show that by capturing genomic fragments, which contain the target sequences, we recover reads extending targeted regions and thus can be used for the determination of potentially unknown flanking sequences. By pooling enriched libraries derived from two distinct E. coli strains and analyzing them in parallel, we demonstrate the efficiency of this method in multiplexed format. Crucially we evaluated the optimal bait size for large fragment libraries and we describe for the first time a standardized method for target enrichment in MinION platform
Cloning production and research of the immulological specifications of core / core +1 proteins of HCH virus
No full textHepatitis C virus (HCV) is a member of Ηepacivirus genus within the Flaviviridae family. It infects the human liver and is a major cause of acute and chronic hepatitis, which in turn leads to severe liver diseases, such as chronic active hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). An estimated 170 million people (3% of world population) is infected by HCV. Comparison of nucleotide sequence data has led to the classification of HCV into six major types (genotypes) that differ from each other by 30% over the entire genome and several closely related subtypes that differ from each other by around 20%. Genotypes 1, 2 and 3 are spread worldwide. In Western Europe, HCV genotype 1 is the most prevalent genotype in individuals aged over 40 years, whereas genotype 3 is mostly common in young people, especially in intravenous drug users. In Greece, HCV genotype 1 is the most prevalent (46.9%), followed by genotype 3 (28.1%), 4 (13.2%), 2 (6.9%) and 5 (0.4%). Moreover, a sharp (13-fold) increase for genotype 3 was observed from 1970 to 1990, suggesting that genotype 3 and intravenous drug use are the major forces for HCV epidemic in the recent cohort of HCV-infected individuals in Greece.
Although there is no vaccine or broadly effective therapy, treatment of HCV infection with standard combination therapy, which includes pegylated interferon-a (Peg-IFN-a-2a) plus ribavirin, has an overall estimated success rate of 50% for genotype 1 and about 80% for genotype 2 and 3. Viral load of less than 600,000 IU/mL at the beginning of the therapy is also a major predictor of a sustained virological response (SVR). Host factors such as age, race, gender, obesity and degree of hepatic fibrosis, also affect the chance of an SVR.
HCV genome consists of a 9.6 kb single-strand, positive-sense RNA, which encodes for a single immature polyprotein of about 3,000 amino acids. This translation product is cleaved by cellular and viral proteases to yield at least four structural (C, E1, E2, p7) and six non structural (NS2, NS3, NS4A, NS4B, NS5A, NS5B) mature proteins. Recent studies by different groups of investigators, have provided strong evidence for the presence of a functional alternative open reading frame (ORF) within the core genomic region in the +1 reading frame (known as ARF or core+1 ORF), that leads to the production of ‘core overlapping’ peptides known as alternative reading frame proteins (ARFPs) or frameshift (F) or core+1 proteins.
Since its discovery, different isoforms of ARF/core+1 protein have been reported based on differences in the translation initiation mechanism that are found to stimulate expression of ARF/core+1 ORF in cultured cells. The biological significance of the ARF/core+1 expression remains elusive. However, several studies imply the presence of this protein in HCV patients via its specific recognition by serum antibodies (anti-ARF/core+1 Abs). Some of these studies suggest a correlation between the presence of anti ARF/core+1 Abs and specific stages of HCV infection, such as the latest stages of liver steatosis and hepatocellular carcinoma (HCC).
In the present study we estimated the prevalence of specific anti-ARF/core+1 Abs in HCV infected patients belonging to genotypes 1a/1b or 3a, treated with Peg-IFN-a-2a plus ribavirin and its association with patients’ age and HCV-RNA levels at baseline. The anti-ARF/core+1 Ab’s titer dynamics during therapy follow up were also investigated.
For these purposes, highly purified HCV core and ARF/core+1 recombinant proteins were expressed in Escherichia coli. Using an enzyme-linked immunosorbent assay (ELISA), we assessed the prevalence of anti-ARF/core+1 antibodies in 90 chronic hepatitis C patients. Samples derived from 92 healthy blood donors were used as negative controls. All HCV-RNA positive serum samples reacted with core 1a antigen while 15 (37.5%) out of 40 and 14 (28%) out of 50 patients infected with HCV-1a/1b and HCV-3a respectively, were found to have anti-ARF/core+1 antibodies into their serum before treatment initiation. These antibodies were persistently present during treatment follow up and linked to elevated levels of HCV RNA at baseline.O ιός της ηπατίτιδας C (HCV) είναι μέλος του γένους των Hepacivirus που ανήκουν στην οικογένεια Flaviviridae. Μολύνει το ανθρώπινο ήπαρ και είναι μία κύρια αιτία οξείας και χρόνιας ηπατίτιδας, η οποία κατά περιπτώσεις οδηγεί σε σοβαρές ηπατικές ασθένειες, όπως χρόνια ενεργό ηπατίτιδα, κίρρωση και ηπατοκυτταρικό καρκίνο (HCC). Περίπου 170 εκατομμύρια άνθρωποι (3% του παγκόσμιου πληθυσμού) έχουν μολυνθεί από τον HCV. H σύγκριση δεδομένων νουκλεοτιδικών αλληλουχιών έχει οδηγήσει στην κατηγοριοποίηση του HCV σε έξι κύριους τύπους (γονότυπους) που διαφέρουν μεταξύ τους κατά 30% σε ολόκληρο το γονιδίωμά τους, σε αρκετούς συγγενικούς υπότυπους που διαφέρουν μεταξύ τους περίπου 20%. Οι γονότυποι 1, 2, και 3 έχουν παγκόσμια διασπορά. Στην Δυτική Ευρώπη ο γονότυπος 1 είναι ο πιο διαδεδομένος σε άτομα άνω των 40 ετών, ενώ ο γονότυπος 3 είναι ο πιο διαδεδομένος ανάμεσα σε νεαρά άτομα και ειδικότερα στους χρήστες ενδοφλέβιων ουσιών. Στην Ελλάδα, ο γονότυπος 1 είναι ο πιο διαδεδομένος (46.9%), ενώ ακολουθεί ο γονότυπος 3 (28.1%), 4 (13.2%), 2 (6.9%), και 5 (0.4%). Επιπρόσθετα, μία απότομη αύξηση του γονότυπου 3 σε χρήστες ενδοφλέβιων ουσιών παρατηρήθηκε μεταξύ του 1970 και 1990, προτείνοντας ότι ο γονότυπος 3 και οι χρήστες ενδοφλέβιων ουσιών είναι οι κινητήριες δυνάμεις της επιδημίας του HCV στον Ελληνικό πληθυσμό.
Παρότι δεν υπάρχει εμβόλιο ή ευρέως αποτελεσματική θεραπεία για την λοίμωξη από τον HCV, η συνδυαστική θεραπεία με πεγκυλιωμένη ιντερφερόνη-a (Peg-IFN-a-2a) και ριμπαβιρίνη, έχει μία συνολική αποτελεσματικότητα γύρω στο 50% για τον γονότυπο 1 και γύρω στο 80% για τους γονότυπους 2 και 3. To χαμηλό ιϊκό φορτίο (<600,000 IU/mL) κατά την εκκίνηση της θεραπείας είναι επίσης ένας κύριος προγνωστικός δείκτης μίας παρατεταμένης ιικής ανταπόκρισης (SVR). Παράγοντες που αφορούν τον ξενιστή όπως η ηλικία, η φυλή, η ηπατική ίνωση επίσης επηρεάζουν την ανταπόκριση στην θεραπεία.
Το γονιδίωμα του HCV αποτελείται από ένα θετικής πολικότητας μονόκλωνο μόριο RNA μήκους 9.6kb το οποίο κωδικοποιεί για μια πολυπρωτεΐνη μήκους 3.000 αμινοξέων. Το μεταφραστικό αυτό προϊόν πρωτεολύεται από κυτταρικές και ιϊκές πρωτεάσες και έτσι παράγει τουλάχιστον τέσσερις δομικές (C, E1, E2, p7) και έξι μη δομικές (NS2, NS3, NS4A, NS4B, NS5A, NS5B) ώριμες πρωτεΐνες. Πρόσφατες μελέτες από ανεξάρτητες ομάδες ερευνητών, έχουν φέρει στο φως ισχυρές ενδείξεις για την παρουσία ενός λειτουργικού εναλλακτικού πλαισίου ανάγνωσης (ORF) μέσα στην γονιδιακέ περιοχή core, στο +1 πλαίσιο ανάγνωσης (γνωστό ως ARF ή core+1 ORF), που οδηγεί στην παραγωγή ‘core-επικαλυπτόμενων’ πεπτιδίων γνωστών ως πρωτεΐνες εναλλακτικού πλαισίου ανάγνωσης (ARFPs) ή frameshift (F) ή core+1 πρωτεΐνες.
Από την ανακάλυψη της μέχρι σήμερα, διάφορες ισομορφές της ARF/core+1 έχουν περιγραφεί, κυρίως λόγω ύπαρξης διαφορετικών μηχανισμών έναρξης της μετάφρασης που έχουν βρεθεί να επάγουν το ARF/core+1 πλαίσιο ανάγνωσης σε καλλιεργούμενα κύτταρα. Η βιολογική σημασία της έκφρασης της ARF/core+1 παραμένει αδιευκρίνιστη. Παρόλα αυτά, αρκετές μελέτες καταδεικνύουν την ύπαρξη αυτής της πρωτεΐνης σε ασθενείς με λοίμωξη από τον HCV, μέσω αναγνώρισής της από αντισώματα του ορού (anti-ARF/core+1 Abs). Κάποιες από αυτές τις μελέτες προτείνουν μία συσχέτιση της παρουσίας αυτών των αντισωμάτων με συγκεκριμένα στάδια της λοίμωξης από τον HCV, όπως τα τελικά στάδια ηπατικής στεάτωσης και τον ηπατοκυτταρικό καρκίνο (HCC).
Στην παρούσα μελέτη εξετάσαμε την παρουσία ειδικών anti-ARF/core+1 αντισωμάτων σε ασθενείς που είχαν μολυνθεί από τον ιό HCV γονότυπου 1a/b ή 3a, και είχαν ακολουθήσει θεραπεία με Peg-IFN-a-2a και ριμπαβιρίνη, καθώς και την συσχέτισή τους με την ηλικία των ασθενών και τα επίπεδα του HCV RNA πριν την έναρξη της θεραπείας. Μελετήθηκε επίσης δυναμική του τίτλου των anti-ARF/core+1 αντισωμάτων κατά την διάρκεια του follow up της θεραπείας.
Για τον σκοπό της μελέτης, υψηλής καθαρότητας HCV core και ARF/core+1 ανασυνδυασμένες πρωτεΐνες εκφράστηκαν σε βακτήρια Escherichia coli. Χρησιμοποιώντας την ανοσοενζυμική μέθοδο ELISA, μελετήσαμε την παρουσία των anti-ARF/core+1 αντισωμάτων σε 90 χρόνιους ασθενείς. Δείγματα πλάσματος από 92 υγιή άτομα χρησιμοποιήθηκαν σαν αρνητικά control. Όλοι οι HCV-RNA θετικοί οροί αντέδρασαν με το core 1a αντιγόνο, ενώ 15 (37.5%) από τους 40 και 14 (28%) από τους 50 ασθενείς που είχαν μολυνθεί από την ιό HCV-1a/1b και HCV-3a αντίστοιχα, βρέθηκε να έχουν anti-ARF/core+1 αντισώματα στον ορό τους πριν την έναρξη της θεραπείας. Αυτά τα αντισώματα ήταν παρόντα καθ’ όλη την διάρκεια της θεραπείας, και συνδέονταν με αυξημένα επίπεδα HCV-RNA σε αυτούς τους ασθενείς
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
