Exploiting zoning based on approximating splines in cursive script recognition

Because of its complexity, handwriting recognition has to exploit many sources of information to be successful, e.g. the handwriting zones. Variability of zone-lines, however, requires a more flexible representation than traditional horizontal or linear methods. The proposed method therefore employs approximating cubic splines. Using entire lines of text rather than individual words is shown to improve the zoning accuracy, especially for short words. The new method represents an improvement over existing methods in terms of range of applicability, zone-line precision and zoning-classification accuracy. Application to several problems of handwriting recognition is demonstrated and evaluated

EuPathDomains: The Divergent Domain Database for Eukaryotic Pathogens

International audienceEukaryotic pathogens (e.g. Plasmodium, Leishmania, Trypanosomes, etc.) are a major source of morbidity and mortality worldwide. In Africa, one of the most impacted continents, they cause millions of deaths and constitute an immense economic burden. While the genome sequence of several of these organisms is now available, the biological functions of more than half of their proteins are still unknown. This is a serious issue for bringing to the foreground the expected new therapeutic targets. In this context, the identification of protein domains is a key step to improve the functional annotation of the proteins. However, several domains are missed in eukaryotic pathogens because of the high phylogenetic distance of these organisms from the classical eukaryote models. We recently proposed a method, co-occurrence domain detection (CODD), that improves the sensitivity of Pfam domain detection by exploiting the tendency of domains to appear preferentially with a few other favorite domains in a protein. In this paper, we present EuPathDomains (http://www.atgc-montpellier.fr/EuPathDomains/), an extended database of protein domains belonging to ten major eukaryotic human pathogens. EuPathDomains gathers known and new domains detected by CODD, along with the associated confidence measurements and the GO annotations that can be deduced from the new domains. This database significantly extends the Pfam domain coverage of all selected genomes, by proposing new occurrences of domains as well as new domain families that have never been reported before. For example, with a false discovery rate lower than 20%, EuPathDomains increases the number of detected domains by 13% in Toxoplasma gondii genome and up to 28% in Cryptospordium parvum, and the total number of domain families by 10% in Plasmodium falciparum and up to 16% in C. parvum genome. The database can be queried by protein names, domain identifiers, Pfam or Interpro identifiers, or organisms, and should become a valuable resource to decipher the protein functions of eukaryotic pathogens

Hidrolitički potencijal β-ksilozidaze iz plijesni Talaromyces thermophilus i njezina primjena u kontinuiranoj proizvodnji ksiloze

We report here the enhanced hemicellulase production by a Talaromyces thermophilus strain in a fed-batch fermentation using 3.6-litre laboratory-controlled bioreactor. When grown on wheat bran, this fungus produces a wide spectrum of polysaccharide-hydrolysing enzymes, mainly endo-β-1,4-xylanase (27 U/mL), β-xylosidase (1.4 U/mL), α-L-arabinofuranosidase (1.05 U/mL) and β-D-mannosidase (0.78 U/mL). The β-xylosidase was purified and shown to hydrolyse xylobiose and short xylooligosaccharides, but it was inactive on xylan. It released xylose from xylooligosaccharides with a degree of polymerisation ranging from 2 to 5. Talaromyces thermophilus β-xylosidase activity was unaffected by high glucose or arabinose concentration (0.5 M) and retained 75 % of its original activity in the presence of 133 mM xylose. Chitosan-immobilised β-xylosidase was used in a continuous process of conversion of wheat bran hydrolysate to xylose in a packed bed reactor. Xylose production of 18.6 mg/g was reached after six hours in the bioreactor and was twofold higher than that produced by the free enzyme. The produced xylose was further converted into xylitol using the crude intracellular enzyme of Talaromyces thermophilus.U radu je opisana mogućnost povećanja proizvodnje hemicelulaze s pomoću soja plijesni Talaromyces thermophilus u šaržnom procesu s pritokom supstrata provedenom u laboratorijski kontroliranom bioreaktoru zapremnine 3,6 L. Na podlozi je od pšeničnih mekinja plijesan proizvela različite enzime što hidroliziraju polisaharide, kao što su: endo-β-1,4-ksilanaza (27 U/mL), β-ksilozidaza (1,4 U/mL), α-L-arabinofuranozidaza (1,05 U/mL) i β-D-manozidaza (0,78 U/mL). Pročišćena je β-ksilozidaza hidrolizirala ksilobiozu i kratkolančane ksilooligosaharide, dok u prisutnosti ksilana nije bila aktivna. Stupanj je polimerizacije ksiloze iz oligosaharida bio u rasponu od 2 do 5. Visoka koncentracija (0,5 M) glukoze ili arabinoze nije utjecala na aktivnost β-ksilozidaze iz plijesni Talaromyces thermophilus, koja je zadržala 75 % aktivnosti u prisutnosti 133 mM ksiloze. U kontinuiranoj proizvodnji ksiloze iz hidrolizata pšeničnih mekinja u reaktoru s nasutim slojem nosača korištena je β-ksilozidaza imobilizirana na kitozanu. Prinos ksiloze od 18,6 mg/g postignut je nakon 6 sati u bioreaktoru, što je dvostruko više od prinosa postignutog pomoću slobodnog enzima. Dobivena je ksiloza prevedena u ksilitol pomoću nepročišćenog intracelularnog enzima iz plijesni Talaromyces thermophilus

Characteristics of epstein barr virus variants associated with gastric carcinoma in Southern Tunisia

<p>Abstract</p> <p>Backgroud</p> <p>EBV-associated Gastric Carcinoma (EBVaGC) has a distinct clinical features and its prevalence is variable worldwide.</p> <p>Results</p> <p>To determine the prevalence of EBVaGC in Tunisia, EBV-encoded small RNA (EBER) expression was assessed in 81 gastric carcinoma (GC) specimens. The nuclear EBER expression was detected in 12 out of 81 GC cases (14.81%) and concordance between the score range of EBER staining and the number of EBV DNA copies as estimate by QPCR is observed. On the other hand, we found that EBVaGC strongly correlated with age at diagnosis, and weakly with tumor differentiation and venous invasion.</p> <p>Furthermore, the EBVaGC specimens were subjected to determine the EBV DNA polymorphisms. Our results show a unique genetic profile of the EBV strains regarding the A and D types, the F prototype, the retention of <it>Xho</it>I restriction site and the 30 bp del-LMP1 variant. <b><it>According to our previous studies on nasopharyngeal carcinoma (NPC), we suggested that EBV strains associated to GC and NPC shared some similarities in Tunisian patients</it>.</b></p> <p>Conclusion</p> <p>The prevalence of EBVaGC is of 14.81% in the southern Tunisia and that common EBV strain are associated with both NPC and GC which are likely to differ from Asian strains. Our findings support therefore a certain geographical distribution of EBV strains which is not restricted to EBV-associated malignancies.</p

Probiotics as a Beneficial Modulator of Gut Microbiota and Environmental Stress for Sustainable Mass-Reared <em>Ceratitis capitata</em>

The Mediterranean fruit fly Ceratitis capitata (medfly) is a major pest throughout the world and one of the most destructive. Several strategies for controlling this pest have been proposed, including the sterile insect technique (SIT). The SIT’s effectiveness against the medfly is well documented. Sterile medflies, on the other hand, can perform poorly. Reduced mating compatibility and mating competitiveness in the field may be caused by genetic and symbiotic differences between natural and laboratory medfly populations. Probiotic gut symbionts have been shown to facilitate control strategies and improve male medfly fitness. They are equally effective in the live and inactivated forms when administered to medfly adults or larvae. They have been shown to modulate a large set of inducible effector molecules including antimicrobial peptides (AMP) and stress-responsive proteins. The selection procedures of probiotics for their use in the medfly rearing process are reviewed, and other pathways for selection are proposed based on recent in silico studies. This chapter summarizes the most relevant evidence from scientific literature regarding potential applications of probiotics in medfly as an innovative tool for biocontrol, while also shedding light on the spectrum of symbiotic relationships in medfly that may serve as a powerful symbiotic integrative control approach

Simultaneous gene expression profiling in human macrophages infected with Leishmania major parasites using SAGE

<p>Abstract</p> <p>Background</p> <p><it>Leishmania </it>(<it>L</it>) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MΦ) striving to eliminate the pathogen and the parasite struggling for its own survival.</p> <p>To investigate this host-parasite conflict at the transcriptional level, in the context of monocyte-derived human MΦs (MDM) infection by <it>L. major </it>metacyclic promastigotes, the quantitative technique of serial analysis of gene expression (SAGE) was used.</p> <p>Results</p> <p>After extracting mRNA from resting human MΦs, <it>Leishmania</it>-infected human MΦs and <it>L. major </it>parasites, three SAGE libraries were constructed and sequenced generating up to 28,173; 57,514 and 33,906 tags respectively (corresponding to 12,946; 23,442 and 9,530 unique tags). Using computational data analysis and direct comparison to 357,888 publicly available experimental human tags, the parasite and the host cell transcriptomes were then simultaneously characterized from the mixed cellular extract, confidently discriminating host from parasite transcripts. This procedure led us to reliably assign 3,814 tags to MΦs' and 3,666 tags to <it>L. major </it>parasites transcripts. We focused on these, showing significant changes in their expression that are likely to be relevant to the pathogenesis of parasite infection: (i) human MΦs genes, belonging to key immune response proteins (e.g., IFNγ pathway, S100 and chemokine families) and (ii) a group of <it>Leishmania </it>genes showing a preferential expression at the parasite's intra-cellular developing stage.</p> <p>Conclusion</p> <p>Dual SAGE transcriptome analysis provided a useful, powerful and accurate approach to discriminating genes of human or parasitic origin in <it>Leishmania</it>-infected human MΦs. The findings presented in this work suggest that the <it>Leishmania </it>parasite modulates key transcripts in human MΦs that may be beneficial for its establishment and survival. Furthermore, these results provide an overview of gene expression at two developmental stages of the parasite, namely metacyclic promastigotes and intracellular amastigotes and indicate a broad difference between their transcriptomic profiles. Finally, our reported set of expressed genes will be useful in future rounds of data mining and gene annotation.</p

Ten simple rules for organizing a bioinformatics training course in low- And middle-income countries

© 2021 Moore et al.Bioinformatics training is required at every stage of a scientist’s research career. Continual bioinformatics training allows exposure to an ever-changing and growing repertoire of techniques and databases, and so biologists, computational scientists, and healthcare practitioners are all seeking learning opportunities in the use of computational resources and tools designed for data storage, retrieval, and analysis. There are abundant opportunities for accessing bioinformatics training for scientists in high-income countries (HICs), with well-equipped facilities and participants and trainers requiring minimal travel and financial costs alongside a range of general advice for developing short bioinformatics training courses [1–3]. However, regionally targeted bioinformatics training in low- and middle-income countries (LMICs) often requires more extensive local and external support, organization, and travel. Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region. A common model of training, used as the basis of this article, includes a local host collaborating with local, regional, and international experts gathering to train local or regional participants. Recently, there has been a growth of capacity strengthening initiatives in LMICs, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [4–6], the Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program [9]. One of the important strands of these initiatives is a drive to organize and deliver valuable bioinformatics training, but organizing and delivering short bioinformatics training workshops in an LMIC present a unique set of challenges. This paper attempts to build upon the sage advice for organizing bioinformatics workshops with specific guidance for organizing and delivering them in LMICs. It describes the processes to follow in organizing courses taking into consideration the low-resource setting. We should also note that LMICs are not a monolithic group and that setting, context, temporality, and specific location matters. LMICs are a complex regional grouping [10] and should be treated as such; however, we will present some common lessons that we hope will help organizers and trainers of bioinformatics training events in LMICs to navigate the often different, challenging, and rewarding experience.The authors who contributed to this manuscript are funded as follows: BM receives salary support from Wellcome Trust grants [WT108749/Z/15/Z, WT108749/Z/15/A], PC, VR, NM, AG’s salaries are funded in whole, or in part, by the NIH Common Fund H3ABioNet grant [U24HG006941], MC, SLFV, AR, PG, PCL’s salaries were partly funded by the UKRI-BBSRC ‘Capacity building for bioinformatics in Latin America’ (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1], JDLR is funded by ISCiii AES [ref. PI18/00591] at the CSIC/USAL (Spain) and by CYTED, RIABIO (Red Iberoamericana 521RT0118), AM’s salary is funded by [WT206194/Z/17/Z], GO is funded by the CABANA grant and SM is funded by the EMBL-EBI

Characterisation of a recombinant β-xylosidase (xylA) from Aspergillus oryzae expressed in Pichia pastoris

β-xylosidases catalyse the hydrolysis of short chain xylooligosaccharides from their non-reducing ends into xylose. In this study we report the heterologous expression of Aspergillus oryzae β-xylosidase (XylA) in Pichia pastoris under the control of the glyceraldehyde-3-phosphate dehydrogenase promoter. The recombinant enzyme was optimally active at 55°C and pH 4.5 with Km and Vmax values of 1.0 mM and 250 μmol min−1 mg−1 respectively against 4-nitrophenyl β-xylopyranoside. Xylose was a competitive inhibitor with a Ki of 2.72 mM, whereas fructose was an uncompetitive inhibitor reducing substrate binding affinity (Km) and conversion efficiency (Vmax). The enzyme was characterised to be an exo-cutting enzyme releasing xylose from the non-reducing ends of β-1,4 linked xylooligosaccharides (X2, X3 and X4). Catalytic conversion of X2, X3 and X4 decreased (Vmax and kcat) with increasing chain length