Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus- Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.published_or_final_versio

Amélioration de l’offre fourragère par l’association culturale céréalelégumineuse à double usage en zone nord soudanienne du Burkina Faso

L’étude a été réalisée dans deux types de terroir du plateau central du Burkina Faso: le centre périurbain de Tenkodogo, situé dans la partie Centre-Est et le terroir agropastoral de Monomtenga, localisé au Centre Sud du pays. Elle a consisté en la mise en place dans chacun des deux sites une association culturale sorgho (variété ICSV 1049) x niébé (variété KVX 745 11P). Ces tests ont été conduits par 74 producteurs volontaires du terroir de Monontenga et 25 agropasteurs péri-urbains de Tenkodogo retenus à partir des critères de choix préalablement élaborés et soumis aux producteurs intéressés par le test dans le village. L’association culturale des deux espèces à double objectif s’est avérée intéressante, eu égard aux productions obtenues bien qu’elles soient modestes. Les rendements de 425,21 kg ha-1 en grain avec 1233,47 kg ha-1 en pailles de sorgho et de 235,34 kg ha-1 en graines avec 891,16 kg ha-1 en fanes de niébé obtenus par le mode d’association introduit constituent un important appoint alimentaire pour les familles et le bétail des producteurs . Ces résultats obtenus en rendements culturaux montrent que les nouvelles variétés des deux espèces proposées en milieu rural sont adaptées à l’amélioration du disponible fourrager local.Mots clés : Association culturale, sorgho, niébé, production, Burkina Faso

Production a double objectif d’Andropogon gayanus Kunth, en culture pluviale dans le plateau central du Burkina Faso

L’influence du rythme d’exploitation sur la production à double finalité a été étudiée chez la graminée pérenne locale Andropogon gayanus, dans le plateau central du Burkina Faso. La culture de l’espèce a consisté en la mise en place, par repiquage, d’éclats de souches, suivie de l’exploitation, durant deux années. Les résultats montrent que la coupe de la plante à 40 jours de repousse permet d’obtenir la production fourragère la plus importante, soit 3434 kg de MS/ha, en première année, et 3500 kg de MS/ha, en deuxième année d’exploitation, avec un rendement en pailles, en fin de cycle, respectivement, de 1337 et 1351 kg de MS/ha. La production de fourrage la plus faible est observée avec la coupe de la plante à 30 jours de repousse, suivie de la récolte de la paille en fin de cycle (1107 kg de MS/ha en première année, et 1095 kg de MS/ha en deuxième année. Quant à la production de pailles, l’exploitation en fin de cycle de la plante est le rythme le mieux indiqué pour une production maximale de paille. La coupe de la plante à 40 jours de repousse (pour la production de fourrage), suivie d’une deuxième en fin de cycle (pour la fourniture de paille) se révèle donc être le meilleur rythme d’exploitation, permettant d’obtenir la production optimale, à double finalité, de l’espèce Andropogon gayanus, dans les conditions climatiques nord-soudaniennes. La conservation du fourrage produit et son utilisation, surtout pendant la période de soudure, de même que la confection des seccos à partir des pailles, contribuent à améliorer les revenus des agrospasteurs de la zone.Mots-clés : Andropogon gayanus Kunth, agropasteur, rythme de coupe, fourrage, pailles Burkina Faso.DUAL PROPOSE PRODUCTION OF Andropogon gayanus KUNTH UNDER PLUVIAL CULTIVATION IN THE CENTRAL PLATEAU OF BURKINA FASOThe influence of the rhythm of exploitation on the production of fodder and stem of a local perennial grass Andropogon gayanus Kunth was studied in the Central Plateau of Burkina Faso. The setting up of the species has consisted of planting out of split stumps the first year, followed by exploitation during two years. The results show that cutting the plant at 40 days after regrowth give higher fodder, 3434 kg/ha DM the first year and 3500 kg/ha DM the second year. The corresponding value for stem at the end of growing cycle were respectively 1337 and 1351 kg/ha of DM. The lowest fodder production is obtained with cutting the plants 30 days after planting (1107 and 1095 kg/ha DM the first and second year respectively). For the maximum production of straw, the plants should be exploited only at the end of the development cycle. The cutting of the plants at 40 days after planting is them the best rhythm of exploitation allowing optimal production of the species in terms of fodder and stem in the climatic condition of north Sudan. The conservation of fodder produced and its utilization during harsh period, as well as the making of straw mat «secco» contributed to improve the incomes of agropastoral farmers in the area.Keywords : Andropogon gayanus Kunth, agropastoral people, rhythm of exploitation, forage, stems, Burkina Faso

Psychological, social and health issues in Hong Kong women with osteoporotic fractures

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Randomized controlled trial of the effect of phytosterols-enriched low-fat milk on lipid profile in Chinese

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Dishevelled-3 phosphorylation is governed by HIPK2/PP1Cα/ITCH axis and the non-phosphorylated form promotes cancer stemness via LGR5 in hepatocellular carcinoma

Dishevelled-3 (Dvl3) is regarded as a binding hub with many different interacting partners. However, its regulation and mechanism on cancer stemness remain to be explored. In this study, we showed that Dvl3 was significantly overexpressed in human hepatocellular carcinomas (HCCs) and promoted cancer stemness both in vitro and in vivo. We found that the non-phosphorylated (NP)-Dvl3 was more stable than the phosphorylated form, more active in activating β-catenin transcriptional activity, and more potent in enhancing self-renewal ability in HCC cells. Mechanistically, we confirmed that the homeodomain-interacting protein kinase-2 (HIPK2) and E3 ubiquitin ligase ITCH were able to physically bind to Dvl3 protein. Knockdown of HIPK2 and the protein phosphatase regulatory unit C-alpha (PP1Cα) resulted in sustained Dvl3 phosphorylation and hence decrease in the NP form of Dvl3. On the other hand, knockdown of E3 ubiquitin ligase ITCH reduced the phosphorylation-induced degradation and stabilized the phosphorylated Dvl3 protein. Furthermore, the NP-Dvl3 enhanced the LGR5 promoter activity to upregulate LGR5 expression, which was associated with increased cancer stemness in HCC. Our findings established that HIPK2/PP1Cα/ITCH axis sustains the de-phosphorylation of Dvl3. This post-translational modification of Dvl3 in turn maintains LGR5 expression and enhances the cancer stemness properties in HCC.published_or_final_versio

Efficiency of rice straw lignocelluloses degradability by Aspergillus terreus ATCC 74135 in solid state fermentation

The ability of Aspergillus terreus for the production of cellulolytic enzymes and reduction of lignocellulose contents of rice straw in solid state fermentation was investigated in this study. Results suggested that, 8 days fermentation was appropriate, with enzymes activities as follows: FPase = 410.76 U/gDM, CMCase = 351.96U/gDM, -glucosidase = 16.37 U/gDM, xylanase = 6166.01 U/gDM and amyloglucosidase = 425.04 U/gDM (with maximum 993.71 U/gDM on day 6). In addition, the solid state fermentation significantly (P < 0.01) reduced the concentrations of NDF, ADF, cellulose and hemicellulose in the rice straw by 19.96, 13.8, 16.32 and 32.87%, respectively. The high degradation of the hemicellulose was reflected by the high activity of xylanase enzyme, which hydrolyses xylan in hemicellulose to xylose. Higher reducing sugar and microbial cell mass productions were also obtained after 8 days fermentation. Present data showed that, A. terreus is capable of producing high quantity of cellulolytic enzymes for the reduction of lignocellulose contents of biomass in a shorter incubation time when compared with the previously reported for biological treatment of agricultural by-products using white rot fungi.Key words: Aspergillus terreus, biomass, biological treatment, enzyme activity, solid state fermentation

Effects of Aspergillus niger (K8) on nutritive value of rice straw

The objective of this study was to evaluate the use of solid state fermentation for the improvement of the quality of rice straw as animal feed. Rice straw was fermented using Aspergillus niger (K8) with and without additional nitrogen source (urea). Cellulose, hemicelluloses, organic matter (OM), dry matter (DM), acid detergent fibre (ADF), neutral detergent fibre (NDF) and acid detergent lignin (ADL) contents of rice straw were determined before and after 10 days of fermentation. Fermentation has significant (P < 0.01) effect on NDF, but not ADF and ADL contents. Addition of urea as nitrogen source significantly reduced (P < 0.01) the NDF and hemicellulose contents of fermented rice straw. Cellulose content of the rice straw was not affected (P > 0.05), but crude protein (CP) increased significantly (P < 0.01) after fermentation. In vitro gas production technique was used to evaluate the effect of the biological treatment on activity of rumen microorganisms. Fermentation of rice straw using A. niger significantly reduced total gas production (P < 0.01), DM disappearance (P < 0.01) and acetate, propionate and  total volatile fatty acids (VFA) production (P < 0.05). Results of the present study showed that solid state fermentation of rice straw using A. niger reduced lignocellulose content, but has negative effect on microbial activity in the rumen ecosystem, presumably due to antagonistic activity of A. niger, or other intermediate products from the fermentation, on the rumen microorganisms.Key words: Aspergillus niger, biomass, solid state fermentation, biological treatment, in vitro gas production

An Internet-Based Intervention to Promote Alcohol-Related Attitudinal and Behavioral Change Among Adolescents: Protocol of a Cluster Randomized Controlled Trial

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Response to novel objects and foraging tasks by common marmoset (Callithrix Jacchus) female Pairs

Many studies have shown that environmental enrichment can significantly improve the psychological well-being of captive primates, increasing the occurrence of explorative behavior and thus reducing boredom. The response of primates to enrichment devices may be affected by many factors such as species, sex, age, personality and social context. Environmental enrichment is particularly important for social primates living in unnatural social groupings (i.e. same-sex pairs or singly housed animals), who have very few, or no, benefits from the presence of social companions in addition to all the problems related to captivity (e.g. increased inactivity). This study analyses the effects of enrichment devices (i.e. novel objects and foraging tasks) on the behavior of common marmoset (Callithrix jacchus) female pairs, a species that usually lives in family groups. It aims to determine which aspects of an enrichment device are more likely to elicit explorative behaviors, and how aggressive and stress-related behaviors are affected by its presence. Overall, the marmosets explored foraging tasks significantly longer than novel objects. The type of object, which varied in size, shape and aural responsiveness (i.e. they made a noise when the monkey touched them), did not affect the response of the monkeys, but they explored objects that were placed higher in the enclosure more than those placed lower down.Younger monkeys were more attracted to the enrichment devices than the older ones. Finally, stress-related behavior (i.e. scratching) significantly decreased when the monkeys were presented with the objects; aggressive behavior as unaffected. This study supports the importance of environmental enrichment for captive primates and shows that in marmosets its effectiveness strongly depends upon the height of the device in the enclosure and the presence of hidden food. The findings can be explained ifone considers the foraging behavior of wild common marmosets. Broader applications for the research findings are suggested in relation to enrichment