Optimization of miRNA-seq data preprocessing.

The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments

3D bioprinting of liver-mimetic construct with alginate/cellulose nanocrystal hybrid bioink

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.bprint.2017.12.001 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/3D bioprinting is a novel platform for engineering complex, three-dimensional (3D) tissues that mimic real ones. The development of hybrid bioinks is a viable strategy that integrates the desirable properties of the constituents. In this work, we present a hybrid bioink composed of alginate and cellulose nanocrystals (CNCs) and explore its suitability for extrusion-based bioprinting. This bioink possesses excellent shear-thinning property, can be easily extruded through the nozzle, and provides good initial shape fidelity. It has been demonstrated that the viscosities during extrusion were at least two orders of magnitude lower than those at small shear rates, enabling the bioinks to be extruded through the nozzle (100µm inner diameter) readily without clogging. This bioink was then used to print a liver-mimetic honeycomb 3D structure containing fibroblast and hepatoma cells. The structures were crosslinked with CaCl2 and incubated and cultured for 3 days. It was found that the bioprinting process resulted in minimal cell damage making the alginate/CNC hybrid bioink an attractive bioprinting material.Natural Sciences and Engineering Research Council (NSERC) of Canada (grant no. RGPIN-2016-04398

Propuesta de plan para la institucionalidad de corto y largo plazo para la revaloración y sostenibilidad de la fiesta del Carnaval de Cajamarca

RESUMEN En el presente trabajo se plantea la “PROPUESTA DE PLAN PARA LA INSTITUCIONALIDAD DE CORTO Y LARGO PLAZO PARA LA REVALORACIÓN Y SOSTENIBILIDAD DE LA FIESTA DEL CARNAVAL DE CAJAMARCA”, con el fin de contribuir a una mejor gestión y administración de este; asimismo para poder preservar las costumbres y tradiciones que se van perdiendo, fortalecer la identidad cultural de los pobladores, así como mejorar la percepción y cumplir las expectativas de los turistas. Con el propósito de determinar las percepciones sobre la Fiesta del Carnaval se aplicaron entrevistas a los miembros y ex miembros del Patronato del Carnaval y entrevistas a Empresas Prestadoras de Servicios Turísticos. En el primer caso, los resultados evidencian que todos los años el Patronato del Carnaval ha venido trabajando de manera empírica, desorganizada y a destiempo; en el segundo caso se determinó que no todas las empresas están comprometidas en proporcionar una experiencia dirigida hacia la revalorización y cuiden el patrimonio cultural y cultura viva de la Fiesta del Carnaval. Utilizando una muestra de 384 pobladores, se determinó que, la Fiesta del Carnaval convoca a grandes masas de la población (71%), que participa activamente en las actividades, mostrando un sentimiento general de unión y compartir. Sin embargo la mayoría de población se siente descontenta (45,5%) con la organización de la Fiesta. Asimismo se aplicaron 381 encuestas a turistas nacionales y extranjeros, quienes manifestaron que sienten interés por las distintas actividades que se desarrollan en la Fiesta (46.9%); sin embargo, lo que más les desagradó fue el desorden generado en el desarrollo de la Fiesta (31.5%). Los resultados sugieren que la Implementación de un Plan Estratégico de institucionalización sería una herramienta de trabajo más eficiente, objetiva y planificada para el Patronato, debiendo ser trabajada todo el año, implementando estrategias y planes de acción en los eventos y actividades de la Fiesta. Se proporcionaría así seguridad preservando la integridad física y mental de sus participantes y, por otro lado, se cumpliría el propósito de recuperar nuestro patrimonio cultural vivo; para así consolidar al Carnaval Cajamarquino como el mejor destino de cultura viva seleccionado por los visitantes. PALABRAS CLAVE: propuesta de institucionalización, valoración y sostenibilidad.ABSTRACT This report had the purpose to present a “Proposal of Plan to institutionalize in a short and long term the Cajamarca’s Carnival Fest toward its valuation and sustainability“, intending to contribute for a better management of this event . The proposal was made as a tool to guide how to preserve this traditional fest and so strengthening cultural i dentity of the Cajamarca’s inhabitants. Likewise, to improve the tourists’ perception and to fulfill their expectations. There were conducted interviews to the members and ex-members of the Carnival Board as well to tourism enterprises. In the first case, the results shows that every year the Carnival Board has been working in an empirical way, casually and out of time; in the second case, it was determined that not all the enterprises are committed to give an experience related with the valuation and care of the cultural heritage and living culture of the carnival’s party. After using a sample of 384 villagers, it was determined that the carnival’s fest brings together a great number of people (71 %) that actively participates in the activities, showing a general feeling of union and sharing. However, most of the people feels disappointed (45.5%) with the fest’s organization. Likewise, there were applied 381 surveys to national tourists and foreigners. The results showed that they feel interested in the several activities developed in the party (46.9%). However, they also said that the worst part was the mess generated in the development of the fest (31.5%). The results suggests that implementing a strategic plan of institutionalization would become an efficient, objective and planned working tool for the Carnival’s Board which should be worked the whole year, implementing strategies and action plans in the events and activities of the fest. It would give security preserving physical and mental integrity of the participants. The final purpose is to recover our living culture heritage in order to consolidate Cajamarca’s carnival as the best destiny selected by visitors. KEYWORDS: proposal of institutionalize, valuation and sustainability

Protein Kinase C α Is a Central Signaling Node and Therapeutic Target for Breast Cancer Stem Cells

The epithelial-mesenchymal transition program becomes activated during malignant progression and can enrich for cancer stem cells (CSCs). We report that inhibition of protein kinase C α (PKCα) specifically targets CSCs but has little effect on non-CSCs. The formation of CSCs from non-stem cells involves a shift from EGFR to PDGFR signaling and results in the PKCα-dependent activation of FRA1. We identified an AP-1 molecular switch in which c-FOS and FRA1 are preferentially utilized in non-CSCs and CSCs, respectively. PKCα and FRA1 expression is associated with the aggressive triple-negative breast cancers, and the depletion of FRA1 results in a mesenchymal-epithelial transition. Hence, identifying molecular features that shift between cell states can be exploited to target signaling components critical to CSCs.National Cancer Institute (U.S.) (Grant P01-CA080111)National Institutes of Health (U.S.) (Grant R01-CA078461

Development of a multi-locus sequence typing scheme for Laribacter hongkongensis, a novel bacterium associated with freshwater fish-borne gastroenteritis and traveler's diarrhea

<p>Abstract</p> <p>Background</p> <p>Laribacter hongkongensis is a newly discovered, facultative anaerobic, Gram-negative, motile, sea gull-shaped rod associated with freshwater fish borne gastroenteritis and traveler's diarrhea. A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of <it>L. hongkongensis</it>. In this study, a multilocus sequence typing (MLST) system was developed for <it>L. hongkongensis</it>. The system was used to characterize 146 <it>L. hongkongensis </it>isolates, including 39 from humans and 107 from fish.</p> <p>Results</p> <p>Fragments (362 to 504 bp) of seven housekeeping genes were amplified and sequenced. Among the 3068 bp of the seven loci, 332 polymorphic sites were observed. The median number of alleles at each locus was 34 [range 22 (<it>ilvC</it>) to 45 (<it>thiC</it>)]. All seven genes showed very low <it>d</it>_<it>n</it>/<it>d</it>_{<it>s </it>}ratios of < 0.04, indicating that no strong positive selective pressure is present. A total of 97 different sequence types (STs) were assigned to the 146 isolates, with 80 STs identified only once. The overall discriminatory power was 0.9861. eBURST grouped the isolates into 12 lineages, with six groups containing only isolates from fish and three groups only isolates from humans. Standardized index of association (<it>I</it>^<it>S</it>_<it>A</it>) measurement showed significant linkage disequilibrium in isolates from both humans and fish. The <it>I</it>^<it>S</it>_{<it>A </it>}for the isolates from humans and fish were 0.270 and 0.636, indicating the isolates from fish were more clonal than the isolates from humans. Only one interconnected network (<it>acnB</it>) was detected in the split graphs. The P-value (P = 0) of sum of the squares of condensed fragments in Sawyer's test showed evidence of intragenic recombination in the <it>rho, acnB </it>and <it>thiC </it>loci, but the P-value (P = 1) of maximum condensed fragment in these gene loci did not show evidence of intragenic recombination. Congruence analysis showed that all the pairwise comparisons of the 7 MLST loci were incongruent, indicating that recombination played a substantial role in the evolution of <it>L. hongkongensis</it>. A website for <it>L. hongkongensis </it>MLST was set up and can be accessed at <url>http://mlstdb.hku.hk:14206/MLST_index.html</url>.</p> <p>Conclusion</p> <p>A highly reproducible and discriminative MLST system was developed for <it>L. hongkongensis</it>.</p

Safety, immunogenicity, and reactogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines given as fourth-dose boosters following two doses of ChAdOx1 nCoV-19 or BNT162b2 and a third dose of BNT162b2 (COV-BOOST): a multicentre, blinded, phase 2, randomised trial

BACKGROUND: Some high-income countries have deployed fourth doses of COVID-19 vaccines, but the clinical need, effectiveness, timing, and dose of a fourth dose remain uncertain. We aimed to investigate the safety, reactogenicity, and immunogenicity of fourth-dose boosters against COVID-19. METHODS: The COV-BOOST trial is a multicentre, blinded, phase 2, randomised controlled trial of seven COVID-19 vaccines given as third-dose boosters at 18 sites in the UK. This sub-study enrolled participants who had received BNT162b2 (Pfizer-BioNTech) as their third dose in COV-BOOST and randomly assigned them (1:1) to receive a fourth dose of either BNT162b2 (30 μg in 0·30 mL; full dose) or mRNA-1273 (Moderna; 50 μg in 0·25 mL; half dose) via intramuscular injection into the upper arm. The computer-generated randomisation list was created by the study statisticians with random block sizes of two or four. Participants and all study staff not delivering the vaccines were masked to treatment allocation. The coprimary outcomes were safety and reactogenicity, and immunogenicity (anti-spike protein IgG titres by ELISA and cellular immune response by ELISpot). We compared immunogenicity at 28 days after the third dose versus 14 days after the fourth dose and at day 0 versus day 14 relative to the fourth dose. Safety and reactogenicity were assessed in the per-protocol population, which comprised all participants who received a fourth-dose booster regardless of their SARS-CoV-2 serostatus. Immunogenicity was primarily analysed in a modified intention-to-treat population comprising seronegative participants who had received a fourth-dose booster and had available endpoint data. This trial is registered with ISRCTN, 73765130, and is ongoing. FINDINGS: Between Jan 11 and Jan 25, 2022, 166 participants were screened, randomly assigned, and received either full-dose BNT162b2 (n=83) or half-dose mRNA-1273 (n=83) as a fourth dose. The median age of these participants was 70·1 years (IQR 51·6-77·5) and 86 (52%) of 166 participants were female and 80 (48%) were male. The median interval between the third and fourth doses was 208·5 days (IQR 203·3-214·8). Pain was the most common local solicited adverse event and fatigue was the most common systemic solicited adverse event after BNT162b2 or mRNA-1273 booster doses. None of three serious adverse events reported after a fourth dose with BNT162b2 were related to the study vaccine. In the BNT162b2 group, geometric mean anti-spike protein IgG concentration at day 28 after the third dose was 23 325 ELISA laboratory units (ELU)/mL (95% CI 20 030-27 162), which increased to 37 460 ELU/mL (31 996-43 857) at day 14 after the fourth dose, representing a significant fold change (geometric mean 1·59, 95% CI 1·41-1·78). There was a significant increase in geometric mean anti-spike protein IgG concentration from 28 days after the third dose (25 317 ELU/mL, 95% CI 20 996-30 528) to 14 days after a fourth dose of mRNA-1273 (54 936 ELU/mL, 46 826-64 452), with a geometric mean fold change of 2·19 (1·90-2·52). The fold changes in anti-spike protein IgG titres from before (day 0) to after (day 14) the fourth dose were 12·19 (95% CI 10·37-14·32) and 15·90 (12·92-19·58) in the BNT162b2 and mRNA-1273 groups, respectively. T-cell responses were also boosted after the fourth dose (eg, the fold changes for the wild-type variant from before to after the fourth dose were 7·32 [95% CI 3·24-16·54] in the BNT162b2 group and 6·22 [3·90-9·92] in the mRNA-1273 group). INTERPRETATION: Fourth-dose COVID-19 mRNA booster vaccines are well tolerated and boost cellular and humoral immunity. Peak responses after the fourth dose were similar to, and possibly better than, peak responses after the third dose. FUNDING: UK Vaccine Task Force and National Institute for Health Research