RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

BACKGROUND: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. RESULTS: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. CONCLUSIONS: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA

Clood CBR: towards microservices oriented case-based reasoning.

CBR applications have been deployed in a wide range of sectors, from pharmaceuticals; to defence and aerospace to IoT and transportation, to poetry and music generation; for example. However, a majority of these have been built using monolithic architectures which impose size and complexity constraints. As such these applications have a barrier to adopting new technologies and remain prohibitively expensive in both time and cost because changes in frameworks or languages affect the application directly. To address this challenge, we introduce a distributed and highly scalable generic CBR system, Clood, which is based on a microservices architecture. This splits the application into a set of smaller, interconnected services that scale to meet varying demands. Experimental results show that our Clood implementation retrieves cases at a fairly consistent rate as the casebase grows by several orders of magnitude and was over 3,700 times faster than a comparable monolithic CBR system when retrieving from half a million cases. Microservices are cloud-native architectures and with the rapid increase in cloud-computing adoption, it is timely for the CBR community to have access to such a framework

Transcriptomic Profiling in Childhood H1N1/09 Influenza Reveals Reduced Expression of Protein Synthesis Genes

We compared the blood RNA transcriptome of children hospitalized with influenza A H1N1/09, respiratory syncytial virus (RSV) or bacterial infection, and healthy controls. Compared to controls, H1N1/09 patients showed increased expression of inflammatory pathway genes and reduced expression of adaptive immune pathway genes. This was validated on an independent cohort. The most significant function distinguishing H1N1/09 patients from controls was protein synthesis, with reduced gene expression. Reduced expression of protein synthesis genes also characterized the H1N1/09 expression profile compared to children with RSV and bacterial infection, suggesting that this is a key component of the pathophysiological response in children hospitalized with H1N1/09 infection

A phase 2 multicenter study of ublituximab, a novel glycoengineered anti-CD20 monoclonal antibody, in patients with relapsing forms of multiple sclerosis.

Background: Ublituximab, a novel monoclonal antibody (mAb) targeting a unique epitope on the CD20 antigen, is glycoengineered for enhanced B-cell targeting through antibody-dependent cellular cytotoxicity (ADCC). Greater ADCC may allow lower doses and shorter infusion times versus other anti-CD20 mAbs. Objective: The objective was to determine optimal dose, infusion time, and activity of ublituximab in relapsing multiple sclerosis. Methods: This is a phase 2, placebo-controlled study. Patients received three ublituximab infusions (150 mg over 1-4 hours on day 1 and 450-600 mg over 1-3 hours on day 15 and week 24) in six dosing cohorts. The primary endpoint was B-cell depletion. Results: In all cohorts (N = 48), median B-cell depletion was >99% by week 4, maintained at weeks 24 and 48. Most common adverse events (AEs) were infusion-related reactions (all grade 1-2), with no apparent increased incidence at shorter infusion times. There were no AE-related discontinuations. At weeks 24 and 48, no T1 gadolinium-enhancing lesions (p = 0.003) and a 10.6% decrease in T2 lesion volume (p = 0.002) were detected. The annualized relapse rate was 0.07; 93% remained relapse free on study. Overall, 74% of patients had no evidence of disease activity (NEDA). Conclusion: Ublituximab was safely infused as rapid as 1 hour, producing robust B-cell depletion and profound reductions in magnetic resonance imaging (MRI) activity and relapses

On the formal foundations of cash management systems

[EN] Cash management aims to find a balance between what is held in cash and what is allocated in other investments in exchange for a given return. Dealing with cash management systems with multiple accounts and different links between them is a complex task. Current cash management models provide analytic solutions without exploring the underlying structure of accounts and its main properties. There is a need for a formal definition of cash management systems. In this work, we introduce a formal approach to manage cash with multiple accounts based on graph theory. Our approach allows a formal reasoning on the relation between accounts in cash management systems. A critical part of this formal reasoning is the characterization of desirable and non-desirable cash management policies. Novel theoretical results guide cash managers in the analysis of complex cash management systems.This work is partially funded by projects Logistar (H2020-769142), AI4EU (H2020-825619) and 2017 SGR 172.Salas-Molina, F.; Rodriguez-Aguilar, JA.; Pla Santamaría, D.; Garcia-Bernabeu, A. (2021). On the formal foundations of cash management systems. Operational Research. 21(2):1081-1095. https://doi.org/10.1007/s12351-019-00464-6S10811095212Baccarin S (2009) Optimal impulse control for a multidimensional cash management system with generalized cost functions. Eur J Oper Res 196(1):198–206Bollobás B (2013) Modern graph theory, vol 184. Springer, BerlinBondy JA, Murty USR (1976) Graph theory with applications, vol 290. Macmillan, LondonChartrand G, Oellermann OR (1993) Applied and algorithmic graph theory, vol 993. McGraw-Hill, New YorkConstantinides GM, Richard SF (1978) Existence of optimal simple policies for discounted-cost inventory and cash management in continuous time. Oper Res 26(4):620–636da Costa Moraes MB, Nagano MS, Sobreiro VA (2015) Stochastic cash flow management models: a literature review since the 1980s. In: Guarnieri P (ed) Decision models in engineering and management. Springer, Berlin, pp 11–28de Avila Pacheco JV, Morabito R (2011) Application of network flow models for the cash management of an agribusiness company. Comput Ind Eng 61(3):848–857Golden B, Liberatore M, Lieberman C (1979) Models and solution techniques for cash flow management. Comput Oper Res 6(1):13–20Gormley FM, Meade N (2007) The utility of cash flow forecasts in the management of corporate cash balances. Eur J Oper Res 182(2):923–935Gregory G (1976) Cash flow models: a review. Omega 4(6):643–656Makridakis S, Wheelwright SC, Hyndman RJ (2008) Forecasting methods and applications. Wiley, New YorkRighetto GM, Morabito R, Alem D (2016) A robust optimization approach for cash flow management in stationery companies. Comput Ind Eng 99:137–152Salas-Molina F (2017) Risk-sensitive control of cash management systems. Oper Res. https://doi.org/10.1007/s12351-017-0371-0Salas-Molina F, Pla-Santamaria D, Rodriguez-Aguilar JA (2018) A multi-objective approach to the cash management problem. Ann Oper Res 267(1):515–529Srinivasan V, Kim YH (1986) Deterministic cash flow management: state of the art and research directions. Omega 14(2):145–166Valiente G (2013) Algorithms on trees and graphs. Springer, Berli

Associations of sedentary behaviour, physical activity, blood pressure and anthropometric measures with cardiorespiratory fitness in children with cerebral palsy

Background - Children with cerebral palsy (CP) have poor cardiorespiratory fitness in comparison to their peers with typical development, which may be due to low levels of physical activity. Poor cardiorespiratory fitness may contribute to increased cardiometabolic risk. Purpose - The aim of this study was to determine the association between sedentary behaviour, physical activity and cardiorespiratory fitness in children with CP. An objective was to determine the association between cardiorespiratory fitness, anthropometric measures and blood pressure in children with CP. Methods- This study included 55 ambulatory children with CP [mean (SD) age 11.3 (0.2) yr, range 6-17 yr; Gross Motor Function Classification System (GMFCS) levels I and II]. Anthropometric measures (BMI, waist circumference and waist-height ratio) and blood pressure were taken. Cardiorespiratory fitness was measured using a 10 m shuttle run test. Children were classified as low, middle and high fitness according to level achieved on the test using reference curves. Physical activity was measured by accelerometry over 7 days. In addition to total activity, time in sedentary behaviour and light, moderate, vigorous, and sustained moderate-to-vigorous activity (≥10 min bouts) were calculated. Results - Multiple regression analyses revealed that vigorous activity (β = 0.339, p<0.01), sustained moderate-to-vigorous activity (β = 0.250, p<0.05) and total activity (β = 0.238, p<0.05) were associated with level achieved on the shuttle run test after adjustment for age, sex and GMFCS level. Children with high fitness spent more time in vigorous activity than children with middle fitness (p<0.05). Shuttle run test level was negatively associated with BMI (r2 = -0.451, p<0.01), waist circumference (r2 = -0.560, p<0.001), waist-height ratio (r2 = -0.560, p<0.001) and systolic blood pressure (r2 = -0.306, p<0.05) after adjustment for age, sex and GMFCS level. Conclusions - Participation in physical activity, particularly at a vigorous intensity, is associated with high cardiorespiratory fitness in children with CP. Low cardiorespiratory fitness is associated with increased cardiometabolic risk

An ethical framework for cardiac report cards: a qualitative study

BACKGROUND: The recent proliferation of health care report cards, especially in cardiac care, has occurred in the absence of an ethical framework to guide in their development and implementation. An ethical framework is a consistent and comprehensive theoretical foundation in ethics, and is formed by integrating ethical theories, relevant literature, and other critical information (such as the views of stakeholders). An ethical framework in the context of cardiac care provides guidance for developing cardiac report cards (CRCs) that are relevant and legitimate to all stakeholders. The purpose of this study is to develop an ethical framework for CRCs. METHODS: Delphi technique – 13 panelists: 2 administrators, 2 cardiac nurses, 5 cardiac patients, 2 cardiologists, 1 member of the media, and 1 outcomes researcher. Panelists' views regarding the ethics of CRCs were analyzed and organized into themes. RESULTS: We have organized panelists' views into ten principles that emerged from the data: 1) improving quality of care, 2) informed understanding, 3) public accountability, 4) transparency, 5) equity, 6) access to information 7) quality of information, 8) multi-stakeholder collaboration, 9) legitimacy, and 10) evaluation and continuous quality improvement. CONCLUSION: We have developed a framework to guide the development and dissemination of CRCs. This ethical framework can provide necessary guidance for those generating CRCs and may help them avoid a number of difficult issues associated with existing ones

Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders

Background Classifying pathogenicity of missense variants represents a major challenge in clinical practice during the diagnoses of rare and genetic heterogeneous neurodevelopmental disorders (NDDs). While orthologous gene conservation is commonly employed in variant annotation, approximately 80% of known disease-associated genes belong to gene families. The use of gene family information for disease gene discovery and variant interpretation has not yet been investigated on a genome-wide scale. We empirically evaluate whether paralog-conserved or non-conserved sites in human gene families are important in NDDs. Methods Gene family information was collected from Ensembl. Paralog-conserved sites were defined based on paralog sequence alignments; 10,068 NDD patients and 2078 controls were statistically evaluated for de novo variant burden in gene families. Results We demonstrate that disease-associated missense variants are enriched at paralog-conserved sites across all disease groups and inheritance models tested. We developed a gene family de novo enrichment framework that identified 43 exome-wide enriched gene families including 98 de novo variant carrying genes in NDD patients of which 28 represent novel candidate genes for NDD which are brain expressed and under evolutionary constraint. Conclusion This study represents the first method to incorporate gene family information into a statistical framework to interpret variant data for NDDs and to discover new NDD-associated genes

Effect of Ultrasonic-Assisted Blanching on Size Variation, Heat Transfer, and Quality Parameters of Mushrooms

The main aim of this work was to assess the influence of the application of power ultrasound during blanching of mushrooms (60 90 °C) on the shrinkage, heat transfer, and quality parameters. Kinetics of mushroom shrinkage was modeled and coupled to a heat transfer model for conventional (CB) and ultrasonic-assisted blanching (UB). Cooking value and the integrated residual enzymatic activity were obtained through predicted temperatures and related to the hardness and color variations of mushrooms, respectively. The application of ultrasound led to an increase of shrinkage and heat transfer rates, being this increase more intense at low process temperatures. Consequently, processing time was decreased (30.7 46.0 %) and a reduction in hardness (25.2 40.8 %) and lightness (13.8 16.8 %) losses were obtained. The best retention of hardness was obtained by the UB at 60 °C, while to maintain the lightness it was the CB and UB at 90 °C. For enhancing both quality parameters simultaneously, a combined treatment (CT), which consisted of a CB 0.5 min at 90 °C and then an UB 19.9min at 60 °C, was designed. In this manner, compared with the conventional treatment at 60 °C, reductions of 39.1, 27.2, and 65.5 % for the process time, hardness and lightness losses were achieved, respectively. These results suggest that the CT could be considered as an interesting alternative to CB in order to reduce the processing time and improve the overall quality of blanched mushrooms.The authors acknowledge the financial support of Consejo Nacional de Investigaciones Cientificas y Tecnicas and Universidad Nacional de La Plata from Argentina, Erasmus Mundus Action 2-Strand 1 and EuroTango II Researcher Training Program and Ministerio de Economia y Competitividad (SPAIN) and the FEDER (project DPI2012-37466-CO3-03).Lespinard, A.; Bon Corbín, J.; Cárcel Carrión, JA.; Benedito Fort, JJ.; Mascheroni, RH. (2015). 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