Comprehension and Maintenance of Large Scale Multi-Language Software Applications: Open Issues and Challenges

During the last decade, the number of software applications that have been deployed as a collection of components implemented in different programming languages and paradigms has increased considerably. When such applications are maintained, traditional program comprehension and reengineering techniques may not be adequate. In this context, this working session aims to stimulate discussion around key issues relating to the comprehension, reengineering, and maintenance of multi-language software applications. Such issues include, but are not limited to, the formalization, management, exploration, and presentation of multi-language program dependencies, as well as the development of practical toolsets for automating and easing the comprehension and maintenance of multi-language software

Capacity building for dementia care in community care services: a mixed methods approach

Background The prevalence of dementia is surging that results in huge service demand in the community care services. Dementia care competence of staff working in these settings is fundamental of the care quality. This project aims to examine the effects of staff training on their competence for the anticipated challenges in dementia care and explore how the training influence their care practices. Methods This study adopted a mixed methods triangulation design, including a prospective multi-center study with pre-test post-test evaluations and a narrative analysis of the participants’ reflective essays. Seventeen experienced health and social care professionals were trained as trainers at the Dementia Services Development Centre of the University of Stirling, UK. The trainers provided local facilitator training to staff members by using training materials that were culturally adapted to the local context. The facilitators were required to deliver 12 two-hour in-service training sessions for 6 months to their colleagues in a small group format in their respective workplace. Eventually a total of 1347 staff members from community care centers, day care centers, outreach teams and care homes of 70 non-government organizations in Hong Kong participated in the study between April 2017 and December 2018. Validated instruments were used to measure knowledge, attitude, sense of competence in dementia care and job satisfaction at the baseline and at 12-month follow-up. All participants were required to write a reflective essay to describe their experiences in dementia care by the end of the training. Results A total of 1264 participants, including 195 facilitators and 1069 learners, completed all assessment were included for analysis. Significant improvements were observed in all outcomes at the 12-month follow-up assessment (Ps ≤ .001). The magnitude of improvements in attitudes was the largest. The findings also showed that the effects of the training program significantly varied across different groups of learners in terms of age, occupation, work and training experience. Conclusions This community-wide large-scale project provided evidence that the train-the-trainer model and reflective learning are effective means to facilitate situated learning that promote awareness and understanding of dementia, and consequently enhance sustainability of changes in care practices

A Genome-Wide siRNA Screen to Identify Modulators of Insulin Sensitivity and Gluconeogenesis

BACKGROUND: Hepatic insulin resistance impairs insulin's ability to suppress hepatic glucose production (HGP) and contributes to the development of type 2 diabetes (T2D). Although the interests to discover novel genes that modulate insulin sensitivity and HGP are high, it remains challenging to have a human cell based system to identify novel genes. METHODOLOGY/PRINCIPAL FINDINGS: To identify genes that modulate hepatic insulin signaling and HGP, we generated a human cell line stably expressing beta-lactamase under the control of the human glucose-6-phosphatase (G6PC) promoter (AH-G6PC cells). Both beta-lactamase activity and endogenous G6PC mRNA were increased in AH-G6PC cells by a combination of dexamethasone and pCPT-cAMP, and reduced by insulin. A 4-gene High-Throughput-Genomics assay was developed to concomitantly measure G6PC and pyruvate-dehydrogenase-kinase-4 (PDK4) mRNA levels. Using this assay, we screened an siRNA library containing pooled siRNA targeting 6650 druggable genes and identified 614 hits that lowered G6PC expression without increasing PDK4 mRNA levels. Pathway analysis indicated that siRNA-mediated knockdown (KD) of genes known to positively or negatively affect insulin signaling increased or decreased G6PC mRNA expression, respectively, thus validating our screening platform. A subset of 270 primary screen hits was selected and 149 hits were confirmed by target gene KD by pooled siRNA and 7 single siRNA for each gene to reduce G6PC expression in 4-gene HTG assay. Subsequently, pooled siRNA KD of 113 genes decreased PEPCK and/or PGC1alpha mRNA expression thereby demonstrating their role in regulating key gluconeogenic genes in addition to G6PC. Last, KD of 61 of the above 113 genes potentiated insulin-stimulated Akt phosphorylation, suggesting that they suppress gluconeogenic gene by enhancing insulin signaling. CONCLUSIONS/SIGNIFICANCE: These results support the proposition that the proteins encoded by the genes identified in our cell-based druggable genome siRNA screen hold the potential to serve as novel pharmacological targets for the treatment of T2D

Will the community nurse continue to function during H1N1 influenza pandemic: a cross-sectional study of Hong Kong community nurses?

<p>Abstract</p> <p>Background</p> <p>Healthcare workers have been identified as one of the high risk groups for being infected with influenza during influenza pandemic. Potential levels of absenteeism among healthcare workers in hospital settings are high. However, there was no study to explore the attitudes of healthcare workers in community setting towards the preparedness to the novel H1N1 influenza pandemic. The aim of this study was to explore the willingness of community nurses in Hong Kong to work during H1N1 influenza pandemic.</p> <p>Methods</p> <p>A cross-sectional survey was conducted among all 401 community nurses employed by the Hospital Authority in Hong Kong when the WHO pandemic alert level was 6.</p> <p>Results</p> <p>The response rate of this study was 66.6%. 76.9% participants reported being "not willing" (33.3%) or "not sure" (43.6%) to take care of patients during H1N1 influenza pandemic. The self-reported reasons for being unwilling to report to duty during H1N1 influenza pandemic were psychological stress (55.0%) and fear of being infected H1N1 influenza (29.2%). The reported unwillingness to report to duty was marginally significantly associated with the request for further training of using infection control clinical guideline (OR: 0.057; CI: 0.25-1.02). Those who reported unwillingness or not being sure about taking care of the patients during H1N1 influenza pandemic were more depressed (p < 0.001) and found work more emotionally stressful (p < 0.001).</p> <p>Conclusions</p> <p>Interventions to provide infection control training and address community nurses' psychological needs might increase their willingness to provide care to patients in the community during H1N1 influenza pandemic. This would help to ensure an effective and appropriate health system response during the H1N1 influenza pandemic.</p

Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release

论文以我校为共同通讯单位，刘文教授为共同第一和通讯作者。论文对去甲基化酶蛋白家族中的成员JMJD6在基因转录中的新颖分子作用机制进行了阐述。研究表明JMJD6和另一热门表观遗传学调控子Brd4通过一种全新的“远程调控”模式调节RNA聚合酶II(PolII)在基因启动子附近停顿后重新激活(promoter-proximal　pause　release)和基因转录延伸过程（transcriptional　elongation）。文章首次将相关的远程调控基因组增强子序列命名为“抗停顿增强子”(Anti-pause　enhancers)。值得一提的是，JMJD6和Brd4与多种人类癌症和其它疾病紧密相联，例如乳腺癌的发生发展。研究成果极大地提高了对基因转录延伸机制的理解，同时也为治疗癌症等相关疾病提供了新的理论依据和思路指导，在理论研究及应用方面意义重大。 　　刘文教授是药学院2013年重点引进的优秀人才，因其出色的学术能力和科研潜力，经学院申报，入选当年的中组部“青年千人计划”和“闽江学者”。刘文教授一直致力于从事表观遗传学调控子以及核受体的分子作用机制及其在癌症等重大疾病发生发展中的应用研究，论文多次发表在Nature，Cell,CancerCell，MolecularCell,PNAS等国际权威科学期刊。Distal enhancers characterized by the H3K4me mark play critical roles in developm ental and transcriptional programs. However, potential roles of specific distal regulatory elements in regulating RNA polymerase II (Pol II) promoter-proximal pause release remain poor lyinves tigated . Here, we report that a unique cohort of jumo njiC-domain-con taining protein 6 (JMJD 6) and bromodomain-containing protein 4 (Brd4) cobound distal enhancers , termed a ntip ause e nhance rs (A-PEs), regulate promoter-proximal pause release of a large subset of transcription units via long-range in teractions. Brd4-dependent JMJD6 recruitment on A-PEs mediates erasure of H4R3me, which is directly read by 7SK snR NA,and decappi ng/demet hylation of 7SK snR NA,ensurin g the dis missal of the 7SK snRNA/HEXIM inhibitory complex. The interactions of both JMJD6 and Brd4 with the P-TEFb complex permit its activation and pause release of regulated coding genes.The functions of JM JD6/Brd4-associated dual histone and RNA demethylase activity on anti-pause enhancers have intriguing implications for these proteins in development, homeostasis, and disease

Engineering the Controlled Assembly of Filamentous Injectisomes in E. coli K-12 for Protein Translocation into Mammalian Cells.

Bacterial pathogens containing type III protein secretion systems (T3SS) assemble large needle-like protein complexes in the bacterial envelope, called injectisomes, for translocation of protein effectors into host cells. The application of these molecular syringes for the injection of proteins into mammalian cells is hindered by their structural and genomic complexity, requiring multiple polypeptides encoded along with effectors in various transcriptional units (TUs) with intricate regulation. In this work, we have rationally designed the controlled expression of the filamentous injectisomes found in enteropathogenic Escherichia coli (EPEC) in the nonpathogenic strain E. coli K-12. All structural components of EPEC injectisomes, encoded in a genomic island called the locus of enterocyte effacement (LEE), were engineered in five TUs (eLEEs) excluding effectors, promoters and transcriptional regulators. These eLEEs were placed under the control of the IPTG-inducible promoter Ptac and integrated into specific chromosomal sites of E. coli K-12 using a marker-less strategy. The resulting strain, named synthetic injector E. coli (SIEC), assembles filamentous injectisomes similar to those in EPEC. SIEC injectisomes form pores in the host plasma membrane and are able to translocate T3-substrate proteins (e.g., translocated intimin receptor, Tir) into the cytoplasm of HeLa cells reproducing the phenotypes of intimate attachment and polymerization of actin-pedestals elicited by EPEC bacteria. Hence, SIEC strain allows the controlled expression of functional filamentous injectisomes for efficient translocation of proteins with T3S-signals into mammalian cells

Attaching and effacing (A/E) lesion formation by enteropathogenic E. coli on human intestinal mucosa is dependent on non-LEE effectors

Enteropathogenic E. coli (EPEC) is a human pathogen that causes acute and chronic pediatric diarrhea. The hallmark of EPEC infection is the formation of attaching and effacing (A/E) lesions in the intestinal epithelium. Formation of A/E lesions is mediated by genes located on the pathogenicity island locus of enterocyte effacement (LEE), which encode the adhesin intimin, a type III secretion system (T3SS) and six effectors, including the essential translocated intimin receptor (Tir). Seventeen additional effectors are encoded by genes located outside the LEE, in insertion elements and prophages. Here, using a stepwise approach, we generated an EPEC mutant lacking the entire effector genes (EPEC0) and intermediate mutants. We show that EPEC0 contains a functional T3SS. An EPEC mutant expressing intimin but lacking all the LEE effectors but Tir (EPEC1) was able to trigger robust actin polymerization in HeLa cells and mucin-producing intestinal LS174T cells. However, EPEC1 was unable to form A/E lesions on human intestinal in vitro organ cultures (IVOC). Screening the intermediate mutants for genes involved in A/E lesion formation on IVOC revealed that strains lacking non-LEE effector/s have a marginal ability to form A/E lesions. Furthermore, we found that Efa1/LifA proteins are important for A/E lesion formation efficiency in EPEC strains lacking multiple effectors. Taken together, these results demonstrate the intricate relationships between T3SS effectors and the essential role non-LEE effectors play in A/E lesion formation on mucosal surfaces

The role of place branding and image in the development of sectoral clusters: the case of Dubai

This paper contextualizes how place branding and image influence the development of Dubai’s key sectoral clusters, including the key determinants of growth and success under the impression of Porter’s cluster theory. The approach is exploratory and of a qualitative inductive nature. Data was collected through conducting 21 semi-structured interviews with Dubai’s marketing/communication managers and stakeholders. Findings suggest that Dubai’s traditional clusters, namely, trading, tourism and logistics that have strong place branding and image show strong signs of success owing to Dubai’s geographical location (i.e., physical conditions). Among the new clusters, the financial sector is also benefitting from place branding. The results suggest that the success of traditional clusters have a positive spill over effect on the new clusters, in particular on construction and real estate. For policy makers it is worth to note that the recent success of the financial services cluster in Dubai will have positive impact on both, the traditional as well new clusters. The marketing and brand communication managers must consider the correlation and interplay of strength of activities amongst trading, tourism and logistics clusters and its implication while undertaking place branding for clients in their sector

Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

Background: Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffinembedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens. Principal Findings: For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll TM Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and-RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and –RNA tha