Eosinophilic pneumonia following occupational smoke exposure

A 21-year-old male patient with a history of occupational exposure to open fire smoke was initially treated with empiric antibiotics for simple community-acquired pneumonia. However, he continued to deteriorate rapidly, developed respiratory failure and needed mechanical ventilation. After possible aetiologies were considered, acute eosinophilic pneumonia was suspected and confirmed by broncho-alveolar lavage. His condition improved dramatically soon after glucocorticoid administration and he was discharged without sequelae. Acute eosinophilic pneumonia should be considered in a patient with a history of exposure to smoke presenting with pneumonia that deteriorates rapidly despite broad antibiotics. An important clue for the diagnosis is eosinophilia in peripheral blood

Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics

Completion of human genome sequencing has greatly accelerated functional genomic research. Full-length cDNA clones are essential experimental tools for functional analysis of human genes. In one of the projects of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, the full-length human cDNA sequencing project (FLJ project), nucleotide sequences of approximately 30 000 human cDNA clones have been analyzed. The Gateway system is a versatile framework to construct a variety of expression clones for various experiments. We have constructed 33 275 human Gateway entry clones from full-length cDNAs, representing to our knowledge the largest collection in the world. Utilizing these clones with a highly efficient cell-free protein synthesis system based on wheat germ extract, we have systematically and comprehensively produced and analyzed human proteins in vitro. Sequence information for both amino acids and nucleotides of open reading frames of cDNAs cloned into Gateway entry clones and in vitro expression data using those clones can be retrieved from the Human Gene and Protein Database (HGPD, http://www.HGPD.jp). HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones

An innovative tailored instructional design for computer programming courses in engineering

Industry 4.0 and 5.0 topics are emerging fields and have seen rising demand recently. There is a critical need, on the other hand, for improved methods of instructing programming languages since a growing lack of student motivation during the pandemic has had a deleterious influence on the education of programmers. In this context, online/hybrid computer programming courses must be addressed with innovative solutions to support the field with well-educated professionals. In this paper, we present a case study to propose an innovative tailored instructional design for the online/hybrid learning environments for programming courses in engineering faculties. To develop the instructional design, the Kemp Instructional Design Model was followed. The instructional design is a result of the main outputs of the RECOM “Redesigning Introductory Computer Programming Using Innovative Online Modules” project, which aims to bridge the gap between the existing course design in programming courses and the needs of "Covid” and “post-Covid” generation students

An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis

Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.Comment: 54 pages (19 pages main text; 11 Figures; 26 pages of supplementary information). Revised after critical reviews. Accepted for Publication in PLoS ON

A human MAP kinase interactome.

Mitogen-activated protein kinase (MAPK) pathways form the backbone of signal transduction in the mammalian cell. Here we applied a systematic experimental and computational approach to map 2,269 interactions between human MAPK-related proteins and other cellular machinery and to assemble these data into functional modules. Multiple lines of evidence including conservation with yeast supported a core network of 641 interactions. Using small interfering RNA knockdowns, we observed that approximately one-third of MAPK-interacting proteins modulated MAPK-mediated signaling. We uncovered the Na-H exchanger NHE1 as a potential MAPK scaffold, found links between HSP90 chaperones and MAPK pathways and identified MUC12 as the human analog to the yeast signaling mucin Msb2. This study makes available a large resource of MAPK interactions and clone libraries, and it illustrates a methodology for probing signaling networks based on functional refinement of experimentally derived protein-interaction maps

Computation of significance scores of unweighted Gene Set Enrichment Analyses

<p>Abstract</p> <p>Background</p> <p>Gene Set Enrichment Analysis (GSEA) is a computational method for the statistical evaluation of sorted lists of genes or proteins. Originally GSEA was developed for interpreting microarray gene expression data, but it can be applied to any sorted list of genes. Given the gene list and an arbitrary biological category, GSEA evaluates whether the genes of the considered category are randomly distributed or accumulated on top or bottom of the list. Usually, significance scores (p-values) of GSEA are computed by nonparametric permutation tests, a time consuming procedure that yields only estimates of the p-values.</p> <p>Results</p> <p>We present a novel dynamic programming algorithm for calculating exact significance values of unweighted Gene Set Enrichment Analyses. Our algorithm avoids typical problems of nonparametric permutation tests, as varying findings in different runs caused by the random sampling procedure. Another advantage of the presented dynamic programming algorithm is its runtime and memory efficiency. To test our algorithm, we applied it not only to simulated data sets, but additionally evaluated expression profiles of squamous cell lung cancer tissue and autologous unaffected tissue.</p

Scoping review : intergenerational resource transfer and possible enabling factors

We explore the intergenerational pattern of resource transfer and possible associated factors. A scoping review was conducted of quantitative, peer-reviewed, English-language studies related to intergenerational transfer or interaction. We searched AgeLine, PsycINFO, Social Work Abstracts, and Sociological Abstracts for articles published between Jane 2008 and December 2018. Seventy-five studies from 25 countries met the inclusion criteria. The scoping review categorised resource transfers into three types: financial, instrumental, and emotional support. Using an intergenerational solidarity framework, factors associated with intergenerational transfer were placed in four categories: (1) demographic factors (e.g., age, gender, marital status, education, and ethno-cultural background); (2) needs and opportunities factors, including health, financial resources, and employment status; (3) family structures, namely, family composition, family relationship, and earlier family events; and (4) cultural-contextual structures, including state policies and social norms. Those factors were connected to the direction of resource transfer between generations. Downward transfers from senior to junior generations occur more frequently than upward transfers in many developed countries. Women dominate instrumental transfers, perhaps influenced by traditional gender roles. Overall, the pattern of resource transfer between generations is shown, and the impact of social norms and social policy on intergenerational transfers is highlighted. Policymakers should recognise the complicated interplay of each factor with different cultural contexts. The findings could inform policies that strengthen intergenerational solidarity and support.</jats:p

PRIDE: new developments and new datasets

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML