Isn't a number and a URL enough? Why PIDs matter and technical solutions alone are not sufficient

In the presentation, we introduce the two projects PID4NFDI and PID Network Germany that deal with PIDs at the national level, present some initial findings and highlight their benefit for NFDI. PIDs are used and needed along the entire lifecycle of research data: from enabling to connecting. However, a particular focus for the presentation will be laid on harmonising and connecting

Measurement and classification of human characteristics and capabilities during interaction tasks

In this paperwe address the need to design adaptive interacting systems for advanced industrial production machines. Modern production systems have become highly complex and include many subsidiary functionalities, thus making it difficult for least skilled human operators interact with them. In this regard, adapting the behavior of the machine and of the operator interface to the characteristics of the user allows a more effective interaction process, with a positive impact on manufacturing efficiency and user's satisfaction. To this end, it is crucial to understandwhich are the user's capabilities that influence the interaction and, hence, should be measured to provide the correct amount of adaptation.Moving along these lines, in this paper we identify groups of users that, despite having different individual capabilities and features, have common needs and response to the interaction with complex production systems. As a consequence,we define clusters of users that have the same need for adaptation. Then, adaptation rules can be defined by considering such users' clusters, rather than addressing specific individual user's needs

Employing an orthotopic model to study the role of epithelial-mesenchymal transition in bladder cancer metastasis.

Epithelial-to-mesenchymal transition (EMT) has been implicated in the progression of bladder cancer. To study its contribution to bladder cancer metastasis, we established new xenograft models derived from human bladder cancer cell lines utilizing an orthotopic "recycling" technique that allowed us to isolate and examine the primary tumor and its corresponding circulating tumor cells (CTC's) and metastatic lesions. Using whole genome mRNA expression profiling, we found that a reversible epithelial-to-mesenchymal transition (EMT) characterized by TGFβ pathway activation and SNAIL expression was associated with the accumulation of CTCs. Finally, we observed that conditional silencing of SNAIL completely blocked CTC production and regional/distant metastasis. Using this unique bladder cancer xenograft model, we conclude that metastasis is dependent on a reversible EMT mediated by SNAIL

“Learning on a chip:” Microfluidics for formal and informal science education

© 2019 Author(s). Microfluidics is a technique for the handling of small volumes of liquids on the order of picoliters to nanoliters and has impact for miniaturized biomedical science and fundamental research. Because of its multi- and interdisciplinary nature (i.e., combining the fields of biology, chemistry, physics, and engineering), microfluidics offers much potential for educational applications, both at the university level as well as primary and secondary education. Microfluidics is also an ideal "tool" to enthuse and educate members of the general public about the interdisciplinary aspects of modern sciences, including concepts of science, technology, engineering, and mathematics subjects such as (bio)engineering, chemistry, and biomedical sciences. Here, we provide an overview of approaches that have been taken to make microfluidics accessible for formal and informal learning. We also point out future avenues and desired developments. At the extreme ends, we can distinguish between projects that teach how to build microfluidic devices vs projects that make various microscopic phenomena (e.g., low Reynolds number hydrodynamics, microbiology) accessible to learners and the general public. Microfluidics also enables educators to make experiments low-cost and scalable, and thereby widely accessible. Our goal for this review is to assist academic researchers working in the field of microfluidics and lab-on-a-chip technologies as well as educators with translating research from the laboratory into the lecture hall, teaching laboratory, or public sphere

Recurrent and multiple bladder tumors show conserved expression profiles

<p>Abstract</p> <p>Background</p> <p>Urothelial carcinomas originate from the epithelial cells of the inner lining of the bladder and may appear as single or as multiple synchronous tumors. Patients with urothelial carcinomas frequently show recurrences after treatment making follow-up necessary. The leading hypothesis explaining the origin of meta- and synchronous tumors assumes a monoclonal origin. However, the genetic relationship among consecutive tumors has been shown to be complex in as much as the genetic evolution does not adhere to the chronological appearance of the metachronous tumors. Consequently, genetically less evolved tumors may appear chronologically later than genetically related but more evolved tumors.</p> <p>Methods</p> <p>Forty-nine meta- or synchronous urothelial tumors from 22 patients were analyzed using expression profiling, conventional CGH, LOH, and mutation analyses.</p> <p>Results</p> <p>We show by CGH that partial chromosomal losses in the initial tumors may not be present in the recurring tumors, by LOH that different haplotypes may be lost and that detected regions of LOH may be smaller in recurring tumors, and that mutations present in the initial tumor may not be present in the recurring ones. In contrast we show that despite apparent genomic differences, the recurrent and multiple bladder tumors from the same patients display remarkably similar expression profiles.</p> <p>Conclusion</p> <p>Our findings show that even though the vast majority of the analyzed meta- and synchronous tumors from the same patients are not likely to have originated directly from the preceding tumor they still show remarkably similar expressions profiles. The presented data suggests that an expression profile is established early in tumor development and that this profile is stable and maintained in recurring tumors.</p

Meta-Analysis of the Luminal and Basal Subtypes of Bladder Cancer and the Identification of Signature Immunohistochemical Markers for Clinical Use

AbstractBackgroundIt has been suggested that bladder cancer can be divided into two molecular subtypes referred to as luminal and basal with distinct clinical behaviors and sensitivities to chemotherapy. We aimed to validate these subtypes in several clinical cohorts and identify signature immunohistochemical markers that would permit simple and cost-effective classification of the disease in primary care centers.MethodsWe analyzed genomic expression profiles of bladder cancer in three cohorts of fresh frozen tumor samples: MD Anderson (n=132), Lund (n=308), and The Cancer Genome Atlas (TCGA) (n=408) to validate the expression signatures of luminal and basal subtypes and relate them to clinical follow-up data. We also used an MD Anderson cohort of archival bladder tumor samples (n=89) and a parallel tissue microarray to identify immunohistochemical markers that permitted the molecular classification of bladder cancer.FindingsBladder cancers could be assigned to two candidate intrinsic molecular subtypes referred to here as luminal and basal in all of the datasets analyzed. Luminal tumors were characterized by the expression signature similar to the intermediate/superficial layers of normal urothelium. They showed the upregulation of PPARγ target genes and the enrichment for FGFR3, ELF3, CDKN1A, and TSC1 mutations. In addition, luminal tumors were characterized by the overexpression of E-Cadherin, HER2/3, Rab-25, and Src. Basal tumors showed the expression signature similar to the basal layer of normal urothelium. They showed the upregulation of p63 target genes, the enrichment for TP53 and RB1 mutations, and overexpression of CD49, Cyclin B1, and EGFR. Survival analyses showed that the muscle-invasive basal bladder cancers were more aggressive when compared to luminal cancers. The immunohistochemical expressions of only two markers, luminal (GATA3) and basal (KRT5/6), were sufficient to identify the molecular subtypes of bladder cancer with over 90% accuracy.InterpretationThe molecular subtypes of bladder cancer have distinct clinical behaviors and sensitivities to chemotherapy, and a simple two-marker immunohistochemical classifier can be used for prognostic and therapeutic stratification.FundingU.S. National Cancer Institute and National Institute of Health

Evidence for the impact of the 8.2-kyBP climate event on Near Eastern early farmers.

The 8.2-thousand years B.P. event is evident in multiple proxy records across the globe, showing generally dry and cold conditions for ca. 160 years. Environmental changes around the event are mainly detected using geochemical or palynological analyses of ice cores, lacustrine, marine, and other sediments often distant from human settlements. The Late Neolithic excavated area of the archaeological site of Çatalhöyük East [Team Poznań (TP) area] was occupied for four centuries in the ninth and eighth millennia B.P., thus encompassing the 8.2-thousand years B.P. climatic event. A Bayesian analysis of 56 radiocarbon dates yielded a high-resolution chronological model comprising six building phases, with dates ranging from before 8325-8205 to 7925-7815 calibrated years (cal) B.P. Here, we correlate an onsite paleoclimate record constructed from δ2H values of lipid biomarkers preserved in pottery vessels recovered from these buildings with changes in architectural, archaeozoological, and consumption records from well-documented archaeological contexts. The overall sequence shows major changes in husbandry and consumption practices at ca. 8.2 thousand years B.P., synchronous with variations in the δ2H values of the animal fat residues. Changes in paleoclimate and archaeological records seem connected with the patterns of atmospheric precipitation during the occupation of the TP area predicted by climate modeling. Our multiproxy approach uses records derived directly from documented archaeological contexts. Through this, we provide compelling evidence for the specific impacts of the 8.2-thousand years B.P. climatic event on the economic and domestic activities of pioneer Neolithic farmers, influencing decisions relating to settlement planning and food procurement strategies

9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy

Immune checkpoint therapy (ICT) provides substantial clinical benefits to cancer patients, but a large proportion of cancers do not respond to ICT. To date, the genomic underpinnings of primary resistance to ICT remain elusive. Here, we performed immunogenomic analysis of data from TCGA and clinical trials of anti-PD-1/PD-L1 therapy, with a particular focus on homozygous deletion of 9p21.3 (9p21 loss), one of the most frequent genomic defects occurring in ~13% of all cancers. We demonstrate that 9p21 loss confers "cold" tumor-immune phenotypes, characterized by reduced abundance of tumor-infiltrating leukocytes (TILs), particularly, T/B/NK cells, altered spatial TILs patterns, diminished immune cell trafficking/activation, decreased rate of PD-L1 positivity, along with activation of immunosuppressive signaling. Notably, patients with 9p21 loss exhibited significantly lower response rates to ICT and worse outcomes, which were corroborated in eight ICT trials of >1,000 patients. Further, 9p21 loss synergizes with PD-L1/TMB for patient stratification. A "response score" was derived by incorporating 9p21 loss, PD-L1 expression and TMB levels in pre-treatment tumors, which outperforms PD-L1, TMB, and their combination in identifying patients with high likelihood of achieving sustained response from otherwise non-responders. Moreover, we describe potential druggable targets in 9p21-loss tumors, which could be exploited to design rational therapeutic interventions