Glycan analysis as biomarkers for testicular cancer

The U.S. Preventive Services Task Force does not recommend routine screening for testicular cancer (TC) in asymptomatic men, essentially because serological testicular cancer (TC) biomarkers are not reliable. The main reason is that two of the most important TC biomarkers, ?-fetoprotein (AFP) and human chorionic gonadotropin (hCG), are not produced solely due to TC. Moreover, up to 40% of patients with TC do not have elevated serological biomarkers, which is why serial imaging with CT is the chief means of monitoring progress. On the other hand, exposure to radiation can lead to an increased risk of secondary malignancies. This review provides the first comprehensive account of the applicability of protein glycoprofiling as a promising biomarker for TC with applications in disease diagnostics, monitoring and recurrence evaluation. The review first deals with the description and classification of TC. Secondly, the limitations of current TC biomarkers such as hCG, AFP and lactate dehydrogenase are provided together with an extensive overview of the glycosylation of hCG and AFP related to TC. The final part of the review summarises the potential of glycan changes on either hCG and AFP as TC biomarkers for diagnostics and prognostics purposes, and for disease recurrence evaluation. Finally, an analysis of glycans in serum and tissues as TC biomarkers is also provided. - 2019 by the authors.Funding: The authors wish to acknowledge the financial support received from the Slovak Research and Development Agency APVV 17-0300. This work was supported by the Ministry of Health of the Slovak Republic under project registration no. 2018/23-SAV-1. P.K. expresses thanks that this work was also made possible by NPRP grants NPRP 6-381-1-078 and NPRP-9-219-2-105 from the Qatar National Research Fund (A Member of The Qatar Foundation). The findings achieved herein are solely the responsibility of the authors.Scopu

Incorporating DNA Methyltransferase Inhibitors (DNMTis) in the Treatment of Genitourinary Malignancies: A Systematic Review

Inhibition of DNA methyltransferases (DNMTs) has emerged as a novel treatment strategy in solid tumors. Aberrant hypermethylation in promoters of critical tumor suppressor genes is the basis for the idea that treatment with hypomethylating agents may lead to the restoration of a “normal” epigenome and produce clinically meaningful therapeutic outcomes. The aim of this review article is to summarize the current state of knowledge of DNMT inhibitors in the treatment of genitourinary malignancies. The efficacy of these agents in genitourinary malignancies was reported in a number of studies and suggests a role of induced DNA hypomethylation in overcoming resistance to conventional cytotoxic treatments. The clinical significance of these findings should be further investigated

Sharp and fuzzy observables on effect algebras

Observables on effect algebras and their fuzzy versions obtained by means of confidence measures (Markov kernels) are studied. It is shown that, on effect algebras with the (E)-property, given an observable and a confidence measure, there exists a fuzzy version of the observable. Ordering of observables according to their fuzzy properties is introduced, and some minimality conditions with respect to this ordering are found. Applications of some results of classical theory of experiments are considered.Comment: 23 page

Assessing the conservation value of waterbodies: the example of the Loire floodplain (France)

In recent decades, two of the main management tools used to stem biodiversity erosion have been biodiversity monitoring and the conservation of natural areas. However, socio-economic pressure means that it is not usually possible to preserve the entire landscape, and so the rational prioritisation of sites has become a crucial issue. In this context, and because floodplains are one of the most threatened ecosystems, we propose a statistical strategy for evaluating conservation value, and used it to prioritise 46 waterbodies in the Loire floodplain (France). We began by determining a synthetic conservation index of fish communities (Q) for each waterbody. This synthetic index includes a conservation status index, an origin index, a rarity index and a richness index. We divided the waterbodies into 6 clusters with distinct structures of the basic indices. One of these clusters, with high Q median value, indicated that 4 waterbodies are important for fish biodiversity conservation. Conversely, two clusters with low Q median values included 11 waterbodies where restoration is called for. The results picked out high connectivity levels and low abundance of aquatic vegetation as the two main environmental characteristics of waterbodies with high conservation value. In addition, assessing the biodiversity and conservation value of territories using our multi-index approach plus an a posteriori hierarchical classification methodology reveals two major interests: (i) a possible geographical extension and (ii) a multi-taxa adaptation

Clinical utility of plasma miR-371a-3p in germ cell tumors

Germ cell tumours predominantly of the testis ((T)GCTs) are remarkably chemotherapy sensitive. However, a small proportion of patients fail to be cured with cisplatin-based combination chemotherapy. miR-371a-3p is a new liquid biopsy biomarker for (T)GCTs. The aim of this study was to evaluate clinical utility of plasma miR-371a-3p level in patients starting systemic chemotherapy. Patients were included before the first cycle (N = 180) and second cycle (N = 101) of systemic first line chemotherapy, treated between July 2010 and May 2017. Plasma miR-371a-3p levels were measured with the ampTSmiR test and compared to disease characteristics and outcome. Pretreatment plasma miR-371a-3p levels were increased in 51.7% of cases and associated with number of metastatic sites, presence of lung, retroperitoneal, and mediastinal lymph node metastases, S – stage, IGCCCG risk group, and response to therapy. Patients with a negative pretreatment plasma level had better progression-free survival (PFS) and overall survival (OS) compared to patients being positive for miR-371a-3p (hazard ratio [HR] = 0.26, 95% confidence interval [CI] 0.09-0.71, P = 0.02 for PFS and HR = 0.21, 95% CI 0.07-0.67, P = 0.03 for OS, respectively). Patients negative for miR-371a-3p in both samples had a superior PFS (HR = 0.10, 95% CI 0.01-21.49, P = 0.02) and OS (HR = 0.08, 95% CI 0.01-27.81, P = 0.008) compared to patients with miR-371a-3p positive in both samples (multivariate analyses were non-significant). In total 68% of the patients were S0. This study demonstrates clinical value of plasma miR-371a-3p level in chemotherapy naïve (T)GCT patients starting first line of chemotherapy to predict prognosis

Transition of cavitating flow to supercavitation within Venturi nozzle – hysteresis investigation

Cavitation is usually considered as undesirable phenomena. On the other hand, it can be utilized in many applications. One of the technical applications is using cavitation in water treatment, where hydrodynamic cavitation seems to be effective way how to reduce cyanobacteria within large bulks of water. The main scope of this paper is investigation of the cavitation within Venturi nozzle during the transition from fully developed cavitation to supercavitation regime and vice versa. Dynamics of cavitation was investigated using experimental data of pressure pulsations and analysis of high speed videos, where FFT of the pixel intensity and Proper Orthogonal Decomposition (POD) of the records were done to identify dominant frequencies connected with the presence of cavitation. The methodology of the high speed (HS) records semiautomated analysis using the FFT was described. Obtained results were correlated and above that the possible presence of hysteresis was discussed

Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States

Human pluripotent stem cells (PSCs) exist in naive and primed states and provide important models to investigate the earliest stages of human development. Naive cells can be obtained through primed-to-naive resetting, but there are no reliable methods to prospectively isolate unmodified naive cells during this process. Here we report comprehensive profiling of cell surface proteins by flow cytometry in naive and primed human PSCs. Several naive-specific, but not primed-specific, proteins were also expressed by pluripotent cells in the human preimplantation embryo. The upregulation of naive-specific cell surface proteins during primed-to-naive resetting enabled the isolation and characterization of live naive cells and intermediate cell populations. This analysis revealed distinct transcriptional and X chromosome inactivation changes associated with the early and late stages of naive cell formation. Thus, identification of state-specific proteins provides a robust set of molecular markers to define the human PSC state and allows new insights into the molecular events leading to naive cell resetting.Imaging was performed at the Live Cell Imaging Facility/Nikon Center of Excellence, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, supported by grants from the Knut and Alice Wallenberg Foundation, the Swedish Research Council, the Centre for Innovative Medicine, and the Jonasson donation to the School of Technology and Health, Royal Institute of Technology, Sweden. We would like to acknowledge the MedH Flow Cytometry facility at Karolinska Institutet, supported by grants from Karolinska Institutet and the Stockholm County Council. We thank Céline Vallot and Claire Rougeulle at the Université Paris Diderot for providing X chromosome SNP coordinates. We are grateful to Rudolph Jaenisch at the Whitehead Institute for Biomedical Research for providing WIBR3 cells and Austin Smith at the WT–MRC Cambridge Stem Cell Institute for providing H9 NK2 and FiPS cells. We thank all couples who donated embryos to this study. S.P., A.P.R., J.P.S., and F.L. are supported by grants from the Swedish Research Council (2013-2570), Ragnar Söderberg Foundation (M67/13), Swedish Foundation for Strategic Research (ICA-5), Knut and Alice Wallenberg Foundation (4-1205/2016 and 4-148/2017), and Centre for Innovative Medicine and by a Lau fellowship. R.W. is an ISAC Shared Resource Laboratory Emerging Leader. A.J.C. is supported by an MRC DTG Studentship (MR/J003808/1). P.J.R.G. is supported by the Wellcome Trust (WT093736) and BBSRC (BBS/ E/B/000C0402)

Socially and biologically inspired computing for self-organizing communications networks

The design and development of future communications networks call for a careful examination of biological and social systems. New technological developments like self-driving cars, wireless sensor networks, drones swarm, Internet of Things, Big Data, and Blockchain are promoting an integration process that will bring together all those technologies in a large-scale heterogeneous network. Most of the challenges related to these new developments cannot be faced using traditional approaches, and require to explore novel paradigms for building computational mechanisms that allow us to deal with the emergent complexity of these new applications. In this article, we show that it is possible to use biologically and socially inspired computing for designing and implementing self-organizing communication systems. We argue that an abstract analysis of biological and social phenomena can be made to develop computational models that provide a suitable conceptual framework for building new networking technologies: biologically inspired computing for achieving efficient and scalable networking under uncertain environments; socially inspired computing for increasing the capacity of a system for solving problems through collective actions. We aim to enhance the state-of-the-art of these approaches and encourage other researchers to use these models in their future work

Metal Bioavailability in the Sava River Water

Metals present one of the major contamination problems for freshwater systems, such as the Sava River, due to their high toxicity, persistence, and tendency to accumulate in sediment and living organisms. The comprehensive assessment of the metal bioavailability in the Sava River encompassed the analyses of dissolved and DGT-labile metal species of nine metals (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) in the river water, as well as the evaluation of the accumulation of five metals (Cd, Cu, Fe, Mn, and Zn) in three organs (liver, gills, and gastrointestinal tissue) of the bioindicator organism, fish species European chub (Squalius cephalus L.).This survey was conducted mainly during the year 2006, in two sampling campaigns, in April/May and September, as periods representative for chub spawning and post-spawning. Additionally, metal concentrations were determined in the intestinal parasites acanthocephalans, which are known for their high affinity for metal accumulation. Metallothionein concentrations were also determined in three chub organs, as a commonly applied biomarker of metal exposure. Based on the metal concentrations in the river water, the Sava River was defined as weakly contaminated and mainly comparable with unpolluted rivers, which enabled the analyses of physiological variability of metal and metallothionein concentrations in the chub organs, as well as the establishment of their constitutive levels

Pot, kettle: Nonliteral titles aren’t (natural) science

© 2020 The Author. Published by MIT Press. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1162/qss_a_00078Researchers may be tempted to attract attention through poetic titles for their publications, but would this be mistaken in some fields? Whilst poetic titles are known to be common in medicine, it is not clear whether the practice is widespread elsewhere. This article investigates the prevalence of poetic expressions in journal article titles 1996-2019 in 3.3 million articles from all 27 Scopus broad fields. Expressions were identified by manually checking all phrases with at least 5 words that occurred at least 25 times, finding 149 stock phrases, idioms, sayings, literary allusions, film names and song titles or lyrics. The expressions found are most common in the social sciences and the humanities. They are also relatively common in medicine, but almost absent from engineering and the natural and formal sciences. The differences may reflect the less hierarchical and more varied nature of the social sciences and humanities, where interesting titles may attract an audience. In engineering, natural science and formal science fields, authors should take extra care with poetic expressions, in case their choice is judged inappropriate. This includes interdisciplinary research overlapping these areas. Conversely, reviewers of interdisciplinary research involving the social sciences should be more tolerant of poetic licens