Identifying Key Nodes for the Influence Spread Using a Machine Learning Approach.

The identification of key nodes in complex networks is an important topic in many network science areas. It is vital to a variety of real-world applications, including viral marketing, epidemic spreading and influence maximization. In recent years, machine learning algorithms have proven to outperform the conventional, centrality-based methods in accuracy and consistency, but this approach still requires further refinement.

Extreme positive epistasis for fitness in monosomic yeast strains.

The loss of a single chromosome in a diploid organism halves the dosage of many genes and is usually accompanied by a substantial decrease in fitness. We asked whether this decrease simply reflects the joint damage caused by individual gene dosage deficiencies. We measured the fitness effects of single heterozygous gene deletions in yeast and combined them for each chromosome.

Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency.

Introduction: Exosome-enriched small extracellular vesicles (sEVs) are nanosized organelles known to participate in long distance communication between cells, including in the skin. Atopic dermatitis (AD) is a chronic inflammatory skin disease for which filaggrin () gene mutations are the strongest genetic risk factor. Filaggrin insufficiency affects multiple cellular function, but it is unclear if sEV-mediated cellular communication originating from the affected keratinocytes is also altered, and if this influences peptide and lipid antigen presentation to T cells in the skin.

Islets-on-Chip: A Tool for Real-Time Assessment of Islet Function Prior to Transplantation.

Islet transplantation improves metabolic control in patients with unstable type 1 diabetes. Clinical outcomes have been improving over the last decade, and the widely used beta-score allows the evaluation of transplantation results. However, predictive pre-transplantation criteria of islet quality for clinical outcomes are lacking.

A Systematic Review on Quiescent State Research Approaches in .

Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast .

Towards the Integration of an Islet-Based Biosensor in Closed-Loop Therapies for Patients With Type 1 Diabetes.

In diabetes mellitus (DM) treatment, Continuous Glucose Monitoring (CGM) linked with insulin delivery becomes the main strategy to improve therapeutic outcomes and quality of patients' lives. However, Blood Glucose (BG) regulation with CGM is still hampered by limitations of algorithms and glucose sensors. Regarding sensor technology, current electrochemical glucose sensors do not capture the full spectrum of other physiological signals, .

Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae.

Former studies have established that loss of heterozygosity can be a key driver of sequence evolution in unicellular eukaryotes and tissues of metazoans. However, little is known about whether the distribution of loss of heterozygosity events is largely random or forms discernible patterns across genomes. To initiate our experiments, we introduced selectable markers to both arms of all chromosomes of the budding yeast.

Vertical Organic Electrochemical Transistors and Electronics for Low Amplitude Micro-Organ Signals.

Electrical signals are fundamental to key biological events such as brain activity, heartbeat, or vital hormone secretion. Their capture and analysis provide insight into cell or organ physiology and a number of bioelectronic medical devices aim to improve signal acquisition. Organic electrochemical transistors (OECT) have proven their capacity to capture neuronal and cardiac signals with high fidelity and amplification.

Integrating an Islet-Based Biosensor in the Artificial Pancreas: In Silico Proof-of-Concept.

Objective: Current treatment of type 1 diabetes by closed-loop therapy depends on continuous glucose monitoring. However, glucose readings alone are insufficient for an artificial pancreas to truthfully restore nutrient homeostasis where additional physiological regulators of insulin secretion play a considerable role. Previously, we have developed an electrophysiological biosensor of pancreatic islet activity, which integrates these additional regulators through electrical measurements.

Comparison of different digestion methods for proteomic analysis of isolated cells and FFPE tissue samples.

Proteomics of human tissues and isolated cellular subpopulations create new opportunities for therapy and monitoring of a patients' treatment in the clinic. Important considerations in such analysis include recovery of adequate amounts of protein for analysis and reproducibility in sample collection. In this study we compared several protocols for proteomic sample preparation: i) filter-aided sample preparation (FASP), ii) in-solution digestion (ISD) and iii) a pressure-assisted digestion (PCT) method.

Overexpression of a single ORF can extend chronological lifespan in yeast if retrograde signaling and stress response are stimulated.

Systematic collections of single-gene deletions have been invaluable in uncovering determinants of lifespan in yeast. Overexpression of a single gene does not have such a clear outcome as cancellation of its function but it can lead to a variety of imbalances, deregulations and compensations, and some of them could be important for longevity. We report an experiment in which a genome-wide collection of strains overexpressing a single gene was assayed for chronological lifespan (CLS).

Two Bacterial Small Heat Shock Proteins, IbpA and IbpB, Form a Functional Heterodimer.

Small heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as a consequence of ibpA gene duplication event, a two-protein sHsp (IbpA and IbpB) system has evolved.

Dynamic Uni- and Multicellular Patterns Encode Biphasic Activity in Pancreatic Islets.

Biphasic secretion is an autonomous feature of many endocrine micro-organs to fulfill physiological demands. The biphasic activity of islet β-cells maintains glucose homeostasis and is altered in type 2 diabetes. Nevertheless, underlying cellular or multicellular functional organizations are only partially understood.

Tuning of an Artificial Pancreas Controller: an in silico methodology based on clinically-relevant criteria.

This paper presents a methodology to tune an artificial pancreas controller by minimizing the time spent in endangering glycaemic ranges (hypo- and hyperglycaemia). The risk associated to the patient's glycaemia is evaluated with an objective metric (the blood glucose risk index), which has an established clinical relevance. The tuned controller is validated in the UVA/Padova environment where the resulting artificial pancreas achieves minimal glucose risk index in realistic 24-hour long scenarios with unannounced glucose intake.

Mass Spectrometry-Based Identification of MHC-Associated Peptides.

Neoantigen-based immunotherapies promise to improve patient outcomes over the current standard of care. However, detecting these cancer-specific antigens is one of the significant challenges in the field of mass spectrometry. Even though the first sequencing of the immunopeptides was done decades ago, today there is still a diversity of the protocols used for neoantigen isolation from the cell surface.

Population structure, connectivity, and demographic history of an apex marine predator, the bull shark .

Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark . This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures.

Duplicate divergence of two bacterial small heat shock proteins reduces the demand for Hsp70 in refolding of substrates.

Small heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones that bind to aggregation-prone polypeptides at stress conditions. sHsps encage these polypeptides in assemblies, shielding them from further aggregation. To facilitate their subsequent solubilization and refolding by Hsp70 (DnaK) and Hsp100 (ClpB) chaperones, first, sHsps need to dissociate from the assemblies.

Reproductive biology, multiple paternity and polyandry of the bull shark Carcharhinus leucas.

To improve understanding of bull shark Carcharhinus leucas reproductive biology, we analysed reproductive traits from 118 bull sharks caught along Reunion Island coasts (Western Indian Ocean), including 16 gravid females. Specific microsatellite loci were used to investigate the frequency of multiple paternity. Males and females reached maturity at c.

Genetic population structure and demography of an apex predator, the tiger shark .

Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, , is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems.

Bioluminescence of Vibrio fischeri: bacteria respond quickly and sensitively to pulsed microwave electric (but not magnetic) fields.

Biological systems with intrinsic luminescent properties serve as powerful and noninvasive bioreporters for real-time and label-free monitoring of cell physiology. This study employs the bioluminescent marine bacterium Vibrio fischeri to investigate the effects of separated microwave electric (E) and magnetic (H) fields. Using a cylindrical TM010 mode aluminum resonant cavity, designed to spatially separate E and H fields of a pulsed microwave (2.

Multimed: An Integrated, Multi-Application Platform for the Real-Time Recording and Sub-Millisecond Processing of Biosignals.

Enhanced understanding and control of electrophysiology mechanisms are increasingly being hailed as key knowledge in the fields of modern biology and medicine. As more and more excitable cell mechanics are being investigated and exploited, the need for flexible electrophysiology setups becomes apparent. With that aim, we designed Multimed, which is a versatile hardware platform for the real-time recording and processing of biosignals.

Bioelectronic organ-based sensor for microfluidic real-time analysis of the demand in insulin.

On-line and real-time analysis of micro-organ activity permits to use the endogenous analytical power of cellular signal transduction algorithms as biosensors. We have developed here such a sensor using only a few pancreatic endocrine islets and the avoidance of transgenes or chemical probes reduces bias and procures general usage. Nutrient and hormone-induced changes in islet ion fluxes through channels provide the first integrative read-out of micro-organ activity.

First detection of Trichinella pseudospiralis infection in raccoon (Procyon lotor) in Central Europe.

The raccoon (Procyon lotor) is a North American carnivore introduced to Europe in the 20th Century. Raccoons are believed to be the potential hosts of many parasites, or to be involved in their transmission to other animals. Nematodes of the genus Trichinella can infect many carnivorous and omnivorous animals worldwide.

Clonal structure through space and time: High stability in the holothurian (Echinodermata).

Sea cucumbers are increasingly exploited for human consumption and for their curative properties, and many wild populations are now depleted or in danger of extinction. While aquaculture is seen as an alternative to fisheries and as a mean to restore wild populations, more knowledge is needed on their reproductive strategies to render this practice efficient, notably for fissiparous holothurians, which are some of the mobile animals able of asexual reproduction by transverse fission. Little information is available on their population genetic diversity and structure.

Simultaneous monitoring of single cell and of micro-organ activity by PEDOT:PSS covered multi-electrode arrays.

Continuous and long-term monitoring of cellular and micro-organ activity is required for new insights into physiology and novel technologies such as Organs-on-Chip. Moreover, recent advances in stem cell technology and especially in the field of diabetes call for non-invasive approaches in quality testing of the large quantities of surrogate pancreatic islets to be generated. Electrical activity of such a micro-organ results in single cell action potentials (APs) of high frequency and in low frequency changes in local field potentials (slow potentials or SPs), reflecting coupled cell activity and overall organ physiology.