Scalable CNN-based classification of selective sweeps using derived allele frequencies.

Motivation: Selective sweeps can successfully be distinguished from neutral genetic data using summary statistics and likelihood-based methods that analyze single nucleotide polymorphisms (SNPs). However, these methods are sensitive to confounding factors, such as severe population bottlenecks and old migration. By virtue of machine learning, and specifically convolutional neural networks (CNNs), new accurate classification models that are robust to confounding factors have been recently proposed.

Gas chromatography-mass spectrometry selected ion monitoring and gas chromatography-tandem mass spectrometry selected reaction monitoring analyses of mono-, di- and tri-unsaturated C highly branched isoprenoid alkene biomarkers in sea ice and sediment samples: A comparative study.

Rationale: The efficiency of selected ion monitoring (SIM) and selected reaction monitoring (SRM) analyses for the quantification of three mono-, di- and tri-unsaturated highly branched isoprenoid (HBI) alkenes (IP , IPSO and HBI III, respectively), often used as proxies for the occurrence of Arctic and Antarctic sea ice or the adjacent open waters, was compared.

Methods: Gas chromatography (GC)-mass spectrometry (MS)/SIM and GC/MS/MS/SRM analyses were carried out on dilute solutions made from purified standards of these three HBIs, and then on hydrocarbon fractions of several sediment and sea ice sample extracts. More efficient and specific SRM transitions were selected after collision-induced dissociation of each precursor ion at different collision energies.

Essential omega-3 fatty acids are depleted in sea ice and pelagic algae of the Central Arctic Ocean.

Microalgae are the main source of the omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), essential for the healthy development of most marine and terrestrial fauna including humans. Inverse correlations of algal EPA and DHA proportions (% of total fatty acids) with temperature have led to suggestions of a warming-induced decline in the global production of these biomolecules and an enhanced importance of high latitude organisms for their provision. The cold Arctic Ocean is a potential hotspot of EPA and DHA production, but consequences of global warming are unknown.

Sea ice-ocean coupling during Heinrich Stadials in the Atlantic-Arctic gateway.

The variability of Arctic sea-ice during abrupt stadial-interstadial shifts in the last glacial period remain poorly understood. Here, we investigated the millennial-scale relationship, with a focus on Heinrich Stadials (HS), between sea-ice cover and bottom water temperature (BWT) during Marine Isotope Stages (MIS) 3 and 2 (64-13 ka) in the Fram Strait using new molecular sea ice biomarker data and published benthic foraminiferal BWT records. Widespread spring sea-ice cover (SpSIC) dominated the studied interval, especially in mid-late MIS 3 (45-29 ka).

Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters.

Chromosome numbers often change dynamically in tumors and cultured cells, which complicates therapy as well as understanding genotype-mechanotype relationships. Here we use a live-cell "ChReporter" method to identify cells with a single chromosomal loss in efforts to better understand differences in cell shape, motility, and growth. We focus on a standard cancer line and first show clonal populations that retain the ChReporter exhibit large differences in cell and nuclear morphology as well as motility.

Albuminuria and markers for cardiovascular risk in 12-year-olds from the general Dutch population: a cross-sectional study.

Unlabelled: In adults, albuminuria represents a risk factor for cardiovascular disease and is associated with hypertension and obesity. Pediatric data from the general population are inconsistent and largely based on randomly collected urine. A possible association between antenatal programming and albuminuria at school age has still to be investigated.

Beyond butyrate: microbial fiber metabolism supporting colonic epithelial homeostasis.

Human gut bacteria produce metabolites that support energy and carbon metabolism of colonic epithelial cells. While butyrate is commonly considered the primary fuel, it alone cannot meet all the carbon requirements for cellular synthetic functions. Glucose, delivered via circulation or microbial metabolism, serves as a universal carbon source for synthetic processes like DNA, RNA, protein, and lipid production.

Longitudinal relationship between albuminuria in infancy and childhood.

Background: Mildly increased albuminuria is common in the general adult population and is a strong predictor for cardiovascular events, even in otherwise healthy individuals. The underlying pathophysiological process could be endothelial dysfunction. Previously, we reported that increased albuminuria can also be found in 2-year-olds from the general population.

Differential and organ-specific functions of organic solute transporter α and β in experimental cholestasis.

Background & Aims: Organic solute transporter (OST) subunits OSTα and OSTβ facilitate bile acid efflux from the enterocyte into the portal circulation. Patients with deficiency of OSTα or OSTβ display considerable variation in the level of bile acid malabsorption, chronic diarrhea, and signs of cholestasis. Herein, we generated and characterized a mouse model of OSTβ deficiency.

Antiphased dust deposition and productivity in the Antarctic Zone over 1.5 million years.

The Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report a high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.

Incorporation of Toll-Like Receptor Ligands and Inflammasome Stimuli in GM3 Liposomes to Induce Dendritic Cell Maturation and T Cell Responses.

Cancer vaccination aims to activate immunity towards cancer cells and can be achieved by delivery of cancer antigens together with immune stimulatory adjuvants to antigen presenting cells (APC). APC maturation and antigen processing is a subsequent prerequisite for T cell priming and anti-tumor immunity. In order to specifically target APC, nanoparticles, such as liposomes, can be used for the delivery of antigen and adjuvant.

Marker-free lineage tracing reveals an environment-instructed clonogenic hierarchy in pancreatic cancer.

Effective treatments for pancreatic ductal adenocarcinoma (PDAC) are lacking, and targeted agents have demonstrated limited efficacy. It has been speculated that a rare population of cancer stem cells (CSCs) drives growth, therapy resistance, and rapid metastatic progression in PDAC. These CSCs demonstrate high clonogenicity in vitro and tumorigenic potential in vivo.

Type II photosensitized oxidation in senescent microalgal cells at different latitudes: Does low under-ice irradiance in polar regions enhance efficiency?

Comparison of Type II photosensitized oxidation of lipids (the photodynamic effect) and photodegradation of chlorophyll (sensitizer photobleaching) in samples of particulate matter collected previously from locations representing a diverse range of latitudes reveals an enhancement of the photooxidation of lipids at the expense of chlorophyll photodegradation in the polar regions. The efficiency of the photodynamic effect appears to be particularly high in sinking particles collected under sea ice and is attributed to the rapid settling of highly aggregated sympagic algae to depths of low light transmission favouring the photodynamic effect at the expense of photobleaching of the sensitizer. Paradoxically, the low efficiency of Type II photosensitized oxidation of lipids observed in temperate and equatorial regions is associated with high solar irradiances in these regions.

Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution.

Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C tetra-unsaturated methyl alkenone (%C). Elevated %C is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive.

Electron ionization mass spectrometric fragmentation and detection of autoxidation products of 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-ene in Arctic sediments.

Rationale: Some highly branched isoprenoid (HBI) alkenes are commonly used as proxies for palaeoceanographic reconstructions. However, there is a need to identify compounds that are sufficiently stable and abundant to be used as tracers of HBI oxidation in sediments. 2,6,10,14-Tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5(Z/E)-en-4-ols resulting from 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-ene appear to be useful for this purpose.

Discontinuation of RAAS Inhibition in Children with Advanced CKD.

Background And Objectives: Although renin-angiotensin-aldosterone system inhibition (RAASi) is a cornerstone in the treatment of children with CKD, it is sometimes discontinued when kidney function declines. We studied the reasons of RAASi discontinuation and associations between RAASi discontinuation and important risk markers of CKD progression and on eGFR decline in the Cardiovascular Comorbidity in Children with CKD study.

Design, Setting, Participants, & Measurements: In this study, 69 children with CKD (67% male, mean age 13.

Nordic Seas polynyas and their role in preconditioning marine productivity during the Last Glacial Maximum.

Arctic and Antarctic polynyas are crucial sites for deep-water formation, which helps sustain global ocean circulation. During glacial times, the occurrence of polynyas proximal to expansive ice sheets in both hemispheres has been proposed to explain limited ocean ventilation and a habitat requirement for marine and higher-trophic terrestrial fauna. Nonetheless, their existence remains equivocal, not least due to the hitherto paucity of sufficiently characteristic proxy data.

Early Proteinuria Lowering by Angiotensin-Converting Enzyme Inhibition Predicts Renal Survival in Children with CKD.

Although pharmacotherapeutic proteinuria lowering was found to be nephroprotective in adults, the predictive value of early drug-induced proteinuria reduction for long-term renal survival in pediatric CKD is unknown. We analyzed data from the ESCAPE Trial for a potential association between initial antiproteinuric effect of standardized angiotensin-converting enzyme (ACE) inhibition and renal disease progression in children with CKD. In total, 280 eligible children with CKD stages 2-4 (mean age 11.

How to measure and monitor albuminuria in healthy toddlers?

Objective: Urinary albumin:creatinine ratio (UACR) in first morning void (FMV) urine samples collected over three days is the recommended method for measuring and monitoring albuminuria in adults in the clinical setting. Such a guideline is not available for toddlers and young children. We tested several urine collection strategies for albuminuria measurement in toddlers in a prospective observational study.

Electron ionization mass spectrometry fragmentation and multiple reaction monitoring quantification of bacterial metabolites of the sea ice biomarker proxy IP in Arctic sediments.

Rationale: 3,9,13-Trimethyl-6-(1,5-dimethylhexyl)tetradecan-1,2-diol and 2,8,12-trimethyl-5-(1,5-dimethylhexyl)tridecanoic acid appear to be produced during the bacterial metabolism of IP , a highly branched isoprenoid lipid often employed for past Arctic sea ice reconstruction. Characterization and quantification of these metabolites in sediments are essential to determine if bacterial degradation may exert a significant influence on IP -based palaeo sea ice reconstructions.

Methods: Electron ionization mass spectrometry (EIMS) fragmentation pathways of 3,9,13-trimethyl-6-(1,5-dimethylhexyl)tetradecan-1,2-diol and 2,8,12-trimethyl-5-(1,5-dimethylhexyl)tridecanoic acid trimethylsilyl (TMS) derivatives were investigated.

Sea ice dynamics across the Mid-Pleistocene transition in the Bering Sea.

Sea ice and associated feedback mechanisms play an important role for both long- and short-term climate change. Our ability to predict future sea ice extent, however, hinges on a greater understanding of past sea ice dynamics. Here we investigate sea ice changes in the eastern Bering Sea prior to, across, and after the Mid-Pleistocene transition (MPT).

High contributions of sea ice derived carbon in polar bear (Ursus maritimus) tissue.

Polar bears (Ursus maritimus) rely upon Arctic sea ice as a physical habitat. Consequently, conservation assessments of polar bears identify the ongoing reduction in sea ice to represent a significant threat to their survival. However, the additional role of sea ice as a potential, indirect, source of energy to bears has been overlooked.

Further spectral and chromatographic studies of ambergris.

Jetsam ambergris, found washed ashore on beaches, is an environmentally modified form of a natural product of Sperm whales which sometimes develops a pleasant odour. Odorous samples have proved valuable in perfumery. Identification of jetsam ambergris by analysis of organic-soluble extracts by Fourier transform infra-red spectroscopy (FTIR) and of derivatised samples by gas chromatography-mass spectrometry (GC-MS) has already been shown.

Visualization of Large-Scale Narrative Data Describing Human Error.

Objective Introduced is a visual data exploration technique for compiling, reducing, organizing, visually rendering, and filtering text-based narratives for detailed analysis. Background The analysis of data sets provides an increasingly difficult problem. The method of visual representation is considered an effective tool in many applications.