Nutrient availability affects carbon turnover and microbial physiology differently in topsoil and subsoil under a temperate grassland

Increasing subsoil organic carbon inputs could potentially mitigate climate change by sequestering atmospheric CO2. Yet, microbial turnover and stabilization of labile carbon in subsoils are regulated by complex mechanisms including the availability of nitrogen (N), phosphorous (P), and sulfur (S). The present study mimicked labile organic carbon input using a versatile substrate (i.e. glucose) to address the interaction between carbon-induced mineralization, N-P-S availability, and microbial physiology in topsoil and subsoils from a temperate agricultural sandy loam soil. A factorial incubation study (42 days) showed that net losses of added carbon in topsoil were constant, whereas carbon losses in subsoils varied according to nutrient treatments. Glucose added to subsoil in combination with N was fully depleted, whereas glucose added alone or in combination with P and S was only partly depleted, and remarkably 59–92% of the added glucose was recovered after the incubation. This showed that N limitation largely controlled carbon turnover in the subsoil, which was also reflected by microbial processes where addition of glucose and N increased β-glucosidase activity, which was positively correlated to the maximum CO2 production rate during incubation. The importance of N limitation was substantiated by subsoil profiles of carbon source utilization, where microbial metabolic diversity was mainly related to the absence or presence of added N. Overall, the results documented that labile carbon turnover and microbial functions in a temperate agricultural subsoil was controlled to a large extent by N availability. Effects of glucoseinduced microbial activity on subsoil physical properties remained ambiguous due to apparent chemical effects of N (nitrate) on clay dispersibility

RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage Service (S3), or at the Sequence Read Archive (SRA). RSEQREP automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations. The framework outputs a file collection that includes a dynamically generated PDF report using R, knitr, and LaTeX, as well as publication-ready table and figure files. A user-friendly configuration file handles sample metadata entry, processing, analysis, and reporting options. The configuration supports time series RNA-Seq experimental designs with at least one pre- and one post-treatment sample for each subject, as well as multiple treatment groups and specimen types. All RSEQREP analyses components are built using open-source R code and R/Bioconductor packages allowing for further customization. As a use case, we provide RSEQREP results for a trivalent influenza vaccine (TIV) RNA-Seq study that collected 1 pre-TIV and 10 post-TIV vaccination samples (days 1-10) for 5 subjects and two specimen types (peripheral blood mononuclear cells and B-cells)

Nonlinear resonant tunneling in systems coupled to quantum reservoirs

An adiabatic approximation in terms of instantaneous resonances is developed to study the steady-state and time-dependent transport of interacting electrons in biased resonant tunneling heterostructures. The resulting model consists of quantum reservoirs coupled to regions where the system is described by nonlinear ordinary differential equations and has a general conceptual interest.Comment: 4 pages, 3 postscript figure

Charge stability and charge-state-based spin readout of shallow nitrogen-vacancy centers in diamond

Spin-based applications of the negatively charged nitrogen-vacancy (NV) center in diamonds require efficient spin readout. One approach is the spin-to-charge conversion (SCC), relying on mapping the spin states onto the neutral (NV$^0$) and negative (NV$^-$) charge states followed by a subsequent charge readout. With high charge-state stability, SCC enables extended measurement times, increasing precision and minimizing noise in the readout compared to the commonly used fluorescence detection. Nano-scale sensing applications, however, require shallow NV centers within a few \si{\nano \meter} distance from the surface where surface related effects might degrade the NV charge state. In this article, we investigate the charge state initialization and stability of single NV centers implanted \approx \SI{5}{\nano \meter} below the surface of a flat diamond plate. We demonstrate the SCC protocol on four shallow NV centers suitable for nano-scale sensing, obtaining a reduced readout noise of 5--6 times the spin-projection noise limit. We investigate the general applicability of SCC for shallow NV centers and observe a correlation between NV charge-state stability and readout noise. Coating the diamond with glycerol improves both charge initialization and stability. Our results reveal the influence of the surface-related charge environment on the NV charge properties and motivate further investigations to functionalize the diamond surface with glycerol or other materials for charge-state stabilization and efficient spin-state readout of shallow NV centers suitable for nano-scale sensing.Comment: 9 pages, 5 figure

Efficacy of FODMAP Elimination and Subsequent Blinded Placebo-Controlled Provocations in a Randomised Controlled Study in Patients with Ulcerative Colitis in Remission and Symptoms of Irritable Bowel Syndrome:A Feasibility Study

Background: Patients with inflammatory bowel disease (IBD) and symptoms of irritable bowel syndrome (IBS) may be intolerant to fermentable carbohydrates (FODMAPs). The aim of this study was to test the feasibility of eliminating and subsequently reintroducing FODMAPs in patients with IBS symptoms as part of the IBD manifestation and to compare the severity of IBS symptoms and pain, bloating and quality of life (QoL). Methods: An eight-week randomised open-label FODMAP elimination with double-blinded, crossover provocations of FODMAP and placebo. Diet patients were on a low-FODMAP diet for eight weeks with blinded two-week provocations after two and six weeks. Questionnaires, blood and stool samples were collected. Results: Patient enrolment was challenging. Nineteen participants were included in the study. Eliminating low FODMAP for two weeks resulted in significant decreases in pain and bloating scores (p 0.05). Conclusions: The results document the possibility of performing a randomised controlled study following the gold standard for testing food intolerance with blinding of the Low FODMAP diet. Recruitment of participants was challenging

RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting [version 2; referees: 2 approved]

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine via a Docker container or installation script. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage Service (S3), or at the Sequence Read Archive (SRA). RSEQREP automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations. The framework outputs a file collection that includes a dynamically generated PDF report using R, knitr, and LaTeX, as well as publication-ready table and figure files. A user-friendly configuration file handles sample metadata entry, processing, analysis, and reporting options. The configuration supports time series RNA-Seq experimental designs with at least one pre- and one post-treatment sample for each subject, as well as multiple treatment groups and specimen types. All RSEQREP analyses components are built using open-source R code and R/Bioconductor packages allowing for further customization. As a use case, we provide RSEQREP results for a trivalent influenza vaccine (TIV) RNA-Seq study that collected 1 pre-TIV and 10 post-TIV vaccination samples (days 1-10) for 5 subjects and two specimen types (peripheral blood mononuclear cells and B-cells)

Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

The U2AF1 gene is a core part of mRNA splicing machinery and frequently contains somatic mutations that contribute to oncogenesis in myelodysplastic syndrome, acute myeloid leukemia, and other cancers. A change introduced in the GRCh38 version of the human reference build prevents detection of mutations in this gene, and others, by variant calling pipelines. This study describes the problem in detail and shows that a modified GRCh38 reference build with unchanged coordinates can be used to ameliorate the issue

Low hospital admission rates for respiratory diseases in children

BACKGROUND: Population-based data on hospital admissions for children aged 0-17 years concerning all respiratory diseases are scarce. This study examined hospital admissions in relation to the preceding consultations in general practice in this age group. METHODS: Data on children aged 0-17 years with respiratory diseases included in the Second Dutch National Survey of General Practice (DNSGP-2) were linked to all hospital admissions in the Dutch National Medical Registration. Admission rates for respiratory diseases were calculated. Data were analysed using multivariate logistic regression. RESULTS: Of all 79,272 children within the DNSGP-2, 1.8% were admitted to hospital for any respiratory diagnosis. The highest admission rates per 1000 children were for chronic disease of tonsils and adenoids (12.9); pneumonia and influenza (0.97); and asthma (0.92). Children aged 0-4 years and boys were admitted more frequently. Of children with asthma, 2.3% were admitted for respiratory diseases. For asthma, admission rates varied by urbanisation level: 0.47/1000 children/year in cities with ≤ 30,000 inhabitants, 1.12 for cities with ≥ 50,000 inhabitants, and 1.73 for the three largest cities (p = 0.002). Multivariate logistic regression showed that within two weeks after a GP consultation, younger age (OR 0.81, 95% CI 0.76-0.88) and more severe respiratory diseases (5.55, 95% CI 2.99-8.11) predicted hospital admission. CONCLUSIONS: Children in the general population with respiratory diseases (especially asthma) had very low hospital admission rates. In urban regions children were more frequently admitted due to respiratory morbidity. For effectiveness studies in a primary care setting, hospital admission rates should not be used as quality end-point