Local Structure and Bonding of Carbon Nanothreads Probed by High-Resolution Transmission Electron Microscopy

Carbon nanothreads are a new one-dimensional sp^3-bonded nanomaterial of CH stoichiometry synthesized from benzene at high pressure and room temperature by slow solid-state polymerization. The resulting threads assume crystalline packing hundreds of micrometers across. We show high-resolution electron microscopy (HREM) images of hexagonal arrays of well-aligned thread columns that traverse the 80–100 nm thickness of the prepared sample. Diffuse scattering in electron diffraction reveals that nanothreads are packed with axial and/or azimuthal disregistry between them. Layer lines in diffraction from annealed nanothreads provide the first evidence of translational order along their length, indicating that this solid-state reaction proceeds with some regularity. HREM also reveals bends and defects in nanothread crystals that can contribute to the broadening of their diffraction spots, and electron energy-loss spectroscopy confirms them to be primarily sp^3-hybridized, with less than 27% sp^2 carbon, most likely associated with partially saturated “degree-4” threads

Renal Effects of Aliskiren Compared With and in Combination With Irbesartan in Patients With Type 2 Diabetes, Hypertension, and Albuminuria

Objective: We investigated if the antiproteinuric effect of the direct renin inhibitor aliskiren is comparable to irbesartan, and the effect of the combination. Research Design and Methods: Double-blind, randomized, cross-over trial. After a one-month washout period 26 patients with type 2 diabetes, hypertension and albuminuria (>100mg/day) were randomized to four 2-month treatment periods in random order with placebo, aliskiren 300 mg once daily, irbesartan 300 mg once daily or the combination using identical doses. Patients received furosemide in a stable dose throughout the study. Primary endpoint was change in albuminuria. Secondary measures included change in 24h blood pressure (24h BP) and glomerular filtration rate (GFR). Results: Placebo geometric mean albuminuria was 258 mg/day (range 84-2361), mean 24h BP was 140/73 (SD 15/8) mmHg, GFR was 89 (SD 27) ml/min/1.73 m(2). Aliskiren treatment reduced albuminuria by 48% (95% confidence interval 27-62) compared to placebo (p<0.001), not significantly different from irbesartan treatment (58% (42-70) (p<0.001 vs. placebo)). Combination treatment reduced albuminuria by 71% (59-79), more than either monotherapy (p<0.001 and p=0.028). Fractional clearances of albumin were significantly reduced (46, 56 and 67% reduction vs. placebo). 24h BP was reduced 3/4 mmHg by aliskiren (NS/p=0.009), 12/5 mmHg by irbesartan (p<0.001/p=0.002) and 10/6 mmHg by the combination (p=0.001/p<0.001). GFR was significantly reduced 4.6 (0.3, 8.8) ml/min/1.73m(2) by aliskiren, 8.0 (3.6, 12.3) ml/min/1.73m(2) by irbesartan and 11.7 (7.4, 15.9) ml/min/1.73m(2) by the combination. Conclusions: Combining aliskiren and irbesartan is more antiproteinuric in type 2 diabetic patients with albuminuria as compared to monotherapy

Earthworm activity and availability for meadow birds is restricted in intensively managed grasslands

Earthworms are an important prey for the endangered meadow birds of northwest Europe. Although intensive grassland management with high manure inputs generally promotes earthworm abundance, it may reduce the effective food availability for meadow birds through desiccation of the topsoil, which causes earthworms to remain deeper in the soil. We studied the response of Red Worm Lumbricus rubellus, a detritivore, and Grey Worm Aporrectodea caliginosa, a geophage, to soil moisture profiles in the field and under experimental conditions. Surfacing earthworms were counted weekly in eight intensively managed grasslands (treated with high inputs of slurry by slit injection) with variable groundwater tables in the Netherlands. At each count, soil penetration resistance, soil moisture tension and groundwater level were measured, while air temperature and humidity were obtained from a nearby weather station. The response to variation in the vertical distribution of soil moisture was also experimentally studied in the two earthworm species. In the field, earthworms’ surfacing activity at night was negatively associated with soil moisture tension and positively by relative air humidity. Surprisingly, there was no effect of groundwater level; an important management variable in meadow bird conservation. Under experimental conditions, both L. rubellus and A. caliginosa moved to deeper soil layers (&gt;20 cm) in drier soil moisture treatments, avoiding the upper layer when moisture levels dropped below 30%. Synthesis and applications. We propose that in intensively managed grasslands with slurry application, topsoil desiccation reduces earthworm availability for meadow birds. This can be counteracted by keeping soil moisture tensions of the top soil above −15 kPa. We suggest that the late raising of groundwater tables in spring and the disturbance of the soil by slit injection of slurry increase topsoil desiccation. This decreases earthworm availability when it matters most for breeding meadow birds. Meadow bird conservation will benefit from revised manure application strategies that promote earthworm activity near or at the soil surface.</p

Local Structure and Bonding of Carbon Nanothreads Probed by High-Resolution Transmission Electron Microscopy

Carbon nanothreads are a new one-dimensional sp^3-bonded nanomaterial of CH stoichiometry synthesized from benzene at high pressure and room temperature by slow solid-state polymerization. The resulting threads assume crystalline packing hundreds of micrometers across. We show high-resolution electron microscopy (HREM) images of hexagonal arrays of well-aligned thread columns that traverse the 80–100 nm thickness of the prepared sample. Diffuse scattering in electron diffraction reveals that nanothreads are packed with axial and/or azimuthal disregistry between them. Layer lines in diffraction from annealed nanothreads provide the first evidence of translational order along their length, indicating that this solid-state reaction proceeds with some regularity. HREM also reveals bends and defects in nanothread crystals that can contribute to the broadening of their diffraction spots, and electron energy-loss spectroscopy confirms them to be primarily sp^3-hybridized, with less than 27% sp^2 carbon, most likely associated with partially saturated “degree-4” threads

Spec2Vec: improved mass spectral similarity scoring through learning of structural relationships

Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm—Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types