Vector space models of ancient Greek word meaning, and a case study on homer

Our paper describes the creation and evaluation of a Distributional Semantics model of ancient Greek. We developed a vector space model where every word is represented by a vector which encodes information about its linguistic context(s). We validate different vector space models by testing their output against benchmarks obtained from scholarship from the ancient world, modern lexicography, and an NLP resource. Finally, to show how the model can be applied to a research task, we provide the example of a small-scale study of semantic variation in epic formulae, recurring units with limited linguistic flexibility

Amino acid sequences of proteins from Leptospira serovar pomona.

Abstracts: This report describes a partial amino acid sequences from three putative outer envelope proteins from Leptospira serovar pomona. In order to obtain internal fragments for protein sequencing, enzymatic and chemical digestion was performed. The enzyme clostripain was used to digest the proteins 32 and 45kDa. In situ digestion of 40kDa molecular weight protein was accomplished using cyanogen bromide. The 32kDa protein generated two fragments, one of 21kDa and another of 10kDa that yielded five residues. A fragment of 24 kDa that yielded nineteen residues of amino acids was obtained from 45 kDa protein. A fragment with a molecular weight of 20 kDa, yielding a twenty amino acids sequence from the 40kDa protein

High temperature decreases the PIC / POC ratio and increases phosphorus requirements in <i>Coccolithus pelagicus</i> (Haptophyta)

Rising ocean temperatures will likely increase stratification of the water column and reduce nutrient input into the photic zone. This will increase the likelihood of nutrient limitation in marine microalgae, leading to changes in the abundance and composition of phytoplankton communities, which in turn will affect global biogeochemical cycles. Calcifying algae, such as coccolithophores, influence the carbon cycle by fixing CO₂ into particulate organic carbon through photosynthesis (POC production) and into particulate inorganic carbon through calcification (PIC production). As calcification produces a net release of CO₂, the ratio of PIC to POC production determines whether coccolithophores act as a source (high PIC / POC) or a sink (low PIC / POC) of atmospheric CO₂. We studied the effect of phosphorus (P-) limitation and high temperature on the physiology and the PIC / POC ratio of two subspecies of Coccolithus pelagicus. This large and heavily calcified species is a major contributor to calcite export from the photic zone into deep-sea reservoirs. Phosphorus limitation did not influence exponential growth rates in either subspecies, but P-limited cells had significantly lower cellular P-content. One of the subspecies was subjected to a 5 °C temperature increase from 10 °C to 15 °C, which did not affect exponential growth rates either, but nearly doubled cellular P-content under both high and low phosphate availability. This temperature increase reduced the PIC / POC ratio by 40–60%, whereas the PIC / POC ratio did not differ between P-limited and nutrient-replete cultures when the subspecies were grown near their respective isolation temperature. Both P-limitation and elevated temperature significantly increased coccolith malformations. Our results suggest that a temperature increase may intensify P-limitation due to a higher P-requirement to maintain growth and POC production rates, possibly reducing abundances in a warmer ocean. Under such a scenario <i>C. pelagicus</i> may decrease its calcification rate relative to photosynthesis, thus favouring CO₂ sequestration over release. It seems unlikely that P-limitation by itself causes changes in the PIC / POC ratio in this species

Oral iron exacerbates colitis and influences the intestinal microbiome

Inflammatory bowel disease (IBD) is associated with anaemia and oral iron replacement to correct this can be problematic, intensifying inflammation and tissue damage. The intestinal microbiota also plays a key role in the pathogenesis of IBD, and iron supplementation likely influences gut bacterial diversity in patients with IBD. Here, we assessed the impact of dietary iron, using chow diets containing either 100, 200 or 400 ppm, fed ad libitum to adult female C57BL/6 mice in the presence or absence of colitis induced using dextran sulfate sodium (DSS), on (i) clinical and histological severity of acute DSS-induced colitis, and (ii) faecal microbial diversity, as assessed by sequencing the V4 region of 16S rRNA. Increasing or decreasing dietary iron concentration from the standard 200 ppm exacerbated both clinical and histological severity of DSS-induced colitis. DSS-treated mice provided only half the standard levels of iron ad libitum (i.e. chow containing 100 ppm iron) lost more body weight than those receiving double the amount of standard iron (i.e. 400 ppm); p<0.01. Faecal calprotectin levels were significantly increased in the presence of colitis in those consuming 100 ppm iron at day 8 (5.94-fold) versus day-10 group (4.14-fold) (p<0.05), and for the 400 ppm day-8 group (8.17-fold) versus day-10 group (4.44-fold) (p<0.001). In the presence of colitis, dietary iron at 400 ppm resulted in a significant reduction in faecal abundance of Firmicutes and Bacteroidetes, and increase of Proteobacteria, changes which were not observed with lower dietary intake of iron at 100 ppm. Overall, altering dietary iron intake exacerbated DSS-induced colitis; increasing the iron content of the diet also led to changes in intestinal bacteria diversity and composition after colitis was induced with DSS

Letter: Faecal volatile organic metabolites, promising biomarkers in inflammatory bowel disease and Letter: Faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Authors' reply

The aetiology of inflammatory bowel disease (IBD) remains poorly understood. Recent evidence suggests an important role of gut microbial dysbiosis in IBD, and this may be associated with changes in faecal volatile organic metabolites (VOMs).To describe the changes in the faecal VOMs of patients with IBD and establish their diagnostic potential as non-invasive biomarkers.Faecal samples were obtained from 117 people with Crohn's disease (CD), 100 with ulcerative colitis (UC), and 109 healthy controls. Faecal VOMs were extracted using solid-phase micro-extraction and analysed by gas chromatography mass spectrometry. Data analysis was carried out using partial least squares-discriminate analysis (PLS-DA) to determine class membership based on distinct metabolomic profiles.The PLS-DA model showed clear separation of active CD from inactive disease and healthy controls (P < 0.001). Heptanal, 1-octen-3-ol, 2-piperidinone and 6-methyl-2-heptanone were up-regulated in the active CD group [variable important in projection (VIP) score 2.8, 2.7, 2.6 and 2.4, respectively], while methanethiol, 3-methyl-phenol, short-chain fatty acids and ester derivatives were found to be less abundant (VIP score of 3.5, 2.6, 1.5 and 1.2, respectively). The PLS-DA model also separated patients with small bowel CD from healthy controls and those with colonic CD from UC (P < 0.001). In contrast, less distinct separation was observed between active UC, inactive UC and healthy controls.Analysis of faecal volatile organic metabolites can provide an understanding of gut metabolomic changes in IBD. It has the potential to provide a non-invasive means of diagnosing IBD, and can differentiate between UC and CD

A study of volatile compounds in the breath of children with type 1 diabetes

A pilot study of exhaled volatile compounds and their correlation with blood glucose levels in eight children with type 1 diabetes is reported. Five paired blood and breath samples were obtained from each child over a 6 hour period. The blood glucose concentration ranged from 41.4 to 435.6 mg/dL. Breath samples were collected in Tedlar bags and immediately evacuated through thermal desorption tubes packed with Carbopack B and C. The VOCs were later recovered by thermal desorption and analysed using gas chromatography mass spectrometry. The study identified 74 volatile compounds present in at least 10% of the patient samples. Of these 74 volatiles 36 were found in all patient samples tested. Further analysis of the 36 compounds found that none showed significant overall correlation with blood glucose levels. Isoprene showed a weak negative correlation with blood glucose levels. Acetone was found to have no correlation with blood glucose levels for the patients studied. Some patients showed significant individual correlation between the relative peak areas of certain compounds and blood glucose levels. However, there was no consistent pattern observed within these results across all 8 patients. Additional breath samples were collected in Tedlar bags and analysed using SIFTMS for 3 of the patients and a healthy control. The levels of 24 volatiles are reported and were found to be generally consistent with previously reported SIFT-MS data. In agreement with the GCMS data, no compounds exhibited a significant overall correlation with blood glucose level