What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms

Weeds in wheat - response to fallow frequency, legume green manure, and wheat class

Non-Peer Reviewe

Butyric acid glycerides in the diet of broiler chickens: effects on gut histology and carcass composition

Aim of the study was to verify the effects of butyric acid glycerides, as a supplemental ingredient in the diet, on live performance of broiler chickens and on the morphology of their small intestine, since short chain fatty acids are known as selective protection factors against intestinal microbial parasites, potent growth promoters of the gut wall tissues, also in terms of immune modulation response. An experiment was carried out on 150 Ross 308 female chickens, allotted to 5 treatments, over a 35 d ays period: the control, with soybean oil as the energy supplement, and 4 treatments with increasing amounts (0.2, 0.35, 0.5, 1% mixed feed) of a mixture of butyric acid glycerides (mono-, di- and tri- glycerides). Treated animals showed a higher live weight at slaughtering (P<0.05) with a better feed conversion rate. The carcase characteristics were not influenced, but the small intestine wall resulted slightly modified with shorter villi, longer microvilli (P<0.01) and larger crypts depth in jejunum (P<0.01), only with lowest concentration of the supplement (0.2%). It is concluded that butyric acid glycerides are an efficient supplement to broilers' diets, deserving particular attention as a possible alternative to antimicrobial drugs, which have been banned in Europe

Butyric acid glycerides in the diet of broiler chickens: effect of gut histology and carcass composition

Aim of the study was to verify the effects of butyric acid glycerides, as a supplemental ingredient in the diet, on live performance of broiler chickens and on the morphology of their small intestine, since short chain fatty acids are known as selective protection factors against intestinal microbial parasites, potent growth promoters of the gut wall tissues, also in terms of immune modulation response. An experiment was carried out on 150 Ross 308 female chickens, allotted to 5 treatments, over a 35 days period: the control, with soybean oil as the energy supplement, and 4 treatments with increasing amounts (0.2, 0.35, 0.5, 1% mixed feed) of a mixture of butyric acid glycerides (mono-, di- and tri-glycerides). Treated animals showed a higher live weight at slaughtering (P<0.05) with a better feed conversion rate. The carcase characteristics were not influenced, but the small intestine wall resulted slightly modified with shorter villi, longer microvilli (P<0.01) and larger crypts depth in jejunum (P<0.01), only with lowest concentration of the supplement (0.2%

Feminist Art Activisms and Artivisms - 2 July 2018, Middlesex University

This event was organised by Katy Deepwell for the Create/Feminisms research cluster in the Visual Arts Department, Faculty of Arts and Creative Industries, Middlesex University

Pre-eclampsia and offspring cardiovascular health: mechanistic insights from experimental studies

Pre-eclampsia is increasingly recognized as more than an isolated disease of pregnancy. Women who have had a pregnancy complicated by pre-eclampsia have a 4-fold increased risk of later cardiovascular disease. Intriguingly, the offspring of affected pregnancies also have an increased risk of higher blood pressure and almost double the risk of stroke in later life. Experimental approaches to identify the key features of pre-eclampsia responsible for this programming of offspring cardiovascular health, or the key biological pathways modified in the offspring, have the potential to highlight novel targets for early primary prevention strategies. As pre-eclampsia occurs in 2–5% of all pregnancies, the findings are relevant to the current healthcare of up to 3 million people in the U.K. and 15 million people in the U.S.A. In the present paper, we review the current literature that concerns potential mechanisms for adverse cardiovascular programming in offspring exposed to pre-eclampsia, considering two major areas of investigation: first, experimental models that mimic features of the in utero environment characteristic of pre-eclampsia, and secondly, how, in humans, offspring cardiovascular phenotype is altered after exposure to pre-eclampsia. We compare and contrast the findings from these two bodies of work to develop insights into the likely key pathways of relevance. The present review and analysis highlights the pivotal role of long-term changes in vascular function and identifies areas of growing interest, specifically, response to hypoxia, immune modification, epigenetics and the anti-angiogenic in utero milieu

A new model for supraglacial hydrology evolution and drainage for the Greenland ice sheet (SHED v1.0)

The Greenland Ice Sheet (GrIS) is losing mass as the climate warms through both increased meltwater runoff and ice discharge at marine terminating sectors. At the ice sheet surface, meltwater runoff forms a dynamic supraglacial hydrological system which includes stream/river networks and large supraglacial lakes (SGLs). Streams/rivers can route water into crevasses, or into supraglacial lakes with crevasses underneath, both of which can then hydrofracture to the ice sheet base, providing a mechanism for the surface meltwater to access the bed. Understanding where, when and how much meltwater is transferred to the bed is important because variability in meltwater supply to the bed can increase ice flow speeds, potentially impacting the hypsometry of the ice sheet in grounded sectors, and iceberg discharge to the ocean. Here we present a new, physically-based, supraglacial hydrology model for the GrIS that is able to simulate a) surface meltwater routing and SGL filling, b) rapid meltwater drainage to the ice-sheet bed via the hydrofracture of surface crevasses both in, and outside of, SGLs, c) slow SGL drainage via overflow in supraglacial meltwater channels and, by offline coupling with a second model, d) the freezing and unfreezing of SGLs from autumn to spring. We call the model Supraglacial Hydrology Evolution and Drainage (or SHED). We apply the model to three study regions in South West Greenland between 2015 and 2019 inclusive and evaluate its performance with respect to observed supraglacial lake extents, and proglacial discharge measurements. We show that the model reproduces 80 % of observed lake locations, and provides good agreement with observations in terms of the temporal evolution of lake extent. Modelled moulin density values are in keeping with those previously published and seasonal and inter-annual variability in proglacial discharge agrees well with that observed, though the observations lag the model by a few days since they include transit time through the subglacial system and the model does not. Our simulations suggest that lake drainage behaviours may be more complex than traditional models suggest, with lakes in our model draining through a combination of both overflow and hydrofracture, and some lakes draining only partially and then refreezing. This suggests that in order to simulate the evolution of Greenland&rsquo;s surface hydrological system with fidelity, then a model that includes all of these processes needs to be used. In future work we will couple our model to a subglacial model and an ice flow model, and thus use our estimates of where, when and how much meltwater gets to the bed to understand the consequences for ice flow.</p

Discovery of TUG-770: a highly potent free fatty acid receptor 1 (FFA1/GPR40) agonist for treatment of type 2 diabetes

Free fatty acid receptor 1 (FFA1 or GPR40) enhances glucose-stimulated insulin secretion from pancreatic β-cells and currently attracts high interest as a new target for the treatment of type 2 diabetes. We here report the discovery of a highly potent FFA1 agonist with favorable physicochemical and pharmacokinetic properties. The compound efficiently normalizes glucose tolerance in diet-induced obese mice, an effect that is fully sustained after 29 days of chronic dosing

From Anti-equilibrium to The Socialist System and Beyond

This essay attempts to understand János Kornai’s works from a political economy perspective. It argues that Kornai has significantly contributed to the formation of a new paradigm of political economy. The main endeavor of Kornai has been the combination of analytical concepts of economics with the empirical description of real economies. After a certain period of theoretical experimentation János Kornai formulated his research program that can be called the shortage economy explanation of the socialist system. The Economics of Shortage and The Socialist System have created a new theoretical paradigm in a framework in which it has become possible to establish a connection between the analytical and empirical, universal and historical aspects of the theory studying the socialist system as a real economic entity. János Kornai has built his analysis of the socialist system on the primary role of politics in the creation of economic institutions. In his present work on capitalism he has extended this thesis to the capitalist system. This seems to be an important contribution of his to a new political economy paradigm that is just in the process of formation

Two-Dimensional Echocardiography Estimates of Fetal Ventricular Mass throughout Gestation.

BACKGROUND: Two-dimensional (2D) ultrasound quality has improved in recent years. Quantification of cardiac dimensions is important to screen and monitor certain fetal conditions. We assessed the feasibility and reproducibility of fetal ventricular measures using 2D echocardiography, reported normal ranges in our cohort, and compared estimates to other modalities. METHODS: Mass and end-diastolic volume were estimated by manual contouring in the four-chamber view using TomTec Image Arena 4.6 in end diastole. Nomograms were created from smoothed centiles of measures, constructed using fractional polynomials after log transformation. The results were compared to those of previous studies using other modalities. RESULTS: A total of 294 scans from 146 fetuses from 15+0 to 41+6 weeks of gestation were included. Seven percent of scans were unanalysable and intraobserver variability was good (intraclass correlation coefficients for left and right ventricular mass 0.97 [0.87-0.99] and 0.99 [0.95-1.0], respectively). Mass and volume increased exponentially, showing good agreement with 3D mass estimates up to 28 weeks of gestation, after which our measurements were in better agreement with neonatal cardiac magnetic resonance imaging. There was good agreement with 4D volume estimates for the left ventricle. CONCLUSION: Current state-of-the-art 2D echocardiography platforms provide accurate, feasible, and reproducible fetal ventricular measures across gestation, and in certain circumstances may be the modality of choice