Ethanol plant location and intensification vs. extensification of corn cropping in Kansas

This is the author final draft. Copyright 2014 Elsevier.Farmers' cropping decisions are a product of a complex mix of socio-economic, cultural, and natural environments in which factors operating at a number of different spatial scales affect how farmers ultimately decide to use their land in any given year or over a set of years. Some environmentalists are concerned that increased demand for corn driven by ethanol production is leading to conversion of non-cropland into corn production (which we label as “extensification”). Ethanol industry advocates counter that more than enough corn supply comes from crop switching to corn and increased yields (which we label as “intensification”). In this study, we determine whether either response to corn demand – intensification or extensification – is supported. This is determined through an analysis of land-use/land-cover (LULC) data that covers the state of Kansas and a measure of a corn demand shifter related to ethanol production – distance to the closest ethanol plant – between 2007 and 2009

Autoantibodies Against Proteins Previously Associated With Autoimmunity in Adult and Pediatric Patients With COVID-19 and Children With MIS-C

The antibody profile against autoantigens previously associated with autoimmune diseases and other human proteins in patients with COVID-19 or multisystem inflammatory syndrome in children (MIS-C) remains poorly defined. Here we show that 30% of adults with COVID-19 had autoantibodies against the lung antigen KCNRG, and 34% had antibodies to the SLE-associated Smith-D3 protein. Children with COVID-19 rarely had autoantibodies; one of 59 children had GAD65 autoantibodies associated with acute onset of insulin-dependent diabetes. While autoantibodies associated with SLE/Sjögren’s syndrome (Ro52, Ro60, and La) and/or autoimmune gastritis (gastric ATPase) were detected in 74% (40/54) of MIS-C patients, further analysis of these patients and of children with Kawasaki disease (KD), showed that the administration of intravenous immunoglobulin (IVIG) was largely responsible for detection of these autoantibodies in both groups of patients. Monitoring in vivo decay of the autoantibodies in MIS-C children showed that the IVIG-derived Ro52, Ro60, and La autoantibodies declined to undetectable levels by 45-60 days, but gastric ATPase autoantibodies declined more slowly requiring >100 days until undetectable. Further testing of IgG and/or IgA antibodies against a subset of potential targets identified by published autoantigen array studies of MIS-C failed to detect autoantibodies against most (16/18) of these proteins in patients with MIS-C who had not received IVIG. However, Troponin C2 and KLHL12 autoantibodies were detected in 2 of 20 and 1 of 20 patients with MIS-C, respectively. Overall, these results suggest that IVIG therapy may be a confounding factor in autoantibody measurements in MIS-C and that antibodies against antigens associated with autoimmune diseases or other human proteins are uncommon in MIS-C

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The National Early Warning Score and its subcomponents recorded within ±24 hours of emergency medical admission are poor predictors of hospital-acquired acute kidney injury

YesBackground: Hospital-acquired Acute Kidney Injury (H-AKI) is a common cause of avoidable morbidity and mortality. Aim: To determine if the patients’ vital signs data as defined by a National Early Warning Score (NEWS), can predict H-AKI following emergency admission to hospital. Methods: Analyses of emergency admissions to York hospital over 24-months with NEWS data. We report the area under the curve (AUC) for logistic regression models that used the index NEWS (model A0), plus age and sex (A1), plus subcomponents of NEWS (A2) and two-way interactions (A3). Likewise for maximum NEWS (models B0,B1,B2,B3). Results: 4.05% (1361/33608) of emergency admissions had H-AKI. Models using the index NEWS had the lower AUCs (0.59 to 0.68) than models using the maximum NEWS AUCs (0.75 to 0.77). The maximum NEWS model (B3) was more sensitivity than the index NEWS model (A0) (67.60% vs 19.84%) but identified twice as many cases as being at risk of H-AKI (9581 vs 4099) at a NEWS of 5. Conclusions: The index NEWS is a poor predictor of H-AKI. The maximum NEWS is a better predictor but seems unfeasible because it is only knowable in retrospect and is associated with a substantial increase in workload albeit with improved sensitivity.The Health Foundatio

Improvements in radiotherapy practice: the impact of new imaging technologies

Improvements in imaging technology are impacting on every stage of the radiotherapy treatment process. Fundamental to this is the move towards computed tomography (CT) simulation as the basis of all radiotherapy planning. Whilst for many treatments, the definition of three-dimensional (3D) tumour volumes is necessary, for geometrically simple treatments virtual simulation may be more speedily performed by utilising the reconstruction of data in multiple imaging planes. These multi-planar reconstructions may be used to define both the treatment volumes (e.g. for palliative lung treatments) and the organs at risk to be avoided (e.g. for para-aortic strip irradiation). For complex treatments such as conformal radiotherapy (CFRT) and intensity-modulated radiotherapy (IMRT) where 3D volumes are defined, improvements in imaging technologies have specific roles to play in defining the gross tumour volume (GTV) and the planning target volume (PTV). Image registration technologies allow the incorporation of functional imaging, such as positron emission tomography and functional magnetic resonance imaging, into the definition of the GTV to result in a biological target volume. Crucial to the successful irradiation of these volumes is the definition of appropriate PTV margins. Again improvements in imaging are revolutionising this process by reducing the necessary margin (active breathing control, treatment gating) and by incorporating patient motion into the planning process (slow CT scans, CT/fluoroscopy units). CFRT and IMRT are leading to far closer conformance of the treated volume to the defined tumour volume. To ensure that this is reliably achieved on a daily basis, new imaging technologies are being incorporated into the verification process. Portal imaging has been transformed by the introduction of electronic portal imaging devices and a move is underway from two-dimensional (2D) to 3D treatment verification (cone beam CT, optical video systems). A parallel development is underway from off-line analysis of portal images to the incorporation of imaging at the time of treatment using image-guided radiotherapy. By impacting on the whole process of radiotherapy (tumour definition, simulation, treatment verification), these new imaging technologies offer improvements in radiotherapy delivery with the potential for greater cure rates and a minimum level of treatment side effects

Complications of radiotherapy: improving the therapeutic index

For every course of radiotherapy treatment, the potential benefit has to be weighed against the risk of normal tissue damage. Radiation-induced proctitis during and after radical radiotherapy for prostate cancer can be decreased by reducing both the size of the target volume and the margins required around this volume. In the future, target volumes could be reduced by both CT/MRI co-registration and dose painting using MR spectroscopy of choline and citrate in the prostate. Improved immobilisation and image-guided radiotherapy should allow reduced margins without compromising the effectiveness of treatment. Similarly, in breast radiotherapy treatment, lung and cardiac complications can be reduced by better patient positioning and ensuring that doses to the heart and lung are minimised during radiotherapy treatment planning. Cosmesis can be improved by using 3D breast planning techniques rather than the conventional 2D approach. These ongoing improvements and developments in radiotherapy treatment planning are leading to treatments which offer both better tumour volume coverage, and are minimising the risk of treatment-related complications. In time, these changes should allow the escalation in dose delivered to the tumour volume with the potential for increased cure rates