Radiative pion capture by a nucleon

The differential cross sections for $\pi^- p \to \gamma n$ and $\pi^+ n \to \gamma p$ are computed up to $O(p^3)$ in heavy baryon chiral perturbation theory (HBChPT). The expressions at $O(p)$ and $O(p^2)$ have no free parameters. There are three unknown parameters at $O(p^3)$, low energy constants of the HBChPT Lagrangian, which are determined by fitting to experimental data. Two acceptable fits are obtained, which can be separated by comparing with earlier dispersion relation calculations of the inverse process. Expressions for the multipoles, with emphasis on the p-wave multipoles, are obtained and evaluated at threshold. Generally the results obtained from the best of the two fits are in good agreement with the dispersion relation predictions.Comment: 24 pages, Latex, using RevTe

Outlining the Hidden Curriculum: Perspectives on Successfully Navigating Scientific Conferences

Scientific conferences and meetings are valuable opportunities for researchers to network, communicate, and develop knowledge. For early career scientists, conferences can also be intimidating, confusing, and overwhelming, especially without having adequate preparation or experience. In this Perspective, we provide advice based on previous experiences navigating scientific meetings and conferences. These guidelines outline parts of the hidden curriculum around preparing for and attending meetings, navigating conference sessions, networking with other scientists, and participating in social activities while upholding a recommended code of conduct

ProPIG - Organic pig health, welfare and environmental impact across Europe

Organic production is perceived by consumers as being superior in animal welfare and sustainability and the demand for organic pork products is slowly increasing. Within the past ten years a variety of husbandry and management systems have been developed across the EU, ranging from farms with pigs outdoors all year round using local breeds to farms with housed pigs having concrete outside runs and using conventional breeds (CorePIG, Rousing et al, 2011). So far, mainly clinical parameters have been used to describe the health situation on organic pig farms, identifying some key problems, such as weaning diarrhoea and piglet mortality. Organic pig production is - amongst others - characterised through a holistic approach based on the EU Regulation (EC) No 834/2007 and the IFOAM principles: ‘health, ecology, fairness and care’. This clearly states that health is more than absence of clinical symptoms and, the relation between animals and their environment is identified: ‘Health’ is defined as ‘the wholeness and integrity of living systems. It is not simply the absence of illness, but the maintenance of physical, mental, social and ecological well-being’ (IFOAM; 2006). Concepts of animal welfare include physical and mental welfare as well as the concept of naturalness (Fraser 2003), which is often interpreted as the ability to perform natural behaviour. Verhoog et al (2003) describe three main approaches within organic agriculture’s concept of nature and naturalness: the no-chemicals approach, the agro-ecology approach and the integrity approach. Applying those concepts to organic pig production can highlight potential conflicts: outdoor systems are perceived as the optimal housing system for pigs, as they allow natural behaviour such as rooting. However, this behaviour can cause damage to the grass cover and furthermore the manure fate in outdoor areas needs to be considered. A few studies on outdoor pig production have shown a clear N and P surplus and a high degree of distribution heterogeneity in outdoor areas, increasing the risk of N and P losses (Watson et al. 2003). Robust and competitive organic pig production needs to encompass low environmental impacts and good animal health and welfare. So far few studies have quantified both aspects in different pig husbandry systems. In addition, the theory that improving animal health and welfare reduces environmental impacts through decreased medicine use, improved growth rate and feed conversion efficiency has still to be verified. The aim of the CoreOrganic2 project ProPIG (2011-2014; carried out in eight European countries) is to examine the relationship between health, welfare and environmental impact. On-farm assessment protocols will be carried out on 75 farms in three pig husbandry systems (outdoor, partly outdoor, indoor with concrete outside run). Environmental impact will be assessed using both Life Cycle Assessment and calculations of nutrient balances at farm and outdoor area level. Animal health and welfare will be evaluated from animal based parameters including clinical and selected behavioural parameters. Results will be fed back and used by the farmers to decide farm specific goals and strategies to achieve these goals. As an outcome, all farms will create their individual health, welfare and environmental plan, which will be reviewed after one year to allow continuous development. This will provide the opportunity not only to investigate, but also improve the influence of organic pig farming systems on animal welfare and environmental impact. This fulfils the fourth IFOAM principle of care: ‘Organic Agriculture should be managed in a precautionary and responsible manner to protect the health and well-being of current and future generations and the environment’ (IFOAM, 2006)

Trading people versus trading time: What is the difference?

BACKGROUND: Person trade-off (PTO) elicitations yield different values than standard utility measures, such as time trade-off (TTO) elicitations. Some people believe this difference arises because the PTO captures the importance of distributive principles other than maximizing treatment benefits. We conducted a qualitative study to determine whether people mention considerations related to distributive principles other than QALY-maximization more often in PTO elicitations than in TTO elicitations and whether this could account for the empirical differences. METHODS: 64 members of the general public were randomized to one of three different face-to-face interviews, thinking aloud as they responded to TTO and PTO elicitations. Participants responded to a TTO followed by a PTO elicitation within contexts that compared either: 1) two life-saving treatments; 2) two cure treatments; or 3) a life-saving treatment versus a cure treatment. RESULTS: When people were asked to choose between life-saving treatments, non-maximizing principles were more common with the PTO than the TTO task. Only 5% of participants considered non-maximizing principles as they responded to the TTO elicitation compared to 68% of participants who did so when responding to the PTO elicitation. Non-maximizing principles that emerged included importance of equality of life and a desire to avoid discrimination. However, these principles were less common in the other two contexts. Regardless of context, though, participants were significantly more likely to respond from a societal perspective with the PTO compared to the TTO elicitation. CONCLUSION: When lives are at stake, within the context of a PTO elicitation, people are more likely to consider non-maximizing principles, including the importance of equal access to a life-saving treatment, avoiding prejudice or discrimination, and in rare cases giving treatment priority based purely on the position of being worse-off

‘ProPIG’ Challenges and opportunities for on farm pig researchers: How to collect sound scientific data on animal health, welfare, nutrition and environmental impact AND act as a facilitator to improve these aspects at the same time?

Challenges and opportunities of on farm research are discussed and it is concluded, that transdisciplinary on-farm research requires from all involved parties: Understanding and willingness to learn from each other Acceptance, that own field of research is only a part of the whole “on farm picture” Sound scientific methods as well as technical tools for support (e.g. tablet PCs) Move from being/expecting “experts” towards “facilitation

Processed pseudogenes acquired somatically during cancer development

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer

Signatures of mutational processes in human cancer.

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy

Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

As mortality rates decline, life expectancy increases, and populations age, non-fatal outcomes of diseases and injuries are becoming a larger component of the global burden of disease. The Global Burden of Diseases, Injuries, and Risk Factors Study 2016 (GBD 2016) provides a comprehensive assessment of prevalence, incidence, and years lived with disability (YLDs) for 328 causes in 195 countries and territories from 1990 to 2016

Global, regional, and national disability-adjusted life-years (DALYs) for 333 diseases and injuries and healthy life expectancy (HALE) for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

BACKGROUND: Measurement of changes in health across locations is useful to compare and contrast changing epidemiological patterns against health system performance and identify specific needs for resource allocation in research, policy development, and programme decision making. Using the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we drew from two widely used summary measures to monitor such changes in population health: disability-adjusted life-years (DALYs) and healthy life expectancy (HALE). We used these measures to track trends and benchmark progress compared with expected trends on the basis of the Socio-demographic Index (SDI). METHODS: We used results from the Global Burden of Diseases, Injuries, and Risk Factors Study 2016 for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2016. We calculated DALYs by summing years of life lost and years of life lived with disability for each location, age group, sex, and year. We estimated HALE using age-specific death rates and years of life lived with disability per capita. We explored how DALYs and HALE differed from expected trends when compared with the SDI: the geometric mean of income per person, educational attainment in the population older than age 15 years, and total fertility rate. FINDINGS: The highest globally observed HALE at birth for both women and men was in Singapore, at 75·2 years (95% uncertainty interval 71·9-78·6) for females and 72·0 years (68·8-75·1) for males. The lowest for females was in the Central African Republic (45·6 years [42·0-49·5]) and for males was in Lesotho (41·5 years [39·0-44·0]). From 1990 to 2016, global HALE increased by an average of 6·24 years (5·97-6·48) for both sexes combined. Global HALE increased by 6·04 years (5·74-6·27) for males and 6·49 years (6·08-6·77) for females, whereas HALE at age 65 years increased by 1·78 years (1·61-1·93) for males and 1·96 years (1·69-2·13) for females. Total global DALYs remained largely unchanged from 1990 to 2016 (-2·3% [-5·9 to 0·9]), with decreases in communicable, maternal, neonatal, and nutritional (CMNN) disease DALYs offset by increased DALYs due to non-communicable diseases (NCDs). The exemplars, calculated as the five lowest ratios of observed to expected age-standardised DALY rates in 2016, were Nicaragua, Costa Rica, the Maldives, Peru, and Israel. The leading three causes of DALYs globally were ischaemic heart disease, cerebrovascular disease, and lower respiratory infections, comprising 16·1% of all DALYs. Total DALYs and age-standardised DALY rates due to most CMNN causes decreased from 1990 to 2016. Conversely, the total DALY burden rose for most NCDs; however, age-standardised DALY rates due to NCDs declined globally. INTERPRETATION: At a global level, DALYs and HALE continue to show improvements. At the same time, we observe that many populations are facing growing functional health loss. Rising SDI was associated with increases in cumulative years of life lived with disability and decreases in CMNN DALYs offset by increased NCD DALYs. Relative compression of morbidity highlights the importance of continued health interventions, which has changed in most locations in pace with the gross domestic product per person, education, and family planning. The analysis of DALYs and HALE and their relationship to SDI represents a robust framework with which to benchmark location-specific health performance. Country-specific drivers of disease burden, particularly for causes with higher-than-expected DALYs, should inform health policies, health system improvement initiatives, targeted prevention efforts, and development assistance for health, including financial and research investments for all countries, regardless of their level of sociodemographic development. The presence of countries that substantially outperform others suggests the need for increased scrutiny for proven examples of best practices, which can help to extend gains, whereas the presence of underperforming countries suggests the need for devotion of extra attention to health systems that need more robust support. FUNDING: Bill & Melinda Gates Foundation