The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation ...becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.
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IJS, NUK, SBMB, UL, UM, UPUK
Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine ...whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.
In this study, the author examines the effects of three forms of gentrification—demographic shifts, private investment, and state intervention—on gang-motivated homicides in Chicago from 1994 to 2005 ...using data from the U.S. Census, the Chicago Police Department, business directories, and the Chicago Housing Authority. The findings suggest that demographic shifts have a strong negative effect on gang homicide. Private investment gentrification, measured here as the proliferation of coffee shops, has a marginally significant and negative effect on gang homicide. In contrast, state-based gentrification, operationalized as the demolition of public housing, has a positive effect on gang homicide.
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NUK, OILJ, SAZU, UKNU, UL, UM, UPUK
•Tracks the national narrative from the Brexit referendum to Article 50.•OR study prioritising researcher creativity through Critical Realism.•Shows how DREI(C) model can help to conceptualise the ...process of causal mapping.•Combines qualitative and quantitative OR through a Critical Realism philosophy.
The UK's journey from the Brexit referendum on 24th June 2016 until activating Article 50 of the Treaty of Lisbon on 29th March 2017 was turbulent. Through applying soft Operational Research (OR) tools within a Critical Realist (CR) philosophy we analyse 86 televised interviews with leading politicians conducted during these nine months, this study uses causal mapping to theorise the changing national narrative. We theorise that, compared to pre-referendum debates, the period was characterised by an inconsistent national narrative where the large volume of information shared did not create a clear message. The study used the philosophy and methodological creativity of CR to justify our development and analysis of causal maps without recourse to interviewees. We apply CR principles of DREI(C) to describe (D) the Brexit and data context, explain the causal mapping process and identify (I) causal generative mechanisms through a process of retroduction (R) to facilitate thematic analysis and develop our theory of the Brexit journey. This combination provides the framework to eliminate (E) and identify corrections (C) to the emerging theory through iterative abstraction. The contribution to soft OR is threefold. First, it shows how CR can justify a soft OR study where researcher creativity is central, thereby differing from interpretivist causal mapping where respondents are central. Second, it shows how DREI(C) can help conceptualise the process of analysing causal maps. Third, it shows how CR can provide a consistent philosophy for OR studies such as those which use researcher creativity to bridge hard and soft OR.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Background
Current enhanced recovery guidelines suggest that opioid sparing medications should be used for analgesia whenever possible following colorectal surgery. The present study aims to assess ...whether post-operative NSAID use is associated with an increased anastomotic leak rate after a colonic or rectal anastomosis.
Methods
A systematic review was performed for studies investigating anastomotic leak rate following NSAID use vs control after colonic or rectal anastomosis. Meta-analysis was performed to assess for overall risk of anastomotic leak with NSAID use, as well as sub-group analysis to compare selective vs non-selective NSAIDs and drug-specific NSAID safety profiles.
Results
Seven studies were included in the final review. Use of an NSAID post-operatively was associated with an overall increased risk of anastomotic leakage OR 1.58 (1.23, 2.03),
P
= 0.0003. Non-selective NSAIDs were associated with an increased risk OR 1.79 (1.47, 2.18),
P
< 0.00001, but selective NSAIDs were not. The non-selective NSAID diclofenac was associated with an increased leak rate OR 2.79 (1.96, 3.96),
P
< 0.00001, but ketorolac was not OR 1.36 (0.89, 2.06),
P
= 0.16.
Conclusions
Great caution must be taken when prescribing NSAIDs following colonic or rectal anastomotic creation. The safety profile varies within the NSAID class and further research is needed to clarify which NSAIDs are safe for use and which are not.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin (HSM), making these ecosystems ...vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site‐level hydraulic diversity of leaf turgor loss point, resistance to embolism (P50), and HSMs is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P50 values (< −2 MPa) are common across the wet and dry tropics. This high site‐level hydraulic diversity, largely decoupled from water stress, could influence which species are favoured and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.
Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin (HSM), making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site‐level hydraulic diversity of leaf turgor loss point, resistance to embolism (P50), and HSMs is high across tropical forests and largely independent of water availability.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Summary
Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these ...carbon‐rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine‐root strategies for soil resource exploration, (2) coupling and trade‐offs in fine‐root water vs nutrient acquisition, and (3) aboveground–belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground–belowground hydro‐nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.
Resumen
Las características de las raíces de los bosques tropicales y las estrategias de adquisición de recursos están subrepresentadas en modelos de vegetación, lo que dificulta la predicción del efecto de cambio de clima para estos ecosistemas ricos en carbono. Los bosques tropicales a menudo tienen combinaciones únicas a nivel mundial de alta biodiversidad taxonómica y funcional, estacionalidad de precipitación, y suelos infértiles, dando lugar a patrones distintos en los rasgos y funciones de las raíces en comparación con los ecosistemas de latitudes más altas. Integramos los avances recientes en nuestra comprensión de la función subterránea de los bosques tropicales en modelos de vegetación, centrándonos en la adquisición de agua y nutrientes. Ofrecemos comparaciones de avances recientes en la comprensión empírica y de modelos de las características de las raíces que representan procesos funcionales importantes en los bosques tropicales. Nos centramos en: (1) estrategias de raíces finas para adquisición de recursos del suelo, (2) acoplamiento y compensaciones entre adquisición del agua y de nutrientes, y (3) vínculos entre funciones sobre tierra y debajo del superficie en bosques tropicales. Sugerimos vías para representar estas comunidades de plantas extremadamente diversas en grupos computacionalmente manejables y ecológicamente significativos en modelos. Los bosques tropicales se están calentando, tienen cambios en los regímenes de lluvias, y tienen una exacerbación de la escasez de nutrientes del suelo causada por el elevado CO2 atmosférico. La representación precisa de las funciones de los bosques tropicales en modelos es crucial para comprender las interacciones de este bioma con el clima.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
In the UK, most people with lung cancer are diagnosed at a late stage when curative treatment is not possible. To aid earlier detection, the socio-demographic and early clinical features predictive ...of lung cancer need to be identified.
We studied 12,074 cases of lung cancer and 120,731 controls in a large general practice database. Logistic regression analyses were used to identify the socio-demographic and clinical features associated with cancer up to 2 years before diagnosis. A risk prediction model was developed using variables that were independently associated with lung cancer up to 4 months before diagnosis. The model performance was assessed in an independent dataset of 1,826,293 patients from the same database. Discrimination was assessed by means of a receiver operating characteristic (ROC) curve.
Clinical and socio-demographic features that were independently associated with lung cancer were patients' age, sex, socioeconomic status and smoking history. From 4 to 12 months before diagnosis, the frequency of consultations and symptom records of cough, haemoptysis, dyspnoea, weight loss, lower respiratory tract infections, non-specific chest infections, chest pain, hoarseness, upper respiratory tract infections and chronic obstructive pulmonary disease were also independently predictive of lung cancer. On validation, the model performed well with an area under the ROC curve of 0.88.
This new model performed substantially better than the current National Institute for Health and Clinical Excellence referral guidelines and all comparable models. It has the potential to predict lung cancer cases sufficiently early to make detection at a curable stage more likely by allowing general practitioners to better risk stratify their patients. A clinical trial is needed to quantify the absolute benefits to patients and the cost effectiveness of this model in practice.
This paper seeks to address the relation between semantics, pragmatics and the productivity of a low level lexico-grammatical construction, Have the N (body part/attitude) to ↔metapragmatic comment. ...The question posed is how semantics affects productivity, in the generative sense of extensibility of a construction (a form meaning pairing). The method identifies the specificity and variations of the Have the N (body part/attitude) to ↔metapragmatic comment construction within the pragmeme of politeness using the COHA. Hereafter, we consider how to measure the extensibility within the onomasiological frame based on the available pool of forms expressing an attitude/emotion, i.e., the coverage or attractivity of the Have the N to construction. The paper discusses the findings, namely, how to overcome methodological issues relating to a qualitative rather than quantitative approach to the constructional architecture and the relative productivity of constructions. The experimental small scale corpus study of Have the N to in the COHA suggests that a global view of constructional architecture at multiple levels should be pertinent to identifying the extensibility potential of the construction.
Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary ...biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo‐observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype‐based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus‐specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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