bluuebunny/crossref_metadata_2025 huggingface dataset:
Pipeline shore crossing approaches in Arctic conditions
Authors: Kurbonshoeva L , Gudmestad O T , Zolotukhin A
Published: November 2019

The development of the Arctic region will entail the construction of new infrastructure, in particular, subsea pipelines. Considering the lack of actual field practice, ecosystem vulnerability and lack of common Arctic international standards, their development will be a big challenge, in particular, in the shore crossing zone. The design and construction of pipelines in the shore crossing area require a special approach that takes into account environmental and technological aspects of development. This work is aimed at analysing and determining environmental and technological factors influencing the design of offshore pipelines in the Arctic coastline. The paper presents theoretical and analytical work and the research is applied to a specific case study (pipelines from the Leningraskoye field to shore), through engineering calculations. Currently, there are five Arctic projects with shore transition areas for which trenching has been implemented. In order to determine the best shore crossing approach, it is important to consider the following environmental conditions: ice encroachment; ice ridges; shoreline erosion; permafrost thawing. Environmental characteristics should predetermine the choice of approach. Among three existing methods: trenching, tunnelling and horizontal directional drilling (HDD), the micro-tunnelling method is recommended for the Leningradskoye field in combination with a cofferdam corridor to protect the buried pipe from waves and ice in the nearshore area. In order to protect the surrounded permafrost from melting seasonal cooling-device is recommended to be used. The burial depth is determined to be more than 3.52 m in accordance with Force model calculations of ice ridges scouring depth. On the basis of research, the general choice-making diagram was proposed for Arctic shore crossing areas.
Features of geotechnical surveys and leg penetration analysis for drilling platforms in the Arctic seas
Authors: Marchenko I
Published: November 2019

In recent years, one of the most important direction in the development of offshore hydrocarbon exploration is the expansion of the oil, gas and gas condensate fields of the Russian Federation to the Arctic shelf areas. Extensive and complex engineering surveys are actively performed in the Barents Sea and the Kara Sea. In the last year, a wide range of engineering investigations has been implemented on prospecting and exploratory wells. The geotechnical surveys are mandatory before the drilling of exploratory and production wells to obtain the data for the upper part of the geological profile to provide necessary information for safe positioning of drilling rigs. This is extremely important as the upper part of the soil interacts with an engineering structure whether it is a drilling rig, pipeline, subsea production system or any other structure. The data of the stated surveys is used for optimal location selection for drilling rig positioning and the necessary stability calculations. The use of geophysical and geotechnical methods in engineering surveys provide an effective solution for the geological challenges and ensures the availability of sufficient information regarding soil composition, properties and strength conditions.
The Barents Sea of the Norwegian Continental Shelf: drilling through carbonates, modelling, risk management and well planning
Authors: Mosesyan M A , Hartwig A , Edin K M , Rabey A S , Surguchev L M
Published: November 2019

There are a number of geological and hydrogeochemical modelling techniques used in order to ascertain formation of the hydrogen sulphide (H2S) in the formation fluid within a geological setting in several blocks of the Norwegian Barents Sea. Careful consideration of the regional and chemical factors causing H2S generation can also be used in the drilling context. Thermochemical sulphate reduction (TSR) is the most likely process of H2S formation in this setting. Risk picture becomes different when presence of H2S is closely coupled with occurrence of Permian and Carboniferous carbonate plays prone to causing severe drilling fluid losses and increasing exposure time of the downhole equipment to the H2S. Using appropriate analogues and adequate well offset analysis tend to demonstrate that most of the risk factors can be well mitigated.
Problem and models of multicriteria decision making and risk assessment of the arctic offshore oil and gas field development
Authors: Zolotuhin A B , Stepin Yu P
Published: November 2019

The article is devoted to the systematic solution of problems of multi-criteria assessment and the possibility of implementing projects for the development of hydrocarbon deposits on the Arctic shelf under conditions of uncertainty and risk. Risks are considered in a narrow and broad sense. It is shown that the solution of tasks, in this case, comes down: 1) to a multi-criteria assessment of the quality level of a field based on a hierarchy analysis method that takes into account uncertainties and risks of operating objects through the relevant necessary indicators (criteria); 2) determining, with the help of game theory adopted with the nature of the criteria for selecting the best Bayesian strategies, of development options under both partial and full uncertainty conditions; 3) selection using the rules of the Borda, Pareto and multi-criteria dispersive risk model for choosing the best development strategy.
Field development optimization of waterflooding process using data assimilation methods
Authors: Guliev R , Zolotukhin A
Published: November 2019

The application of data assimilation methods for field development optimization has been the subject of intense investigation during the past 10 years. Lately has seen remarkable progress in the ability of data assimilation approach in reservoir characterization and based on this, improvements of field development optimization. In this review paper, we have summarized key achievements in field development optimization of waterflooding process with data assimilation approach and review many of the achievements of the past time, including developments in the field of search for modifications of Ensemble Kalman Filter (EnKF) and Ensemble Smoothers (ES). An attempt has been made to discuss different data assimilation methods and to identify possible limitations of each. Current challenges and future research opportunities for improved data assimilation methods for field development optimization of waterflooding process are also discussed.
Work on structural integrity for semi submersibles exposed to bergy bits – integrated analysis of ice structure impacts
Authors: Lu W , Yu Z , Van D Berg M , Lubbad R , Kim E , Amdahl J , Bjørheim L G , Langøy M A , Løset S
Published: November 2019

Bergy bits and growlers (i.e., glacial ice features with a waterline diameter < 15 m) travelling with waves are identified as risk to the integrity of offshore structure and ships operating in the high North. It is generally more difficult to detect and monitor these small ice features and apply concurrent ice management operations. Therefore, it is important to study the corresponding damage assessment of a potential impact with such glacial ice features. Traditionally, while carrying out a structural damage assessment, the ice feature is often treated as a rigid body, whereas structural deformation and fractures are simulated with, e.g., NonLinear Finite Element Method (NLFEM). However, this method is too conservative and neglects that the ice feature crushes and dissipates part of the impact energy (often obtained with the so-called external mechanics). On the other hand, it is possible to treat both the ice and the structure deformable, and a fully coupled simulation can be carried out with NLFEM. This method can capture the physical essence that the impact energy dissipation is shared by both ice crushing and structural deformation, thus leading to a less conservative structural damage assessment. However, this method is often too computationally expensive and can only take care of the so-called ‘internal mechanics’ part. In this paper, we propose an integrated approach. This approach is mainly based on the innovative Simulator for Arctic Marine Structures (SAMS) to calculate the impact energy following the principle of ‘external mechanics’. Afterwards, the simulated results are integrated with NLFEM simulations to re-construct the shared impact energy dissipation between both the ice feature and structure. A case study regarding a glacial ice feature (diameter = 15 m) impacting a semi-submersible is carried out in this paper. This integrated simulation approach (i.e., SAMS + NLFEM) is proved to be significantly more effective than the fully coupled analysis; more versatile and less conservative than the limiting scenario analysis when dealing with the impact between ice features and man-made structures.
A summary of adapting Industry 4.0 vision into engineering education in Azerbaijan
Authors: Ahadov A , Asgarov E S , El-Thalji I
Published: November 2019

Industry 4.0 vision and associated technologies are rapidly adopted in several industrial sectors to gain the benefits of creating smart cyber-physical systems and operations. Some sectors, e.g. manufacturing, oil and gas, offshore wind energy, have progressed in developing digitization strategies, executing pilot projects and progressing toward mature implementation of industry 4.0 vision. Offshore Oil and Gas industry highly believes in the potential industrial and societal impacts of digital transformation, due to the need for stochastic and remote operations. Azerbaijan as one of the countries that heavily depend on the Oil and Gas industry is developing more projects in the Caspian Sea. There are several worldwide challenges, mainly, lack of standards, business models, ready products/services and competent and skilled employees. Fortunately, specific developed countries are working hard to standardize industry 4.0 architecture. Moreover, large-scale companies are creating alliances to create a trustful and long-term business model. Furthermore, large-scale companies of information and operational technology are creating robust products and services to be commercially available off the shelf. In terms of education and training, many worldwide universities are upgrading their programs, curriculums, teaching approaches with the goal to support the industry with competent future employees and entrepreneurs. Therefore, the purpose of this paper is, to present the status of engineering education programs in adapting the industry 4.0 vision in Azerbaijan and address the skills that are required for future employment. In order to present the targeted status, the curriculums of all engineering education programs at the master level were collected and analyzed. However, five of them were directly adapting industry 4.0 vision and relevant for industry 4.0. Moreover, a semi-structured interview with industrial managers was applied to extract the future required skills. This study can be considered as a first step in developing a roadmap for engineering education, particularly industrial engineering, to adopt industry 4.0 vision at the national level.
Context analysis of Offshore Fish Farming
Authors: El-Thalji I
Published: November 2019

The in-land and nearshore fish farming is facing capacity limitation and onshore push-out regulations. Huge technological innovations are rapidly evolving toward developing competitive Offshore fish farming. These technological innovations are mainly targeting to innovate new farming concepts that dynamically stable, reliable and compatible with offshore environmental loads and conditions. The dynamic operational behaviour of each farming concept is quite complicated. It is a combination of reinforcing behaviours (Loads, cage deformations, welfare issues, e.g. escaping, stress-related disease) and leveraging behaviours (Biofouling-cleaning, Deterioration-maintenance) and all influenced by fluctuating and harsh environmental loads and conditions. Therefore, the purpose of this paper is to analyse the context of offshore fish farming and explore quantitative descriptions of its reinforcement and leveraging behaviours. The context analysis is a well-known method within systems engineering methodology to illustrate and extract critical interfaces. The context analysis is considered as the first step in building simulation model to quantify the impact of systems interfaces on the entire farming economics, i.e. income and cost.
Development and characterization of jute composites for sustainable product: effect of chemical treatments and polymer coating
Authors: Yadav Arun , Gupta M K
Published: November 2019

In this work, woven jute fibres were subjected to ecofriendly and chemical treatments (alkali, benzoylation and sodium bicarbonate) and PLA coating in order to improve the adhesion with epoxy thereby improvement in the performances of their composites. Treated and coated jute fibres reinforced epoxy composites were prepared by hand lay-up technique keeping constant 30 wt% of fibres content in the each composite. Mechanical properties (i.e. tensile, flexural and impact) and dynamic mechanical properties (i.e. storage modulus, loss modulus, damping and glass transition temperature) of prepared composites were studied. The outcomes from the experimental results suggested that benzoyl chloride treated and PLA coated jute composite exhibited the best performance as compared to other all the composites. There were 21%, 40.6% and 27.5% improvement in tensile strength, flexural strength and impact strength respectively for this composite as compared to that of untreated jute fibre reinforced composites. Moreover, storage and loss modulus of jute composites were also significantly enhanced by treatment and coating. The present developed composites can be used for medium strength application in the field of automobile, building and construction and packaging.
An exploration of the freeform two-mirror off-axis solution space
Authors: Volatier Jean-Baptiste , Duveau Louis , Druart Guillaume
Published: November 2019

We use a differential construction procedure to construct three starting solutions for a thermal infrared telescope design problem. We further refine these solutions with a simple optimization procedure. We show that this hybrid method is interesting by its flexibility that makes it suitable to find solutions to problems with tight volume constraints and its ease of use with little designer interaction required. Taking advantage of a fully automated process, we are able to investigate for each solution and its starting geometry, the impact of the Zernike order on the final performance obtained. Finally we show the systems proposed are sufficient for thermal infrared applications and while not as performant as the three mirror system used for comparison, their simplicity makes them an interesting alternative.
Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation
Authors: Honjo Mie N , Kudoh Hiroshi
Published: November 2019

Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.
Extra-pair mating opportunities mediate parenting and mating effort trade-offs in a songbird
Authors: Lv Lei , Zhang Zhengwang , Groenewoud Frank , Kingma Sjouke A , Li Jianqiang , van der Velde Marco , Komdeur Jan
Published: November 2019

In socially monogamous species with bi-parental care, males may face a trade-off between providing parental care and pursuing extra-pair matings. The “parenting-mating trade-off” hypothesis predicts that high-quality males—who have greater potential to gain extra-pair matings, for example, larger males usually win the competition for extra-pair mating—should reduce parental care and spend more time looking for extra-pair matings. However, the trade-off between parenting and mating efforts may be complicated by variation in the availability of extra-pair mating opportunities. By using field data of hair-crested drongos (Dicrurus hottentottus), a species exhibiting bi-parental incubation behavior, collected in central China from 2010 to 2017, we tested whether the potential negative relationship between male quality and paternal care was dependent on the number of nearby fertile females. We found that male drongos mainly seek extra-pair matings during the incubation period and high-quality individuals (males with longer tarsi) are more likely to sire extra-pair offspring. In agreement with the “parenting-mating trade-off” hypothesis, high-quality males incubated less by recessing longer between incubation bouts. However, this was only the case when sufficient fertile females nearby for extra-pair mating opportunities. Females compensated for reduced male care, but this was independent of male quality. This suggests that the reduction in care by high-quality males might be a direct response to extra-pair mating opportunities rather than facilitated by differential allocation of females. Our results indicate that individual quality and available mating opportunities may shape the optimal trade-off between parental care and seeking additional matings for males.
Morphological and physiological consequences of a dietary restriction during early life in bats
Authors: Meniri Magali , Hebinger Doriane , Sorlin Mahaut , Ramirez Marine , Kauffmann Emilie , Vallat Armelle J , Glauser Gaëtan , Fasel Nicolas , Helfenstein Fabrice
Published: November 2019

Early life adverse conditions can have major consequences on an individual’s life history traits. Oxidative stress has been hypothesized to be one main mechanism underlying the negative consequences of early life adverse conditions. To test this hypothesis, we restricted the food availability of Seba’s short-tailed bat (Carollia perspicillata) mothers of unweaned pups for 10 days, followed by ad libitum provisioning. We also had a control, unrestricted group. We explored the morphological consequences of dietary restriction during early life by measuring growth rate. We also measured four markers of blood oxidative balance during growth. We assessed the level of cortisol, and its inactive form cortisone, in the hair of the pups at the end of growth. Finally, we monitored survival during the first year. Food restriction triggered a slowdown in growth followed by catch-up growth when ad libitum feeding was restored which did not lead to full compensation in size or mass compared to control individuals. We found that higher growth rate was associated with elevated oxidative damage, suggesting an oxidative cost to growth. However, we found no clear evidence for physiological costs specific to the catch-up growth. Survival after a year was not impacted by the treatment, the oxidative balance or the level of glucocorticoids at the end of growth. In conclusion, our results show that individuals were able to efficiently mitigate the short-term consequences of adverse early life conditions. However, consequences might arise in the long-term, and could impact reproductive success or lifespan.
Organoid model of mammographic density displays a higher frequency of aberrant colony formations with radiation exposure
Authors: Cheng Qingsu , Parvin Bahram
Published: November 2019

Motivation

Aberrant three-dimensional (3D) colony organization of premalignant human mammary epithelial cells (HMECs) is one of the indices of dysplasia. An experiment has been designed where the stiffness of the microenvironment, in 3D culture, has been set at either low or high level of mammographic density (MD) and the organoid models are exposed to 50 cGy X-ray radiation. This study utilizes published bioinformatics tools to quantify the frequency of aberrant colony formations by the combined stressors of stiffness and X-ray exposure. One of the goals is to develop a quantitative assay for evaluating the risk factors associated with women with high MD exposed to X-ray radiation.

Results

Analysis of 3D colony formations indicate that high stiffness, within the range of high MD, and X-ray radiation have an approximately additive effect on increasing the frequency of aberrant colony formations. Since both stiffness and X-ray radiation are DNA-damaging stressors, the additive effect of these stressors is also independently validated by profiling activin A-secreted protein. Secretion of activin A is known to be higher in tissues with a high MD as well as tumor cells. In addition, we show that increased stiffness of the microenvironment also induces phosphorylation of γH2AX-positive foci. The study uses two HMECs derived from a diseased tissue (e.g. MCF10A) and reduction mammoplasty of normal breast tissue (e.g. 184A1) to further demonstrate similar traits in the frequency of aberrant colony organization.

Supplementary information

Supplementary data are available at Bioinformatics online.
Social Workers under the Spotlight: An Analysis of Fitness to Practise Referrals to the Regulatory Body in England, 2014–2016
Authors: Banks Sarah , Zasada Magdalena , Jago Robert , Gallagher Ann , Austin Zubin , van der Gaag Anna
Published: November 2019

This article examines the nature of, and reasons for, the disproportionately high rates of fitness to practise referrals of social workers in England to the Health and Care Professions Council (HCPC), compared with other professions regulated by HCPC during 2014–2016. In 2014–2015, the rate of referrals for social workers was 1.42 per cent of registrants, compared with an average for the sixteen professions regulated by HCPC of 0.66 per cent. Drawing on published statistics and unique analysis of a sample of 232 case files undertaken as part of a research project in 2016–2017, the article highlights relatively high rates of inappropriate referrals from ‘members of the public’ (mainly service users) particularly in relation to child placements and contact. A detailed picture is offered of the variety of referrals dealt with at each stage of the fitness to practise process (from initial triage to final hearings), with recommendations for how to prevent inappropriate referrals, whilst focusing concern on the most serious cases of incompetence and misconduct. This research is of significance at a time of increasing pressure for social workers, social services and service users under conditions of austerity and managerialism; on-going concerns about standards in social work; and recent changes in social work regulation.
Reduced drift rate: a biomarker of impaired information processing in functional movement disorders
Authors: Sadnicka Anna , Daum Corinna , Meppelink Anne-Marthe , Manohar Sanjay , Edwards Mark
Published: November 2019

Functional neurological disorder is a common and phenomenologically diverse condition. Resultant disability is caused by both the dominant clinical presentation, e.g. paralysis or tremor and additional symptomatology such as cognitive symptoms. Recently the similarity of neuropsychiatric profiles across a range of functional syndromes has been highlighted. This is suggestive of a common underlying mechanism with a theoretical deficit of information processing proposed. Identification of an experimental biomarker for such deficits could offer novel assessment and therapeutic strategies. In this study, we took the temporal discrimination threshold as a paradigm that can be used to model sensory processing in functional movement disorders. Our hypothesis was that we would be able to delineate markers of slowed information processing in this paradigm removed from the phenomenological presentation with a movement disorder. We recorded both response accuracy and reaction time in a two-choice temporal resolution/discrimination task in 36 patients with functional movement disorders and 36 control subjects. A psychometric function was fitted to accuracy data for each individual revealing both abnormally high threshold values (P = 0.0053) and shallow psychometric slopes in patients (P = 0.0015). Patients with functional movement disorders also had significantly slower response times (P = 0.0065). We then used a well-established model for decision-making (the drift diffusion model) that uses both response accuracy and reaction time data to estimate mechanistic physiological dimensions of decision-making and sensory processing. This revealed pathologically reduced drift rate in the patient group, a parameter that quantifies the quality and rate of information accumulation within this sensory task (P = 0.002). We discuss how the deficits we observed in patients with functional movement disorders are likely to stem from abnormal allocation of attention that impairs the quality of sensory information available. Within a predictive coding framework sensory information could be down-weighted in favour of predictions encoded by the prior. Our results therefore offer a parsimonious account for a range of experimental and clinical findings. Reduced drift rate is a potential experimental marker for a generalized deficit in information processing across functional disorders that allows diverse symptomatology to be quantified under a common disease framework.
Associating Psychotic Symptoms with Altered Brain Anatomy in Psychotic Disorders Using Multidimensional Item Response Theory Models
Authors: Stan Ana D , Tamminga Carol A , Han Kihwan , Kim Jong Bae , Padmanabhan Jaya , Tandon Neeraj , Hudgens-Haney Matthew E , Keshavan Matcheri S , Clementz Brett A , Pearlson Godfrey D , Sweeney John A , Gibbons Robert D
Published: November 2019

Reduced cortical thickness has been demonstrated in psychotic disorders, but its relationship to clinical symptoms has not been established. We aimed to identify the regions throughout neocortex where clinical psychosis manifestations correlate with cortical thickness. Rather than perform a traditional correlation analysis using total scores on psychiatric rating scales, we applied multidimensional item response theory to identify a profile of psychotic symptoms that was related to a region where cortical thickness was reduced. This analysis was performed using a large population of probands with psychotic disorders (N = 865), their family members (N = 678) and healthy volunteers (N = 347), from the 5-site Bipolar-Schizophrenia Network for Intermediate Phenotypes. Regional cortical thickness from structural magnetic resonance scans was measured using FreeSurfer; individual symptoms were rated using the Positive and Negative Syndrome Scale, Montgomery-Asberg Depression Rating Scale, and Young Mania Rating Scale. A cluster of cortical regions whose thickness was inversely related to severity of psychosis symptoms was identified. The regions turned out to be located contiguously in a large region of heteromodal association cortex including temporal, parietal and frontal lobe regions, suggesting a cluster of contiguous neocortical regions important to psychosis expression. When we tested the relationship between reduced cortical surface area and high psychotic symptoms we found no linked regions describing a related cortical set.
Liver Fibrosis Progression and Mortality in Hepatitis B– and C–Coinfected Persons Treated With Directly Acting Antiviral Agents: Results From ERCHIVES
Authors: Butt Adeel A , Yan Peng , Aslam Samia , Abou-Samra Abdul-Badi , Sherman Kenneth E , Shaikh Obaid S
Published: November 2019

For persons with baseline Fibrosis-4 1.46–3.25, cirrhosis incidence/1000 patient-years was 49.3 among hepatitis B virus (HBV)/hepatitis C virus (HCV) coinfected and 18.2 among HCV monoinfected (P = .03). Cirrhosis risk was numerically higher but statistically nonsignificant among HBV/HCV coinfected (hazards ratio [HR] 1.51; 95% confidence intervals [CI], .37–6.05) but lower among those who attained sustained virologic response (HR, .52; 95% CI, .42–.63).
Long-Term Sequelae and Health-Related Quality of Life Associated With Lyme Disease: A Systematic Review
Authors: Mac Stephen , Bahia Simran , Simbulan Frances , Pullenayegum Eleanor M , Evans Gerald A , Patel Samir N , Sander Beate
Published: November 2019

Lyme disease (LD) is the most commonly reported vector-borne disease, but its clinical consequences remain uncertain. We conducted a systematic review of the long-term sequelae and health-related quality of life (HRQoL) associated with LD in North America and Europe. We performed searches in 6 electronic databases up to December 2018 following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, including observational studies reporting long-term sequelae, HRQoL, and prognostic factors. We included 46 studies, published between 1994 and 2019. Based on 21 studies reporting attributable outcomes, higher proportions of sequelae reported from exposed patients were: neck pain, myalgia, arthralgia, paresthesia, sleep disorder, poor appetite, and concentration difficulties. Patients with PTLDS reported impaired HRQoL compared to the general US population. Included studies were highly heterogeneous in terms of study design, settings, patient characteristics, and quality. Patients with LD are more likely to report nonspecific long-term sequelae, especially those experiencing persistent symptoms posttreatment. Opportunities exist for prospective longitudinal studies to better understand LD outcomes.
A comparison of fecal sampling and direct feeding observations for quantifying the diet of a frugivorous primate
Authors: Matthews Jaya K , Ridley Amanda , Kaplin Beth A , Grueter Cyril C
Published: November 2019

Both observational and indirect evidence are widely used to determine the diets of wild animals. Direct observations are often assumed to provide the most comprehensive reflection of diet, but many wild animals are logistically challenging to observe. Despite the regular use of observational and indirect methods for inferring diet in wild animals, they have rarely been compared in detail for the same study population. Over 12 months this study assessed the congruence of methods in estimating the diet of a montane community of eastern chimpanzees Pan troglodytes schweinfurthii in Nyungwe National Park, Rwanda using observational scan samples and macroscopic fecal inspection. The assessment of the number of food species consumed each month was comparable between methods, but the estimation of the composition of items in the diet differed significantly. Most notably, the fecal samples significantly underestimated the consumption of flowers, and certain fruit species, which based on direct behavioral observations were seasonally consumed at very high rates. Conversely, direct observations underestimated the consumption of leaves and pith in comparison to results present in the fecal samples. These results suggest that combining methods where possible is most useful for accurate monitoring of dietary trends, particularly for species that experience significant seasonal shifts in their diet.
The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations
Authors: Manni Mosè , Simao Felipe A , Robertson Hugh M , Gabaglio Marco A , Waterhouse Robert M , Misof Bernhard , Niehuis Oliver , Szucsich Nikolaus U , Zdobnov Evgeny M
Published: November 2019

The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
Age and Gender Stereotypes Reflected in Google’s “Autocomplete” Function: The Portrayal and Possible Spread of Societal Stereotypes
Authors: Roy Senjooti , Ayalon Liat
Published: November 2019

Background and Objectives

Google’s autocomplete function provides “predictors” to enable quick completion of intended search terms. The predictors reflect the search trends of a population; they capture societal beliefs and perceptions about a variety of subjects. This study explores the predictors provided by Google United States when searching for information about older men and women.

Research Design and Methods

The Google search engine of the United States was used to record predictors in response to 720 search terms. Inductive content analysis method was used to categorize and interpret the results.

Results

There was prevalence of age and gender stereotypes in the predictors offered by Google. Queries about older men were primarily associated with romance and sexuality whereas those for older women centered on changes in the body as well as sexual and reproductive health.

Discussion and Implications

The appearance of such predictors in response to a potential search query may lead to the spread of harmful stereotypes about older adults.
Naturally occurring NOTCH3 exon skipping attenuates NOTCH3 protein aggregation and disease severity in CADASIL patients
Authors: Gravesteijn Gido , Dauwerse Johannes G , Overzier Maurice , Brouwer Gwendolyn , Hegeman Ingrid , Mulder Aat A , Baas Frank , Kruit Mark C , Terwindt Gisela M , van Duinen Sjoerd G , Jost Carolina R , Aartsma-Rus Annemieke , Lesnik Oberstein Saskia A J , Rutten Julie W
Published: November 2019

CADASIL is a vascular protein aggregation disorder caused by cysteine-altering NOTCH3 variants, leading to mid-adult-onset stroke and dementia. Here, we report individuals with a cysteine-altering NOTCH3 variant that induces exon 9 skipping, mimicking therapeutic NOTCH3 cysteine correction. The index came to our attention after a coincidental finding on a commercial screening MRI, revealing white matter hyperintensities. A heterozygous NOTCH3 c.1492G>T, p.Gly498Cys variant, was identified using a gene panel, which was also present in four first- and second-degree relatives. Although some degree of white matter hyperintensities was present on MRI in all family members with the NOTCH3 variant, the CADASIL phenotype was mild, as none had lacunes on MRI and there was no disability or cognitive impairment above the age of 60 years. RT-PCR and Sanger sequencing analysis on patient fibroblast RNA revealed that exon 9 was absent from the majority of NOTCH3 transcripts of the mutant allele, effectively excluding the mutation. NOTCH3 aggregation was assessed in skin biopsies using electron microscopy and immunohistochemistry and did not show granular osmiophilic material and only very mild NOTCH3 staining. For purposes of therapeutic translatability, we show that, in cell models, exon 9 exclusion can be obtained using antisense-mediated exon skipping and CRISPR/Cas9-mediated genome editing. In conclusion, this study provides the first in-human evidence that cysteine corrective NOTCH3 exon skipping is associated with less NOTCH3 aggregation and an attenuated phenotype, justifying further therapeutic development of NOTCH3 cysteine correction for CADASIL.
Sources of Stability in Social and Economic Ideological Orientations: Cohort, Context, and Construct Effects
Authors: Ksiazkiewicz Aleksander , Klemmensen Robert , Dawes Christopher T , Christensen Kaare , McGue Matt , Krueger Robert F , Nørgaard Asbjørn Sonne
Published: November 2019

Existing research shows that ideological orientations are stable after young adulthood. Extending research on the sources of ideological stability, we examine social and economic ideology over a 3- to 4-year period in two twin panels (one Danish and one American). We find evidence for the importance of genetic influences and individual life experiences on the stability of social ideology in both contexts; shared environmental factors play an important role in the younger, Danish sample only. For economic ideology, genetic factors contribute to stability in the American sample only. Our findings show that the role of genetic and environmental factors in the stability of ideological orientations varies by type of ideology, national context, and, possibly, age cohort.
A Malaria Transmission Model Predicts Holoendemic, Hyperendemic, and Hypoendemic Transmission Patterns Under Varied Seasonal Vector Dynamics
Authors: Ratti Vardayani , Wallace Dorothy I
Published: November 2019

A model is developed of malaria (Plasmodium falciparum) transmission in vector (Anopheles gambiae) and human populations that include the capacity for both clinical and parasite suppressing immunity. This model is coupled with a population model for Anopheles gambiae that varies seasonal with temperature and larval habitat availability. At steady state, the model clearly distinguishes uns hypoendemic transmission patterns from stable hyperendemic and holoendemic patterns of transmission. The model further distinguishes hyperendemic from holoendemic disease based on seasonality of infection. For hyperendemic and holoendemic transmission, the model produces the relationship between entomological inoculation rate and disease prevalence observed in the field. It further produces expected rates of immunity and prevalence across all three endemic patterns. The model does not produce mesoendemic transmission patterns at steady state for any parameter choices, leading to the conclusion that mesoendemic patterns occur during transient states or as a result of factors not included in this study. The model shows that coupling the effect of varying larval habitat availability with the effects of clinical and parasite-suppressing immunity is enough to produce known patterns of malaria transmission.
Double-blind reviewing and gender biases at EvoLang conferences: An update
Authors: Cuskley Christine , Roberts Seán G , Politzer-Ahles Stephen , Verhoef Tessa
Published: November 2019

A previous study of reviewing at the Evolution of Language conferences found effects that suggested that gender bias against female authors was alleviated under double-blind review at EvoLang 11. We update this analysis in two specific ways. First, we add data from the most recent EvoLang 12 conference, providing a comprehensive picture of the conference over five iterations. Like EvoLang 11, EvoLang 12 used double-blind review, but EvoLang 12 showed no significant difference in review scores between genders. We discuss potential explanations for why there was a strong effect in EvoLang 11, which is largely absent in EvoLang 12. These include testing whether readability differs between genders, though we find no evidence to support this. Although gender differences seem to have declined for EvoLang 12, we suggest that double-blind review provides a more equitable evaluation process.
Time-dependent behaviour of quasar proximity zones at z ∼ 6
Authors: Davies Frederick B , Hennawi Joseph F , Eilers Anna-Christina
Published: November 2019

Since the discovery of z ∼ 6 quasars two decades ago, studies of their Ly α-transparent proximity zones have largely focused on their utility as a probe of cosmic reionization. But even when in a highly ionized intergalactic medium, these zones provide a rich laboratory for determining the time-scales that govern quasar activity and the concomitant growth of their supermassive black holes. In this work, we use a suite of 1D radiative transfer simulations of quasar proximity zones to explore their time-dependent behaviour for activity time-scales from ∼103 to 108 yr. The sizes of the simulated proximity zones, as quantified by the distance at which the smoothed Ly α transmission drops below 10 per cent (denoted Rp), are in excellent agreement with observations, with the exception of a handful of particularly small zones that have been attributed to extremely short ≲104 lifetimes. We develop a physically motivated semi-analytic model of proximity zones which captures the bulk of their equilibrium and non-equilibrium behaviour, and use this model to investigate how quasar variability on ≲105 yr time-scales is imprinted on the distribution of observed proximity zone sizes. We show that large variations in the ionizing luminosity of quasars on time-scales of ≲104 yr are disfavoured based on the good agreement between the observed distribution of Rp and our model prediction based on ‘lightbulb’ (i.e. steady constant emission) light curves.
Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography
Authors: Peter Benjamin M , Petkova Desislava , Novembre John
Published: November 2019

Geographic patterns in human genetic diversity carry footprints of population history and provide insights for genetic medicine and its application across human populations. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure do not incorporate geography directly, and it must be considered post hoc alongside a visual summary of the genetic structure. Here, we estimate “effective migration” surfaces to visualize how human genetic diversity is geographically structured. The results reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, the relationship is often subtly distorted. Overall, the visualizations provide a new perspective on genetics and geography in humans and insight to the geographic distribution of human genetic variation.
Mutations Beget More Mutations—Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation
Authors: Ruan Yongsen , Wang Haiyu , Chen Bingjie , Wen Haijun , Wu Chung-I
Published: November 2019

The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
Chronic kidney disease progression and mortality risk profiles in Germany: results from the Chronic Kidney Disease Outcomes and Practice Patterns Study
Authors: Reichel Helmut , Zee Jarcy , Tu Charlotte , Young Eric , Pisoni Ronald L , Stengel Bénédicte , Duttlinger Johannes , Lonnemann Gerhard , Robinson Bruce M , Pecoits-Filho Roberto , Fliser Danilo
Published: November 2019

Background

Chronic kidney disease (CKD) progression among German patients in a representative setting has not been described previously. The Verband Deutsche Nierenzentren and Chronic Kidney Disease Outcomes and Practice Patterns Study established a longitudinal observational cohort among German CKD patients to research variations in patient care and outcomes in real-world nephrology practices.

Methods

A cohort of CKD Stages 3 (25%) and 4 (75%) patients was established from German nephrologist-run CKD clinics in 2013–16. Linear models were used to determine the estimated glomerular filtration rate (eGFR) slope during follow-up and Cox models were used to assess outcomes of end-stage kidney disease (ESKD) and death.

Results

A total of 1834 patients (median age 75 years, 58% male, 42% diabetics, median baseline eGFR 25 mL/min/1.73 m2) were followed for a median of 29 months. More than 50% had slow or no decline and 17% declined ≥5 mL/min/1.73 m2/year. After 4.5 years, the incidence of ESKD was 8% and of deaths without ESKD 16% among patients with eGFR ≥30 mL/min/1.73 m2 and 37% and 19% for eGFR <30 mL/min/1.73 m2. Adjusted models showed higher risks of ESKD or death for patients with worse kidney function at baseline, male sex, diabetes and higher blood pressure; a higher risk of ESKD with higher albuminuria; and a higher risk of death with older age or cardiovascular comorbidity.

Conclusions

Routine nephrology care of patients in Germany comprises mostly elderly patients, many with slow CKD progression. Identification of risk factors for CKD progression and mortality may help guide resources by closer follow-up of high-risk patients.