bluuebunny/crossref_metadata_2025 huggingface dataset:
Mortality after emergency abdominal surgery in a non‐metropolitan Australian centre
Authors: Tocaciu Shreya , Thiagarajan Jayaraman , Maddern Guy J. , Wichmann Matthias W.
Published: November 2018

Objective

Emergency abdominal surgery has poorer outcomes and higher mortality rates, compared with elective surgery. Serious morbidity or mortality occurs in up to 40% of patients. No information is available with regard to the outcome of patients undergoing emergency abdominal surgery in rural Australia.

Methods

Patients undergoing emergency abdominal surgery in a 110‐bed rural surgical centre in South Australia over a 5 year period (January 2010–December 2014) were included in the study. Patient data were retrieved using the hospital database and review of patient records.

Results

A total of 4396 general surgical emergency admissions was recorded. Emergency admissions without intervention, endoscopic intervention only, appendectomy, cholecystectomy or urological or gynaecological diagnoses were excluded from mortality analysis. The remaining 237 patients underwent major abdominal emergency surgery for bowel obstruction (benign and malignant: n = 143, 60%), injury/inflammation/perforation/peritonitis (n = 85, 36%) or haemorrhage/ischaemia (n = 9, 3.8%). Thirty‐ (n = 9) and 90‐ (n = 12) day mortality rates were 3.8% and 5.1%, respectively.

Conclusion

Emergency abdominal surgery can be safely provided in non‐metropolitan Australian centres, with a low 30‐day mortality rate of 3.8% and a 90‐day mortality rate of 5.1%. This compares well with results published by other national and international investigators.
CCR10+ILC2s with ILC1‐like properties exhibit a protective function in severe allergic asthma
Authors: Beuraud Chloé , Lombardi Vincent , Luce Sonia , Horiot Stéphane , Naline Emmanuel , Neukirch Catherine , Airouche Sabi , Perchet Thibaut , Golub Rachel , Devillier Philippe , Chollet‐Martin Sylvie , Baron‐Bodo Véronique , Nony Emmanuel , Aubier Michel , Mascarell Laurent , Moingeon Philippe
Published: November 2018

Background

We previously showed that patients with severe allergic asthma have high numbers of circulating ILC2s expressing CCR10.

Method

Herein, CCR10+ ILC2s were further analyzed in the blood of healthy individuals or patients with allergic and non−allergic asthma. Characteristics of human CCR10+ and CCR10− ILC2s were assessed by flow cytometry as well as single‐cell multiplex RT‐qPCR. The role of CCR10+ ILC2s in asthma pathophysiology was studied in allergen‐treated mice.

Results

When compared to healthy controls, CCR10+ ILC2s are enriched in the blood of both allergic and non‐allergic severe asthmatic patients, and these cells are recruited to the lungs. Plasma concentrations of the CCR10 ligand CCL27 are significantly increased in severe asthmatics when compared to non‐asthmatic patients. CCR10+ ILC2s secrete little TH2 cytokines, but exhibit ILC1‐like properties, including a capacity to produce IFN‐γ. Also, single‐cell analysis reveals that the CCR10+ ILC2 subset is enriched in cells expressing amphiregulin. CCR10+ ILC2 depletion, as well as blocking of IFN‐γ activity, exacerbates airway hyperreactivity in allergen‐challenged mice, providing evidence for a protective role of these cells in allergic inflammation.

Conclusions

Frequencies of circulating CCR10+ ILC2s and CCL27 plasma concentrations represent candidate markers of asthma severity. The characterization of CCR10+ ILC2s in human samples and in mouse asthma models suggests that these cells downregulate allergic inflammation through IFN‐γ production.
RNA is taking its Toll: Impact of RNA‐specific Toll‐like receptors on health and disease
Authors: Vierbuchen Tim , Stein Karina , Heine Holger
Published: November 2018

RNA‐sensing Toll‐like receptors (TLRs) are often described as antiviral receptors of the innate immune system. However, the past decade has shown that the function and relevance of these receptors are far more complex. They were found to be essential for the detection of various bacterial, archaeal, and eukaryotic microorganisms and facilitate the discrimination between dead and living microbes. The cytokine and interferon response profile that is triggered has the potential to improve the efficacy of next‐generation vaccines and may prevent the development of asthma and allergy. Nevertheless, the ability to recognize foreign RNA comes with a cost as also damaged host cells can release nucleic acids that might induce an inappropriate immune response. Thus, it is not surprising that RNA‐sensing TLRs play a key role in various autoimmune diseases. However, promising new inhibitors and antagonists are on the horizon to improve their treatment.
One year investigation of the prevalence and diversity of clostridial spores in raw milk from the Tokachi area of Hokkaido
Authors: Komori Kazuhiro , Ohkubo Yoshiaki , Katano Naoya , Motoshima Hidemasa
Published: November 2018

We investigated the seasonal prevalence and diversity of clostridial spores in raw milk from the Tokachi area of Hokkaido. Samples of raw milk were collected quarterly from May 2013 through February 2014. The mean clostridial spore count for the raw milk from 336 milk tankers was 27.6 CFU/100 ml. The clostridial species isolated most frequently from raw milk samples was Clostridium tyrobutyricum. The dominant species was C. tyrobutyricum regardless of the season. The percentage of samples with low spore counts (<10 CFU/100 ml) was highest (60.9%) during winter (February) and lowest (34.5%) in autumn (November). In comparison, the percentage of samples with high spore counts (>100 CFU/100 ml) was highest (5.7%) in autumn (November) and lowest (1.1%) during spring (May).
Erosion of informed consent in U.S. research
Authors: Shepherd Lois , Macklin Ruth
Published: November 2018

This paper evaluates four recent randomized clinical trials in which the informed consent of participants was either not sought at all, or else was conducted with critical information missing from the consent documents. As these studies have been taking place, various proposals to conduct randomized clinical trials without consent have been appearing in the medical literature. Some of the explanations offered for why it is appropriate to bypass consent or disclosure requirements appear to represent a fundamental misunderstanding of applicable government regulations and even the research enterprise. Others are the result of conceptual disagreements about the importance and application of traditional research ethics norms to ‘comparative effectiveness research’ and modern research environments. Common among these explanations, however, is a failure to appreciate when a research intervention, rather than merely an observation or review of data, is taking place. Review committees and investigators are failing to see, or choosing to ignore, interventions in the lives of research subjects. When these studies have come to light, government agencies with oversight authority have done little or backed down. Prestigious medical journals have published research results knowing that the required consent was not obtained, or they have stood by the published studies even after the inadequacy of consent is discovered. This article critically examines this erosion of consent in theory and practice and calls for restoring the requirement of informed consent to its proper place as a priority in human subjects research.
Insight and the no‐self in deep brain stimulation
Authors: Specker Sullivan Laura
Published: November 2018

Ethical analyses of the effects of neural interventions commonly focus on changes to personality and behavior, interpreting these changes in terms of authenticity and identity. These phenomena have led to debate among ethicists about the meaning of these terms for ethical analysis of such interventions. While these theoretical approaches have different criteria for ethical significance, they agree that patients’ reports are concerning because a sense of self is valuable. In this paper, I question this assumption. I propose that the Buddhist theory of no‐self offers a novel approach to making ethical sense of patients’ claims following deep brain stimulation. This alternative approach is based on the value of insight into patterns of cause and effect among mental states and actions.
The common rule's ‘reasonable person’ standard for informed consent
Authors: Greenblum Jake , Hubbard Ryan
Published: November 2018

Laura Odwazny and Benjamin Berkman have raised several challenges regarding the new reasonable person standard in the revised Common Rule, which states that informed consent requires potential research subjects be provided with information a reasonable person would want to know to make an informed decision on whether to participate in a study. Our aim is to offer a response to the challenges Odwazny and Berkman raise, which include the need for a reasonable person standard that can be applied consistently across institutional review boards and that does not stigmatize marginal groups. In response, we argue that the standard ought to be based in an ordinary rather than ideal person conception of reasonable person and that the standard ought to employ what we call a liberal constraint: the reasonability standard must be malleable enough such that a wide variety of individuals with different, unique value systems would endorse it. We conclude by suggesting some of the likely consequences our view would have, if adopted.
Erythropoietin and ferritin response in native highlanders aged 4–19 years from the Leh‐Ladakh region of India
Authors: Yanamandra Uday , Senee Harikishan , Yanamadra Sushma , Das Subrat K. , Bhattachar Srinivas A. , Das Reena , Kumar Suman , Malhotra Pankaj , Varma Subhash , Varma Neelam , Nair Velu
Published: November 2018

The pivotal role of erythropoietin (EPO) in hypoxic adaptation has led to various studies assessing the EPO and ferritin response in native highlanders from Andes and Tibet. We assessed the relationship between EPO, haemoglobin and ferritin in 335 native highlanders (172 boys and 163 girls, aged 4 to 19 years) from Leh‐Ladakh, India, who had no history of travel to lowland areas. Complete blood counts, serum EPO and ferritin levels were measured. We stratified study subjects based on age, gender, pubertal status and analysed the EPO and ferritin levels between the stratified groups respectively. The mean EPO level in boys was lower than girls. The mean ferritin level in boys was significantly higher (P = 0·013) than in girls. There was no significant variation in the EPO and ferritin levels amongst the various age groups in our study. Near normal EPO levels since childhood with a negative correlation with haemoglobin is suggestive of a robust adaptive mechanism to high altitude from the early years of life. Low ferritin levels are indicative of decreased iron stores in these native highlanders.
Accelerating the Development of Second‐Order False Belief Reasoning: A Training Study With Different Feedback Methods
Authors: Arslan Burcu , Verbrugge Rineke , Taatgen Niels , Hollebrandse Bart
Published: November 2018

One‐hundred‐six 5‐year‐olds’ (Mage = 5;6; SD = 0.40) were trained with second‐order false belief tasks in one of the following conditions: (a) feedback with explanation; (b) feedback without explanation; (c) no feedback; (d) active control. The results showed that there were significant improvements in children's scores from pretest to posttest in the three experimental conditions even when children's age, verbal abilities, or working memory scores were controlled for. The training effect was stable at a follow‐up session 4 months after the pretest. Overall, our results suggest that 5‐year‐olds’ failures in second‐order false belief tasks are due to lack of experience and that they can be helped over the threshold by exposure to many stories involving second‐order false belief reasoning, including why questions.
Style Invariant Locomotion Classification for Character Control
Authors: Boehs G.E. , Vieira M.L.H.
Published: November 2018

We present a real‐time system for character control that relies on the classification of locomotive actions in skeletal motion capture data. Our method is both progress dependent and style invariant. Two deep neural networks are used to correlate body shape and implicit dynamics to locomotive types and their respective progress. In comparison to related work, our approach does not require a setup step and enables the user to act in a natural, unconstrained manner. Also, our method displays better performance than the related work in scenarios where the actor performs sharp changes in direction and highly stylized motions while maintaining at least as good performance in other scenarios. Our motivation is to enable character control of non‐bipedal characters in virtual production and live immersive experiences, where mannerisms in the actor's performance may be an issue for previous methods.
Plant adaptation and speciation studied by population genomic approaches
Authors: Bamba Masaru , Kawaguchi Yawako W. , Tsuchimatsu Takashi
Published: November 2018

Ever since Darwin, one of the major challenges in evolutionary biology is to unravel the process and mechanisms of adaptation and speciation. Population genomics—the analysis of whole‐genome polymorphism data from large population samples—is a critical approach to study adaptation and speciation, as population genomics datasets enable us to: (1) perform genome‐wide association studies (GWAS) to find genes underlying adaptive phenotypic variations; (2) scan the footprints of selection across the genome to pinpoint loci under selection; and (3) infer the structure and demographic history of populations. Here, we review recent studies of plants using population genomics, covering those focusing on interactions with other organisms, adaptations to local climatic conditions, and the genomic causes and consequences of reproductive isolation. Integrative studies involving GWAS, selection scans, functional studies, and fitness measurements in the field have successfully identified loci for adaptation, revealed the molecular basis of genetic trade‐offs, and shown that fitness can be predicted by polygenic effects of a number of loci associated with local climate. We highlight the importance of the measurement of fitness and phenotypes in the field, which can be powerful tools when combined with population genomic analyses.
Long‐term muscle changes after hamstring lengthening in children with bilateral cerebral palsy
Authors: Salami Firooz , Brosa Julia , Van Drongelen Stefan , Klotz Matthias C M , Dreher Thomas , Wolf Sebastian I , Thielen Mirjam
Published: November 2018

Aim

To evaluate short‐term (1y postoperatively; E1) and long‐term (at least 4y postoperatively; E2) changes in hamstring muscle‐tendon length (MTL) and lengthening velocity after hamstring lengthening in children with bilateral cerebral palsy (CP).

Method

Three‐dimensional gait analysis was performed in 19 children (16 males, 3 females; 36 limbs; mean age at surgery 9y [SD 3y]; range 6–10y) with flexed knee gait, preoperative ankle dorsiflexion lower than 20 degrees, and CP before bilateral hamstring lengthening (E0), at E1 and E2. Hamstring MTL (normalized by leg length) and velocity were assessed via OpenSim software.

Results

MTL increased from E0 to E1 (p=0.004) and decreased from E1 to E2 (p<0.020). Hamstring lengthening velocity did not change. In the subgroup with short, not slow hamstrings, the increase in MTL was maintained at E2.

Interpretation

Hamstring lengthening is an efficient procedure to lengthen short and/or slow hamstrings short‐term. The desired outcome with maintenance of the postoperative changes in hamstring MTL is only achieved for preoperatively short, not slow hamstrings.

What this paper adds

Surgical hamstring lengthening can be confirmed via musculoskeletal modelling in OpenSim software.

Surgical hamstring lengthening in cerebral palsy does not change hamstring lengthening velocity.

Short, not slow hamstrings present a long‐lasting muscle‐tendon length (MTL) increase after hamstring lengthening.

Changes in MTL after hamstring lengthening cannot be maintained for slow hamstrings.

MTL does not change after hamstring lengthening for neither short nor slow hamstrings.
Mycophenolate mofetil in the treatment of pediatric autoimmune central nervous system disease
Authors: Stingl Cory , Van Mater Heather
Published: November 2018

This commentary is on the original article by Nosadini et al. on pages 458–468 of this issue.
Prefrontal and temporal cortical thickness in adolescents with traumatic brain injury
Authors: Vander Linden Catharine , Verhelst Helena , Verleysen Gregory , Caeyenberghs Karen , Deblaere Karel , Vingerhoets Guy
Published: November 2018

Aim

To investigate the impact of traumatic injury on the developing prefrontal‐temporal adolescent cortex, and correlated brain structural measures with neurocognitive functioning.

Method

Nineteen adolescents (12 males, 7 females, age range: 11–17y, mean 15y 8mo, standard deviation 1y 7mo, median 15y 11mo) with traumatic brain injury (TBI) were included. Cortical thickness of frontal and temporal lobes was assessed using magnetic resonance imaging. We correlated cortical thickness of prefrontal‐temporal regions with age, time since injury, and neurocognitive functioning, and compared these results with a matched control cohort without TBI.

Results

We found thinner prefrontal (p=0.039) and temporal cortices (p=0.002) in adolescents with TBI compared to typically developing children. Furthermore, significant age effect was observed on the prefrontal (r=−0.75, p=0.003) and temporal (r=−0.66, p=0.013) cortical thickness in typically developing adolescents, but not in adolescents with TBI. Executive function (measured using the Behaviour Rating Inventory of Executive Function questionnaire, with lower scores meaning higher functioning) was correlated with prefrontal cortical thickness in typically developing adolescents (r=0.72, p=0.009). Opposite trends were found for correlations between cortical thickness and executive function in the TBI and control cohort.

Interpretation

Structural maturation in typically developing adolescents correlates with functional development: the older the adolescent, the thinner the prefrontal cortex, the better executive function. In adolescents with TBI we observed an opposite trend, that appeared significantly different from the control group: the thinner the prefrontal and temporal cortex, the worse executive functioning.

What this paper adds

Cortical thickness is negatively correlated with age in typically developing adolescents.

Prefrontal cortex thickness correlates negatively with executive function in typically developing adolescents.

Correlations between cortical thickness and executive functioning rise for adolescents without traumatic brain injury (TBI).

Correlations between cortical thickness and executive functioning fall for adolescents with TBI.

Adolescents with TBI have a long‐term impairment of adaptive functioning in daily living.
The crisis in replicability
Authors: Rigby Alan S , Day Steven M
Published: November 2018

This commentary is on the invited review by Nuijten on pages 535–539 of this issue.
Exenatide use and incidence of pancreatic and thyroid cancer: A retrospective cohort study
Authors: Liang Caihua , Bertoia Monica L. , Ding Yan , Clifford C. Robin , Qiao Qing , Gagne Joshua J. , Dore David D.
Published: November 2018

A retrospective cohort study, supplemented with a nested case‐control study, was performed using two administrative databases from commercial health plans in the United States to compare the incidence of pancreatic and thyroid cancer among users of exenatide versus other antidiabetic drugs (OADs). Patients with type 2 diabetes who initiated exenatide or OADs between 1 June 2005 and 30 June 2015 were included. Pancreatic and thyroid cancers were identified using chart‐validated algorithms in the cohort study. Cases in the nested case‐control study were chart‐confirmed pancreatic or thyroid cancers, and controls were sampled using risk‐set sampling. The time‐fixed analyses comparing 33 629 exenatide initiators with 49 317 propensity‐score‐matched OAD initiators yielded hazard ratios of 0.76 (95% confidence interval [CI] 0.47‐1.21) for pancreatic cancer and 1.46 (95% CI 0.98‐2.19) for thyroid cancer. Results in the time‐dependent analyses by cumulative duration or dose were similar. Nested case‐control analyses yielded rate ratios of 0.61 (95%CI, 0.37–1.00) for pancreatic cancer and 0.89 (95% CI, 0.64–1.24) for thyroid cancer. This observational study suggested exenatide use was not associated with an increased risk of pancreatic or thyroid cancer.
Ethiopia's developmental state: A building stability framework assessment
Authors: Dejene Melisew , Cochrane Logan
Published: November 2018

Ethiopia has been lauded for its economic growth and progress in human development indicators. For some, that success is rooted in the developmental state approach advocated by the government. For others, the theory of the developmental state and the practice in Ethiopia were often at odds. Up until 2018, ideas that challenged the state and its approaches were not welcome, and politicians, academics and journalists were jailed for expressing alternative views. However, this appears to have changed, and in June 2018 the Deputy Prime Minister called for debate on the developmental state model. This article explores Ethiopia's developmental state model using the building stability framework, analysing its ability to establish fair power structures, foster inclusive economic growth, develop conflict‐resolution mechanisms, create effective and legitimate institutions, and enable a supportive regional environment. We find the developmental state was effective in a number of ways, but that this modality of governance appears to have passed its peak of securing advantage in Ethiopia. A shift from the developmental state to developmental democracy appears to be underway. Decision‐making and economic policies need to align with this change.
Foraging preferences of ants on a heterogeneous Brazilian sandy shore habitat
Authors: Vidal Mayra C. , Silva Ana K. , Sendoya Sebastián F.
Published: November 2018

1. Ants may select their food in response to nutritional needs of the colony and forage in a way that optimises a complementary nutrition. Even though resource availability is known to affect ant colony and individual health, there is still no study that has investigated the plastic preferences of ants according to spatial resource availability in naturally heterogeneous conditions.

2. Beaches are great biomes to test spatial foraging preference because a complete absence of nectaries can be found. Dorymyrmex nigra Pergande 1896 was found inhabiting a beach in southeastern Brazil, in which nectar sources are heterogeneously distributed. This study tested whether the foraging preference to sugar baits depended on the availability of nectar sources surrounding the nests.

3. We found that more D. nigra workers foraged on sugar baits when the colonies lacked naturally occurring nectar in their vicinity compared with colonies with abundant nectar nearby.

4. These results show that the foraging preference of ants depends upon resource availability. This is the first study to use a natural mosaic of resource availability to show that resource preference of ants is plastic and varies spatially.
Adaptive foraging of leaf‐cutter ants to spatiotemporal changes in resource availability in Neotropical savannas
Authors: Costa Alan N. , Vasconcelos Heraldo L. , Vieira‐Neto Ernane H.M. , Bruna Emilio M.
Published: November 2018

1. Generalist herbivores feed on a wide and diverse set of species, but fine‐scale foraging patterns may be affected by the interplay between the quality, quantity and spatial distribution of host plants.

2. The foraging patterns of a prevalent Neotropical herbivore, the leaf‐cutter ant Atta laevigata, in the Brazilian Cerrado savannas were examined in order to determine if patterns observed are in concert with central‐place foraging predictions.

3. The results showed that A. laevigata acts as a polyphagous but highly selective herbivore, with ant attacks often resulting in partial defoliation of less‐preferred species and full defoliation of preferred ones. It was found, for the first time, that there is a strong and positive relationship between the relative attack frequency on plants from preferred species and foraging distance to the nest. This suggests a balance between the quality of plant resources harvested and costs involved in their transportation. It was also observed that colonies focused their harvest on preferred species in months with low availability of young leaves. Consequently, high herbivory rate was more frequent in plants attacked far away from the nest and in dry months.

4. These assessments highlight the fact that Atta colonies may become more selective as foraging distance to the nest increases and in response to fluctuations in the availability of palatable resources throughout the year. The results also show some dissimilarities in the foraging behaviours of A. laevigata when compared with other locations, suggesting that widely distributed herbivores may modify foraging strategies across their geographic range.
An interspecific test of Bergmann's rule reveals inconsistent body size patterns across several lineages of water beetles (Coleoptera: Dytiscidae)
Authors: Pallarés Susana , Lai Michele , Abellán Pedro , Ribera Ignacio , Sánchez‐Fernández David
Published: November 2018

1. Bergmann's rule sensu lato, the ecogeographic pattern relating animals' body size with environmental temperature (or latitude), has been shown to be inconsistent among insect taxa. Body size clines remain largely unexplored in aquatic insects, which may show contrasting patterns to those found in terrestrial groups because of the physiological or mechanical constraints of the aquatic environment.

2. Bergmann's rule was tested using data on body size, phylogeny and distribution for 93 species belonging to four lineages of dytiscid water beetles. The relationship between size and latitude was explored at two taxonomic resolutions – within each independent lineage, and for the whole dataset – employing phylogenetic generalised least‐squares to control for phylogenetic inertia. The potential influence of habitat preference (lotic versus lentic) on body size clines was also considered.

3. Within‐lineage analyses showed negative relationships (i.e. converse Bergmann's rule), but only in two lineages (specifically in those that included both lotic and lentic species). By contrast, no relationship was found between body size and latitude for the whole dataset.

4. These results suggest that there may be no universal interspecific trends in latitudinal variation of body size in aquatic insects, even among closely related groups, and show the need to account for phylogenetic inertia. Furthermore, habitat preferences should be considered when exploring latitudinal clines in body size in aquatic taxa at the interspecific level.
Price shocks in regional markets: Japan's Great Kantō Earthquake of 1923
Authors: Hunter Janet , Ogasawara Kota
Published: November 2018

Japan's Great Kantō Earthquake of 1 September 1923 devastated the area around Tokyo and the country's main port of Yokohama. This article uses the earthquake as a case study to inform our understanding of the economics of disasters and the history of market integration. It seeks to test two main assumptions: first, that shifting demand and supply curves consequent on a disaster will have some impact on prices; and second, that any local changes in the disaster region are likely to be diffused across a wider geographical area. We make use of a unique monthly wholesale price dataset for a number of cities across Japan, and our analysis suggests three main findings: that price changes in the affected areas immediately following the disaster were in most cases reflected in price changes in Japan's provincial cities; that cities further away from the devastation witnessed smaller price changes than those nearer to the affected area; and that the observed pattern of price changes reflects the regional heterogeneity identified by scholars who have worked on market integration in Japan.
The relationship between the temporal structure of magnetoencephalography recorded brain activity and capacity to form discrete auditory representations
Authors: Allen Christopher
Published: November 2018

A function of oscillatory brain activity may be to align activity relative to threshold potentials and in doing so provide limited opportunities for representational neuronal assemblies to form. This low‐level function could apply across frequency bands and potentially affect the temporal dynamics of experience. To test these possibilities, a magnetoencephalography protocol was developed where capacity to form discrete auditory representations over time was assessed relative to oscillatory brain activity. Three sets of preregistered analyses were conducted. First, the capacity to form representations correlated with the prevalence and durations of activity localised to the auditory cortex. Second, brain oscillations became entrained to stimuli over a broad range of frequencies. Finally, a sequence of gamma (γ) band events predicted successful discrete representation, where previous research had indicated similar individuation‐related differences within the alpha (α) range. Together, these findings indicate that a low‐level function of cortical oscillations, which may apply across a range of frequency bands, is periodically to set conditions in which representational neuronal assemblies can manifest, limiting and so affecting the flow of experience.
Estimating effective population size of large marine populations, is it feasible?
Authors: Marandel Florianne , Lorance Pascal , Berthelé Olivier , Trenkel Verena M. , Waples Robin S. , Lamy Jean‐Baptiste
Published: November 2018

Sustainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries‐related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size (Ne), a concept founded in population genetics. We reviewed recent empirical studies on Ne and carried out a simulation study to evaluate the feasibility of estimating Ne in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical Ne values were very similar despite differences in species and total population sizes (N). Genetic simulations for an age‐structured fish population were carried out for a range of population and samples sizes, and Ne was estimated using the Linkage Disequilibrium method. The results showed that already for medium‐sized populations (1 million individuals) and common sample sizes (50 individuals), negative estimates were likely to occur which for real applications is commonly interpreted as indicating very large (infinite) Ne. Moreover, on average, Ne estimates were negatively biased. The simulations further indicated that around 1% of the total number of individuals might have to be sampled to ensure sufficiently precise estimates of Ne. For large marine populations, this implies rather large samples (several thousands to millions of individuals). If however such large samples were to be collected, many more population parameters than only Ne could be estimated.
Spatial variability in ocean‐mediated growth potential is linked to Chinook salmon survival
Authors: Henderson Mark , Fiechter Jerome , Huff David D. , Wells Brian K.
Published: November 2018

Early ocean survival of Chinook salmon, Oncorhynchus tshawytscha, varies greatly inter‐annually and may be the period during which later spawning abundance and fishery recruitment are set. Therefore, identifying environmental drivers related to early survival may inform better models for management and sustainability of salmon in a variable environment. With this in mind, our main objectives were to (a) identify regions of high temporal variability in growth potential over a 23‐year time series, (b) determine whether the spatial distribution of growth potential was correlated with observed oceanographic conditions, and (c) determine whether these spatial patterns in growth potential could be used to estimate juvenile salmon survival. We applied this method to the fall run of the Central Valley Chinook salmon population, focusing on the spring and summer period after emigration into central California coastal waters. For the period from 1988 to 2010, juvenile salmon growth potential on the central California continental shelf was described by three spatial patterns. These three patterns were most correlated with upwelling, detrended sea level anomalies, and the strength of onshore/offshore currents, respectively. Using the annual strength of these three patterns, as well as the overall growth potential throughout central California coastal waters, in a generalized linear model we explained 82% of the variation in juvenile salmon survival estimates. We attributed the relationship between growth potential and survival to variability in environmental conditions experienced by juvenile salmon during their first year at sea, as well as potential shifts in predation pressure following out‐migration into coastal waters.
Arctic browning: Impacts of extreme climatic events on heathland ecosystem CO2 fluxes
Authors: Treharne Rachael , Bjerke Jarle W. , Tømmervik Hans , Stendardi Laura , Phoenix Gareth K.
Published: November 2018

Extreme climatic events are among the drivers of recent declines in plant biomass and productivity observed across Arctic ecosystems, known as “Arctic browning.” These events can cause landscape‐scale vegetation damage and so are likely to have major impacts on ecosystem CO2 balance. However, there is little understanding of the impacts on CO2 fluxes, especially across the growing season. Furthermore, while widespread shoot mortality is commonly observed with browning events, recent observations show that shoot stress responses are also common, and manifest as high levels of persistent anthocyanin pigmentation. Whether or how this response impacts ecosystem CO2 fluxes is not known. To address these research needs, a growing season assessment of browning impacts following frost drought and extreme winter warming (both extreme climatic events) on the key ecosystem CO2 fluxes Net Ecosystem Exchange (NEE), Gross Primary Productivity (GPP), ecosystem respiration (Reco) and soil respiration (Rsoil) was carried out in widespread sub‐Arctic dwarf shrub heathland, incorporating both mortality and stress responses. Browning (mortality and stress responses combined) caused considerable site‐level reductions in GPP and NEE (of up to 44%), with greatest impacts occurring at early and late season. Furthermore, impacts on CO2 fluxes associated with stress often equalled or exceeded those resulting from vegetation mortality. This demonstrates that extreme events can have major impacts on ecosystem CO2 balance, considerably reducing the carbon sink capacity of the ecosystem, even where vegetation is not killed. Structural Equation Modelling and additional measurements, including decomposition rates and leaf respiration, provided further insight into mechanisms underlying impacts of mortality and stress on CO2 fluxes. The scale of reductions in ecosystem CO2 uptake highlights the need for a process‐based understanding of Arctic browning in order to predict how vegetation and CO2 balance will respond to continuing climate change.
A Geographic Network Automata Approach for Modeling Dynamic Ecological Systems
Authors: Anderson Taylor , Dragićević Suzana
Published: November 2018

Landscape connectivity networks are composed of nodes representing georeferenced habitat patches that link together based on a species’ maximum dispersal distance. These static representations cannot capture the complexity in species dispersal where the network of habitat patch nodes changes structure over time as a function of local dispersal dynamics. Therefore, the objective of this study is to integrate geographic information, complexity, and network science to propose a novel Geographic Network Automata (GNA) modeling approach for the simulation of dynamic spatial ecological networks. The proposed GNA modeling approach is applied to the emerald ash borer (EAB) forest insect infestation using geospatial data sets from Michigan, U.S.A. and simulates the evolution of the EAB spatiotemporal dispersal network structures across a large regional scale. The GNA model calibration and sensitivity analysis are performed. The simulated spatial network structures are quantified using graph theory measures. Results indicate that the spatial distribution of habitat patch nodes across the landscape in combination with EAB dispersal processes generate a highly connected small‐world dispersal network that is robust to node removal. The presented GNA model framework is general and flexible so that different types of geospatial phenomena can be modeled, providing valuable insights for management and decision‐making.
A murine model of acute lung injury identifies growth factors to promote tissue repair and their biomarkers
Authors: Kurosawa Takeyuki , Miyoshi Shion , Yamazaki Soh , Nishina Takashi , Mikami Tetuo , Oikawa Akira , Homma Sakae , Nakano Hiroyasu
Published: November 2018

Type II alveolar epithelial cells (AEC2s) play a crucial role in the regeneration of type I AECs after acute lung injury. The mechanisms underlying the regeneration of AEC2s are not fully understood. To address this issue, here, we investigated a murine model of acute lung injury using mice expressing human Diphtheria Toxin Receptor (DTR) under the control of Lysozyme M promoter (LysM‐DTR). DT injection induced the depletion of AEC2s, alveolar macrophages, and bone marrow (BM)‐derived myeloid cells in LysM‐DTR mice, and the mice died within 6 days after DT injection. Apoptotic AEC2s and bronchiolar epithelial cells appeared at 24 hr, whereas Ki67‐positive proliferating cells appeared in the alveoli and bronchioles in the lung of LysM‐DTR mice at 72–96 hr after DT injection. Transfer of wild‐type BM cells into LysM‐DTR mice accelerated the regeneration of AEC2s along with the up‐regulation of several growth factors. Moreover, several metabolites were significantly decreased in the sera of LysM‐DTR mice compared with WT mice after DT injection, suggesting that these metabolites might be biomarkers to predict AEC2s injury. Together, LysM‐DTR mice might be useful to identify growth factors to promote lung repair and the metabolites to predict the severity of lung injury.
Lost but not forgotten: A population‐based study of mortality and care trajectories among people living with HIV who are lost to follow‐up in Ontario, Canada
Authors: Kendall CE , Raboud J , Donelle J , Loutfy M , Rourke SB , Kroch A , Liddy C , Rosenes R ,   Ontario HIV Treatment Network (OHTN) Cohort Study Team, Burchell AN
Published: November 2018

Objectives

Selection as a consequence of volunteer participation in, and loss to follow‐up from, cohort studies may bias estimates of mortality and other health outcomes. To quantify this potential, we estimated mortality and health service use among people living with HIV (PLWH) who were lost to cohort follow‐up (LTCFU) from a volunteer clinical HIV‐infected cohort, and compared these to mortality and health service use in active cohort participants and non‐cohort‐participants living with HIV in Ontario, Canada.

Methods

We analysed population‐based provincial health databases from 1995 to 2014, identifying PLWH ≥ 18 years old; these included data from participants in the Ontario HIV Treatment Network Cohort Study (OCS), a volunteer, multi‐site clinical HIV‐infected cohort. We calculated all‐cause mortality, hospitalization and emergency department (ED) visit rates per 100 person‐years (PY) and estimated hazard ratios (HRs) of mortality, adjusting for age, sex, income, rurality, and immigration status.

Results

Among 23 043 PLWH, 5568 were OCS participants. Compared with nonparticipants, participants were younger and less likely to be female, to be an immigrant and to reside in a major urban centre, and had lower comorbidity. Mortality among active participants, participants LTCFU and nonparticipants was 2.52, 3.30 and 2.20 per 100 PY, respectively. After adjustment for covariates, mortality risk was elevated among participants LTCFU compared with active participants (HR 2.26; 95% confidence interval 1.91, 2.68). Age‐adjusted hospitalization rates and ED visit rates were highest among participants LTCFU.

Conclusions

Mortality risk and use of health care resources were lower among active cohort participants. Our findings may inform health outcome estimates based on volunteer cohorts, as well as quantitative bias adjustment to correct for such biases.
Green recovery of phenolic compounds from rice byproduct (rice bran) using glycerol based on viscosity, conductivity and density
Authors: Huang Hao , Wang Zhenni , Aalim Halah , Limwachiranon Jarukitt , Li Li , Duan Zhenhua , Ren Guoping , Luo Zisheng
Published: November 2018

Rice bran, the industry byproduct, contains high levels of phenolic compounds. Based on glycerol, a green recovery of phenolics from rice bran was proposed. Extraction temperature (X1), glycerol concentration (X2) and liquid‐to‐solid ratio (X3) were optimised by response surface methodology. Basic physical properties, that is, viscosity, conductivity, density were analysed and UPLC‐Triple‐TOF/MS method was applied for phenolic identification. Results showed the optimum conditions were X1 = 66.76 °C, X2 = 19.47% and X3 = 32.92 mL g−1. Under these conditions, the recovery yield in total polyphenols was 708.58 ± 12.36 mg GAE/100 g DW. Moreover, the recovery capacity of phenolic compounds was significantly correlated with viscosity, conductivity and density of glycerol solution. Under the optimal conditions, totals of thirteen phenolic compounds were identified and phenolic acids (4‐hydroxybenzoic acid, vanillic acid, syringic acid, 4‐coumaric acid, ferulic acid and salicylic acid) were quantified. These results demonstrate glycerol can serve as an ideal green solvent to recover phenolic compounds from rice bran.
Effect of barley β‐glucan on water redistribution and thermal properties of dough
Authors: Huang Ze‐Hua , Zhao Yang , Zhu Ke‐Xue , Guo Xiao‐Na , Peng Wei , Zhou Hui‐Ming
Published: November 2018

The effect of adding barley (Hordeum vulgare L.) β‐glucan (BBG) to dough on the water redistribution and the thermal properties of dough was studied by TGA and DSC. Combined with LF‐NMR to analyse the competition and redistribution mechanism of water at the 1H level. The mass loss of the dough measured by TGA was reduced by an average of 2.11% with BBG added. BBG increased the water retention of the dough, delayed the water loss process. The LF‐NMR results showed that at the same water absorption the T21 of the 3% BBG dough was longer while its T22 was shorter than those of the control. BBG has different effects on the different states of water in the dough. BBG increased the free sulfhydryl content in dough during heating, while the adverse effects of BBG on the biopolymer reactions, such as disulfide bond, could be partially relieved by regulating water content.
Valorisation of protein hydrolysates from animal by‐products: perspectives on bitter taste and debittering methods: a review
Authors: Fu Yu , Chen Jingru , Bak Kathrine H. , Lametsch René
Published: November 2018

Conversion of animal by‐products to high value‐added food ingredients is one of the top trends in the slaughter industry. Enzymatic hydrolysis of animal by‐products can generate protein hydrolysates, which provides an opportunity for effective utilisation. However, bitterness of protein hydrolysate is a major undesirable aspect for various applications. In this review, the current knowledge on protein hydrolysates from animal by‐products is briefly reviewed. The structural features of bitter peptides and bitter taste receptors are summarised. Moreover, the potential approaches for debittering protein hydrolysates are highlighted, including exopeptidase treatment, Maillard reaction, plastein reaction and encapsulation. In addition, the current debittering strategies and challenges are also discussed. This article presents some opportunities to utilise protein hydrolysates from animal by‐products and their debittering methods.
Autochthonous white grape pomaces as bioactive source for functional jams
Authors: Restuccia Donatella , Giorgi Gianluca , Gianfranco Spizzirri Umile , Sciubba Fabio , Capuani Giorgio , Rago Vittoria , Carullo Gabriele , Aiello Francesca
Published: November 2018

Seeds and skins from grape pomaces of Pecorello and Mantonico cv underwent extraction (ultrasound–assisted or maceration), in order to obtain added‐value ingredients for the production of a functional pear jam. The antioxidant features of the extracts were tested by in vitro colorimetric assays. Among seeds, Mantonico by maceration (MSC) showed the best results, as well as Mantonico by ultrasound‐assisted extraction (MBs) among skin extracts. The selected extracts were fully characterised by NMR and MS techniques, confirming the presence of many polyphenols, flavonoids and tannins among others. Pectin was then derivatised by the grafting procedure with the active molecules of MBs and MSC. The latter produced the best antioxidant polymer also without toxicity evaluated using Caco‐2 cells and was used for the jam preparation. The functional pear jam showed improved antioxidant performances in comparison with its non‐functional counterparts as well as its maintenance over time (15 days).
TRB‐J1 usage, in combination with the HLA‐A*01:01 allele, represents an apparent survival advantage for uterine corpus endometrial carcinoma: Comparisons with microscopic assessments of lymphocyte infiltrates
Authors: Clark Kendall R. , Tong Wei Lue , Callahan Blake M. , Yavorski John M. , Tu Yaping N. , Blanck George
Published: November 2018

The opportunity for the highly efficient recovery of immune receptor recombination data from cancer specimens, including the ready assessment of immune receptor V and J usage, raises the issue of establishing precise values of assessing the immune receptor status as opposed to obtaining basic information regarding lymphocyte infiltration, in the cancer setting. In this report, we obtained the lymphocyte infiltration percentages from the cancer digital slide archive representing uterine corpus endometrial carcinoma (UCEC) and correlated these data with recovery of the immune receptor recombination reads from corresponding UCEC exome files. Results indicated a basic correlation of the recovery of productive T‐cell receptor beta (TRB) recombination reads with lymphocyte infiltration percentages. However, the recovery of specific immune receptor recombination reads did not indicate the same survival outcomes as microscope detection of lymphocyte infiltrate percentages. To further exploit the value of recovery of the TRB recombination reads from the UCEC exome files, we determined the survival outcomes for combinations of TRB gene segment usage and HLA class I alleles, with the most important result being that the combination of HLA‐A*01:01 and TRB‐J1 segment usage reflected a strikingly high survival rate. Overall, this report emphasized the increased value of the knowledge of the immune receptor recombinations, in comparison with basic lymphocyte infiltration percentages, in assessing cancer survival rates.