bluuebunny/crossref_metadata_2025 huggingface dataset:
Widespread warming trends in storm temperatures and snowpack fate across the Western United States
Authors: Hu J Michelle , Nolin Anne W
Published: February 2020

Western United States snowpacks are generated by cold-season storms, yet the vast majority of snow trend studies utilize undifferentiated air temperature records. Previous studies do not distinguish between days with and without precipitation, which effectively dilutes temperature trends relevant for snowpack monitoring. We examined trends in cold-season precipitation and impacts on snow in nine mountain regions across the western United States. Using 33 years of daily meteorological data (1984–2016) from 567 Snow Telemetry (SNOTEL) sites and a homogenized daily temperature dataset (TopoWx), we investigated seasonal and regional trends in storm day temperatures, storm day frequency, and resulting snowpack fate. We found widespread warming of 0.4 °C–1.2 °C per decade, especially during the fall and in the Interior West using tests for statistically significant trends. Disaggregation showed that days with precipitation are warming nearly twice as fast as dry days in the fall and winter. We also observed increases in November dry days, increased melt on dry days throughout the accumulation season, spring cooling and declines in daily snowmelt during snow-depleting storm days. These findings demonstrate the importance of disaggregating temperature data to elucidate trends (in storm day frequency, accumulation and melt, and warming and cooling) and their impacts on snow in the western US.
The effect of the mineral supplement “Permait” and vitamin B13 on the productivity of broiler chickens
Authors: Alekseev V A , Yu Nemtseva E , Evdokimov N V , Yu Lavrentiev A , Sherne V S , Petrov N S , Danilova N V
Published: February 2020

The article presents the materials obtained in experiments to study the feasibility of using a zeolite-containing additive “Permait” and poorly studied vitamin B13, The results of the experiments showed that the optimal dose of using a zeolite-containing additive in compound feeds is 2% of the dry matter of the feed. At this level, compared with the control, the growth energy of broiler chickens increased by 9.1-10.7 % compared to the control groups. The feeding of this drug contributed to an increase in slaughter of meat in the first experiment by 3.1%, in the second experiment - by 4.6%. Per 1 kg gain in live weight of experimental birds was spent from 2.02 to 2.56 kg of feed. The use of potassium orotate in the composition of complete feed contributed to an increase in the average daily growth of broiler chickens from the experimental groups only by 0.8 - 2.5% relative to the control (p <0.05). Higher rates are obtained with a dose of 10 mg. The slaughter yield of the half-gutted carcass of broiler chickens ranged from 78.1 to 81.2%, and the gutted - 64.7-66.8%.
Non-specific resistance and specific immunogenesis of the body of the bird cross Loman Brown on the background of biostimulation
Authors: Tyurin V , Semenov V , Kozak S , Ivanov N , Koshich O , Tikhonova G , Lyagina E
Published: February 2020

PV-1 immunostimulant influence on the parameters of non-specific resistance and specific immunogenesis of bird cross Loman Brown is discussed in the paper. It was established experimentally that feeding chickens by the PV-1 preparation in doses of 0.05 ml/kg, 0.10 and 0.15 ml/kg of body weight, respectively, once a day within 10 days with a 10-day break, with repeating cycles up to 111-day of their age, stimulates the growth and development of young. Immunization of a bird against the background of the use of the immunotropic drug PV-1 is accompanied by an increase in immunity: when chickens are vaccinated against Gumboro disease, the titers of specific antibodies are increased by 53.3%, against Newcastle’s disease - by 50.0% and against egg drop syndrome-76 - by 26.5%. An increase in the egg productivity of laying hens grown on the background of the use of PV-1 was established: egg production for the initial hen increased by 9.2 - 17.8%, egg weight - by 0.5 - 4.6%. Studying the meat productivity of poultry grown on the background of the use of the PV-1 preparation, an increase in the slaughter yield of 1.7–5.0% was established, the yield of edible parts increased by 6 ±3.20 – 155±3.40 g (P <0.001).
Veterinary-sanitary evaluation of fish when applying the Akwa-Biot-Norm nutrient feed additive
Authors: Semenov V , Petryankin F , Kosyaev N , Nikitin D , Nikitina A , Tikhonova G , Grigorieva V
Published: February 2020

The paper presents the data of veterinary-sanitary assessment of the Lena sturgeon grown using the nutrient feed additive Akwa-Biot-Norm. It has been revealed that organoleptic characteristics of fish samples correspond to the benign products. The chemical composition of the muscle tissue of the experimental and control groups of fish was almost the same. The cadmium level in both fish groups was 0.007 mg/kg; the mercury level was 0.00019 mg/kg and 0.00018 mg/kg in the control and in the experimental group respectively, which does not exceed the maximum permissible concentrations. Microbiological studies of Lena sturgeon meat have shown that the number of mesophilic aerobic and facultative anaerobic microorganisms (NMAFAnM) in fish samples does not exceed the safety requirements and nutritional value of food products. Coliform bacteria (BGKP), Staphylococcus, Salmonella, and Listeria monocytogenes were not isolated from all selected samples (control and experimental). The results of the veterinary-sanitary assessment of the Lena sturgeon grown with the use of the nutrient feed additive Akwa-Biot-Norm indicate that the fish meets the requirements of the technical regulations of the Eurasian Economic Union “On the safety of fish and fish products” (EEU TR 040/2016) and is safe for the consumer.
Management of competitiveness of organizations through improved product quality
Authors: Nechaeva M L , Kutaeva T N , Borovitskaya M V , Semenova A N , Abrosimova M S
Published: February 2020

Analysis and evaluation of approaches to management of quality of food products, development of directions of their management are shown. Also the goal is selection of tools for transformation of competitive position through the formation of a single evaluation model. The current economic situation in Russia, complicated by economic sanctions, shows the importance of studying consumer preferences for the analysis of product quality at a new level. The development of the market of domestic bakery products is mainly hampered by non-compliance with the basic parameters of non-price competition. Therefore, there is a need to systematize the factors affecting competitiveness, their analysis and ranking, decision-making, taking into account the capabilities of a particular enterprise. The methods of analysis of quality management of bakery products to ensure a competitive position at the regional level are implemented. The most significant parameters influencing formation of consumer preferences and perception of quality of bakery products are defined. The econometric model of dependence of parameters of quality of food products which description allows defining and carrying out coordination of strategic decisions on operational management competitiveness of the enterprises of the food industry is developed.
Mathematical approach to the validation of field surface texture parameter software
Authors: Todhunter Luke , Leach Richard , Lawes Simon , Harris Peter , Blateyron François
Published: February 2020

A new method for performance validation of surface texture parameter calculation software is introduced, focussing on field surface texture parameters. Surface height functions are defined mathematically, either using Fourier series or polynomials, and are then input into the surface texture parameter definitions to obtain mathematical parameter values. A series of user-adjustable parametric surface functions are defined that correspond to each surface texture parameter, enabling users to create a variety of surfaces to assess their software whilst still retaining mathematical traceability. This method is expanded to include complex surface textures. Chebyshev polynomials are used to perform numerical calculations of surface texture parameters for a selection of polynomial surface functions. Mathematical reference parameter values are calculated for a series of fifteen predefined surfaces and ten parametric surfaces to assess the performance of the software under test for a given dataset resolution. Assessment of the number of significant figures of the software-obtained values that agree with the reference values is used as a performance metric that enables comparison between different third-party software applications for a given dataset resolution. An assessment of the sampling methods used to create discrete datasets of a mathematical surface function for use with numerical third-party software is performed. Two implementations of surface height sampling are used to create datasets that are input into four third-party surface texture parameter calculation software packages, and the results compared, showing a significant variation in the performance metric values for different sampling methods.
Influence of oxidized ceramics on the tribological properties of Ni60/WC composite coatings
Authors: Wang Xinsheng , Xing Zhiguo , Hou Junjian , Liu Kun
Published: February 2020

Ni-based composite ceramic coatings with good comprehensive performance are obtained by a supersonic plasma spraying process. A ceramic powder is added to a Ni60/WC powder to make the surface of the sprayed sample more uniform and compact. Pores are present on the surface of the two composite ceramic coatings prepared by NiWT(Ni60/WC + TiO2) and NiWA(Ni60/WC + Al2O3), as well as five phase components. In the microscopic morphology of the two composite ceramic coatings, the surface composition of the NiWT coating is relatively uniform and the surface of NiWA exhibits a cluster structure with more pits than NiWT. The friction coefficient of the NiWT coating at 200 r min−1 is between 0.40 and 0.43 and that of the NiWA coating is between 0.35 and 0.38. Simultaneously, the abrasion width and wear volume of the NiWT and NiWA coatings are small compared with the substrate, while the abrasion width and volume of the NiWT coating are smaller. The composite ceramic coatings prepared by the addition of two kinds of oxidized ceramics, through comparative analysis of the experiment, showed that NiWT had an improved surface micro-morphology and wear resistance than NiWA. The wear morphology of NiWT showed a wear mechanism of abrasive particles and the wear morphology of NiWA showed a fatigue wear mechanism.
The consistent burden in published estimates of delirium occurrence in medical inpatients over four decades: a systematic review and meta-analysis study
Authors: Gibb Kate , Seeley Anna , Quinn Terry , Siddiqi Najma , Shenkin Susan , Rockwood Kenneth , Davis Daniel
Published: February 2020

Introduction

Delirium is associated with a wide range of adverse patient safety outcomes, yet it remains consistently under-diagnosed. We undertook a systematic review of studies describing delirium in adult medical patients in secondary care. We investigated if changes in healthcare complexity were associated with trends in reported delirium over the last four decades.

Methods

We used identical criteria to a previous systematic review, only including studies using internationally accepted diagnostic criteria for delirium (the Diagnostic and Statistical Manual of Mental Disorders and the International Statistical Classification of Diseases). Estimates were pooled across studies using random effects meta-analysis, and we estimated temporal changes using meta-regression. We investigated publication bias with funnel plots.

Results

We identified 15 further studies to add to 18 studies from the original review. Overall delirium occurrence was 23% (95% CI 19–26%) (33 studies) though this varied according to diagnostic criteria used (highest in DSM-IV, lowest in DSM-5). There was no change from 1980 to 2019, nor was case-mix (average age of sample, proportion with dementia) different. Overall, risk of bias was moderate or low, though there was evidence of increasing publication bias over time.

Discussion

The incidence and prevalence of delirium in hospitals appears to be stable, though publication bias may have masked true changes. Nonetheless, delirium remains a challenging and urgent priority for clinical diagnosis and care pathways.
53 Does the Community Geriatrician’s Role in Advanced Care Planning Help Community Dwellers Achieve Their Preferred Place of Care?
Authors: Honney K , Judd H , Mitchell A , Nash H , Ford J , Schweigart A , Griffiths B , Sira A
Published: February 2020

Introduction

Advanced Care Planning (ACP) is well established for patients with terminal cancer diagnoses but is poorly utilised when caring for elderly patients with other terminal illnesses. We aimed to assess the effectiveness of ACP in our older, community dwellers following a period of increased awareness.

Methods

A closed loop audit was undertaken, assessing deaths from a dementia care home within rural Norfolk, before and after implementation of an education and focus programme (cycle 1=Jan 2017-Jan 2018, cycle 2: Feb 2018-Jan-2019). Deceased patients were identified from care home records and data from electronic hospital and general practice records were analysed. Results were compared according to existing guidance outlined in the Palliative Gold Standards Framework (GSF) and Department of Health End of Life Care Strategy 2009. Compliance between cycles was compared using the chi-square test with p=.05 indicative of statistical significance.

Results

59 patients were included (median age=84, male=31). Results of the audit for each criterion are shown in table 1. More patients achieved their preferred place of care (PPOC) following the implementation of the education programme, with access to end of life medications significantly improving.

Conclusions

Increasing awareness and understanding of ACP in the community has been shown to improve compliance with GSF standards, particularly access to end of life medications. Further efforts are still required to improve care and a third cycle is scheduled for January 2020, following further training.
73 Is There A Real Relationship Between Body Mass Index and Vasovagal Syncope or is it Just Anecdote?
Authors: Cohen S , Young E , Hunt S , Garimella S , Lakhani D R
Published: February 2020

Introduction

Syncope is characterised by global cerebral hypoperfusion rapidly causing a transient loss of consciousness with loss of voluntary muscle tone and a subsequent spontaneous, prompt and complete recovery. It is often caused by Neurally mediated reflex syncope syndromes of which Vasovagal syncope (VVS) is the commonest form. The prodromal symptoms of VVS are explained by circulatory alterations (vasodilatation and bradycardia) and autonomic activation. Whilst many triggers and risk factors for such alterations are recognised, they are incompletely understood. Anecdotally, being “young and thin” is a risk factor but there is little published data evaluating the relationship between body weight and VVS. Whilst VVS can often be diagnosed on clinical history alone, further evaluation is warranted in some patients. The validated test to assess susceptibility to VVS is the head-up-tilt table (HUT) test. We set out to evaluate the relationship between Body Mass Index (BMI) and the outcome of HUT testing.

Methods

We reviewed the outcomes of 1193 patients attending for HUT testing at the University Hospitals of Leicester between December 2014 and October 2017. The protocol used was a 40 minute passive HUT (70 degree) followed by sublingual nitroglyserin. The parameters of height, weight, gender and test outcome were recorded prospectively and interrogated retrospectively.

Results

Of the 1193 patients, the passive HUT test was positive for VVS in 293 patients. These patients were then sub-grouped by BMI as set out in the table. The chances of VVS, as diagnosed by HUT testing are almost doubled in those with a (clinically underweight) BMI range 16-20. (p value 0.002-0.001)

Discussion

The presented data supports the anecdotal experience of many clinicians: that low BMI may be associated with an increased tendency to VVS. The physiological basis for this (if it is real) is not understood and requires further evaluation since it may have implications for future management strategies. Larger studies are required to further analyse this relationship to determine if BMI is an independent predictor or risk factor for VVS.
Age and location influence the costs of compensatory and accelerated growth in a hibernating mammal
Authors: Heissenberger Sarah , de Pinho Gabriela Medeiros , Martin Julien G A , Blumstein Daniel T
Published: February 2020

The increase of structural growth rates to compensate for a poor initial body condition, defined as compensatory growth, may have physiological costs, but little is known about its effects on individual fitness in the wild. Yellow-bellied marmots (Marmota flaviventer) are obligate hibernators and depend on fat accumulation acquired during an approximately 4-month summer to survive overwinter. We investigated the costs of survival and longevity of rapid growth in a wild population of yellow-bellied marmots. We used trapping data collected from 2002 to 2014 to calculate individual relative seasonal growth and assess its effects on longevity and annual survival of juveniles, yearlings, and adults. Sites were distributed in two main areas, down-valley and up-valley; the latter has a higher elevation and is an overall harsher environment. We found that relative seasonal growth had no effect on individual longevity or on juvenile and adult annual survival. For yearlings, the effect of relative seasonal growth on survival depended on the location: yearlings with high relative seasonal growth had lower survival if located up-valley, and higher survival if located down-valley. In conclusion, juveniles and adults do not appear to have detectable costs of rapid growth, although there are costs to yearling survival depending on environmental conditions. Substantial structural growth occurs when marmots are yearlings and our results are likely driven by the high conflicting demands of somatic growth versus maintenance at this stage. Thus, the costs of rapid growth are age and site dependent and may be seen in the short term for species facing temporal constraints on growth.
Adaptive critical value for constrained likelihood ratio testing
Authors: Al Mohamad Diaa , Van Zwet Erik W , Cator Eric , Goeman Jelle J
Published: February 2020

We present a new general method for constrained likelihood ratio testing which, when few constraints are violated, improves upon the existing approach in the literature that compares the likelihood ratio with the quantile of a mixture of chi-squared distributions; the improvement is in terms of both simplicity and power. The proposed method compares the constrained likelihood ratio statistic against the quantile of only one chi-squared random variable with data-dependent degrees of freedom. The new test is shown to have a valid exact significance level $\alpha$. It also has more power than the classical approach against alternatives for which the number of violations is not large. We provide more details for testing a simple order $\mu_1\leqslant\cdots\leqslant\mu_p$ against all alternatives using the proposed approach and give clear guidelines as to when the new method would be advantageous. A simulation study suggests that for testing a simple order, the new approach is more powerful in many scenarios than the existing method that uses a mixture of chi-squared variables. We illustrate the results of our adaptive procedure using real data on the liquidity preference hypothesis.
Case report: changes in creatine kinase isoenzymes after myocardial infarction in a patient with prostatic carcinoma.
Authors: Alexander R L
Published: February 2020

The detection of serum proteins that can serve as tumor markers has been reported with increased frequency in patients with various localized or metastatic cancers. Many of these reports have concerned patients with prostatic carcinoma, who had normal or increased concentrations of creatine kinase (EC 2.7.3.2) in serum. In many instances the creatine kinase BB isoenzyme was increased in these patients. I describe the case of a patient with carcinoma of the prostate (stage D), who had a myocardial infarction three to four days after admission. The serum activity of the MM, MB, and BB isoenzymes changed markedly after the infarction. These changes and the possible tissue source(s) of this isoenzyme are discussed in relationship to the clinical symptoms of the patient.
Striving for population-level conservation: integrating physiology across the biological hierarchy
Authors: Ames Elizabeth M , Gade Meaghan R , Nieman Chelsey L , Wright James R , Tonra Christopher M , Marroquin Cynthia M , Tutterow Annalee M , Gray Suzanne M
Published: February 2020

The field of conservation physiology strives to achieve conservation goals by revealing physiological mechanisms that drive population declines in the face of human-induced rapid environmental change (HIREC) and has informed many successful conservation actions. However, many studies still struggle to explicitly link individual physiological measures to impacts across the biological hierarchy (to population and ecosystem levels) and instead rely on a ‘black box’ of assumptions to scale up results for conservation implications. Here, we highlight some examples of studies that were successful in scaling beyond the individual level, including two case studies of well-researched species, and using other studies we highlight challenges and future opportunities to increase the impact of research by scaling up the biological hierarchy. We first examine studies that use individual physiological measures to scale up to population-level impacts and discuss several emerging fields that have made significant steps toward addressing the gap between individual-based and demographic studies, such as macrophysiology and landscape physiology. Next, we examine how future studies can scale from population or species-level to community- and ecosystem-level impacts and discuss avenues of research that can lead to conservation implications at the ecosystem level, such as abiotic gradients and interspecific interactions. In the process, we review methods that researchers can use to make links across the biological hierarchy, including crossing disciplinary boundaries, collaboration and data sharing, spatial modelling and incorporating multiple markers (e.g. physiological, behavioural or demographic) into their research. We recommend future studies incorporating tools that consider the diversity of ‘landscapes’ experienced by animals at higher levels of the biological hierarchy, will make more effective contributions to conservation and management decisions.
Outcome, complication and follow-up of patients with esophageal foreign body impaction: an academic institute’s 15 years of experience
Authors: Marashi Nia Seyed Farzad , Aghaie Meybodi Mohamad , Sutton Richard , Bansal Ajay , Olyaee Mojtaba , Hejazi Reza
Published: February 2020

Esophageal foreign body impaction (EFBI) is a gastrointestinal emergency, mostly requiring endoscopic management. The aim of this study is to evaluate the epidemiology, adverse events, and outcomes of patients following the episode of EFBI. All esophagogastroduodenoscopy (EGD) reports of admitted patients for EFBI at the University of Kansas Medical Center between 2003 and 2018 were retrospectively reviewed. Of 204 patients, who met the inclusion criteria, 60% were male and the mean age was 54.7 ± 17.7 years. The encounter was the first episode of EFBI in 76% of cases. EGD in less than 24 hours of patients’ admission was required in 79% of cases. The distal esophagus was the most common site of impaction (44%). Push and pull techniques were used in 38 and 35.2% of cases, respectively, while 11% were managed by a combination of both techniques. Structural causes were the most common etiologic findings including benign strictures and stenosis in 21.5% of patients, followed by Schatzki’s ring (7.8%) and hiatal hernia (6.9%). Of all cases, 45% did follow-up in up to 1 year, and biopsy was done in 34% of cases. Out of 43 patients who had endoscopic findings suspicious for eosinophilic esophagitis (EoE), the diagnosis was confirmed by pathology in 37. The rate of recurrence EFBI was significantly higher in patients with EoE (P < 0.001). EFBI-related esophageal adverse events (AEs) occurred in 4.9% of cases. Cardiovascular and pulmonary AEs occurred in 1.5 and 2.9%, respectively. Logistic regression did not find any predictor for AEs occurrence. EFBI managed very well with endoscopic treatments. Despite the emerging data about the safety of the push technique, there are still concerns regarding its adverse events especially the risk of perforations. Our study shows no significant difference in adverse events between different types of techniques.
The Fate of Ornamental White Fringetree Through the Invasion Wave of Emerald Ash Borer and Implications for Novel Host Use by This Beetle
Authors: Ellison E A , Peterson D L , Cipollini D
Published: February 2020

Emerald ash borer (EAB, Agrilus planipennis Fairmaire [Coleoptera: Buprestidae]) is a wood boring beetle that is an invasive pest of ash trees (Fraxinus spp.) in North America. In 2014, it was reported that EAB had infested white fringetree (Chionanthus virginicus L. [Lamiales: Oleaceae]) in Ohio and was since found to have infested this species across its invasive range. In 2018, we reexamined 166 white fringetrees in Illinois, Indiana, Ohio, and Pennsylvania that had been previously examined for EAB attack in 2015 to determine their fate. We assessed tree health and EAB infestation in each tree, assigned an infestation status of newly, continuously, not reinfested, or never infested, and compared the trees’ current status to their 2015 status. This assessment was done to determine whether their health and infestation status had changed through the EAB invasion wave. We found that attack rates declined: 26% of trees were infested in 2015 whereas only 13% were in 2018, likely coinciding with declining beetle populations in the area. Overall tree health improved for trees that were not reinfested by EAB after a record of attack in 2015, suggesting that they can survive and recover from EAB attack. Conversely, health declined for newly and continuously infested trees, indicating that they became stressed from EAB attack. Although the majority of the trees survived the invasion wave, several were removed from various sites due to EAB attack suggesting that white fringetree varies in its resistance and tolerance to attack. As beetle populations continue to expand geographically, infestation rates will likely increase and health of white fringetrees will decrease with the EAB attack wave, especially as EAB reaches denser populations of fringetrees.
Employing Very High Frequency (VHF) Radio Telemetry to Recreate Monarch Butterfly Flight Paths
Authors: Fisher Kelsey E , Adelman James S , Bradbury Steven P
Published: February 2020

The overwintering population of eastern North American monarch butterflies (Danaus plexippus) has declined significantly. Loss of milkweed (Asclepias sp.), the monarch’s obligate host plant in the Midwest United States, is considered to be a major cause of the decline. Restoring breeding habitat is an actionable step towards population recovery. Monarch butterflies are highly vagile; therefore, the spatial arrangement of milkweed in the landscape influences movement patterns, habitat utilization, and reproductive output. Empirical studies of female movement patterns within and between habitat patches in representative agricultural landscapes support recommendations for habitat restoration. To track monarch movement at distances beyond human visual range, we employed very high frequency radio telemetry with handheld antennae to collect movement bearings on a biologically relevant time scale. Attachment of 220–300 mg transmitters did not significantly affect behavior and flight capability. Thirteen radio-tagged monarchs were released in a restored prairie, and locations were estimated every minute for up to 39 min by simultaneous triangulation from four operators. Monarchs that left the prairie were tracked and relocated at distances up to 250 m. Assuming straight flights between locations, the majority of steps within the prairie were below 50 m. Steps associated with exiting the prairie exceeded 50 m with high directionality. Because butterflies do not fly in straight lines between stationary points, we also illustrate how occurrence models can use location data obtained through radio telemetry to estimate movement within a prairie and over multiple land cover types.
Elite Schools, Elite Ambitions? The Consequences of Secondary-Level School Choice Sorting for Tertiary-Level Educational Choices
Authors: Bygren Magnus , Rosenqvist Erik
Published: February 2020

We ask if school choice, through its effect on sorting across schools, affects high school graduates’ application decisions to higher education. We exploit a school choice reform that dramatically increased achievement sorting across secondary schools in the municipality of Stockholm, employing a before–after design with a control group of students in similar schools located outside this municipality. The reform had a close to zero mean effect on the propensity to apply for tertiary educational programs, but strongly affected the self-selection by achievement into the kinds of higher educational programs applied for. Low achievers increased their propensity to apply for the ‘low-status’ educational programs, on average destining them to less prestigious, less well-paid occupations, and high achievers increased their propensity to apply for ‘high-status’ educational programs, on average destining them to more prestigious, well-paid occupations. The results suggest that increased sorting across schools reinforces differences across schools and groups in ‘cultures of ambition’. Although these effects translate into relatively small increases in the gender gap, the immigration gap, and the parental education gap in educational choice, our results indicate that school choice, and the increased sorting it leads to, through conformity mechanisms in schools polarizes educational choices of students across achievement groups.
Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension
Authors: Eaaswarkhanth Muthukrishnan , dos Santos Andre Luiz Campelo , Gokcumen Omer , Al-Mulla Fahd , Thanaraj Thangavel Alphonse
Published: February 2020

Despite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlapping TNKS that showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, the TNKS haplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.
GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms
Authors: Browne Patrick Denis , Nielsen Tue Kjærgaard , Kot Witold , Aggerholm Anni , Gilbert M Thomas P , Puetz Lara , Rasmussen Morten , Zervas Athanasios , Hansen Lars Hestbjerg
Published: February 2020

Background

Metagenomic sequencing is a well-established tool in the modern biosciences. While it promises unparalleled insights into the genetic content of the biological samples studied, conclusions drawn are at risk from biases inherent to the DNA sequencing methods, including inaccurate abundance estimates as a function of genomic guanine-cytosine (GC) contents.

Results

We explored such GC biases across many commonly used platforms in experiments sequencing multiple genomes (with mean GC contents ranging from 28.9% to 62.4%) and metagenomes. GC bias profiles varied among different library preparation protocols and sequencing platforms. We found that our workflows using MiSeq and NextSeq were hindered by major GC biases, with problems becoming increasingly severe outside the 45–65% GC range, leading to a falsely low coverage in GC-rich and especially GC-poor sequences, where genomic windows with 30% GC content had >10-fold less coverage than windows close to 50% GC content. We also showed that GC content correlates tightly with coverage biases. The PacBio and HiSeq platforms also evidenced similar profiles of GC biases to each other, which were distinct from those seen in the MiSeq and NextSeq workflows. The Oxford Nanopore workflow was not afflicted by GC bias.

Conclusions

These findings indicate potential sources of difficulty, arising from GC biases, in genome sequencing that could be pre-emptively addressed with methodological optimizations provided that the GC biases inherent to the relevant workflow are understood. Furthermore, it is recommended that a more critical approach be taken in quantitative abundance estimates in metagenomic studies. In the future, metagenomic studies should take steps to account for the effects of GC bias before drawing conclusions, or they should use a demonstrably unbiased workflow.
Lithofacies classification based on a hybrid system of artificial neural networks and hidden Markov models
Authors: Feng Runhai
Published: February 2020

Lithofacies is one of the most important reservoir parameters, which could provide a qualitative description for hydrocarbon and geothermal reservoirs. Various techniques, such as artificial neural networks (ANN) and hidden Markov models (HMM), have been applied to extract this information, with the well log suites as inputs. However, both of these methods have their own limitations, such as no geological priors in ANN, since log samples along the depth direction are treated independently. While in HMM, a simple Gaussian assumption is usually adopted, which may not be sufficient for complex data distributions. In order to address these problems, a new method is proposed, which combines ANN and HMM into a hybrid system. This new technique allows for a more flexible approach to the probability distributions of rock properties, without any Gaussian assumption being made. At the same time, the geological dependence between adjacent samples is introduced by a representative transition matrix of lithofacies. The output probability from ANN must be reformulated to an emission function before it can be fed into the HMM, which is achieved via the Bayes’ rule. Then the Viterbi algorithm in HMM is applied for the decoding of sequential patterns in the subsurface. In this fashion, the classification process can be proceeded statistically and geologically. Better performance of the proposed approach, compared with other classification methods, is demonstrated in two case studies.
Anti-obesity public health messages and risk factors for disordered eating: a systematic review
Authors: Bristow Claire , Meurer Capella , Simmonds Janette , Snell Tristan
Published: February 2020

In response to the increasing prevalence of overweight and obesity, public health efforts to curb these conditions have been delivered in abundance. There is concern however that the messages used to target these conditions may be increasing risk factors for disordered eating. Therefore, we sought to systematically review the literature on the effects of anti-obesity public health messages on risk factors for disordered eating. Seven electronic databases were searched for articles meeting the inclusion criteria, resulting in the inclusion of 12 studies of various methodologies that measured one or more risk factors for disordered eating following exposure to public health messages. Few studies specifically and accurately measured disordered eating behaviours. Most studies found that messages were stigmatizing towards persons who are overweight/obese, and exacerbate thin ideals and drive for thinness. Interestingly, the same was not found for measures of body dissatisfaction. Messages promoting smaller meals were also thought to be potential triggers for disordered eating. Whilst the studies included in this review offered both quantitative and qualitative insights into how public health messages may have adverse effects on eating behaviours, there was a consistent lack of valid reporting measures and clear classification of outcomes overall. Hence, future research is recommended using valid reporting tools such as validated questionnaires, as well as prolonged exposure to the intervention condition to determine longer-term impact.
Analysis of fibroblasts from patients with cblC and cblG genetic defects of cobalamin metabolism reveals global dysregulation of alternative splicing
Authors: Rashka Charif , Hergalant Sébastien , Dreumont Natacha , Oussalah Abderrahim , Camadro Jean-Michel , Marchand Virginie , Hassan Ziad , Baumgartner Matthias R , Rosenblatt David S , Feillet François , Guéant Jean-Louis , Flayac Justine , Coelho David
Published: February 2020

Vitamin B12 or cobalamin (Cbl) metabolism can be affected by genetic defects leading to defective activity of either methylmalonyl-CoA mutase or methionine synthase or both enzymes. Patients usually present with a wide spectrum of pathologies suggesting that various cellular processes could be affected by modifications in gene expression. We have previously demonstrated that these genetic defects are associated with subcellular mislocalization of RNA-binding proteins (RBP) and subsequent altered nucleo-cytoplasmic shuttling of mRNAs. In order to characterize the possible changes of gene expression in these diseases, we have investigated global gene expression in fibroblasts from patients with cblC and cblG inherited disorders by RNA-seq. The most differentially expressed genes are strongly associated with developmental processes, neurological, ophthalmologic and cardiovascular diseases. These associations are consistent with the clinical presentation of cblC and cblG disorders. Multivariate analysis of transcript processing revaled splicing alterations that led to dramatic changes in cytoskeleton organization, response to stress, methylation of macromolecules and RNA binding. The RNA motifs associated with this differential splicing reflected a potential role of RBP such as HuR and HNRNPL. Proteomic analysis confirmed that mRNA processing was significantly disturbed. This study reports a dramatic alteration of gene expression in fibroblasts of patients with cblC and cblG disorders, which resulted partly from disturbed function of RBP. These data suggest to evaluate the rescue of the mislocalization of RBP as a potential strategy in the treatment of severe cases who are resistant to classical treatments with co-enzyme supplements.
Shrinking Scale Equidistribution for Monochromatic Random Waves on Compact Manifolds
Authors: de Courcy-Ireland Matthew
Published: February 2020

We prove equidistribution at shrinking scales for the monochromatic ensemble on a compact Riemannian manifold of any dimension. This ensemble on an arbitrary manifold takes a slowly growing spectral window in order to synthesize a random function. With high probability, equidistribution takes place close to the optimal wave scale and simultaneously over the whole manifold. The proof uses Weyl’s law to approximate the two-point correlation function of the ensemble, and a Chernoff bound to deduce concentration.
Effects of feed removal on thermoregulation and intestinal morphology in pigs recovering from acute hyperthermia
Authors: Kpodo Kouassi R , Duttlinger Alan W , Maskal Jacob M , Johnson Jay S
Published: February 2020

Feed consumption increases body temperature and may delay a return to euthermia and exacerbate intestinal injury following acute hyperthermia recovery in pigs. Therefore, the study objective was to evaluate the effects of feed removal on body temperature and intestinal morphology in pigs exposed to acute hyperthermia and then rapidly cooled. Twenty-four gilts (78.53 ± 5.46 kg) were exposed to thermoneutral (TN; n = 12 pigs; 21.21 ± 0.31 °C; 61.88 ± 6.93% RH) conditions for 6 h, or heat stress (HS; 38.51 ± 0.60 °C; 36.38 ± 3.40% RH) conditions for 3 h followed by a 3-h recovery period of rapid cooling (HSC;n = 12 pigs; TN conditions and cold water dousing). Within each recovery treatment, one-half of the pigs were provided feed ad libitum (AF; n = 6 pigs per recovery treatment) and one-half of the pigs were not provided feed (NF; n = 6 pigs per recovery treatment). Gastrointestinal (TGI), vaginal (TV), and skin (TSK) temperatures and respiration rate (RR) were recorded every 15 min. Pigs were video-recorded to assess feeding and drinking attempts. Immediately following the 6-h thermal stress period, pigs were euthanized, and intestinal samples were collected to assess morphology. During the HS period, Tv, TGI, TSK, and RR were increased (P < 0.01; 1.63, 2.05, 8.32 °C, and 88 breaths per min, respectively) in HSC vs. TN pigs, regardless of feeding treatment. Gastrointestinal temperature was greater (P = 0.03; 0.97 °C) in HSC + AF vs. HSC + NF pigs from 45 to 180 min of the recovery period. During the recovery period, feeding attempts were greater (P = 0.02; 195.38%) in AF vs. NF pigs. No drinking attempt differences were detected with any comparison (P > 0.05). A decrease (P < 0.01) in jejunum and ileum villus height (24.72% and 26.11%, respectively) and villus height-to-crypt depth ratio (24.03% and 25.29%, respectively) was observed in HSC vs. TN pigs, regardless of feeding treatment. Ileum goblet cells were reduced (P = 0.01; 37.87%) in HSC vs. TN pigs, regardless of feeding treatment. In summary, TGI decreased more rapidly following acute hyperthermia when the feed was removed, and this may have implications toward using feed removal as a strategy to promote acute hyperthermia recovery in pigs.
Light or Dark Pigmentation of Engineered Skin Substitutes Containing Melanocytes Protects Against Ultraviolet Light-Induced DNA Damage In Vivo
Authors: Supp Dorothy M , Hahn Jennifer M , Lloyd Christopher M , Combs Kelly A , Swope Viki B , Abdel-Malek Zalfa , Boyce Steven T
Published: February 2020

Engineered skin substitutes (ESS) containing autologous fibroblasts and keratinocytes provide stable wound closure in patients with large, full-thickness burns, but are limited by hypopigmentation due to absence of added melanocytes. DNA damage caused by ultraviolet radiation (UV) increases risk for skin cancer development. In human skin, melanocytes provide pigmentation that protects skin from UV-induced DNA damage. This study investigated whether inclusion of human melanocytes (hM) affects the response of ESS to UV in vivo. Specifically, pigmentation and formation of cyclobutane pyrimidine dimers (CPDs), the most prevalent UV-induced DNA photoproduct, were analyzed. Three groups of ESS were prepared with fibroblasts and keratinocytes, ± melanocytes, and grafted orthotopically to immunodeficient mice: ESS without melanocytes (ESS-hM), ESS with light skin-derived (Caucasian) melanocytes (ESS+hM-L), and ESS with dark skin-derived (African-American) melanocytes (ESS+hM-D). Pigmentation of ESS+hM-L and ESS+hM-D increased significantly after grafting; pigmentation levels were significantly different among groups. Mean melanocyte densities in ESS+hM-L and ESS+hM-D were similar to each other and to densities in normal human skin. After 8 weeks in vivo, grafts were irradiated with 135 mJ/cm2 UV; non-UV-treated mice served as controls. UV modestly increased pigmentation in the ESS+hM groups. UV significantly increased CPD levels in ESS-hM, and levels in ESS-hM were significantly greater than in ESS+hM-L or ESS+hM-D. The results demonstrate that light or dark melanocytes in ESS decreased UV-induced DNA damage. Therefore, melanocytes in ESS play a photoprotective role. Protection against UV-induced DNA damage is expected to reduce skin cancer risk in patients grafted with ESS containing autologous melanocytes.
Insomnia and Neurocognitive Functioning in Adult Survivors of Childhood Cancer
Authors: Tonning Olsson Ingrid , Lubas Margaret M , Li Chenghong , Mandrell Belinda N , Banerjee Pia , Howell Carrie R , Ness Kirsten K , Srivastava Deokumar , Robison Leslie L , Hudson Melissa M , Krull Kevin R , Brinkman Tara M
Published: February 2020

Background

In noncancer populations, insomnia is known to affect neurocognitive processes. Although the prevalence of insomnia appears to be elevated in survivors of childhood cancer, relatively little is known about its association with neurocognitive performance in this at-risk population.

Methods

A total of 911 survivors (51.9% female; mean [SD] age, 34 [9.0] years; time since diagnosis, 26 [9.1] years) completed direct assessments of attention, memory, processing speed, and executive functioning and self-reported symptoms of sleep (Pittsburgh Sleep Quality Index), fatigue (Functional Assessment of Chronic Illness Therapy-Fatigue), and daytime sleepiness (Epworth Sleepiness Scale). Sex-stratified general linear models were used to examine associations between insomnia and neurocognitive performance, with adjustment for treatment exposures and chronic health conditions. All statistical tests were two-sided.

Results

Insomnia was reported by 22.1% of females and 12.3% of males (P < .001). After adjustment for neurotoxic treatment exposures, insomnia (vs healthy sleepers with no daytime fatigue or sleepiness) was associated with worse neurocognitive performance in the domains of verbal reasoning, memory, attention, executive function, and processing speed (verbal reasoning: males β = −0.34, P = .04, females β = −0.57, P < .001; long-term memory: males β = −0.60, P < .001, females β = −0.36, P = .02; sustained attention: males β = −0.85, P < .001, females β = −0.42, P = .006; cognitive flexibility: males β = −0.70, P = .002, females β = −0.40, P = .02). Self-reported sleep disturbance without daytime fatigue or sleepiness or daytime fatigue or sleepiness alone were not consistently associated with poorer neurocognitive performance.

Conclusions

Insomnia was highly prevalent and contributed to the neurocognitive burden experienced by adult survivors of childhood cancer. Treatment of insomnia may improve neurocognitive problems in survivors.