bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables
Authors: Kusstatscher Peter , Cernava Tomislav , Abdelfattah Ahmed , Gokul Jarishma , Korsten Lise , Berg Gabriele
Published: June 2020

Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.
The Role of Polygenic Score and Cognitive Activity in Cognitive Functioning Among Older Adults
Authors: Shin Su Hyun , Park Soohyun , Wright Cheryl , D’astous Valerie Anne , Kim Giyeon
Published: June 2020

Background and Objectives

This study explored whether the intensity of cognitive activities could moderate the relationship between a genetic predisposition for developing Alzheimer’s disease (AD) and cognitive functioning among older adults in the United States. Furthermore, we examined whether the same moderating effects were dependent on different measures of cognition.

Research Design and Methods

We used a data set from the 2000–2014 waves of the Health and Retirement Study and the Consumption and Activities Mail Survey. Our sample included 3,793 individuals aged 50 or older. We used the polygenic score (PGS) for AD as a genetic trait for cognitive functioning. Reading, listening to music, using a computer, playing cards/games/solving puzzles, singing/playing musical instruments, and creating art and crafts were included as cognitive activities, and TV viewing as passive activities. We used total cognition, fluid intelligence, and crystallized intelligence as proxies for cognitive functioning. Growth-curve models were conducted.

Results

After controlling for covariates, we found that reading books, using a computer, and playing cards/games/solving puzzles had a positive effect on cognitive functioning. An additional hour spent reading books moderated the negative effect of AD PGS on cognition. The measure of fluid, when compared with crystallized intelligence, appeared to drive these results.

Discussion and Implications

Reading could be a protective factor against cognitive decline among older adults who are genetically predisposed to developing AD. Implications for individuals, caregivers, clinicians, and policymakers are suggested. Furthermore, the onset of AD in those at greater genetic risk may be delayed with this intervention.
The UPC without the UK: Consequences and Alternatives
Authors: Tilmann Winfried
Published: June 2020

The UK has announced its withdrawal from the UPCA. In order to effectively leave the group of CMS it would have to notify its departure from the UPCA and the two Regulations to the EU Council and from the Protocol on provisional application to the Council of Europe. The UPCA-CMS on the continent should quickly pick up preparatory work after a new ratification law has been enacted in Germany consequential to the decision of the German Constitutional Court. The alternative of merging the UPC with a new specialised court within the Court of the CJEU has no realistic prospect of succeeding because ratification by all EU Member States is necessary.
Geometric curve flows in low dimensional Cayley–Klein geometries
Authors: Benson Joseph , Valiquette Francis
Published: June 2020

Using the method of equivariant moving frames, we derive the evolution equations for the curvature invariants of arc-length parametrized curves under arc-length preserving geometric flows in two-, three- and four-dimensional Cayley–Klein geometries. In two and three dimensions, we obtain recursion operators, which show that the curvature evolution equations obtained are completely integrable.
The impact of metabolites derived from the gut microbiota on immune regulation and diseases
Authors: Ohno Hiroshi
Published: June 2020

Abstract

The gut microbiota strongly impacts the physiology and pathology in the host. To understand the complex interactions between host and gut microbiota, an ‘integrated omics’ approach has been employed, where exhaustive analyses for the different layers of cellular functions, such as epigenomics, transcriptomics and metabolomics, in addition to metagenomics, are combined. With this approach, the mechanisms whereby short-chain fatty acids (SCFAs) regulate host defense and the immune system have been elucidated. In a gnotobiotic mouse model of enterohemorrhagic Escherichia coli infection, Bifidobacterium-derived acetate can protect from infection-mediated death by changing the gene expression profile of colonic epithelial cells. It has also been shown that gut microbiota-derived butyrate enhances colonic regulatory T-cell differentiation through its epigenetic modulatory ability via histone deacetylase inhibition. SCFAs are involved in many other immunomodulatory effects as well as host pathophysiological conditions. Dysbiosis in the gut has been implicated in the pathogenesis of many diseases. Although the causal relationship of gut microbial dysbiosis and/or metabolites with pathogenesis is mostly unknown, mechanistic insights have been elucidated in some cases. Metabolism in the gut microbiota and host liver produces trimethylamine N-oxide, which is known to aggravate atherosclerosis, and a secondary bile acid deoxycholate, which reportedly induces non-alcoholic steatohepatitis-related hepatocellular carcinoma. It has been reported that secondary bile acids could also induce the differentiation of peripherally derived regulatory T cells in the gut. Further studies on the interactions between the host and gut microbiota could lead to the development of new therapeutic strategies as well as in preventive medicine.
Outdoor Programs for Veterans: Public Land Policies and Practices to Support Therapeutic Opportunities
Authors: Derrien Monika M , Cerveny Lee K , Havlick David G
Published: June 2020

Many veterans returning from military deployment experience stress- or trauma-related symptoms that make reintegration with civilian society difficult. Nature exposure and outdoor recreation can be important parts of alternative and complementary approaches to reduce symptoms and build on veterans’ pre-existing strengths. Multiple outdoor programs now exist for veterans; many of these occur on federal public lands and present a variety of needs, opportunities, and challenges. This paper relies on interviews (n = 36) with public land managers, program providers and participants, health professionals, and veterans to enhance understanding about outdoor programs for veterans (OPVs). We develop a typology of OPVs to help land managers understand current and potential programs, and then describe programs’ varying dimensions. We examine opportunities and challenges for land managers in their interactions with OPVs. Results inform policymakers and public officials interested in developing more effective institutional partnerships and programs that engage and serve veterans and their communities.

Study Implications: With growing scientific evidence of the benefits of nature-based therapy, nature exposure, and outdoor recreation for veterans, programming for veterans on public lands has proliferated. Public land-management agencies vary in the extent to which they have systematically organized to provide opportunities for veterans, developed partnerships to support veterans’ health, and explicitly acknowledged agency roles in serving veterans. We describe seven types of outdoor programs for veterans (OPVs) that currently serve this population: supported outdoor activity; guided outdoor activity; retreat; outdoor job training; stewardship or service; horticulture, farming or gardening; and animal-assisted therapy. Each OPV type has different needs for infrastructure, outdoor spaces, and administrative or programmatic engagement. OPVs occurring on public lands typically involve one or more partner organizations, such as commercial outfitters and guides, health providers, veterans’ associations, foundations, corporations, and research institutions. There is potential for public land-management agencies to expand their role as institutional leaders in support of veterans’ health by facilitating the use of public lands as therapeutic landscapes. By enhancing new and existing relations with OPV providers, health providers, and other government agencies, public land agencies could expand benefits to veterans and spur broader societal benefits.
Repair of a recurrent symptomatic hernia through the foramen of Morgagni: a case study and review of the literature
Authors: Ben-Yaacov Almog , Menasherov Nikolay , Bard Vyacheslav
Published: June 2020

The prevalence and natural history in adults of Morgagni hernias have been relatively poorly characterized. A case is presented of a 31-year-old man where the hernia recurred following a laparoscopic mesh repair. In the era of minimally invasive surgery, debate concerns whether the peritoneal sac should be excised and if the insertion of mesh is superior to primary diaphragmatic repair.
High-voltage, diffuse delta rhythms coincide with wakeful consciousness and complexity in Angelman syndrome
Authors: Frohlich Joel , Bird Lynne M , Dell’Italia John , Johnson Micah A , Hipp Joerg F , Monti Martin M
Published: June 2020

Abundant evidence from slow wave sleep, anesthesia, coma, and epileptic seizures links high-voltage, slow electroencephalogram (EEG) activity to loss of consciousness. This well-established correlation is challenged by the observation that children with Angelman syndrome (AS), while fully awake and displaying volitional behavior, display a hypersynchronous delta (1–4 Hz) frequency EEG phenotype typical of unconsciousness. Because the trough of the delta oscillation is associated with down-states in which cortical neurons are silenced, the presence of volitional behavior and wakefulness in AS amidst diffuse delta rhythms presents a paradox. Moreover, high-voltage, slow EEG activity is generally assumed to lack complexity, yet many theories view functional brain complexity as necessary for consciousness. Here, we use abnormal cortical dynamics in AS to assess whether EEG complexity may scale with the relative level of consciousness despite a background of hypersynchronous delta activity. As characterized by multiscale metrics, EEGs from 35 children with AS feature significantly greater complexity during wakefulness compared with sleep, even when comparing the most pathological segments of wakeful EEG to the segments of sleep EEG least likely to contain conscious mentation and when factoring out delta power differences across states. These findings (i) warn against reverse inferring an absence of consciousness solely on the basis of high-amplitude EEG delta oscillations, (ii) corroborate rare observations of preserved consciousness under hypersynchronization in other conditions, (iii) identify biomarkers of consciousness that have been validated under conditions of abnormal cortical dynamics, and (iv) lend credence to theories linking consciousness with complexity.
How Reliable Are Volumetric Techniques for High-Grade Gliomas? A Comparison Study of Different Available Tools
Authors: Zeppa Pietro , Neitzert Luca , Mammi Marco , Monticelli Matteo , Altieri Roberto , Castaldo Margherita , Cofano Fabio , Borrè Alda , Zenga Francesco , Melcarne Antonio , Garbossa Diego
Published: June 2020

BACKGROUND

Gliomas are the most common malignant primary brain tumors. Assessment of the tumor volume represents a crucial point in preoperative and postoperative evaluation.

OBJECTIVE

To compare pre- and postoperative tumor volumes obtained with an automated, semi-automatic, and manual segmentation tool. Mean processing time of each segmentation techniques was measured.

METHODS

Manual segmentation was performed on preoperative and postoperative magnetic resonance images with the open-source software Horos (Horos Project). “SmartBrush,” a tool of the IPlan Cranial software (Brainlab, Feldkirchen, Germany), was used to carry out the semi-automatic segmentation. The open-source BraTumIA software (NeuroImaging Tools and Resources Collaboratory) was employed for the automated segmentation. Pearson correlation coefficient was used to assess volumetric comparison. Subsequently deviation/range and average discrepancy were determined. The Wilcoxon signed-rank test was used to assess statistical significance.

RESULTS

A total of 58 patients with a newly diagnosed high-grade glioma were enrolled. The comparison of the volumes calculated with Horos and IPlan showed a strong agreement both on preoperative and postoperative images (respectively: “enhancing” ρ = 0.99-0.78, “fluid-attenuated inversion recovery” ρ = 0.97-0.92, and “total tumor volume” ρ = 0.98-0.95). Agreement between BraTumIA and the other 2 techniques appeared to be strong for preoperative images, but showed a higher disagreement on postoperative images. Mean time expenditure for tumor segmentation was 27 min with manual segmentation, 17 min with semi-automated, and 8 min with automated software.

CONCLUSION

The considered segmentation tools showed high agreement in preoperative volumetric assessment. Both manual and semi-automated software appear adequate for the postoperative quantification of residual volume. The evaluated automated software is not yet reliable. Automated software considerably reduces the time expenditure.
MI5, the Cold War, and the Rule of Law
Authors: Ewing Keith , Mahoney Joan , Moretta Andrew
Published: June 2020

This title is concerned with the powers, activities, and accountability of MI5 principally in the period from 1945 to 1964. It was a body without statutory authority, with no statutory powers, and with no obvious forms of statutory accountability. It was established as a counter-espionage agency, yet was beset by espionage scandals on a frequency that suggested if not high levels of incompetence, then high levels of distraction and the squandering of resources. The book addresses the evolution of MI5’s mandate which set out its role and functions and to a limited extent the lines of accountability, the surveillance targets of MI5, and the surveillance methods that it used for this purpose, with a focus in two chapters on MPs and lawyers, respectively; the purposes for which this information was used, principally to exclude people from certain forms of employment; and the accountability of MI5 or the lack thereof for the way in which it discharged its responsibilities under the mandate.
Quantum Mechanics for Beginners
Authors: Zubairy M. Suhail
Published: June 2020

Quantum mechanics is a highly successful yet a mysterious theory. Quantum Mechanics for Beginners provides an introduction of this fascinating subject to someone with only a high school background in physics and mathematics. This book, except the last chapter on the Schrödinger equation, is entirely algebra-based. A major strength of this book is that, in addition to the foundation of quantum mechanics, it provides an introduction to the fields of quantum communication and quantum computing. The topics covered include wave–particle duality, the Heisenberg uncertainty relation, Bohr’s principle of complementarity, quantum superposition and entanglement, Schrödinger’s cat, Einstein–Podolsky–Rosen paradox, Bell theorem, quantum no-cloning theorem and quantum copying, quantum eraser and delayed choice, quantum teleportation, quantum key distribution protocols such as BB-84 and B-92, counterfactual communication, quantum money, quantum Fourier transform, quantum computing protocols including Shor and Grover algorithms, quantum dense coding, and quantum tunneling. All these topics and more are explained fully but using only elementary mathematics. Each chapter is followed by a short list of references and some exercises. This book is meant for an advanced high school student and a beginning college student and can be used as a text for a one semester course at the undergraduate level. However it can also be a useful and accessible book for those who are not familiar but want to learn some of the fascinating recent and ongoing developments in areas related to the foundations of quantum mechanics and its applications to quantum communication and quantum computing.
What Do We Owe to Animals? Kant on Non-Intrinsic Value
Authors: Hay Carol
Published: June 2020

This chapter argues that intrinsic value is necessarily connected to the rational ability people have to value things. Because animals do not have this ability, they cannot have intrinsic value. This means that if animals are to have any value at all, their value must be non-intrinsic. I argue that, despite their seemingly second-rate moral status, we can construct a surprisingly robust Kantian account of what we owe to animals. Kant is usually interpreted as arguing that the only reason we have to avoid cruelty to animals is that such behaviour is likely to harden our characters, making us more likely to behave cruelly towards people. I argue here that we can affirm the basic Kantian story about the loci and sources of both intrinsic and non-intrinsic value without being committed to a variety of morally problematic conclusions about animals. On this picture, we can still say that animals matter morally, that their interests must be taken into account, that they are moral patients or subjects, and that they deserve genuine moral consideration or regard.
RADIATION DOSE ASSESSMENT TO FAMILY MEMBERS TAKING CARE OF NON-CANCEROUS THYROID PATIENTS TREATED WITH I-131 THERAPY IN NUCLEAR MEDICINE DEPARTMENT
Authors: Kadhim Ali Abdulhasan , Sheikhzadeh Peyman , Farzanefar Saeed , Yavari Shima , Ay Mohammad Reza
Published: June 2020

This study aimed to determine the effective doses of caregivers taking care of non-cancerous patients treated with iodine-131 (I-131). Patients (administered 185–1110 MBq of I-131) were given specific radiation safety instructions (RSI). Afterwards, caregivers were provided with thermoluminescent (TLD) dosimeter badges to be worn for 12–28 days when taking care of the patients. At the end of this period, TLD measurements were obtained. Results showed that caregivers’ mean effective dose was 0.15 ± 0.15 mSv, which is far less than the international recommendations of 5 mSv. Furthermore, the effective doses had no significant correlation with administered I-131 activity to the patients, distance from the hospital, caregivers’ age, educational level and mode of transport. Our study showed that radiation doses received by caregivers of non-cancerous patients are higher than that of cancerous patients, nevertheless their received doses were within the international limits, thereby indicating good compliance by the caregivers to RSI.
Skin Lesions Classification Based on Deep Learning Approach
Authors: Deif Mohanad A. , Hammam Rania E.
Published: June 2020

As one kind of skin cancer, melanoma is very dangerous. Dermoscopy-based early detection and reorganization strategy is critical for melanoma therapy. Skin imaging is essential in order to diagnose the tumor type; this had to be accomplished by taking a biopsy from patients. This procedure is very uncomfortable for patients and requires time and highly qualified dermatologists to precisely differentiate between different types of skin cancer. In order to solve these problems, many efforts focused on developing automatic image analysis systems that reduce the suffering of patients, time, and tumor classification error. Here we report a novel strategy based on deep learning technique, which achieved very high skin melanoma diagnosis accuracy. Different pretrained architectures (VGG16, Inception_v3, and ResNet-50) were proposed and applied on 10,135 dermoscopy skin images. A comparison between these models was accomplished with hair removal and nonremoval algorithms. Experimental results showed that the removal of hair had a significant effect on the skin imaging as it helped to improve the training accuracy results. The VGG16 model achieved the highest accuracy (96.9%) with hair removal algorithm, followed by Inception_v3 and ResNet-50 model with an accuracy of 94.2% and 91.8% respectively.
The critical importance of experimentation in biomarker-based trophic ecology
Authors: Galloway Aaron W. E. , Budge Suzanne M.
Published: June 2020

Fatty acids are commonly used as biomarkers for making inferences about trophic relationships in aquatic and soil food webs. However, researchers are often unaware of the physiological constraints within organisms on the trophic transfer and modification of dietary biomarkers in consumers. Fatty acids are bioactive molecules, which have diverse structures and functions that both complicate and enhance their value as trophic tracers. For instance, consumers may synthesize confounding non-dietary sourced markers from precursor molecules, and environmental conditions also affect fatty acid composition. There is a vital need for more research on the uptake and transfer of trophic biomarkers in individual organisms in order to advance the field and make meaningful use of these tools at the scale of populations or ecosystems. This special issue is focused on controlled feeding experiments on a diverse taxonomic breadth of model consumers from freshwater, marine and soil ecosystems with a goal of creating a more integrated understanding of the connection between consumer physiology and trophic ecology.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids'.
Unlocking the power of fatty acids as dietary tracers and metabolic signals in fishes and aquatic invertebrates
Authors: Jardine Timothy D. , Galloway Aaron W. E. , Kainz Martin J.
Published: June 2020

Determining the transfer and transformation of organic matter in food webs is a fundamental challenge that has implications for sustainable management of ecosystems. Fatty acids (FA) offer a potential approach for resolving complex diet mixtures of organisms because they provide a suite of molecular tracers. Yet, uncertainties in the degree of their biochemical modification by consumers, due to selective retention or metabolism, have limited their application. Here, we consolidated 316 controlled feeding studies of aquatic ectotherms (fishes and invertebrates) involving 1404 species–diet combinations to assess the degree of trophic modification of FA in muscle tissue. We found a high degree of variability within and among taxa in the %FA in consumer muscle tissue versus %FA in diet regression equations. Most saturated FA had weak relationships with the diet (
r
2
< 0.30) and shallow slopes (
m
< 0.30), suggesting a lack of retention in muscle when fed in increasing amounts. Contrarily, several essential FA, including linoleic (18:2n-6) and α-linolenic acid (18:3n-3), exhibited significant relationships with the diet (
m
> 0.35,
r
2
> 0.50), suggesting supply limitations and selective retention in muscle by consumers. For all FA, relationships strengthened with increasing taxonomic specificity. We also demonstrated the utility of new correction equations by calculating the potential contributions of approximately 20 prey items to the diet of selected species of generalist fishes using a FA mixing model. Our analyses further reveal how a broad range of fishes and invertebrates convert or store these compounds in muscle tissue to meet physiological needs and point to their power in resolving complex diets in aquatic food webs.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Fatty acid metabolism and modifications in
Chironomus riparius
Authors: Strandberg Ursula , Vesterinen Jussi , Ilo Timo , Akkanen Jarkko , Melanen Miina , Kankaala Paula
Published: June 2020

A priori
knowledge of fatty acid modifications in consumers is essential for studies using fatty acids as biomarkers. We investigated fatty acid metabolism and possible modification pathways in benthic invertebrate
Chironomus riparius
larvae (Diptera). We conducted diet manipulation experiments using natural food sources (two chlorophyte algae, a diatom and a non-toxic cyanobacterium). We also did a diet-switch experiment on two different resources, fish food flakes TetraMin
®
and cyanobacterium
Spirulina
, to study fatty acid turnover in
Chironomus
. Results of the diet manipulation experiments indicate that
Chironomus
larvae have a strong tendency to biosynthesize 20:5n-3 and 20:4n-6 from precursor fatty acids, and that the dietary availability of polyunsaturated fatty acids (PUFA) does not control larval growth. Fatty acid modifications explain why low dietary availability of PUFA did not significantly limit growth. This has ecologically relevant implications on the role of benthic chironomids in conveying energy to upper trophic level consumers. A diet-switch experiment showed that the turnover rate of fatty acids in
Chironomus
is relatively fast––a few days. The compositional differences of algal diets were large enough to separate
Chironomus
larvae into distinct groups even if significant modification of PUFA was observed. In summary, fatty acids are excellent dietary biomarkers for
Chironomus
, if modifications of PUFA are considered, and will provide high-resolution data on resource use.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
Assimilation and turnover rates of lipid compounds in dominant Antarctic copepods fed with
13
C-enriched diatoms
Authors: Graeve Martin , Boissonnot Lauris , Niehoff Barbara , Hagen Wilhelm , Kattner Gerhard
Published: June 2020

The study revealed species- and stage-specific differences in lipid accumulation of the dominant Antarctic copepods, the primarily herbivorous
Calanoides acutus
(copepodite stage V (CV), females) and the more omnivorous
Calanus propinquus
(females) storing wax esters and triacylglycerols, respectively, which were collected in summer (end of December). Feeding carbon-labelled diatoms to these copepods,
13
C elucidated assimilation and turnover rates of copepod total lipids as well as specific fatty acids and alcohols. The
13
C incorporation was monitored by compound-specific stable isotope analysis (CSIA). CV stages of
C. acutus
exhibited an intense total lipid turnover and 55% of total lipids were labelled after 9 days of feeding. By contrast, total lipid assimilation of female
C. acutus
and
C. propinquus
was lower with 29% and 32%, respectively. The major dietary fatty acids 16:0, 16:1(n − 7) and 20:5(n − 3) had high turnover rates in all specimens. In
C. acutus
CV, the high rates of the de novo synthesized long-chain monounsaturated fatty acids and alcohols 20:1(n − 9) and 22:1(n − 11) indicate intense lipid deposition, whereas these rates were low in females. The differences in lipid assimilation and turnover clearly show that the copepod species exhibit a high variability and plasticity to adapt their lipid production to their various life phases.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
Interaction between
ω
6 and
ω
3 fatty acids of different chain lengths regulates Atlantic salmon hepatic gene expression and muscle fatty acid profiles
Authors: Emam Mohamed , Katan Tomer , Caballero-Solares Albert , Taylor Richard G. , Parrish Kathleen S. , Rise Matthew L. , Parrish Christopher C.
Published: June 2020

Atlantic salmon smolts (approx. 20-months old) were fed experimental diets with different combinations of omega-6:omega-3 fatty acids (FAs) (high-ω6, high-ω3, or balanced) and eicosapentaenoic acid plus docosahexaenoic acid (EPA + DHA) levels (0.3, 1.0 or 1.4%) for 12 weeks. Muscle FA (% total FA) reflected dietary C
18
-polyunsaturated FA; however, muscle EPA per cent and content (mg g
−1
) were not different in salmon fed high-ω3 or balanced diets. Muscle DHA per cent was similar among treatments, while DHA content increased in fish fed 1.4% EPA + DHA, compared with those fed 0.3–1.0% EPA + DHA combined with high-ω6 FA. Muscle 20:3
ω
6 (DGLA) content was highest in those fed high-ω6 with 0.3% EPA + DHA. Quantitative polymerase chain reaction analyses on liver RNA showed that the monounsaturated FA synthesis-related gene,
scdb,
was upregulated in fish fed 1.0% EPA + DHA with high-ω6 compared to those fed 0.3% EPA + DHA. In high-ω3-fed salmon, liver
elovl2
transcript levels were higher with 0.3% EPA + DHA than with 1.0% EPA + DHA. In high-ω6-fed fish,
elovl2
did not vary with EPA + DHA levels, but it was positively correlated with muscle ARA, 22:4
ω
3 and DGLA. These results suggest dietary 18:3
ω
3 elongation contributed to maintaining muscle EPA + DHA levels despite a two- to threefold change in dietary proportions, while 18:2
ω
6 with 0.3% EPA + DHA increased muscle DGLA more than arachidonic acid (ARA). Positive correlations between hepatic
elovl2
and
fabp10a
with muscle
ω
6:
ω
3 and EPA + DHA + ARA, respectively, were confirmed by reanalysing data from a previous salmon trial with lower variations in dietary EPA + DHA and
ω
6:
ω
3 ratios.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Comparison of Bayesian and numerical optimization-based diet estimation on herbivorous zooplankton
Authors: Litmanen Jaakko J. , Perälä Tommi A. , Taipale Sami J.
Published: June 2020

Consumer diet estimation with biotracer-based mixing models provides valuable information about trophic interactions and the dynamics of complex ecosystems. Here, we assessed the performance of four Bayesian and three numerical optimization-based diet estimation methods for estimating the diet composition of herbivorous zooplankton using consumer fatty acid (FA) profiles and resource library consisting of the results of homogeneous diet feeding experiments. The method performance was evaluated in terms of absolute errors, central probability interval checks, the success in identifying the primary resource in the diet, and the ability to detect the absence of resources in the diet. Despite occasional large inconsistencies, all the methods were able to identify the primary resource most of the time. The numerical optimization method QFASA using χ
2
(QFASA-CS) or Kullback­–Leibler (QFASA-KL) distance measures had the smallest absolute errors, most frequently found the primary resource, and adequately detected the absence of resources. While the Bayesian methods usually performed well, some of the methods produced ambiguous results and some had much longer computing times than QFASA. Therefore, we recommend using QFASA-CS or QFASA-KL. Our systematic tests showed that FA models can be used to accurately estimate complex dietary mixtures in herbivorous zooplankton.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
The potential of fatty acid isotopes to trace trophic transfer in aquatic food-webs
Authors: Burian Alfred , Nielsen Jens M. , Hansen Thomas , Bermudez Rafael , Winder Monika
Published: June 2020

Compound-specific isotope analyses (CSIA) of fatty acids (FA) constitute a promising tool for tracing energy flows in food-webs. However, past applications of FA-specific carbon isotope analyses have been restricted to a relatively coarse food-source separation and mainly quantified dietary contributions from different habitats. Our aim was to evaluate the potential of FA-CSIA to provide high-resolution data on within-system energy flows using algae and zooplankton as model organisms. First, we investigated the power of FA-CSIA to distinguish among four different algae groups, namely cyanobacteria, chlorophytes, haptophytes and diatoms. We found substantial within-group variation but also demonstrated that δ
13
C of several FA (e.g. 18:3
ω
3 or 18:4
ω
3) differed among taxa, resulting in group-specific isotopic fingerprints. Second, we assessed changes in FA isotope ratios with trophic transfer. Isotope fractionation was highly variable in daphnids and rotifers exposed to different food sources. Only δ
13
C of nutritionally valuable poly-unsaturated FA remained relatively constant, highlighting their potential as dietary tracers. The variability in fractionation was partly driven by the identity of food sources. Such systematic effects likely reflect the impact of dietary quality on consumers' metabolism and suggest that FA isotopes could be useful nutritional indicators in the field. Overall, our results reveal that the variability of FA isotope ratios provides a substantial challenge, but that FA-CSIA nevertheless have several promising applications in food-web ecology.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Unique fatty acid desaturase capacities uncovered in
Hediste diversicolor
illustrate the roles of aquatic invertebrates in trophic upgrading
Authors: Kabeya Naoki , Gür İbrahim , Oboh Angela , Evjemo Jan Ove , Malzahn Arne M. , Hontoria Francisco , Navarro Juan C. , Monroig Óscar
Published: June 2020

Omega-3 (
ω
3 or
n
-3) long-chain polyunsaturated fatty acids (PUFA), including eicosapentaenoic acid and docosahexaenoic acid (DHA), play physiologically important roles in vertebrates. These compounds have long been believed to have originated almost exclusively from aquatic (mostly marine) single-cell organisms. Yet, a recent study has discovered that many invertebrates possess a type of enzymes called methyl-end desaturases (
ω
x
) that enables them to endogenously produce
n
-3 long-chain PUFA and could make a significant contribution to production of these compounds in the marine environment. Polychaetes are major components of benthic fauna and thus important to maintain a robust food web as a recycler of organic matter and a prey item for higher trophic level species like fish. In the present study, we investigated the
ω
x
enzymes from the common ragworm,
Hediste diversicolor
, a common inhabitant in sedimentary littoral ecosystems of the North Atlantic. Functional assays of the
H. diversicolor
ω
x
demonstrated unique desaturation capacities. An
ω
3 desaturase mediated the conversion of
n
-6 fatty acid substrates into their corresponding
n
-3 products including DHA. A further enzyme possessed unique regioselectivities combining both
ω
6 and
ω
3 desaturase activities. These results illustrate that the long-chain PUFA biosynthetic enzymatic machinery of aquatic invertebrates such as polychaetes is highly diverse and clarify that invertebrates can be major contributors to fatty acid trophic upgrading in aquatic food webs.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Ambient temperature and algal prey type affect essential fatty acid incorporation and trophic upgrading in a herbivorous marine copepod
Authors: Helenius Laura , Budge Suzanne M. , Nadeau Heather , Johnson Catherine L.
Published: June 2020

The essential fatty acids (EFA) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are critical nutrients for all organisms, and the temperature sensitivity of their trophic transfer in marine systems is of concern because of rising ocean temperatures. Laboratory-reared copepodites of the marine calanoid
Calanus finmarchicus
were used to test the effects of temperature (at 6°C, 12°C and increasing temperature stress) and prey type (the dinoflagellate
Heterocapsa triquetra
and the diatom
Thalassiosira weissflogii
) on the extent and efficiency of dietary EPA and DHA incorporation from phytoplankton to copepods in a set of feeding experiments using
13
C labelling. Temperature was a significant determinant of
C
.
finmarchicus
copepodites' EFA incorporation and gross growth efficiency, defined as the fraction of ingested EFA retained in copepod tissue. Ingestion and incorporation of both EFA were higher at warmer temperature, except in the case of DHA in copepods feeding on diatoms. DHA-associated growth efficiency was higher at the higher temperature for copepodites consuming the dinoflagellate, but temperature-related variation in algal EFA content was also a predictive factor. Moreover, our results strongly suggest that copepodites are capable of synthesizing EPA when consuming an EPA-depleted diet. Our study implies that the copepod link of marine food webs is resilient in terms of EFA transfer when confronted with alterations of ambient temperature and prey type availability. Measurements presented here are critical for estimating how EFA transfer dynamics respond to intra- and interannual environmental variability.

This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care
Authors: Jones Nick K. , Conway Morris Andrew , Curran Martin D. , Parmar Surendra , Sule Olajumoke , Enoch David A. , Aliyu Sani H. , Zhang Hongyi , Jalal Hamid , Navapurkar Vilas , Murphy Michael E.
Published: June 2020

Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis.

Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs.

Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge’s Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records.

Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected

Streptococcus pneumoniae

more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and

Mycobacterium tuberculosis

culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation.

Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.
Feasibility of dual phase 99mTc-MDP SPECT/CT imaging in rheumatoid arthritis evaluation
Authors: Abdelhafez Yasser G. , Godinez Felipe , Sood Kanika , Hagge Rosalie J. , Boutin Robert D. , Raychaudhuri Siba P. , Badawi Ramsey D. , Chaudhari Abhijit J.
Published: June 2020

Objectives

To prospectively demonstrate the feasibility of performing dual-phase SPECT/CT for the assessment of the small joints of the hands of rheumatoid arthritis (RA) patients, and to evaluate the reliability of the quantitative and qualitative measures derived from the resulting images.

Methods

A SPECT/CT imaging protocol was developed in this pilot study to scan both hands simultaneously in RA patients, in two phases of 99mTc-MDP radiotracer uptake; namely the soft-tissue blood pool phase (within 15 minutes after radiotracer injection) and osseous phase (after 3 hours). Joints were evaluated qualitatively (normal vs. abnormal uptake) and quantitatively (by measuring the maximum corrected count ratio [MCCR]). Qualitative and quantitative evaluations were repeated to assess reliability.

Results

Four participants completed seven studies (all four were imaged at baseline, and three of them at follow-up after 1-month of arthritis therapy). A total of 280 joints (20 per hand) were evaluated. The MCCR from soft-tissue phase scans was significantly higher for clinically abnormal joints compared to clinically normal ones; p<0.001, however the MCCR from the osseous phase scans were not different between the two groups. Intraclass Correlation Coefficient (ICC) for MCCR was excellent (0.9789, 95% confidence interval [CI]: 0.9734-0.9833). Intra-observer agreement for qualitative SPECT findings was good for both the soft-tissue phase (kappa=0.78, 95%CI: 0.72-0.83) and osseous-phase (kappa=0.70, 95%CI: 0.64-0.76) scans.

Conclusion

Extracting reliable quantitative and qualitative measures from dual-phase 99mTc-MDP SPECT/CT hand scans is feasible in RA patients. SPECT/CT may provide a unique means for assessing both synovitis and osseous involvement in RA joints using the same radiotracer injection.
Copper deficiency alters shoot architecture and reduces fertility of both gynoecium and androecium inArabidopsis thaliana
Authors: Ishka Maryam Rahmati , Vatamaniuk Olena K.
Published: June 2020

Copper deficiency reduces plant growth, male fertility and seed set. The contribution of copper to female fertility and the underlying molecular aspects of copper deficiency-caused phenotypes are not well-known. We show that among copper deficiency-caused defects inArabidopsis thalianawere the increased shoot branching, delayed flowering and senescence, and entirely abolished gynoecium fertility. The increased shoot branching of copper-deficient plants was rescued by the exogenous application of auxin or copper. The delayed flowering was associated with the decreased expression of the floral activator,FT. Copper deficiency also decreased the expression of senescence-associated genes,WRKY53andSAG13, but increased the expression ofSAG12. The reduced fertility of copper-deficient plants stemmed from multiple factors including the abnormal stigma papillae development, the abolished gynoecium fertility, and the failure of anthers to dehisce. The latter defect was associated with reduced lignification, the upregulation of copper microRNAs and the downregulation of their targets, laccases, implicated in lignin synthesis. Copper-deficient plants accumulated ROS in pollen and had reduced cytochromecoxidase activity in leaves. This study opens new avenues for the investigation into the relationship between copper homeostasis, hormone-mediated shoot architecture, gynoecium fertility and copper deficiency-derived nutritional signals leading to the delay in flowering and senescence.

Highlight

Copper deficiency alters shoot architecture, delays flowering and senescence, and compromises fertility by altering stigma morphology, disrupting anther lignification and dehiscence, and pollen redox status inArabidopsis thaliana.
Colon Cancer and SARS-CoV-2: Impact of ACE2 Expression in Susceptibility to COVID-19
Authors: Ahmadi Mohsen , Saffarzadeh Negin , Habibi Mohammad Amin , Hajiesmaeili Fatemeh , Rezaei Nima
Published: June 2020

Novel coronavirus disease (COVID-19) pandemic has become a global health emergency. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interacts with angiotensin-converting enzyme 2 (ACE2) to enter the cells and infects diverse human tissues. It has been reported that a few conditions, including cancer, predispose individuals to SARS-CoV-2 infection and severe form of COVID-19. These findings led us to evaluate the susceptibility of colon adenocarcinoma (COAD) patients to SARS-CoV-2 infection by investigation of ACE2 expression in their tumor tissues. The expression analysis revealed that both mRNA and protein levels of ACE2 had increased in colon cancer samples than normal group. Next, the prognosis analysis has indicated that the upregulation of ACE2 was not correlated with patient survival outcomes. Further assessment displayed the hypomethylation of the ACE2 gene promoter in COAD patients. Surprisingly, this methylation status has a strong negative correlation with ACE2 gene expression. The functional enrichment analysis of the genes that had similar expression patterns with ACE2 in colon cancer tissues demonstrated that they mainly enriched in Vitamin digestion and absorption, Sulfur relay system, and Fat digestion and absorption pathways. Finally, we found that ACE2 gene expression had a significant association with the immune cell infiltration levels in COAD patients. In conclusion, it has plausible that COAD patients are more likely to be infected with SARS-CoV-2 and experience severe injuries. Moreover, COVID-19 would bring unfavorable survival outcomes of patients with colon cancer by the way of immune cell infiltration linked process. The present study highlights the importance of preventive actions for COAD patients during the COVID-19 pandemic.