bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources
Authors: Brandt Sophie C. , Brognaro Hévila , Ali Arslan , Ellinger Bernhard , Maibach Katharina , Rühl Martin , Wrenger Carsten , Schlüter Hartmut , Schäfer Wilhelm , Betzel Christian , Janssen Stefan , Gand Martin
Published: March 2021

Background

The transition to a biobased economy involving the depolymerization and fermentation of renewable agro-industrial sources is a challenge that can only be met by achieving the efficient hydrolysis of biomass to monosaccharides. In nature, lignocellulosic biomass is mainly decomposed by fungi. We recently identified six efficient cellulose degraders by screening fungi from Vietnam.

Results

We characterized a high-performance cellulase-producing strain, with an activity of 0.06 U/mg, which was identified as a member of theFusarium solanispecies complex linkage 6 (Fusarium metavorans), isolated from mangrove wood (FW16.1, deposited as DSM105788). The genome, representing nine potential chromosomes, was sequenced using PacBio and Illumina technology. In-depth secretome analysis using six different synthetic and artificial cellulose substrates and two agro-industrial waste products identified 500 proteins, including 135 enzymes assigned to five different carbohydrate-active enzyme (CAZyme) classes. TheF. metavoransenzyme cocktail was tested for saccharification activity on pre-treated sugarcane bagasse, as well as untreated sugarcane bagasse and maize leaves, where it was complemented with the commercial enzyme mixture Accellerase 1500. In the untreated sugarcane bagasse and maize leaves, initial cell wall degradation was observed in the presence of at least 196 µg/mL of the in-house cocktail. Increasing the dose to 336 µg/mL facilitated the saccharification of untreated sugarcane biomass, but had no further effect on the pre-treated biomass.

Conclusion

Our results show thatF. metavoransDSM105788 is a promising alternative pre-treatment for the degradation of agro-industrial lignocellulosic materials. The enzyme cocktail promotes the debranching of biopolymers surrounding the cellulose fibers and releases reduced sugars without process disadvantages or loss of carbohydrates.
Masting by beech trees predicts the risk of Lyme disease
Authors: Bregnard Cindy , Rais Olivier , Voordouw Maarten Jeroen
Published: March 2021

Background

The incidence of Lyme borreliosis and other tick-borne diseases is increasing in Europe and North America. There is currently much interest in identifying the ecological factors that determine the density of infected ticks as this variable determines the risk of Lyme borreliosis to vertebrate hosts, including humans. Lyme borreliosis is caused by the bacteriumBorrelia burgdorferisensu lato (s.l.) and in western Europe, the hard tickIxodes ricinusis the most important vector.

Methods

Over a 15-year period (2004–2018), we monitored the monthly abundance ofI. ricinusticks (nymphs and adults) and theirB. burgdorferis.l. infection status at four different elevations on a mountain in western Switzerland. We collected climate variables in the field and from nearby weather stations. We obtained data on beech tree seed production (masting) from the literature, as the abundance ofIxodesnymphs can increase dramatically 2 years after a masting event. We used generalized linear mixed effects models and AIC-based model selection to identify the ecological factors that influence inter-annual variation in the nymphal infection prevalence (NIP) and the density of infected nymphs (DIN).

Results

We found that the NIP decreased by 78% over the study period. Inter-annual variation in the NIP was explained by the mean precipitation in the present year, and the duration that the DNA extraction was stored in the freezer prior to pathogen detection. The DIN decreased over the study period at all four elevation sites, and the decrease was significant at the top elevation. Inter-annual variation in the DIN was best explained by elevation site, year, beech tree masting index 2 years prior and the mean relative humidity in the present year. This is the first study in Europe to demonstrate that seed production by deciduous trees influences the density of nymphs infected withB. burgdorferis.l. and hence the risk of Lyme borreliosis.

Conclusions

Public health officials in Europe should be aware that masting by deciduous trees is an important predictor of the risk of Lyme borreliosis.

Graphical Abstract
Potential metabolic resistance mechanisms to ivermectin in Anopheles gambiae: a synergist bioassay study
Authors: Nicolas Patricia , Kiuru Caroline , Wagah Martin G. , Muturi Martha , Duthaler Urs , Hammann Felix , Maia Marta , Chaccour Carlos
Published: March 2021

Background

Despite remarkable success obtained with current malaria vector control strategies in the last 15 years, additional innovative measures will be needed to achieve the ambitious goals for malaria control set for 2030 by the World Health Organization (WHO). New tools will need to address insecticide resistance and residual transmission as key challenges. Endectocides such as ivermectin are drugs that kill mosquitoes which feed on treated subjects. Mass administration of ivermectin can effectively target outdoor and early biting vectors, complementing the still effective conventional tools. Although this approach has garnered attention, development of ivermectin resistance is a potential pitfall. Herein, we evaluate the potential role of xenobiotic pumps and cytochrome P450 enzymes in protecting mosquitoes against ivermectin by active efflux and metabolic detoxification, respectively.

Methods

We determined the lethal concentration 50 for ivermectin in colonized Anopheles gambiae; then we used chemical inhibitors and inducers of xenobiotic pumps and cytochrome P450 enzymes in combination with ivermectin to probe the mechanism of ivermectin detoxification.

Results

Dual inhibition of xenobiotic pumps and cytochromes was found to have a synergistic effect with ivermectin, greatly increasing mosquito mortality. Inhibition of xenobiotic pumps alone had no effect on ivermectin-induced mortality. Induction of xenobiotic pumps and cytochromes may confer partial protection from ivermectin.

Conclusion

There is a clear pathway for development of ivermectin resistance in malaria vectors. Detoxification mechanisms mediated by cytochrome P450 enzymes are more important than xenobiotic pumps in protecting mosquitoes against ivermectin.

Graphical Abstract
A 3-year retrospective analysis of canine intestinal parasites: fecal testing positivity by age, U.S. geographical region and reason for veterinary visit
Authors: Sweet Sarah , Hegarty Evan , McCrann Donald J. , Coyne Michael , Kincaid Dave , Szlosek Donald
Published: March 2021

Background

Canine life stage is a key factor in parasite prevalence as clinical signs associated with parasitism are more common in pups. In adult dogs, health status and geographical region may also play a role in parasite prevalence. The purpose of this study was to evaluate fecal test results using zinc sulfate flotation by centrifugation combined with fecal antigen testing for hookworms (Ancylostomaspp.Uncinaria stenocephala), ascarids (Toxocara canis, Toxascarisspp., Baylisascarisspp.) and whipworms (Trichuris vulpis) sorted by age, geographical region and veterinary visit type.

Methods

A retrospective sample of intestinal parasite panels submitted to IDEXX Laboratories from 1,626,104 individual dogs were selected from the continental USA from 1 January 2017 to 31 December 2019. These data contain results from fecal exams performed using zinc sulfate flotation by centrifugation paired with coproantigen immunoassay results for hookworms, ascarids, whipworms andGiardia(Fecal Dx® withGiardia coproantigen immunoassay plate). For paired testing, if either the coproantigen assay or flotation test was positive, the sample was considered to be positive. Data were summarized by age category, U.S. Census Bureau geographical region (Northeast, South, Midwest, West) and veterinary visit type. Visit types were subdivided into Wellness Visits and Other Clinical Visits in which a fecal sample was submitted.

Results

In dogs presenting for either Wellness Visits or Other Clinical Visits in whichGiardiatesting was included,Giardiahad the highest positivity (combined results for microscopy and coproantigen: 12.2 and 10.8%, respectively), followed by hookworms (combined microscopy and coproantigen: 4.1 and 4.2%, respectively), ascarids (combined microscopy and coproantigen: 2.5 and 1.7%, respectively) and whipworms (combined microscopy and coproantigen: 1.1 and 1.4%, respectively). When all test results were pooled together, pups aged 2–6 months were observed to have the highest proportion of positive results by either microscopy or coproantigen immunoassay regardless of clinical visit type. Parasite positivity varied by geographical region. Regardless of visit type, age or geographical region, the coproantigen method was observed to find a higher proportion of positive test results than microscopy inGiardia, ascarids, hookworms and whipworms.

Conclusions

The Fecal Dx® coproantigen immunoassay combined with the zinc sulfate flotation by centrifugation method uncovers a higher number of positive hookworm, ascarid and whipworm infections than zinc sulfate flotation alone in both pups and adult dogs across all geographical regions of the USA regardless of visit type.

Graphical Abstract
Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster
Authors: Sabirov Marat , Kyrchanova Olga , Pokholkova Galina V. , Bonchuk Artem , Klimenko Natalia , Belova Elena , Zhimulev Igor F. , Maksimenko Oksana , Georgiev Pavel
Published: March 2021

Background

Pita is required for Drosophila development and binds specifically to a long motif in active promoters and insulators. Pita belongs to the Drosophila family of zinc-finger architectural proteins, which also includes Su(Hw) and the conserved among higher eukaryotes CTCF. The architectural proteins maintain the active state of regulatory elements and the long-distance interactions between them. In particular, Pita is involved in the formation of several boundaries between regulatory domains that controlled the expression of threehoxgenes in the Bithorax complex (BX-C). The CP190 protein is recruited to chromatin through interaction with the architectural proteins.

Results

Using in vitro pull-down analysis, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. Then we constructed transgenic lines expressing the Pita protein of thewild-typeand mutant variants lacking CP190-interacting regions. We have demonstrated that CP190-interacting region of the Pita can maintain nucleosome-free open chromatin and is critical for Pita-mediated enhancer blocking activity in BX-C. At the same time, interaction with CP190 is not required for the in vivo function of the mutant Pita protein, which binds to the same regions of the genome as the wild-type protein. Unexpectedly, we found that CP190 was still associated with the most of genome regions bound by the mutant Pita protein, which suggested that other architectural proteins were continuing to recruit CP190 to these regions.

Conclusions

The results directly demonstrate role of CP190 in insulation and support a model in which the regulatory elements are composed of combinations of binding sites that interact with several architectural proteins with similar functions.
Vision loss in patients with giant cell arteritis treated with tocilizumab
Authors: Amsler Jennifer , Kysela Iveta , Tappeiner Christoph , Seitz Luca , Christ Lisa , Scholz Godehard , Stalder Odile , Kollert Florian , Reichenbach Stephan , Villiger Peter M.
Published: March 2021

Objectives

Giant cell arteritis (GCA) may lead to vision loss. To what extent tocilizumab (TCZ) is able to prevent vision loss is unknown. The aim was to analyze the occurrence of vision loss in a large GCA cohort treated with TCZ.

Methods

In this observational monocentric study, GCA patients treated with TCZ between the years 2010 and 2018 were studied. Demographic, clinical, and laboratory data were analyzed.

Results

A total of 186 patients were included (62% female); 109 (59%) fulfilled the American College of Rheumatology (ACR) criteria, in 123 (66%) patients, large vessel vasculitis was diagnosed by magnetic resonance-angiography (MRA). Cumulative duration of TCZ treatment was 224 years, median treatment duration was 11.1 (IQR 5.6–17.9) months. Glucocorticoids (GC) were tapered over a median of 5.8 (IQR 3.0–8.5) months. At baseline, visual symptoms were present in 70 (38%) and vision loss in 21 (11%) patients. Patients with vision loss at baseline were older (p = 0.032), had a lower C-reactive protein (p = 0.002), and showed a negative association with MRA of the aorta (p = 0.006). Two patients (1.1%) developed vision loss, both at the initiation of TCZ treatment.

Conclusion

Our data show a very low incidence of vision loss in TCZ-treated patient. The two cases of AION occurred at the initiation of therapy, they support the hypothesis that advanced, and established structural changes of arteries are key factors for this accident. Whether a shorter duration of concomitant GC treatment is risky regarding vision loss needs to be studied.
Abdominal ectopic pregnancy complicated with a large bowel injury: a case report
Authors: Fessehaye Abraham , Gashawbeza Biruck , Daba Mekdes , Arusi Muhudin , Terefe Tsega
Published: March 2021

Background

Abdominal pregnancy accounts for 0.6 to 4% of all ectopic pregnancies. Due to delays in diagnosis and difficulties in the management of abdominal pregnancy, the risk of mortality is significantly higher than for uncomplicated ectopic pregnancies.

Case summary

A 23 years-old gravida-II, ectopic-I Ethiopian woman was initially managed as a case of missed second trimester abortion. Later on, abdominal ectopic pregnancy was diagnosed with ultrasound and she underwent a laparotomy. Though fetus and placenta was removed successfully without significant hemorrhage, there was inadvertent sigmoid colon injury.

Conclusion

In the management of abdominal ectopic pregnancy, the possibility of bowel injury during entry to the abdominal cavity at laparotomy should always be considered and an experienced general surgeon should always be in attendance before opening the abdomen, to prevent it from happening.
Successful treatment of intubation-induced severe neurogenic post-extubation dysphagia using pharyngeal electrical stimulation in a COVID-19 survivor: a case report
Authors: Traugott Marianna , Hoepler Wolfgang , Kitzberger Reinhard , Pavlata Sophie , Seitz Tamara , Baumgartner Sebastian , Placher-Sorko Gudrun , Pirker-Krassnig Daniela , Ehehalt Urs , Grasnek Andreas , Beham-Kacerovsky Michaela , Friese Emanuela , Wenisch Christoph , Neuhold Stephanie
Published: March 2021

Background

A significant portion of critically ill patients with coronavirus disease 2019 (COVID-19) are at high risk of developing intensive care unit (ICU)-acquired swallowing dysfunction (neurogenic dysphagia) as a consequence of requiring prolonged mechanical ventilation. Pharyngeal electrical stimulation (PES) is a simple and safe treatment for neurogenic dysphagia. It has been shown that PES can restore safe swallowing in orally intubated or tracheotomized ICU patients with neurogenic dysphagia following severe stroke. We report the case of a patient with severe neurogenic post-extubation dysphagia (PED) due to prolonged intubation and severe general muscle weakness related to COVID-19, which was successfully treated using PES.

Case presentation

A 71-year-old Caucasian female patient with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection developed neurogenic dysphagia following prolonged intubation in the ICU. To avoid aerosol-generating procedures, her swallowing function was evaluated non-instrumentally as recommended by recently published international guidelines in response to the COVID-19 pandemic. Her swallowing function was markedly impaired and PES therapy was recommended. PES led to a rapid improvement of the PED, as evaluated by bedside swallowing assessments using the Gugging Swallowing Screen (GUSS) and Dysphagia Severity Rating Scale (DSRS), and diet screening using the Functional Oral Intake Scale (FOIS). The improved swallowing, as reflected by these measures, allowed this patient to transfer from the ICU to a non-intensive medical department 5 days after completing PES treatment.

Conclusions

PES treatment contributed to the restoration of a safe swallowing function in this critically ill patient with COVID-19 and ICU-acquired swallowing dysfunction. Early clinical bedside swallowing assessment and dysphagia intervention in COVID-19 patients is crucial to optimize their full recovery. PES may contribute to a safe and earlier ICU discharge of patients with ICU-acquired swallowing dysfunction. Earlier ICU discharge and reduced rates of re-intubation following PES can help alleviate some of the pressure on ICU bed capacity, which is critical in times of a health emergency such as the ongoing COVID-19 pandemic.
Optimizing the acceleration of Cheddar cheese ripening using response surface methodology by microbial protease without altering its quality features
Authors: Alhelli Amaal Mohammed , Mohammed Nameer Khairulla , Khalil Eilaf Suliman , Hussin Anis Shobirin Meor
Published: March 2021

Cheddar cheese proteolysis were accelerated employingPenicillium candidumPCA1/TT031 protease into cheese curd. In the present study, several of the significant factors such as protease purification factor (PF), protease concentration and ripening time were optimized via the response surface methodology (RSM). The ideal accelerated Cheddar cheese environment consisted of 3.12 PF, 0.01% (v/v) protease concentration and 0.6/3 months ripening time at 10 °C. The RSM models was verified to be the most proper methodology for the maintain of chosen Cheddar cheese. Under this experimental environment, the pH, acid degree value (ADV), moisture, water activity (aw), soluble nitrogen (SN)%, fat and overall acceptability were found to be 5.4, 6.6, 35%, 0.9348, 18.8%, 34% and 13.6, respectively of ideal Cheddar cheese. Furthermore, the predicted and experimental results were in significant agreement, which confirmed the validity and reliability of the suggested method. In spite of the difference between the ideal and commercial Cheddar cheese in the concentration of some of amino acids and free fatty acids, the sensory evaluation did not show any significant difference in aroma profile between them.
A characterization of nonhomogeneous wavelet bi-frames for reducing subspaces of Sobolev spaces
Authors: Jia Hui-Fang , Zhang Jianping
Published: March 2021

For nonhomogeneous wavelet bi-frames in a pair of dual spaces $(H^{s}(\mathbb{R}^{d}), H^{-s}(\mathbb{R}^{d}))$
(

H
s

(

R
d

)
,

H

−
s

(

R
d

)
)
with $s\neq 0$
s
≠
0
, smoothness and vanishing moment requirements are separated from each other, that is, one system is for smoothness and the other one for vanishing moments. This gives us more flexibility to construct nonhomogeneous wavelet bi-frames than in $L^{2}(\mathbb{R}^{d})$

L
2

(

R
d

)
. In this paper, we introduce the reducing subspaces of Sobolev spaces, and characterize the nonhomogeneous wavelet bi-frames under the setting of a general pair of dual reducing subspaces of Sobolev spaces.
A finite point algorithm for soil water-salt movement equation
Authors: Li Fenhong , Hu Gang , Abdeljawad Thabet , Abbas Muhammad
Published: March 2021

In this paper, we propose the meshless finite point method for solving a type of fluid flow problem. The moving least square function is combined with the collocation method to treat nonlinear one- and two-dimensional soil water-salt movement equations. An adaptive windward scheme is used to stabilize the numerical solution in regions with a large gradient change. Numerical examples with the comparison among the proposed method, finite element method and characteristic finite element method show that the meshless finite point method is more accurate and is used to eliminate the numerical oscillation phenomenon.
AdipoR2 inhibits human glioblastoma cell growth through the AMPK/mTOR pathway
Authors: Jie Chen , Xuan Wang , Feng Han-Dong , Hua Ding-Mao , Bo Wang , Fei Sun , Hao Zhang
Published: March 2021

Background

AdipoR2, which belongs to the seven-transmembrane-domain receptor family, has been shown to play an important role in the development of human tumours, but the underlying mechanisms are poorly understood. In this study, we found that AdipoR2 expression correlates with glioma grade. In addition, we also investigated the mechanisms behind the antiproliferative effects of AdipoR2 in U251 cells (a human glioma cell line) using colony formation and WST-8 growth assays.

Methods

The U251 cell line was cultured in vitro. Western blotting was used to detect the expression of relevant proteins. Quantitative RT-PCR was used to detect AdipoR1 and AdipoR2 expression. Flow cytometry was used to detect cell cycle assay results. The gene expression profiles of glioma samples from the CGGA database were analysed by MATLAB and GSEA software.

Results

The AMPK/mTOR pathway plays a central role in the regulation of cell proliferation, differentiation and migration and may promote tumorigenesis. Therefore, we can control cancer progression by modulating the AMPK/mTOR pathway. However, there is no information on the relationship between AdipoR and AMPK/mTOR in central nervous system tumours such as GBM. In this study. We found 648 upregulated genes and 436 downregulated genes correlated with AdipoR2 expression in 158 glioma samples. GSEA suggested that AdipoR2 is a cell cycle-associated gene. The results of the flow cytometry analysis indicated that AdipoR2 induced G0/G1 cell cycle arrest in U251 cells. Furthermore, we identified the AMPK/mTOR signalling axis to be involved in AdipoR2-induced cell cycle arrest.

Conclusions

Our results suggest that AdipoR2 may represent a novel endogenous negative regulator of GBM cell proliferation. These findings also suggest that AdipoR2 may be a promising therapeutic target in GBM patients.
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens
Authors: Cook Ryan , Hooton Steve , Trivedi Urmi , King Liz , Dodd Christine E. R. , Hobman Jon L. , Stekel Dov J. , Jones Michael A. , Millard Andrew D.
Published: March 2021

Background

Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7–8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing.

Results

Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut.

Conclusions

The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment.
TOX as a potential target for immunotherapy in lymphocytic malignancies
Authors: Liang Chaofeng , Huang Shuxin , Zhao Yujie , Chen Shaohua , Li Yangqiu
Published: March 2021

TOX (thymocyte selection-associated HMG BOX) is a member of a family of transcriptional factors that contain the highly conserved high mobility group box (HMG-box) region. Increasing studies have shown that TOX is involved in maintaining tumors and promoting T cell exhaustion. In this review, we summarized the biological functions of TOX and its contribution as related to lymphocytic malignancies. We also discussed the potential role of TOX as an immune biomarker and target in immunotherapy for hematological malignancies.
The collaboration between Swiss initial vocational education and training partners: perceptions of apprentices, teachers, and in-company trainers
Authors: Sauli Florinda
Published: March 2021

This study aims to investigate the Swiss initial vocational education and training (IVET) partnership from the perspective of several stakeholders on the ground. Collaboration between stakeholders is essential in dual IVET to connect school- and workplace-based learning and to ensure the quality of the entire system. However, such collaboration can be challenging, given the different epistemic natures of the school and the training company. Apprentices, that regularly cross the boundaries of vocational school and training company, often struggle to connect the learnings that they have acquired from both places. Adopting a boundary crossing perspective, we explore perceptions of IVET partnership in terms of challenges and learning opportunities for the stakeholders on the ground. We realized focus groups with apprentices, vocational teachers, and in-company trainers (N = 64) from several professional fields. The data were analyzed in an inductive and deductive manner, using a thematic analysis. The main results highlight that the participants consider the collaboration between stakeholders to be weak: the links between schools and training companies appear to be scarce and not supported by explicit or formal strategies. Further, the apprentices act as brokers, but they are often not supported in connecting school- and workplace-based learning. These results can provide new insights into how the IVET partnership could be designed.
Wave-slope soaring of the brown pelican
Authors: Stokes Ian A. , Lucas Andrew J.
Published: March 2021

Background

From the laboratory at Scripps Institution of Oceanography, it is common to see the brown pelican (Pelecanus occidentalis) traveling along the crests of ocean waves just offshore of the surf-zone. When flying in this manner, the birds can travel long distances without flapping, centimeters above the ocean’s surface. Here we derive a theoretical framework for assessing the energetic savings related to this behavior, ‘wave-slope soaring,’ in which an organism in flight takes advantage of localized updrafts caused by traveling ocean surface gravity waves.

Methods

The energy cost of steady, constant altitude flight in and out of ground effect are analyzed as controls. Potential flow theory is used to quantify the ocean wave-induced wind associated with near-shoaling, weakly nonlinear, shallow water ocean surface gravity waves moving through an atmosphere initially at rest. Using perturbation theory and the Green’s function for Laplace’s equation in 2D with Dirichlet boundary conditions, we obtain integrals for the horizontal and vertical components of the wave-induced wind in a frame of reference moving with the wave. Wave-slope soaring flight is then analyzed using an energetics-based approach for waves under a range of ocean conditions and the body plan of P. occidentalis.

Results

For ground effect flight, we calculate a ∼15 - 25% reduction in cost of transport as compared with steady, level flight out of ground effect. When wave-slope soaring is employed at flight heights ∼2m in typical ocean conditions (2m wave height, 15s period), we calculate 60-70% reduction in cost of transport as compared with flight in ground effect. A relatively small increase in swell amplitude or decrease in flight height allows up to 100% of the cost of transport to be offset by wave-slope soaring behavior.

Conclusions

The theoretical development presented here suggests there are energy savings associated with wave-slope soaring. Individual brown pelicans may significantly decrease their cost of transport utilizing this mode of flight under typical ocean conditions. Thus wave-slope soaring may provide fitness benefit to these highly mobile organisms that depend on patchy prey distribution over large home ranges.
Prey and habitat distribution are not enough to explain predator habitat selection: addressing intraspecific interactions, behavioural state and time
Authors: Grenier-Potvin Alexis , Clermont Jeanne , Gauthier Gilles , Berteaux Dominique
Published: March 2021

Background

Movements and habitat selection of predators shape ecological communities by determining the spatiotemporal distribution of predation risk. Although intraspecific interactions associated to territoriality and parental care are involved in predator habitat selection, few studies have addressed their effects simultaneously with those of prey and habitat distribution. Moreover, individuals require behavioural and temporal flexibility in their movement decisions to meet various motivations in a heterogeneous environment. To untangle the relative importance of ecological determinants of predator fine-scale habitat selection, we studied simultaneously several spatial, temporal, and behavioural predictors of habitat selection in territorial arctic foxes (Vulpes lagopus) living within a Greater snow goose (Anser caerulescens atlantica) colony during the reproductive season.

Methods

Using GPS locations collected at 4-min intervals and behavioural state classification (active and resting), we quantified how foxes modulate state-specific habitat selection in response to territory edges, den proximity, prey distribution, and habitats. We also assessed whether foxes varied their habitat selection in response to an important phenological transition marked by decreasing prey availability (goose egg hatching) and decreasing den dependency (emancipation of cubs).

Results

Multiple factors simultaneously played a key role in driving habitat selection, and their relative strength differed with respect to the behavioural state and study period. Foxes avoided territory edges, and reproductive individuals selected den proximity before the phenological transition. Higher goose nest density was selected when foxes were active but avoided when resting, and was less selected after egg hatching. Selection for tundra habitats also varied through the summer, but effects were not consistent.

Conclusions

We conclude that constraints imposed by intraspecific interactions can play, relative to prey distribution and habitat characteristics, an important role in the habitat selection of a keystone predator. Our results highlight the benefits of considering behavioural state and seasonal phenology when assessing the flexibility of predator habitat selection. Our findings indicate that considering intraspecific interactions is essential to understand predator space use, and suggest that using predator habitat selection to advance community ecology requires an explicit assessment of the social context in which movements occur.
Accumulation of alpha-synuclein within the liver, potential role in the clearance of brain pathology associated with Parkinson’s disease
Authors: Reyes Juan F. , Ekmark-Léwen Sara , Perdiki Marina , Klingstedt Therése , Hoffmann Alana , Wiechec Emilia , Nilsson Per , Nilsson K. Peter R. , Alafuzoff Irina , Ingelsson Martin , Hallbeck Martin
Published: March 2021

Alpha-synuclein (α-syn) aggregation is the hallmark pathological lesion in brains of patients with Parkinson’s disease (PD) and related neurological disorders characterized as synucleinopathies. Accumulating evidence now indicates that α-syn deposition is also present within the gut and other peripheral organs outside the central nervous system (CNS). In the current study, we demonstrate for the first time that α-syn pathology also accumulates within the liver, the main organ responsible for substance clearance and detoxification. We further demonstrate that cultured human hepatocytes readily internalize oligomeric α-syn assemblies mediated, at least in part, by the gap junction protein connexin-32 (Cx32). Moreover, we identified a time-dependent accumulation of α-syn within the liver of three different transgenic (tg) mouse models expressing human α-syn under CNS-specific promoters, despite the lack of α-syn mRNA expression within the liver. Such a brain-to-liver transmission route could be further corroborated by detection of α-syn pathology within the liver of wild type mice one month after a single striatal α-syn injection. In contrast to the synucleinopathy models, aged mice modeling AD rarely show any amyloid-beta (Aß) deposition within the liver. In human post-mortem liver tissue, we identified cases with neuropathologically confirmed α-syn pathology containing α-syn within hepatocellular structures to a higher degree (75%) than control subjects without α-syn accumulation in the brain (57%). Our results reveal that α-syn accumulates within the liver and may be derived from the brain or other peripheral sources. Collectively, our findings indicate that the liver may play a role in the clearance and detoxification of pathological proteins in PD and related synucleinopathies.
Fungal communities in the biofilms colonizing the basalt sculptures of the Leizhou Stone Dogs and assessment of a conservation measure
Authors: Wang Yali , Zhang Huan , Liu Xiaobo , Liu Xiaoqing , Song Wei
Published: March 2021

The Leizhou Peninsula in China is very famous for its unique folk art creation, especially for the stonework, like the basalt sculptures of the Leizhou Stone Dogs, which have a history of more than two thousand years. Since these sculptures are usually exposed outdoors, many of them are suffering from severe damage by lichen and fungi. To protect them from microbial attack, we determined fungal communities in the biofilms colonizing the stone dogs and explored an effective conservation measure. Specifically, the micromorphology analysis of the biofilms on the stone dogs was performed through both on-site and laboratory-based microscopies in order to provide an overview of the fungal community structure. High-throughput sequencing analysis revealed that the predominant fungi in the biofilms belong to the following genera Caloplaca, Chaetomium, Clitopilus, Acanthostigma, Tolypocladium, Aspergillus, and Toxicocladosporium. The energy dispersive X-ray spectrometry (EDS) showed that the basalt is mainly composed of silica (53% by weight), followed by Al2O3 (14.4%), Fe2O3 (10.1%), CaO (8.4%), and MgO (7.4%) that are oxides susceptible to corrosion of biogenic acids. The EDS analysis of the hyphae provided the direct evidence on the leaching of the minerals of the sculptures. To control microbial attack, three kinds of antimicrobial agents were tested for 2 years. As a result, the mixture of biocide and water repellent showed the best effectiveness. Our findings provide an overview of fungi diversity in the biofilms on the stone dogs and help the investigation of fungi-induced biodeterioration and the exploration of specific conservation measure.
An A-E assessment of post-ICU COVID-19 recovery
Authors: Cadd Matthew , Nunn Maya
Published: March 2021

The COVID-19 global pandemic has placed unprecedented strain on healthcare and critical care services around the world. Whilst most resources have focused on the acute phase of the disease, there is likely to be an untold burden of patients chronically affected.

A wide range of sequelae contribute to post intensive care syndrome (PICS); from our current knowledge of COVID-19, a few of these have the potential to be more prevalent following critical care admission. Follow-up assessment, diagnosis and treatment in an increasingly virtual setting will provide challenges but also opportunities to develop these services. Here, we propose an A to E approach to consider the potential long-term effects of COVID-19 following critical care admission.

Anxiety and other mental health diagnoses

Breathlessness

Central nervous system impairment

Dietary insufficiency and malnutrition

Embolic events

Developing strategies to mitigate these during admission and providing follow-up, assessment and treatment of persistent multiple organ dysfunction will be essential to improve morbidity, mortality and patient quality of life.
Validation of CARE kV automated tube voltage selection for PET-CT: PET quantification and CT radiation dose reduction in phantoms
Authors: Bebbington Natalie A. , Jørgensen Troels , Dupont Erik , Micheelsen Mille A.
Published: March 2021

Background

Applied tube voltage (kilovolts, kV) and tube current (milliampere seconds, mAs) affect CT radiation dose and image quality and should be optimised for the individual patient. CARE kV determines the kV and mAs providing the lowest dose to the patient, whilst maintaining user-defined reference image quality. Given that kV changes affect CT values which are used to obtain attenuation maps, the aim was to evaluate the effect of kV changes on PET quantification and CT radiation dose using phantoms.

Method

Four phantoms (‘Lungman’, ‘Lungman plus fat’, ‘Esser’ and ‘NEMA image quality’ (NEMA IQ)) containing F-18 sources underwent 1 PET and 5 CT scans, with CARE kV on (automatic kV selection and mAs modulation) and in semi mode with specified tube voltages of 140, 120, 100 and 80 kV (mAs modulation only). A CARE kV image quality reference of 120 kV/50 mAs was used. Impact on PET quantification was determined by comparing measured activity concentrations for PET reconstructions from different CT scans with the reconstruction using the 120 kV reference, and dose (DLP, CTDIvol) differences calculated by comparing doses from all kV settings with the 120 kV reference.

Results

CARE kV-determined optimal tube voltage and CARE kV ‘on’ dose (DLP) savings compared with the 120 kV reference were: Lungman, 100 kV, 2.0%; Lungman plus fat, 120 kV, 0%; Esser, 100 kV, 9.3%; NEMA IQ, 100 kV, 3.4%. Using tube voltages in CARE kV ‘semi’ mode which were not advised by CARE kV ‘on’ resulted in dose increases ≤ 65% compared with the 120 kV reference (greatest difference Lungman plus fat, 80 kV). Clinically insignificant differences in PET activity quantification of up to 0.7% (Lungman, 100 kV, mean measured activity concentration) were observed when using the optimal tube voltage advised by CARE kV. Differences in PET quantification of up to 4.0% (Lungman, 140 kV, maximum measured activity concentration) were found over the full selection of tube voltages in semi mode, with the greatest differences seen at the most suboptimal kV for each phantom. However, most differences were within 1%.

Conclusions

CARE kV on can provide CT radiation dose savings without concern over changes in PET quantification.
Protocol for an open-label feasibility study for a randomised controlled trial of vitamin D supplementation in Crohn’s Disease patients with vitamin D deficiency: D-CODE Feasiblity study
Authors: Fletcher Jane , Bedson Emma , Brown Michaela , Hewison Martin , Swift Amelia , Cooper Sheldon C.
Published: March 2021

Background

Crohn's disease (CD) is a principal form of inflammatory bowel disease, affecting approximately 1 in every 650 people in the UK. Vitamin D deficiency is common in approximately 57.7% of CD patients; with anaemia occurring in about 43% of patients. There is growing evidence that supplementing CD patients who are vitamin D deficient may be effective in reducing the severity of CD symptoms and reducing iron-deficiency anaemia. Nevertheless, National Institute for Health and Care Excellence guidance regarding the management of CD does not address vitamin D deficiency in these patients. The aims of the study are (1) to determine the prevalence of vitamin D deficiency in adults with CD in Birmingham, UK and (2) to assess the feasibility of conducting a multi-site randomised controlled trial in adult patients with CD and vitamin D deficiency.

Methods

D-CODE consists of two parts—a screening study and an open-label randomised controlled feasibility study.

Vitamin D screening

Three hundred patients, 18 years or older with CD will have a dried blood spot test to measure vitamin D levels. Dietary and sun exposure data will be collected. Eligible patients with low levels of vitamin D will be invited to participate in the feasibility study.

Feasibility study

Fifty participants with CD and vitamin D deficiency will be randomised to receive either a low (400 IU daily for 24 weeks) or high (3200 IU daily for 12 weeks then vitamin D3 800 IU daily for 12 weeks) dose of vitamin D3 oral supplementation.

Patient-reported outcomes (Inflammatory Bowel Disease Questionnaire, EQ-5D-5L and Crohn’s Disease Activity Index Score) will be collected at weeks 0 and 24. Biochemical monitoring will take place at weeks 0, 12 and 24 and will measure 25-hydroxyvitamin D, corrected calcium, albumin, parathyroid hormone, hepcidin, other vitamin D metabolites, iron studies and C-reactive protein. Faecal calprotectin will be measured at weeks 0 and 24.

Discussion

A key aspect of D-CODE is the identification of vitamin D deficiency prior to supplementation. It is hoped that this feasibility study will lead to a definitive trial that will investigate the benefits of treating vitamin D deficiency in patients with CD.

Trial registration

The trial has been registered with EudraCT number 2018-003910-42, ClinicalTrials.gov identifier NCT03718182 and ISRCTN number 15717783.
d-Tryptophan enhances the reproductive organ-specific expression of the amino acid transporter homolog Dr-SLC38A9 involved in the sexual induction of planarian Dugesia ryukyuensis
Authors: Maezawa Takanobu , Ishikawa Masaki , Sekii Kiyono , Nagamatsu Go , Furukawa Ryohei , Kobayashi Kazuya
Published: March 2021

Background

Many animals switch between asexual and sexual reproduction in nature. We previously established a system for the sexual induction of planarian Dugesia ryukyuensis by feeding asexual planarians with minced sexual planarians. We identified dl-tryptophan (Trp) as one of the sex-inducing substances. dl-Trp can induce ovarian development, the first and essential step of sexual induction. d-Trp must act as a principal bioactive compound in terms of ovarian development, because the ovary-inducing activity of d-Trp was 500 times more potent than that of l-Trp. However, how Trp controls sexual induction is still unknown.

Results

In this study, qRT-PCR analyses suggested that the putative amino acid transporter gene Dr-SLC38A9 is highly expressed in sexual worms, especially in the yolk glands. In situ hybridization analyses showed that Dr-SLC38A9 is expressed in the ovarian primordia of asexual worms and in the mature ovaries, testes, and yolk glands of sexual worms. In addition, Dr-SLC38A9 RNA interference during sexual induction resulted in the suppression of the development of reproductive organs. These results suggest that Dr-SLC38A9 is involved in the development of these organs. Moreover, we demonstrated that the reproductive organ-specific expression of Dr-SLC38A9 is enhanced by the addition of d-Trp.

Conclusion

We propose that d-Trp activates the expression of Dr-SLC38A9 to promote sexual induction in the planarian D. ryukyuensis.
Identification of struggling readers or at risk of reading difficulties with one-minute fluency measures
Authors: Martins Maíra Anelli , Capellini Simone Aparecida
Published: March 2021

Background

To identify readers who are struggling or at risk of reading difficulties, reference standards in oral reading fluency (ORF) are used to conduct an assessment that is based on a widely reported method known as curriculum-based measurement (CBM), which itself is based on 1-min fluency measures. The purpose of this study was to evaluate students’ ORF (with a 1-min fluency measure) to characterize their fluency and to determine references of appropriate development in reading at the 50th percentile.

Method

For this study, a database of readings made available by the Learning Studies Research Laboratory was used. This database consisted of 365 readings by elementary-school students from the third to fifth grades in two cities in the interior of the state of São Paulo from two different public school systems that use the same teaching methodology. The data consisted of digital audio recordings of the passage “The Umbrella” (text suitable for schooling levels) of the Protocol for Assessment of Reading Comprehension procedure. For this procedure, three steps were performed: step 1—listening to the 365 readings and assessing the scores for the number of words read correctly per minute; step 2—the calculation of the mean and percentiles for each grade; and step 3—the adaptation of the reference table to indicate students eligible to receive reading fluency intervention.

Results

Third-year students who correctly read 86 or more words per minute, fourth-year students who correctly read 104 or more words per minute, and fifth-year students who correctly read 117 or more words per minute were considered students who had made adequate progress in reading.

Conclusion

It was possible to classify students based on the 1-min fluency measures, with reference intervals of words read correctly per minute per school year (for the third, fourth, and fifth years) for those who were making adequate progress in reading and reference intervals for those who were considered readers who were struggling or at risk of reading difficulties.