bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleeping with the enemy: unravelling the symbiotic relationships between the scale wormNeopolynoe chondrocladiae(Annelida: Polynoidae) and its carnivorous sponge hosts
Authors: Taboada Sergi , Serra Silva Ana , Díez-Vives Cristina , Neal Lenka , Cristobo Javier , Ríos Pilar , Hestetun Jon Thomassen , Clark Brett , Rossi Maria Eleonora , Junoy Juan , Navarro Joan , Riesgo Ana
Published: October 2020

The North Atlantic deep-water polynoid worm Neopolynoe chondrocladiae is involved in an exceptional symbiotic relationship with two hosts: the carnivorous sponges Chondrocladia robertballardi and Chondrocladia virgata. While this is an obligate symbiotic relationship, its real nature is unclear. We used a multidisciplinary approach to narrow down the type of symbiotic relationship between symbiont and hosts. Molecular connectivity analyses using COI and 16S suggest that N. chondrocladiae has high potential for dispersal, connecting sites hundreds of kilometres apart, likely aided by oceanographic currents. Microbial analyses on different anatomical parts of five Chondrocladia species suggest that the presence of the worm in C. robertballardi does not affect the microbiome of the sponge. MicroCT analysis on N. chondrocladiae show that it has dorsally oriented parapodia, which might prevent the worm from getting trapped in the sponge. A faecal pellet recovered from the worm suggests that the polynoid feeds on the crustacean prey captured by the sponge, something corroborated by our stable isotope analysis. Light and confocal microscopy images suggest that N. chondrocladiae elytra produce bioluminescence. We propose that the worm might use bioluminescence as a lure for prey (increasing the food available for both the sponge and the polynoid) and thus fuelling a mutualistic relationship.
Four Reference Quality Genome Assemblies of Pyrenophora teres f. maculata: A Resource for Studying the Barley Spot Form Net Blotch Interaction
Authors: Wyatt Nathan A. , Friesen Timothy L.
Published: October 2020

Pyrenophora teres is the causal agent of net blotch, the most devastating foliar disease of barley. In nature, net blotch is seen in two forms, net form net blotch, caused by P. teres f. teres, and spot form net blotch, caused by P. teres f. maculata. To date, 11 P. teres f. teres genomes have been sequenced and deposited in publicly available repositories, but only one P. teres f. maculata genome has been publicly deposited. Here, we present four additional reference-quality full-genome sequences of P. teres f. maculata isolates with good geographical and phenotypic diversity, with accompanying RNA sequencing-based genome annotations. These additional P. teres f. maculata genomes will aid in the understanding of the genomic complexities of this important barley pathogen.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Comparing DNA Extraction and 16S rRNA Gene Amplification Methods for Plant-Associated Bacterial Communities
Authors: Giangacomo Cecelia , Mohseni Mohsen , Kovar Lynsey , Wallace Jason G.
Published: October 2020

Plant-associated microbes play important roles in global ecology and agriculture. The most common method to profile these microbial communities is amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene. Both the DNA extraction and PCR amplification steps of this process are subject to bias, especially because the latter requires some way to exclude DNA from plant organelles, which would otherwise dominate the sample. We compared several common DNA extraction kits and 16S rRNA gene amplification protocols to determine the relative biases of each and to make recommendations for plant microbial researchers. For DNA extraction, we found that, as expected, kits optimized for soil were the best for soil, though each still included a distinct “fingerprint” of its own biases. Plant samples were less clear, with different species having different “best” options. For 16S rRNA gene amplification, we found that using peptide nucleic acid clamps provides the least taxonomic distortion, while chloroplast-discriminating primers are easy and inexpensive but present significant bias in the results. Blocking oligos require a more complex protocol and optimization for each species and showed significant taxonomic distortion; therefore, we do not recommend them for off-the-shelf applications. Further methods development will hopefully result in protocols that are even more reliable and less biased than these.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Characterization of the Populations of Botrytis cinerea Infecting Plastic Tunnel-Grown Strawberry and Tomato in the Hubei Province of China
Authors: Yang Rui , Li Na , Zhou Ziliang , Li Guoqing
Published: October 2020

A total of 707 isolates of Botrytis were collected from plastic tunnel-grown strawberry and tomato in the Hubei province of China. They were identified based on the specific molecular markers. Diversity of the B. cinerea (Bc) isolates was evaluated by typing the transposable elements (Boty, Flipper) and the mating types (MAT1-1, MAT1-2), as well as by determining virulence on tobacco (Nicotiana benthamiana) and fenhexamid sensitivity in agar medium. The results showed that 706 isolates (99.9%) were Bc and 1 isolate (0.1%) was B. pseudocinerea. The Bc isolates (n = 706) were classified into four transposable element types, Vacuma (3.1%), Boty (9.6%), Flipper (18.4%), and Transposa (68.8%). The strawberry and tomato subpopulations of Bc had significantly different (P < 0.05) compositions of the four transposable element types. The overall ratio of MAT1-1 to MAT1-2 deviated from 1:1 (n = 706; P = 0.0002), and MAT1-2 (56.9%) predominated over MAT1-1 (43.1%). In 7 of 12 geographic subpopulations, the ratio of MAT1-1 to MAT1-2 matched 1:1; however, in the remaining five geographic subpopulations, the ratio of MAT1-1 to MAT1-2 did not match 1:1. Results of the biological characterizations showed that most Bc isolates were highly sensitive or sensitive to fenhexamid, and the majority of Bc isolates were highly virulent or virulent on tobacco. Moreover, the relationship between genetic diversity and biological characteristics was analyzed. The results achieved during this study are helpful for understanding of the populations of B. cinerea.
Waitea circinata var. zeae Causing Root Rot of Cabbage and Oilseed Rape
Authors: Vojvodić Mira , Tanović Brankica , Mitrović Petar , Vico Ivana , Bulajić Aleksandra
Published: October 2020

Cabbage, a widely used and popular vegetable, and oilseed rape, the second most valuable oilseed crop in the world, are two important species from the Brassicaceae family. Two geographically separated outbreaks of cabbage and oilseed rape root rot with estimated incidence of 15 and 20%, respectively, were recorded during 2017 in the Vojvodina region, Serbia. Twelve hyphal-tip isolates were obtained from symptomatic cabbage and oilseed rape plants and identified as Waitea circinata var. zeae based on morphological and molecular features. This indicates that W. circinata var. zeae has expanded its host range to the Brassicaceae family. Sequence analyses of internal transcribed spacer (ITS) and large subunit of the ribosomal DNA, RPB2, and β-tubulin genes revealed the highest similarity with multiple W. circinata var. zeae. Neighbor-joining analyses of ITS sequences resulted in a phylogenetic tree with one well-defined branch of W. circinata var. zeae, with two separate groups. All Serbian isolates and the majority of isolates originating from natural infection of dicotyledonous plants grouped together in group I. Following artificial inoculation, W. circinata var. zeae isolates caused mild to medium root necrosis of seedlings of 2 monocotyledonous and 12 dicotyledonous plant species, implying a wider host range than was known for W. circinata var. zeae. Additionally, this is the first occurrence of W. circinata var. zeae on dicotyledonous host plants in Europe. Because cabbage and oilseed rape are important crops grown worldwide, the occurrence of this new soilborne pathogen with a broad host range imposes the necessity for changes in routine disease control practices, particularly crop rotation.
The Impact of Asymptomatic Congenital Cytomegalovirus on Adult Quality of Life
Authors: Katusic Maja Z. , Mensah-Bonsu Noël E. , Miller Jerry A. , Turcich Marie R. , Iovino Isabella , Vinson-Sellers Sherry , Voigt Robert G. , Demmler-Harrison Gail J. ,   on behalf of the Houston Congenital CMV Longitudinal Study
Published: October 2020

Objective:

Children born with asymptomatic congenital cytomegalovirus infection (AcCMV) have increased risk for hearing loss, which may affect their quality of life into adulthood. We aim to determine quality of life outcomes among adults who were identified at birth with AcCMV compared with controls, using the cohort of the Houston Congenital CMV Longitudinal Study.

Methods:

Quality of life was determined using the self-reported Quality of Life Inventory (QOLI). Sixty-one of 109 AcCMV subjects and 23 of 51 controls completed QOLI. Percentile scores of subjects were compared with percentile scores of controls using Student t tests. QOLI percentile scores were compared among AcCMV subjects with (N = 14) and without hearing loss (N = 47).

Results:

There was no difference in mean percentile scores on QOLI between AcCMV subjects (59.8 [SD = 27.6]) and controls (57.3 [SD = 35.3]; p = 0.754). Percentile scores indicate an average overall quality of life classification for AcCMV subjects and controls. There was no difference in mean percentile scores on the QOLI between AcCMV subjects with and without hearing loss (54.8 [SD = 25.2]) and 61.3 [SD = 28.3]; p = 0.440, respectively).

Conclusion:

Adults born with AcCMV do not seem to have lower ratings of quality of life compared with uninfected controls. Although our study had small sample size, hearing loss does not seem to be a significant predictor of QOLI percentile scores among AcCMV subjects. Quality of life in adulthood does not seem to be affected by an individual's awareness of screening positive for CMV, which supports the notion of “no harm” occurring from universal newborn screening for congenital CMV infection.
Philadelphia Chromosome‐positive Acute Myeloid Leukemia With e1a3 BCR‐ABL1 Fusion Transcript
Authors: Sheets Julia W. , Eulitt Patrick , He Rong , Olteanu Horatiu , Coombs Catherine C. , Foster Matthew C. , Montgomery Nathan D. , Zeidner Joshua F.
Published: October 2020

Supplemental Digital Content is available in the text
Investigation of Surrogate Biomarkers Associated with Macular Pigment Status in a Group of Older Irish Adults
Authors: Scanlon Grainne , Butler John S. , McCartney Daniel , Loskutova Ekaterina , Kenny Rose A. , Loughman James
Published: October 2020

SIGNIFICANCE

Macular pigment (MP) confers potent antioxidant and anti-inflammatory effects at the macula; however, its optical density in the eye is not routinely measured in clinical practice.

PURPOSE

This study explored a range of surrogate biomarkers including anthropometric, clinical, and plasma measures that may be associated with lower MP optical density (MPOD).

METHODS

Two thousand five hundred ninety-four subjects completed a full MP assessment as part of wave 1 of The Irish Longitudinal Study of Aging. Macular pigment optical density was measured using customized heterochromatic flicker photometry. Clinical (blood pressure), plasma (lipoproteins, inflammatory markers), and anthropometric (waist, hip, height, weight) biomarkers were measured for each participant.

RESULTS

Mean (standard deviation) MPOD for the study group was 0.223 (0.161), with a range of 0 to 1.08. One-way ANOVA revealed that MPOD was significantly lower among participants with low plasma high-density lipoprotein (HDL;P= .04), raised plasma triglyceride-to-HDL ratio (P= .003), and raised total cholesterol–to–HDL ratio (P= .03). Subjects with an elevated waist circumference (WC) had a significantly lower MPOD (mean, 0.216 [0.159]) compared with those with an ideal WC (mean, 0.229 [0.162];P= .03). Significant correlates of MPOD on mixed linear model analysis included education, smoking status, and WC.

CONCLUSIONS

Higher abdominal fat is associated with lower MPOD in this representative sample of older Irish adults. Although altered lipoprotein profiles (low HDL, raised triglyceride-to-HDL ratio, raised total cholesterol–to–HDL ratio) may affect the transport, uptake, and stabilization of carotenoids in the retina, these plasma biomarkers were not predictive of low MPOD after adjustment for abdominal circumference. Although WC emerged as a viable anthropometric predictor of lower MPOD, its effect size seems to be small.
Randomized Controlled Trial of a Spectacle Lens for Macular Degeneration
Authors: Visser Martijn S. , Timman Reinier , Kampen-Smalbrugge Joanneke , Buis Karin , Polling Jan Roelof , Busschbach J. J. V.
Published: October 2020

SIGNIFICANCE

E-Scoop, a spectacle lens, provides no clinically relevant improvements on quality of life, visual acuity, and contrast sensitivity for patients with AMD. Because patients' burden is high and therapeutic options are scarce, the incentive to develop effective vision rehabilitation interventions remains.

PURPOSE

Patients with AMD experience low quality of life due to vision loss, despite angiogenesis inhibitor interventions that slow down progression for some patients. E-Scoop, which includes low-power prisms, 6% magnification, yellow tint, and antireflection coating, might aid in daily activities by improving distance viewing. Separately, these features have little proven effectiveness. E-Scoop has not been formally tested. This study aimed to determine the impact of E-Scoop on quality of life and the effect on visual acuity and contrast sensitivity.

METHODS

In this randomized controlled, open-label trial, 190 of 226 eligible patients were included. The primary outcome was quality of life measured with the 25-item National Eye Institute Visual Function Questionnaire. Secondary outcomes were visual acuity and contrast sensitivity. The follow-up for quality of life was after 6 weeks for controls and after 3 weeks of use for E-Scoop wearers. The visual measures were repeated after 6 weeks, with optimal refractive correction, with and without E-Scoop.

RESULTS

Randomization resulted in 99 E-Scoop and 86 control group patients for intention-to-treat analysis. No differential change was found between the E-Scoop and control groups on the 25-item National Eye Institute Visual Function Questionnaire using Rasch analysis (Cohen d = −0.07, P = .53). Statistically significant but small effects were found in favor of E-Scoop on binocular visual acuity (mean difference, 0.05 logMAR [2.5 letters, P < .001]) and contrast sensitivity (mean difference, 0.10 logCS [2 letters, P < .001]).

CONCLUSIONS

No effect of E-Scoop on quality of life was found. E-Scoop showed effects that were statistically significant, although not clinically meaningful and within typical variability, on visual measures.
Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell
Authors: Britton Samuel , Alber Mark , Cannon William R.
Published: October 2020

Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization–reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of
E. coli
(gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.
On the importance of trip destination for modelling individual human mobility patterns
Authors: Lenormand Maxime , Arias Juan Murillo , San Miguel Maxi , Ramasco José J.
Published: October 2020

Obtaining insights into human mobility patterns and being able to reproduce them accurately is of the utmost importance in a wide range of applications from public health, to transport and urban planning. Still the relationship between the effort individuals will invest in a trip and the importance of its purpose is not taken into account in individual mobility models that can be found in the recent literature. Here, we address this issue by introducing a model hypothesizing a relation between the importance of a trip and the distance travelled. In most practical cases, quantifying such importance is undoable. We overcome this difficulty by focusing on shopping trips (for which we have empirical data) and by taking the price of items as a proxy. Our model is able to reproduce the long-tailed distribution in travel distances empirically observed and to explain the scaling relationship between distance travelled and item value found in the data.
RNA editing in mesothelioma: a look forward
Authors: Hariharan Ananya , Sun Suna , Wipplinger Martin , Felley-Bosco Emanuela
Published: October 2020

RNA editing is a post-transcriptional process increasing transcript diversity, thereby regulating different biological processes. We recently observed that mutations resulting from RNA editing due to hydrolytic deamination of adenosine increase during the development of mesothelioma, a rare cancer linked to chronic exposure to asbestos. This review gathers information from the published literature and public data mining to explore several aspects of RNA editing and their possible implications for cancer growth and therapy. We address possible links between RNA editing and particular types of mesothelioma genetic and epigenetic alterations and discuss the relevance of an edited substrate in the context of current chemotherapy or immunotherapy.
Polo-like kinase in trypanosomes: an odd member out of the Polo family
Authors: Kurasawa Yasuhiro , An Tai , Li Ziyin
Published: October 2020

Polo-like kinases (Plks) are evolutionarily conserved serine/threonine protein kinases playing crucial roles during multiple stages of mitosis and cytokinesis in yeast and animals. Plks are characterized by a unique Polo-box domain, which plays regulatory roles in controlling Plk activation, interacting with substrates and targeting Plk to specific subcellular locations. Plk activity and protein abundance are subject to temporal and spatial control through transcription, phosphorylation and proteolysis. In the early branching protists, Plk orthologues are present in some taxa, such as kinetoplastids and
Giardia
, but are lost in apicomplexans, such as
Plasmodium
. Works from characterizing a Plk orthologue in
Trypanosoma brucei
, a kinetoplastid protozoan, discover its essential roles in regulating the inheritance of flagellum-associated cytoskeleton and the initiation of cytokinesis, but not any stage of mitosis. These studies reveal evolutionarily conserved and species-specific features in the control of Plk activation, substrate recognition and protein abundance, and suggest the divergence of Plk function and regulation for specialized needs in this flagellated unicellular eukaryote.
Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan
Authors: Yorisue Takefumi , Iguchi Akira , Yasuda Nina , Mizuyama Masaru , Yoshioka Yuki , Miyagi Aika , Fujita Yoshihisa
Published: October 2020

Marine cave habitats in the Ryukyu Islands, Indo-West Pacific, are located at the northern edge of the distribution of many cave-dwelling species. At distribution margins, gene flow is often more restricted than that among core populations due to the smaller effective population size. Here, we used high-throughput sequencing technology to investigate the gene flow pattern among three sampling sites of a marine cave-dwelling species at the margin of its distribution range. We collected individuals of the barbouriid shrimpParhippolyte misticiafrom three marine caves in the Ryukyu Islands and performed population genetic analyses by means of multiplexed inter-simple sequence repeat genotyping by sequencing. Based on 62 single-nucleotide polymorphism markers, no clear population structure or directional gene flow pattern was found among the three sites. These results were unexpected because previous studies of other stygobitic shrimps in this region did find significant population genetic structures and northward directional gene flow patterns.Together, these inconsistent findings imply that marine cave-dwelling species in the region have different mechanisms of larval dispersal. Future studies on larval ecology and the biotic and abiotic factors influencing gene flow patterns are needed to clarify the mechanisms underlying the population dynamics of marine cave-dwelling species.
The pantophysin gene and its relationship with survival in early life stages of Atlantic cod
Authors: Otterå Håkon , Johansen Torild , Folkvord Arild , Dahle Geir , Solvang Bingh Marte Kristine , Westgaard Jon-Ivar , Glover Kevin A.
Published: October 2020

Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series ofin vitrocrosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAAgenotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.
Actions do not speak louder than words in an interactive false belief task
Authors: Wenzel Lisa , Dörrenberg Sebastian , Proft Marina , Liszkowski Ulf , Rakoczy Hannes
Published: October 2020

Traditionally, it had been assumed that meta-representational Theory of Mind (ToM) emerges around the age of 4 when children come to master standard false belief (FB) tasks. More recent research with various implicit measures, though, has documented much earlier competence and thus challenged the traditional picture. In interactive FB tasks, for instance, infants have been shown to track an interlocutor's false or true belief when interpreting her ambiguous communicative acts (Southgate
et al
. 2010
Dev. Sci.
13
, 907–912. (
doi:10.1111/j.1467-7687.2009.00946.x
)). However, several replication attempts so far have produced mixed findings (e.g. Dörrenberg
et al
. 2018
Cogn. Dev.
46
, 12–30. (
doi:10.1016/j.cogdev.2018.01.001
); Grosse Wiesmann
et al.
2017
Dev. Sci.
20
, e12445. (
doi:10.1111/desc.12445
); Király
et al
. 2018
Proc. Natl Acad. Sci. USA
115
, 11 477–11 482. (
doi:10.1073/pnas.1803505115
)). Therefore, we conducted a systematic replication study, across two laboratories, of an influential interactive FB task (the so-called ‘Sefo’ tasks by Southgate
et al
. 2010
Dev. Sci.
13
, 907–912. (
doi:10.1111/j.1467-7687.2009.00946.x
)). First, we implemented close direct replications with the original age group (17-month-olds) and compared their performance to those of 3-year-olds. Second, we designed conceptual replications with modifications and improvements regarding pragmatic ambiguities for 2-year-olds. Third, we validated the task with explicit verbal test versions in older children and adults. Results revealed the following: the original results could not be replicated, and there was no evidence for FB understanding measured by the Sefo task in any age group except for adults. Comparisons to explicit FB tasks suggest that the Sefo task may not be a sensitive measure of FB understanding in children and even underestimate their ToM abilities. The findings add to the growing replication crisis in implicit ToM research and highlight the challenge of developing sensitive, reliable and valid measures of early implicit social cognition.
Cellulose nanocrystals/graphene oxide composite for the adsorption and removal of levofloxacin hydrochloride antibiotic from aqueous solution
Authors: Tao Junhong , Yang Jie , Ma Chengxiao , Li Junfeng , Du Keqing , Wei Zhen , Chen Cuizhong , Wang Zhaoyang , Zhao Chun , Deng Xiaoya
Published: October 2020

Residual antibiotics in water are often persistent organic pollutants. The purpose of this study was to prepare a cellulose nanocrystals/graphene oxide composite (CNCs-GO) with a three-dimensional structure for the removal of the antibiotic levofloxacin hydrochloride (Levo-HCl) in water by adsorption. The scanning electron microscope, Fourier transform infrared (FT-IR), energy-dispersive spectroscopy, X-ray photoelectron spectroscopy and other characterization methods were used to study the physical structure and chemical properties of the CNCs-GO. The three-dimensional structure of the composite material rendered a high surface area and electrostatic attraction, resulting in increased adsorption capacity of the CNCs-GO for Levo-HCl. Based on the Box–Behnken design, the effects of different factors on the removal of Levo-HCl by the CNCs-GO were explored. The composite material exhibited good antibiotic adsorption capacity, with a removal percentage exceeding 80.1% at an optimal pH of 4, the adsorbent dosage of 1.0 g l
−1
, initial pollutant concentration of 10.0 mg l
−1
and contact time of 4 h. The adsorption isotherm was well fitted by the Sips model, and kinetics studies demonstrated that the adsorption process conformed to a quasi-second-order kinetics model. Consequently, the as-synthesized CNCs-GO demonstrates good potential for the effective removal of antibiotics such as levofloxacin hydrochloride from aqueous media.
Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study
Authors: Shou Keyun , Sarter Mona , de Souza Nicolas R. , de Campo Liliana , Whitten Andrew E. , Kuchel Philip W. , Garvey Christopher J. , Stadler Andreas M.
Published: October 2020

By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein–protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and Å length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na
+
-selective ionophore monensin and the K
+
-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.
On the asymptotic properties of a canonical diffraction integral
Authors: Assier Raphaël C. , Abrahams I. David
Published: October 2020

We introduce and study a new canonical integral, denoted

I

+
−

ε

, depending on two complex parameters
α
1
and
α
2
. It arises from the problem of wave diffraction by a quarter-plane and is heuristically constructed to capture the complex field near the tip and edges. We establish some region of analyticity of this integral in

C

2

, and derive its rich asymptotic behaviour as |
α
1
| and |
α
2
| tend to infinity. We also study the decay properties of the function obtained from applying a specific double Cauchy integral operator to this integral. These results allow us to show that this integral shares all of the asymptotic properties expected from the key unknown function
G
+−
arising when the quarter-plane diffraction problem is studied via a two-complex-variables Wiener–Hopf technique (see Assier & Abrahams,
SIAM J. Appl. Math.
, in press). As a result, the integral

I

+
−

ε

can be used to mimic the unknown function
G
+−
and to build an efficient ‘educated’ approximation to the quarter-plane problem.
Rayleigh–Bénard magnetoconvection with temperature modulation
Authors: Hazra Suparna , Kumar Krishna , Mitra Saheli
Published: October 2020

Floquet analysis of modulated magnetoconvection in Rayleigh–Bénard geometry is performed. A sinusoidally varying temperature is imposed on the lower plate. As Rayleigh number Ra is increased above a critical value Ra
o
, the oscillatory magnetoconvection begins. The flow at the onset of magnetoconvection may oscillate either subhar- monically or harmonically with the external modulation. The critical Rayleigh number Ra
o
varies non-monotonically with the modulation frequency
ω
for appreciable value of the modulation amplitude
a
. The temperature modulation may either postpone or prepone the appearance of magnetoconvection. The magnetoconvective flow always oscillates harmonically at larger values of
ω
. The threshold Ra
o
and the corresponding wavenumber
k
o
approach to their values for the stationary magnetoconvection in the absence of modulation (
a
 = 0), as
ω
 → ∞. Two different zones of harmonic instability merge to form a single instability zone with two local minima for higher values of Chandrasekhar’s number
Q
, which is qualitatively new. We have also observed a new type of bicritical point, which involves two different sets of harmonic oscillations. The effects of variation of
Q
and Pr on the threshold Ra
o
and critical wavenumber
k
o
are also investigated.
Unitary unfoldings of a Bose–Hubbard exceptional point with and without particle number conservation
Authors: Znojil Miloslav
Published: October 2020

The conventional non-Hermitian but

P

T

-symmetric three-parametric Bose–Hubbard Hamiltonian
H
(
γ
,
v
,
c
) represents a quantum system of
N
bosons, unitary only for parameters
γ
,
v
and
c
in a domain

D

. Its boundary

∂

D

contains an exceptional point of order
K
(EPK;
K
 = 
N
 + 1) at
c
 = 0 and
γ
 = 
v
, but even at the smallest non-vanishing parameter
c
 ≠ ~0 the spectrum of
H
(
v
,
v
,
c
) ceases to be real, i.e. the system ceases to be observable. In this paper, the question is inverted: all of the stable, unitary and observable Bose–Hubbard quantum systems are sought which would lie close to the phenomenologically most interesting EPK-related dynamical regime. Two different families of such systems are found. Both of them are characterized by the perturbed Hamiltonians

H

(
λ
)
=
H
(
v
,
v
,
0
)
+
λ
 

V

for which the unitarity and stability of the system is guaranteed. In the first family the number
N
of bosons is assumed conserved while in the second family such an assumption is relaxed. Attention is paid mainly to an anisotropy of the physical Hilbert space near the EPK extreme. We show that it is reflected by a specific, operationally realizable structure of perturbations

λ
 

V

which can be considered small.
Target competition for resources under multiple search-and-capture events with stochastic resetting
Authors: Bressloff P. C.
Published: October 2020

We develop a general framework for analysing the distribution of resources in a population of targets under multiple independent search-and-capture events. Each event involves a single particle executing a stochastic search that resets to a fixed location
x

r

at a random sequence of times. Whenever the particle is captured by a target, it delivers a packet of resources and then returns to
x

r

, where it is reloaded with cargo and a new round of search and capture begins. Using renewal theory, we determine the mean number of resources in each target as a function of the splitting probabilities and unconditional mean first passage times of the corresponding search process without resetting. We then use asymptotic PDE methods to determine the effects of resetting on the distribution of resources generated by diffusive search in a bounded two-dimensional domain with
N
small interior targets. We show that slow resetting increases the total number of resources
M
tot
across all targets provided that

∑

j
=
1

N

G
(

x

r

,

x

j

)
<
0

, where
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A case report: insights into reducing plastic waste in a microbiology laboratory
Authors: Alves Joana , Sargison Fiona A. , Stawarz Hanne , Fox Willow B. , Huete Samuel G. , Hassan Amany , McTeir Brian , Pickering Amy C.
Published: October 2020

Single-use plastics have often replaced more sustainable materials in microbiology laboratories. Keeping in mind that one of the objectives of the United Nations Sustainable Development Goals is responsible consumption and production, we wanted to document how many single-use plastic items could be saved by taking reduction and reuse approaches in a microbiology laboratory. After taking 4 weeks to document the baseline levels of single-use plastic waste being generated in our laboratory and identifying ways to reduce our reliance on them, we implemented various reduction and reuse approaches and then documented our plastic use over a 7-week period. Reduction approaches included moving to sustainable materials, such as reusable wooden sticks for patch plating and metal loops for inoculation. Reuse approaches focused on reusing plastic tubes via a chemical decontamination station and autoclaving, facilitating the reduction of single-use plastics and a decrease in the amount of waste generated. By utilizing reduction and reuse strategies, which could be implemented in other microbiology laboratories, substantial single-use plastic savings were achieved. These savings had an impact on the amount of biohazard waste being autoclaved and incinerated, as well as generating substantial cost savings for the research institute. The reductions in waste documented in this study could act as a benchmark for others wanting to implement the changes described.
Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment
Authors: Zhang Weiyan , Zhu Suting , Cheng Yuping , Ding Lijian , Li Shengying , Peng Nan , He Shan
Published: October 2020

A Gram-stain-negative, rod-shaped, motile and strictly aerobic bacterium, designated LHK132T, was isolated from a mangrove sediment sample collected in Haikou, Hainan Province, PR China. Strain LHK132T was able to grow at temperatures of 10–45 °C, at salinities of 0–7.0 % (w/v) and at pH 6.0–9.0. Catalase and oxidase activities, H2S production, urease and methyl red reaction were positive. Indole, nitrate reduction, hydrolysis of gelatin, starch, casein and Tweens 20, 40, 60 and 80 were negative. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1
 ω7c and/or C16 : 1
 ω6c). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. According to 16S rRNA gene sequence analysis, strain LHK132T had 98.3, 97.5, 97.4, 97.2 and 97.1% similarities to

Rheinheimera soli

BD-d46T,

Rheinheimera sediminis

YQF-1T,

Rheinheimera tangshanensis

JA3-B52T,

Rheinheimera mesophila

IITR-13T and

Rheinheimera arenilitoris

J-MS1T, respectively. Phylogenetic analyses indicated that strain LHK132T formed a distinct lineage with

R. soli

BD-d46T within the genus

Rheinheimera

. The average nucleotide identity and digital DNA–DNA hybridization values between strain LHK132T and related species of the genus

Rheinheimera

were well below the thresholds for species delineation. The DNA G+C content was 46.7 mol%. On the basis of its phenotypic, chemotaxonomic and genotypic data, strain LHK132T is considered a representative of a novel species in the genus

Rheinheimera

, for which the name Rheinheimera mangrovi sp. nov. is proposed. The type strain is LHK132T (=KCTC 62580T=MCCC 1K03529T).
Novel Mutations in Human Luteinizing Hormone Beta Subunit Related to Polycystic Ovary Syndrome among Sudanese Women
Authors: Essa Nidal , Osman Suliman , Jemaah Salah , Hassan Mohamed A. , Eltayeb Rashid
Published: October 2020

Introduction

Polycystic ovary syndrome (PCOS) is a common disorder that is not fully understood. Multiple hormonal and metabolic factors impact on disease pathophysiology resulting in various phenotypic characteristics among the PCOS population. Luteinizing hormone beta subunit (LHB) (protein ID P01229) is mapped on (chr19p13.3) and consists of three exons. Luteinizing hormone (LH) has a central role in stimulation ovarian steroidogenesis, in particular androgen production, and the promotion of ovulation.

Objectives

To determine if genetic variations of LHB are associated with PCOS among Sudanese families.

Methods

A prospective laboratory based cross-sectional study to examine genetic mutations in LHB that associate with PCOS in families (cases; n=35 families, 90 females and controls; n=11 families, 30 females) in Khartoum State, Sudan. Quantitative enzyme linked immuno-sorbent assay (ELISA) and polymerase chain reaction (PCR) with Sanger sequencing were used to analyze biochemical parameters and detect polymorphisms. Protein structure and function bioinformatics analysis was conducted using standard software.

Results

PCOS cases had significantly different biochemical parameters from the controls (LH: p<0.001; testosterone: p<0.001; fasting glucose: p=0.02; insulin: p=0.01; triglycerides: p=0.03; total cholesterol: p<0.001; high density lipoprotein (HDL): p=0.012;low density lipoprotein (LDL): p<0.001). There were no differences in follicle stimulating hormone (FSH) (p=0.984) or prolactin (p=0.068). Sanger sequencing revealed 5 single nucleotide polymorphisms (rs5030775, A18T; rs746167425, R22K; rs1800447, W28R; rs35270001, H30R; and rs34349826, I35T) located on (exon 2) of LHB gene that were statistically correlated with serum LH, Testosterone and insulin levels among PCOS families.

Conclusion

This is the first molecular family-based study in Sudan exploring the genetics of the LHB gene in women manifesting PCOS. These novel mutations give further information about the role of genetic inheritance and may explain some of the altered ovarian function and responses in women with PCOS.
Association between TM6SF2 rs58542926 T/C gene polymorphism and significant liver fibrosis: A meta-analysis
Authors: Mei Ting-Ting , Zhang Jing , Tang Shan , Guo Hai-Qing , Wei Xin-Huan , Zhang Wen-Yan , Liu Ya-Li , Liang Shan , Fan Zuo-Peng , Ma Li-Xia , Qiu Li-Xia , Liu Yi-Rong , Yu Hai-Bin
Published: October 2020

Aim

To further explore the association between Transmembrane 6 superfamily member 2 (TM6SF2) rs58542926 T/C gene polymorphism and hepatic fibrosis.

Materials and Methods

In this study the MEDLINE, PubMed, EMBASE, and CENTRAL databases were queried from inception to March 21, 2020. According to inclusion and exclusion criteria, case-control studies assessing the relationship between TM6SF2 rs58542926 T/C gene polymorphism and significant liver fibrosis were selected. NOS scale was used to evaluate the included literature. Stata 12.0 software was used for data analysis.

Results

In this meta-analysis,a total of 7 articles, including 2286 patients were included. Statistical analysis showed that the TM6SF2 gene polymorphism was associated with significant liver fibrosis in the allele contrast, recessive dominant models (T vs. C, OR=1.292, 95%CI 1.035-1.611, P=0.023; TT vs. CT+CC, OR=2.829, 95%CI 1.101-7.267, P=0.031). No significant publication bias was found after Egger’s test.

Conclusion

The present findings suggest that the TT genotype and T gene of TM6SF2 rs58542926 T/C gene polymorphism are associated with susceptibility to significant hepatic fibrosis.
COVID-19 behavioural insights study: Preliminary findings from Finland, April-May, 2020
Authors: Cristea Veronica , Dub Timothee , Luomala Oskari , Sivelä Jonas
Published: October 2020

The COVID-19 monitoring behavioural insights study was conducted from April-May 2020 in Finland. Respondents reported feeling confident protecting themselves against COVID-19 infection. Worries shifted from overloading the health system (mean value 5.5 [95% CI: 5.4-5.6]) to mental health concerns (mean value 5.3 [95% CI 5.2-5.4]). Maintaining physical distancing from families and friends decreased by 7% and 6%. Respondents mostly agreed that if a vaccine would become available, they would get it. The decrease in acceptance of recommended measures needs further analysis, but current results provide evidence to support the response.

Key points

Currently limited information available on the complex interaction between epidemiology, media attention, pandemic control measures, risk perception and compliance with public health measures.

Despite the relatively high risk perception of a possible infection with COVID-19, we observed a steady decrease in adherence to public health measures.

Throughout the study, information-seeking behaviour shifted.

We observed a decrease in acceptance among the participants in regards to avoiding physical contact.
Histopathological findings in COVID-19 cases: A Systematic Review
Authors: Hammoud Hamed , Bendari Ahmed , Bendari Tasneem , Bougmiza Iheb
Published: October 2020

Background

The current COVID-19 pandemic is considered one of the most serious public health crisis over the last few decades. Although the disease can result in diverse, multiorgan pathology, there have been very few studies addressing the postmortem pathological findings of the cases. Active autopsy amid this pandemic could be an essential tool for diagnosis, surveillance, and research.

Objective

To provide a total picture of the SARS-CoV-2 histopathological features of different body organs through a systematic search of the published literature.

Methods

A systematic search of electronic databases (PubMed, ScienceDirect, Google scholar, Medrxiv & Biorxiv) was carried out from December 2019 to August, 15th2020, for journal articles of different study designs reporting postmortem pathological findings in COVID-19 cases. PRISMA guidelines were used for reporting the review.

Results

A total of 50 articles reporting 430 cases were included in our analysis. Postmortem pathological findings were reported for different body organs, pulmonary system (42 articles), cardiovascular system ( 23 articles), hepatobiliary system (22 articles), kidney (16 articles), spleen, and lymph nodes (12 articles), and central nervous system (7 articles). In lung samples, diffuse alveolar damage (DAD) was the most commonly reported findings in 239 cases (84.4%). Myocardial hypertrophy (87 cases by 51.2%), arteriosclerosis (121 cases by 62%), and steatosis ( 118 cases by 59.3%) were the most commonly reported pathological findings in the heart, kidney, and hepatobiliary system respectively.

Conclusion

Autopsy examination as an investigation tool could help in a better understanding of SARS-CoV-2 pathophysiology, diagnosis, management, and subsequently improving patient care.