bluuebunny/crossref_metadata_2025_split huggingface dataset:
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 .
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

ABSTRACT:

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.
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

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

IntroductionPolycystic 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.ObjectivesTo determine if genetic variations of LHB are associated with PCOS among Sudanese families.MethodsA 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.ResultsPCOS 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.ConclusionThis 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

AbstractAimTo further explore the association between Transmembrane 6 superfamily member 2 (TM6SF2) rs58542926 T/C gene polymorphism and hepatic fibrosis.Materials and MethodsIn 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.ResultsIn 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.ConclusionThe 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

AbstractThe 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 pointsCurrently 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

AbstractBackgroundThe 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.ObjectiveTo provide a total picture of the SARS-CoV-2 histopathological features of different body organs through a systematic search of the published literature.MethodsA 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.ResultsA 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.ConclusionAutopsy examination as an investigation tool could help in a better understanding of SARS-CoV-2 pathophysiology, diagnosis, management, and subsequently improving patient care.
Awareness, Perception and Practice of COVID 19 Prevention among Residents of a State in the South-South Region of Nigeria: Implications for Public Health Control Efforts
Authors: Owhonda Golden , Maduka Omosivie , Nwadiuto Ifeoma , Tobin-West Charles , Azi Esther , Ojimah Chibianotu , Alasia Datonye , Olofinuka Ayo-Maria , Agala Vetty , Paul John Nwolim , Nria Doris , Okafor Chinenye , Ndekwu Ifeoma , Opara Chikezie , Newsom Chris 
Published: October 2020

AbstractBackgroundThis research explored awareness, perception, and practice of COVID 19 prevention among residents of communities in all the local government areas (districts) in Rivers State during the early stages of the pandemic response.DesignThis was a descriptive cross-sectional survey which employed an interviewer-administered four-page questionnaire built into the Open Data Kit application for android phones. Knowledge and practice scores were computed by scoring every correct response/action as 1 and wrong responses as 0. Knowledge was graded as excellent for scores of ≥80%, good for scores of 50-79% and poor for scores of <50%. Respondents who washed all critical parts of the hand were categorized as having correct handwashing practice.SettingRivers State in the South-South region of Nigeria had recorded over 2000 cases of COVID 19 as of 18th August 2020, ranking 5th among the high burden states in Nigeria. As with any epidemic of an infectious nature, panic, fear, and misconceptions are rife. Risk communication utilizes multi-faceted activities geared towards facilitating correct and consistent knowledge and prevention practice.ParticipantsStudy involved 1,294 adult community residents in the 23 districts of the state.ResultsThe respondents were aged between 18 and 80 years with average age of 39.6 years (SD = 11.9 years). A total of 710 (54.9%) were male, 476 (36.8%) were unemployed with 685 (52.9%) having secondary education. Almost all respondents 1,271 (98.2%) had heard about COVID 19. The three most common sources of information about COVID 19 were radio jingles 1102 (86.7%), television adverts 940 (74.0%) and announcements in Church 612 (48.2%). Overall, 608 (47.0%) of the respondents had poor knowledge of COVID 19. About 1167 (90.2%) of the respondents who were aware of COVID 19 acknowledged that COVID 19 is a problem in the state while 443 (34.9%) respondents believed they were unlikely contract the virus. Only 505 (39.0%) of the respondents washed all critical parts of the hand correctly.ConclusionsRisk communication interventions during pandemics need to be based on an understanding of the gaps in knowledge, attitude, perceptions, and practice. Broadcast media has a pivotal role to play in risk communication for behaviour change for the control of current and future epidemics in this population.