Phase Variants Research Articles

Loss of glycerol catabolism confers carbon-source-dependent artemisinin resistance in Mycobacterium tuberculosis.

In view of the urgent need for new antibiotics to treat human infections caused by multidrug-resistant pathogens, drug repurposing is gaining strength due to the relatively low research costs and shorter clinical trials. Such is the case of artemisinin, an antimalarial drug that has recently been shown to display activity against Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To gain insight into how Mtb is affected by artemisinin, we used RNAseq to assess the impact of artemisinin on gene expression profiles, revealing the induction of several efflux pumps and the KstR2 regulon. To anticipate the artemisinin resistance-conferring mutations that could arise in clinical Mtb strains, we performed an in vitro evolution experiment in the presence of lethal concentrations of artemisinin. We obtained artemisinin-resistant isolates displaying different growth kinetics and drug phenotypes, suggesting that resistance evolved through different pathways. Whole-genome sequencing of nine isolates revealed alterations in the glpK and glpQ1 genes, both involved in glycerol metabolism, in seven and one strains, respectively. We then constructed a glpK mutant and found that loss of glpK increases artemisinin resistance only when glycerol is present as a major carbon source. Our results suggest that mutations in glycerol catabolism genes could be selected during the evolution of resistance to artemisinin when glycerol is available as a carbon source. These results add to recent findings of mutations and phase variants that reduce drug efficacy in carbon-source-dependent ways.

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs

BackgroundMetagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read.ResultsHere, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3–40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes.ConclusionPenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities.C22dm7AjjRZTtiuc33W1snVideo

Phase variable colony variants are conserved across Gardnerella spp. and exhibit different virulence-associated phenotypes.

The Gardnerella genus, comprising at least 13 species, is associated with the polymicrobial disorder bacterial vaginosis (BV). However, the details of BV pathogenesis are poorly defined, and the contributions made by individual species, including Gardnerella spp., are largely unknown. We report here that colony phenotypes characterized by size (large and small) and opacity (opaque and translucent) are phase variable and are conserved among all tested Gardnerella strains, representing at least 10 different species. With the hypothesis that these different variants could be an important missing piece to the enigma of how BV develops in vivo, we characterized their phenotypic, proteomic, and genomic differences. Beyond increased colony size, large colony variants showed reduced vaginolysin secretion and faster growth rate relative to small colony variants. The ability to inhibit the growth of Neisseria gonorrhoeae and commensal Lactobacillus species varied by strain and, in some instances, differed between variants. Proteomics analyses indicated that 127-173 proteins were differentially expressed between variants. Proteins with increased expression in large variants of both strains were associated with amino acid and protein synthesis and protein folding, whereas those increased in small variants were related to nucleotide synthesis, phosphate transport, ABC transport, and glycogen breakdown. Furthermore, whole genome sequencing analyses revealed an abundance of genes associated with variable homopolymer tracts, implicating slipped strand mispairing in Gardnerella phase variation and illuminating the potential for previously unrecognized heterogeneity within clonal populations. Collectively, these results suggest that phase variants may be primed to serve different roles in BV pathogenesis.IMPORTANCEBacterial vaginosis is the most common gynecological disorder in women of childbearing age. Gardnerella species are crucial to the development of this dysbiosis, but the mechanisms involved in the infection are not understood. We discovered that Gardnerella species vary between two different forms, reflected in bacterial colony size. A slow-growing form makes large amounts of the toxin vaginolysin and is better able to survive in human cervix tissue. A fast-growing form is likely the one that proliferates to high numbers just prior to symptom onset and forms the biofilm that serves as a scaffold for multiple BV-associated anaerobic bacteria. Identification of the proteins that vary between different forms of the bacteria as well as those that vary randomly provides insight into the factors important for Gardnerella infection and immune avoidance.

Low-loss vanadium dioxide-enabled mmWave tunable reflective electromagnetic surface with complementary unit cells for wave manipulation

This study presents a novel implementation of vanadium dioxide (VO2) phase change material in an electromagnetic (EM) surface with beam steering capabilities. For the first time, we present the design, fabrication, and measurement of a globally actuated, VO2-based beamforming reflective EM surface. We propose a design featuring complementary unit cells that enable beam steering with a single excitation, marking a pioneering use of low-loss VO2 in creating a complementary EM surface for the mmWave band. The unit cells incorporating VO2 exhibit low-loss characteristics, with −0.92 and −1.9 dB in the hot state and −0.49 and −0.25 dB in the cold state, respectively. We incorporate both positive and negative phase variants alongside two temperature-independent phase unit cells. The complementary design enables us to utilize two beam operating states, effectively exploiting the otherwise unused cold state. We experimentally demonstrated beamforming at ±5° and ±10° from the broadside. In the case of ±10°, the measured gains at 35 GHz in the cold and hot states were 19.4 and 20.3 dB, respectively, which aligned well with the simulated gains of 20.9 and 21.5 dB. Manipulation of the electromagnetic wave direction with a single excitation has the potential for imaging, sensing, and communication applications. The complementary unit cell design methodology can be further adapted for mmWave beamforming, absorbing, and cloaking reconfigurable EM surfaces. Furthermore, the use of VO2 can be extended up to sub-THz frequencies due to the wideband, low-loss characteristics compared with conventional reconfigurable devices, such as PIN diodes or MEMS switches.

Effects of shear strain on shock response in single crystal iron

With large-scale non-equilibrium molecular dynamics simulations and in situ x-ray diffraction analysis, we conducted a systematic investigation into the effects of pre-existing shear strain (γxy) on the shock response of single crystal iron. Our findings reveal significant effects of γxy on the deformation of the crystal structure during shock loading, leading to noticeable alterations in the propagation of shock waves. Specifically, during the elastic stage, the presence of γxy results in a reduction of shock strength, consequently diminishing the magnitude of elastic lattice strain (εe). In the plastic stage, γxy stimulates the α–ε phase transformation, and structure deformation undergoes a transition from the sequential activity of dislocation-to-transformation to the synchronous activity of dislocation and transformation. This transition inhibits the propagation of plastic waves and consequently broadens the elastic regime. Additionally, the introduction of γxy activates different slip systems, as it alters the corresponding resolved shear stress. Concurrently, the presence of γxy triggers the activation of different high-pressure phase variants. Our investigation sheds light on the fundamental physics of iron under shock compression and the influence of pre-existing shear strain on its behavior.

Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield.

Rare or novel missense variants in large genes such as TTN and NEB are frequent in the general population, which hampers the interpretation of putative disease-causing biallelic variants in patients with sporadic neuromuscular disorders. Often, when the first initial genetic analysis is performed, the reconstructed haplotype, i.e. phasing information of the variants is missing. Segregation analysis increases the diagnostic turnaround time and is not always possible if samples from family members are lacking. To overcome this difficulty, we investigated how well the linked-read technology succeeded to phase variants in these large genes, and whether it improved the identification of structural variants. Linked-read sequencing data of nemaline myopathy, distal myopathy, and proximal myopathy patients were analyzed for phasing, single nucleotide variants, and structural variants. Variant phasing was successful in the large muscle genes studied. The longest continuous phase blocks were gained using high-quality DNA samples with long DNA fragments. Homozygosity increased the number of phase blocks, especially in exome sequencing samples lacking intronic variation. In our cohort, linked-read sequencing added more information about the structural variation but did not lead to a molecular genetic diagnosis. The linked-read technology can support the clinical diagnosis of neuromuscular and other genetic disorders.

Identification of the Vulnerability of Atherosclerotic Plaques by a Photoacoustic/Ultrasonic Dual-Modal cRGD Nanomolecular Probe.

To explore the feasibility of using cRGD-GNR-PFP-NPs to assess plaque vulnerability in an atherosclerotic plaque mouse model by dual-modal photoacoustic/ultrasonic imaging. A nanomolecular probe containing gold nanorods (GNRs) and perfluoropentane (PFP) coated with the cyclic Arg-Gly-Asp (cRGD) peptide were prepared by double emulsion solvent evaporation and carbodiimide methods. The morphology, particle size, potential, cRGD conjugation and absorption features of the nanomolecular probe were characterized, along with its in vitro phase transformation and photoacoustic/ultrasonic dual-modal imaging properties. In vivo fluorescence imaging was used to determine the distribution of cRGD-GNR-PFP-NPs in vivo in apolipoprotein E-deficient (ApoE-/-) atherosclerotic plaque model mice, the optimal imaging time was determined, and photoacoustic/ultrasonic dual-modal molecular imaging of integrin αvβ3 expressed in atherosclerotic plaques was performed. Pathological assessments verified the imaging results in terms of integrin αvβ3 expression and plaque vulnerability. cRGD-GNR-PFP-NPs were spherical with an appropriate particle size (average of approximately 258.03±6.75 nm), a uniform dispersion, and a potential of approximately -9.36±0.53 mV. The probe had a characteristic absorption peak at 780~790 nm, and the surface conjugation of the cRGD peptide reached 92.79%. cRGD-GNR-PFP-NPs were very stable in the non-excited state but very easily underwent phase transformation under low-intensity focused ultrasound (LIFU) and had excellent photoacoustic/ultrasonic dual-modal imaging capability. Mice fed a high-fat diet for 20 weeks had obvious hyperlipidemia with larger, more vulnerable plaques. These plaques could be specifically targeted by cRGD-GNR-PFP-NPs as determined by in vivo fluorescence imaging, and the enrichment of nanomolecular probe increased with the increasing of plaque vulnerability; the photoacoustic/ultrasound signals of the plaques in the high-fat group were stronger. The pathological assessments were in good agreement with the cRGD-GNR-PFP-NPs plaque accumulation, integrin αvβ3 expression and plaque vulnerability results. A phase variant photoacoustic/ultrasonic dual-modal cRGD nanomolecular probe was successfully prepared and can be used to identify plaque vulnerability safely and effectively.

Visualization of therapeutic intervention for acute liver injury using low-intensity pulsed ultrasound-responsive phase variant nanoparticles.

Acute liver injury (ALI) is a highly fatal condition characterized by sudden massive necrosis of liver cells, inflammation, and impaired coagulation function. Currently, the primary clinical approach for managing ALI involves symptom management based on the underlying causes. The association between excessive reactive oxygen species originating from macrophages and acute liver injury is noteworthy. Therefore, we designed a novel nanoscale phase variant contrast agent, denoted as PFP@CeO2@Lips, which effectively scavenges reactive oxygen species, and enables visualization through low intensity pulsed ultrasound activation. The efficacy of the nanoparticles in scavenging excess reactive oxygen species from RAW264.7 and protective AML12 cells has been demonstrated through in vitro and in vivo experiments. Additionally, these nanoparticles have shown a protective effect against LPS/D-GalN attack in C57BL/6J mice. Furthermore, when exposed to LIPUS irritation, the nanoparticles undergo liquid-gas phase transition and enable ultrasound imaging.

Mechanical properties anisotropy of Ti−6Al−4V alloy fabricated by β forging

The anisotropy of tensile properties and fracture toughness of Ti−6Al−4V (Ti64) alloy fabricated by β forging was investigated. In order to evaluate anisotropic mechanical properties, the microstructure and crystallographic texture of billets with different orientations were characterized, and the influence of sampling direction on tensile properties and fracture toughness was studied. The results reveal that the prior β grains of Ti64 billet display pan-cake-type characteristics. At room temperature, the alloy is mainly composed of α phase, and several α phase variants produced by β→α phase transformation decrease the α texture intensity. The anisotropy of mechanical properties is affected by prior β grain morphology and the slip activation related to α texture. The initiation toughness was obtained by the J-integral resistance curve method. The initiation toughness was divided into intrinsic and extrinsic toughness by calculation. The anisotropy of intrinsic toughness is mainly attributed to the size of crack tip plastic zone, which is affected by prior β grain morphology. In contrast, the extrinsic toughness is affected by zigzag degree of crack, which is mainly influenced by α lamellae and colonies.

Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae.

Despite enabling Streptococcus pneumoniae to acquire antibiotic resistance and evade vaccine-induced immunity, transformation occurs at variable rates across pneumococci. Phase variants of isolate RMV7, distinguished by altered methylation patterns driven by the translocating variable restriction-modification (tvr) locus, differed significantly in their transformation efficiencies and biofilm thicknesses. These differences were replicated when the corresponding tvr alleles were introduced into an RMV7 derivative lacking the locus. RNA-seq identified differential expression of the type 1 pilus, causing the variation in biofilm formation, and inhibition of competence induction in the less transformable variant, RMV7domi. This was partly attributable to RMV7domi's lower expression of ManLMN, which promoted competence induction through importing N-acetylglucosamine. This effect was potentiated by analogues of some proteobacterial competence regulatory machinery. Additionally, one of RMV7domi's phage-related chromosomal island was relatively active, which inhibited transformation by increasing expression of the stress response proteins ClpP and HrcA. However, HrcA increased competence induction in the other variant, with its effects depending on Ca2+ supplementation and heat shock. Hence the heterogeneity in transformation efficiency likely reflects the diverse signalling pathways by which it is affected. This regulatory complexity will modulate population-wide responses to synchronising quorum sensing signals to produce co-ordinated yet stochastic bet hedging behaviour.

Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function

Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.

Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis.

Bacterial virulence, persistence and defence are affected by epigenetic modifications, including DNA methylation. Solitary DNA methyltransferases modulate a variety of cellular processes and influence bacterial virulence; as part of a restriction-modification (RM) system, they act as a primitive immune system in methylating the own DNA, while unmethylated foreign DNA is restricted. We identified a large family of type II DNA methyltransferases in Metamycoplasma hominis, comprising six solitary methyltransferases and four RM systems. Motif-specific 5mC and 6mA methylations were identified with a tailored Tombo analysis on Nanopore reads. Selected motifs with methylation scores >0.5 fit with the gene presence of DAM1 and DAM2, DCM2, DCM3, and DCM6, but not for DCM1, whose activity was strain-dependent. The activity of DCM1 for CmCWGG and of both DAM1 and DAM2 for GmATC was proven in methylation-sensitive restriction and finally for recombinant rDCM1 and rDAM2 against a dam-, dcm-negative background. A hitherto unknown dcm8/dam3 gene fusion containing a (TA) repeat region of varying length was characterized within a single strain, suggesting the expression of DCM8/DAM3 phase variants. The combination of genetic, bioinformatics, and enzymatic approaches enabled the detection of a huge family of type II DNA MTases in M. hominis, whose involvement in virulence and defence can now be characterized in future work.

Haplotyping Using Long-Range PCR and Nanopore Sequencing to Phase Variants: Lessons Learned From the ABCA4 Locus

Short-read next-generation sequencing has revolutionized our ability to identify variants underlying inherited diseases; however, it does not allow the phasing of variants to clarify their diagnostic interpretation. The advent of widespread, increasingly accurate long-read sequencing has opened up new applications not currently available through short-read next-generation sequencing. One such use is the ability to phase variants to clarify their diagnostic interpretation and to investigate the increasingly prevalent role of cis-acting variants in the pathogenesis of the inherited disease, so-called complex alleles. Complex alleles are becoming an increasingly prevalent part of the study of genes associated with inherited diseases, for example, in ABCA4-related diseases. We sought to establish a cost-effective method to phase contiguous segments of the 130-kb ABCA4 locus by long-read sequencing of overlapping amplification products. Using the comprehensively characterized CEPH sample, NA12878, we verified the accuracy and robustness of our assay. However, in-field assessment of its utility using clinical test cases was hampered by the paucity and distribution of identified variants and by PCR chimerism, particularly where the number of PCR cycles was high. Despite this, we were able to construct robust phase blocks of up to 94.9 kb, representing 73% of the ABCA4 locus. We conclude that, although haplotype analysis of variants located within discrete amplification products was robust and informative, the stitching together of larger phase blocks using overlapping single-molecule reads remained practically challenging.

Calling and Phasing of Single-Nucleotide and Structural Variants of the LDLR Gene Using Oxford Nanopore MinION

The LDLR locus has clinical significance for lipid metabolism, Mendelian familial hypercholesterolemia (FH), and common lipid metabolism-related diseases (coronary artery disease and Alzheimer's disease), but its intronic and structural variants are underinvestigated. The aim of this study was to design and validate a method for nearly complete sequencing of the LDLR gene using long-read Oxford Nanopore sequencing technology (ONT). Five PCR amplicons from LDLR of three patients with compound heterozygous FH were analyzed. We used standard workflows of EPI2ME Labs for variant calling. All rare missense and small deletion variants detected previously by massively parallel sequencing and Sanger sequencing were identified using ONT. One patient had a 6976 bp deletion (exons 15 and 16) that was detected by ONT with precisely located breakpoints between AluY and AluSx1. Trans-heterozygous associations between mutation c.530C>T and c.1054T>C, c.2141-966_2390-330del, and c.1327T>C, and between mutations c.1246C>T and c.940+3_940+6del of LDLR, were confirmed. We demonstrated the ability of ONT to phase variants, thereby enabling haplotype assignment for LDLR with personalized resolution. The ONT-based method was able to detect exonic variants with the additional benefit of intronic analysis in one run. This method can serve as an efficient and cost-effective tool for diagnosing FH and conducting research on extended LDLR haplotype reconstruction.

Phase transition and birefringence studies on some ferroelectric liquid crystals

In the present studies the homologous series of hydroxy phenylamino methyl phenoxy benzoate liquid crystals (n = 8,9 and m = 6) are used. The temperature variation of density is measured. Using density data the phase variants in the compounds are identified. All the compounds exhibit first-order phase transitions. By Newton rings method the birefringence is measured directly in smectic and nematic phases. The advantages of the newton ring technique are presented over the conventional methods for the determination of orientational order parameter. The orientational order parameter attained by the newton rings scheme is equated through the literature data, the results are discussed.

Application of Long-Read Nanopore Sequencing to the Search for Mutations in Hypertrophic Cardiomyopathy.

Increasing evidence suggests that both coding and non-coding regions of sarcomeric protein genes can contribute to hypertrophic cardiomyopathy (HCM). Here, we introduce an experimental workflow (tested on four patients) for complete sequencing of the most common HCM genes (MYBPC3, MYH7, TPM1, TNNT2, and TNNI3) via long-range PCR, Oxford Nanopore Technology (ONT) sequencing, and bioinformatic analysis. We applied Illumina and Sanger sequencing to validate the results, FastQC, Qualimap, and MultiQC for quality evaluations, MiniMap2 to align data, Clair3 to call and phase variants, and Annovar's tools and CADD to assess pathogenicity of variants. We could not amplify the region encompassing exons 6-12 of MYBPC3. A higher sequencing error rate was observed with ONT (6.86-6.92%) than with Illumina technology (1.14-1.35%), mostly for small indels. Pathogenic variant p.Gln1233Ter and benign polymorphism p.Arg326Gln in MYBPC3 in a heterozygous state were found in one patient. We demonstrated the ability of ONT to phase single-nucleotide variants, enabling direct haplotype determination for genes TNNT2 and TPM1. These findings highlight the importance of long-range PCR efficiency, as well as lower accuracy of variant calling by ONT than by Illumina technology; these differences should be clarified prior to clinical application of the ONT method.

A New Nanoscale Ultrasound Phase-Variant Contrast Agent for Phase Variant Low-Frequency Medical Ultrasound Imaging That Can Scavenge Reactive Oxygen Species

Nanoscale phase-variant ultrasound contrast agents have attracted the interest of many researchers. However, it is a challenge to design nanobubbles that are activated by low-frequency medical ultrasound that do not cause damage to normal tissues. In this study, we designed a new type of nanoparticle consisting of perfluoropentane and iron polyphthalocyanine loaded into liposomes. These nanoparticles can be activated by a low-frequency medical ultrasound imager at a frequency of 5 MHz for ultrasound imaging and clear reactive oxygen species at a rate of more than 50%. This ability to scavenge excess reactive oxygen species can alleviate the damage these species cause and protect macrophages. Moreover, these nanoparticles can effectively enhance ultrasound contrast imaging for real-time visualization in the diagnosis and treatment of diseases.

Supramolecular ferroelectric nematic materials

ABSTRACT The discovery of a new nematic phase variant with polar order and ferroelectricity, the NF phase, is a significant milestone in soft matter research. Herein we describe the preparation of hydrogen-bonded complexes between 4-(2,4-dimethoxybenzoyloxy)benzoic acid and either 4-nitropyridine or 3-fluoro-4-nitropyridine, these being analogous in structure to the archetypal NF material RM734. Complexes were isolated using a semi-automated process we term Machine Vision Aided Crystallisation. We find these complexes exhibit classical and polar (NF) nematic phases despite the large reduction in electric dipole moment that results from swapping a phenyl ring for 4-pyridyl. DFT calculations support the hypothesis that the onset of polar order is not simply a product of electric dipole magnitude, but rather results from more subtle interactions between regions of opposing electrostatic potential.

The impact of Mendelian sleep and circadian genetic variants in a population setting.

Rare variants in ten genes have been reported to cause Mendelian sleep conditions characterised by extreme sleep duration or timing. These include familial natural short sleep (ADRB1, DEC2/BHLHE41, GRM1 and NPSR1), advanced sleep phase (PER2, PER3, CRY2, CSNK1D and TIMELESS) and delayed sleep phase (CRY1). The association of variants in these genes with extreme sleep conditions were usually based on clinically ascertained families, and their effects when identified in the population are unknown. We aimed to determine the effects of these variants on sleep traits in large population-based cohorts. We performed genetic association analysis of variants previously reported to be causal for Mendelian sleep and circadian conditions. Analyses were performed using 191,929 individuals with data on sleep and whole-exome or genome-sequence data from 4 population-based studies: UK Biobank, FINRISK, Health-2000-2001, and the Multi-Ethnic Study of Atherosclerosis (MESA). We identified sleep disorders from self-report, hospital and primary care data. We estimated sleep duration and timing measures from self-report and accelerometery data. We identified carriers for 10 out of 12 previously reported pathogenic variants for 8 of the 10 genes. They ranged in frequency from 1 individual with the variant in CSNK1D to 1,574 individuals with a reported variant in the PER3 gene in the UK Biobank. No carriers for variants reported in NPSR1 or PER2 were identified. We found no association between variants analyzed and extreme sleep or circadian phenotypes. Using sleep timing as a proxy measure for sleep phase, only PER3 and CRY1 variants demonstrated association with earlier and later sleep timing, respectively; however, the magnitude of effect was smaller than previously reported (sleep midpoint ~7 mins earlier and ~5 mins later, respectively). We also performed burden tests of protein truncating (PTVs) or rare missense variants for the 10 genes. Only PTVs in PER2 and PER3 were associated with a relevant trait (for example, 64 individuals with a PTV in PER2 had an odds ratio of 4.4 for being "definitely a morning person", P = 4x10-8; and had a 57-minute earlier midpoint sleep, P = 5x10-7). Our results indicate that previously reported variants for Mendelian sleep and circadian conditions are often not highly penetrant when ascertained incidentally from the general population.

COVID-19 trends, public restrictions policies and vaccination status by economic ranking of countries: a longitudinal study from 110 countries

BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has transitioned to a third phase and many variants have been originated. There has been millions of lives loss as well as billions in economic loss. The morbidity and mortality for COVID-19 varies by country. There were different preventive approaches and public restrictions policies have been applied to control the COVID-19 impacts and usually measured by Stringency Index. This study aimed to explore the COVID-19 trend, public restriction policies and vaccination status with economic ranking of countries.MethodsWe received open access data from Our World in Data. Data from 210 countries were available. Countries (n = 110) data related to testing, which is a key variable in the present study, were included for the analysis and remaining 100 countries were excluded due to incomplete data. The analysis period was set between January 22, 2020 (when COVID-19 was first officially reported) and December 28, 2021. All analyses were stratified by year and the World Bank income group. To analyze the associations among the major variables, we used a longitudinal fixed-effects model.ResultsOut of the 110 countries included in our analysis, there were 9 (8.18%), 25 (22.72%), 31 (28.18%), and 45 (40.90%) countries from low income countries (LIC), low and middle income countries (LMIC), upper middle income countries (UMIC) and high income countries (HIC) respectively. New case per million was similar in LMIC, UMIC and HIC but lower in LIC. The number of new COVID-19 test were reduced in HIC and LMIC but similar in UMIC and LIC. Stringency Index was negligible in LIC and similar in LMIC, UMIC and HIC. New positivity rate increased in LMIC and UMIC. The daily incidence rate was positively correlated with the daily mortality rate in both 2020 and 2021. In 2020, Stringency Index was positive in LIC and HIC but a negative association in LMIC and in 2021 there was a positive association between UMIC and HIC. Vaccination coverage did not appear to change with mortality in 2021.ConclusionNew COVID-19 cases, tests, vaccinations, positivity rates, and Stringency indices were low in LIC and highest in UMIC. Our findings suggest that the available resources of COVID-19 pandemic would be allocated by need of countries; LIC and UMIC.