Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes.

Premise: Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods: The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results: Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion: While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.

Inferior vena cava thrombosis attributable to hyperhomocysteinemia: A case report from Nepal.

Inferior vena cava thrombosis (IVCT) is a rare complication of deep vein thrombosis (DVT) in the legs. The etiology of IVC thrombosis can be divided into genetic versus nongenetic (environmental/acquired) etiological factors found in Virchow's triad of stasis, endothelial injury, and hypercoagulability. Hyperhomocysteinemia is a rare risk factor for venous thromboembolism and atherosclerotic disease. Hence, very few cases have been described to date to knowledge. A case of a 78-year-old hypertensive man who presented with hyperhomocysteinemia-induced DVT of the left leg extending toward an anatomically normal IVC is discussed in the report.

The Impact of Basic Police Training and Scale Diet on Body Composition and Aerobic Performance of Nepal Police Officers Trainees.

INTRODUCTION: Executing their daily duties, police officers are expected to perform complex, physically demanding activities, often at maximal levels of exertion. Given these criteria, training must be rigorous enough to ensure that when trainees graduate, they are competent in their response to crisis and flexible enough to sustain this for the span of their career. The present study aimed to determine the impact of scale diet and physical training (SDPT) on body composition and aerobic performance among Nepal police officer trainees. METHOD: We conducted a cross-sectional analytic study among 570 Nepal Police recruits from Nepal Police Academy of Butwal and Kathmandu. Null hypothesis was created followed by an alternative hypothesis. Alpha (1 - ?) for the above-mentioned study design were set. Parametric statistical analysis was done with criteria set for acceptance or rejection of the null hypothesis. We collected the data from the field as per Nepal police basic exercise and diet  protocol to determine the effect of physical training and scale diet on body composition and aerobic performance. We enrolled all the recruits  from March to May, 2019 who met the eligibility criteria in the study. We used Microsoft Excel 2013 for data entry and R program (version: 4.0.3) for statistical analysis.  Results:There was a significant rise in aerobic performance (4.51 ± 3.39 ml/kg/min) and remarkable reduction in body fat (-4.49 ± 2.33 %) and Body Mass Index (-0.433 ± 1.00 kg/m2) after SDPT among participants with normal BMI at the time of recruitment. Body fat was significantly reduced (-4.36 ± 2.3%) and aerobic performance was significantly increased (6.93±4.70 ml/kg/min) among overweight participants at the time of recruitment. CONCLUSIONS: The methodology adopted in the physical training of Nepal Police was effective in reducing body mass index and fat, improving the physical capacity. .   Key words: Scale Diet; Physical Training, Body Fat; Aerobic Performance; VO2max, Body Mass Index.

Scoring protein sequence alignments using deep learning.

MOTIVATION: A high-quality sequence alignment (SA) is the most important input feature for accurate protein structure prediction. For a protein sequence, there are many methods to generate a SA. However, when given a choice of more than one SA for a protein sequence, there are no methods to predict which SA may lead to more accurate models without actually building the models. In this work, we describe a method to predict the quality of a protein's SA. RESULTS: We created our own dataset by generating a variety of SAs for a set of 1351 representative proteins and investigated various deep learning architectures to predict the local distance difference test (lDDT) scores of distance maps predicted with SAs as the input. These lDDT scores serve as indicators of the quality of the SAs.Using two independent test datasets consisting of CASP13 and CASP14 targets, we show that our method is effective for scoring and ranking SAs when a pool of SAs is available for a protein sequence. With an example, we further discuss that SA selection using our method can lead to improved structure prediction. AVAILABILITY AND IMPLEMENTATION: Code and the data underlying this article are available at https://github.com/ba-lab/Alignment-Score/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Tocilizumab therapy for persistent high-grade fever in systemic lupus erythematosus: two cases and a literature review.

Tocilizumab (TCZ) is a humanized immunoglobulin (Ig) G1 monoclonal antibody directed against the interleukin (IL)-6 receptor. We report on two patients with persistent high-grade fever and systemic lupus erythematosus (SLE) who were treated with TCZ. Two female Chinese patients presented with SLE and high-grade fever, with raised inflammatory markers including C-reactive protein, erythrocyte sedimentation rate, and IL-6, but no signs of opportunistic infections. Their fever and other symptoms responded poorly to broad-spectrum antibiotics, antifungals, antivirals, and glucocorticoids. They were both treated with TCZ. Their body temperatures returned to normal after treatment with TCZ, and other symptoms, including arthralgia, gradually improved. Both patients were followed-up and their conditions remained steady to date. TCZ may thus be an alternative treatment for patients with SLE and persistent high-grade fever who fail to respond to initial antibiotics and high-dose glucocorticoids.

Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.

Long Term Versus Short Term Hearing Results in Endoscopic Sandwich Myringoplasty.

INTRODUCTION: The use of the endoscope in otological surgeries has both diagnostic and therapeutic values. It provides an excellent view in difficult nooks and corners. The use of endoscopic sandwich myringoplasty using cartilage and perichondrium has its benefit in hearing outcome and graft uptake in long-term follow-up. The main objective was to compare the long-term with short- term hearing outcomes in those who have undergone endoscopic sandwich myringoplasty with Dhulikhel hospital (D­HOS) technique. MATERIALS AND METHODS: Forty-two patients who underwent endoscopic sandwich myringoplasty with D-HOS technique using tragal cartilage perichondrium were enrolled in the study. The hearing outcome was analyzed by comparing the pre-operative findings with post-operative findings and amongst post-operative patients, long-term with short-term air bone gap (ABG) and ABG closure in speech frequencies (0.5kHz, 1kHz, 2kHz, 4kHz) were compared. RESULTS: Amongst forty-two patients, 40 (95.2%) had graft uptake in both short-term (6.08 months) and in long-term (20 months) follow-up. The mean pre-operative ABG was 28.1±9.3dB whereas the mean short-term post-operative ABG was 14.5±7.2dB, it showed statistical significance (P=0.001). Likewise, while comparing pre-operative with long-term post-operative ABG (13.4±4.8 dB), it showed statistical significance of P=0.000. While comparing short-term with long-term post-operative ABG, it did not show any statistical significance (P=0.065).The mean closure in ABG in both short-term and long-term hearing assessment was not statistically significant (P=0.077). CONCLUSION: Endoscopic sandwich myringoplasty with D-HOS technique is a reliable procedure with good hearing outcome and graft uptake in both short and long-term follow-up.

Deep Learning-Based Advances in Protein Structure Prediction.

Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine protein structures, the gap between the number of protein sequences and known protein structures is ever increasing. Computational protein structure prediction is one of the ways to fill this gap. Recently, the protein structure prediction field has witnessed a lot of advances due to Deep Learning (DL)-based approaches as evidenced by the success of AlphaFold2 in the most recent Critical Assessment of protein Structure Prediction (CASP14). In this article, we highlight important milestones and progresses in the field of protein structure prediction due to DL-based methods as observed in CASP experiments. We describe advances in various steps of protein structure prediction pipeline viz. protein contact map prediction, protein distogram prediction, protein real-valued distance prediction, and Quality Assessment/refinement. We also highlight some end-to-end DL-based approaches for protein structure prediction approaches. Additionally, as there have been some recent DL-based advances in protein structure determination using Cryo-Electron (Cryo-EM) microscopy based, we also highlight some of the important progress in the field. Finally, we provide an outlook and possible future research directions for DL-based approaches in the protein structure prediction arena.

Clade-Specific Plastid Inheritance Patterns Including Frequent Biparental Inheritance in Passiflora Interspecific Crosses.

Plastid inheritance in angiosperms is presumed to be largely maternal, with the potential to inherit plastids biparentally estimated for about 20% of species. In Passiflora, maternal, paternal and biparental inheritance has been reported; however, these studies were limited in the number of crosses and progeny examined. To improve the understanding of plastid transmission in Passiflora, the progeny of 45 interspecific crosses were analyzed in the three subgenera: Passiflora, Decaloba and Astrophea. Plastid types were assessed following restriction digestion of PCR amplified plastid DNA in hybrid embryos, cotyledons and leaves at different developmental stages. Clade-specific patterns of inheritance were detected such that hybrid progeny from subgenera Passiflora and Astrophea predominantly inherited paternal plastids with occasional incidences of maternal inheritance, whereas subgenus Decaloba showed predominantly maternal and biparental inheritance. Biparental plastid inheritance was also detected in some hybrids from subgenus Passiflora. Heteroplasmy due to biparental inheritance was restricted to hybrid cotyledons and first leaves with a single parental plastid type detectable in mature plants. This indicates that in Passiflora, plastid retention at later stages of plant development may not reflect the plastid inheritance patterns in embryos. Passiflora exhibits diverse patterns of plastid inheritance, providing an excellent system to investigate underlying mechanisms in angiosperms.

DISTEVAL: a web server for evaluating predicted protein distances.

BACKGROUND: Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and 'binned' distograms, which are a more finely grained variant of the binary contact prediction problem. The latter has been introduced as a new challenge in the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14) 2020 experiment. Despite the recent proliferation of methods for predicting distances, few methods exist for evaluating these predictions. Currently only numerical metrics, which evaluate the entire prediction at once, are used. These give no insight into the structural details of a prediction. For this reason, new methods and tools are needed. RESULTS: We have developed a web server for evaluating predicted inter-residue distances. Our server, DISTEVAL, accepts predicted contacts, distances, and a true structure as optional inputs to generate informative heatmaps, chord diagrams, and 3D models. All of these outputs facilitate visual and qualitative assessment. The server also evaluates predictions using other metrics such as mean absolute error, root mean squared error, and contact precision. CONCLUSIONS: The visualizations generated by DISTEVAL complement each other and collectively serve as a powerful tool for both quantitative and qualitative assessments of predicted contacts and distances, even in the absence of a true 3D structure.

Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora.

Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.

Prevalence of Aeroallergens in Allergic Rhinitis in a Tertiary Care Hospital.

INTRODUCTION: The prevalence of allergic rhinitis has increased significantly globally over the last two decades. Detection of sensitizing aeroallergens plays a crucial role in the diagnosis and management of this troublesome disease. This study aims to investigate the spectrum of aeroallergens sensitization in patients with allergic rhinitis in a tertiary care hospital. METHODS: A descriptive cross-sectional study conducted in the Department of Otorhinolaryngology of our hospital between January 2016 to December 2019. Ethical approval was taken from the Institutional Review Committee (No: 210/19). Patients diagnosed with allergic rhinitis were enrolled using the convenience sampling technique. Data entry and analysis was done using IBM Statistical Package for Social Sciences version 20.0. RESULTS: Among 170 patients, altogether 103 (60.6%) patients yielded positive responses on the skin prick test. The most prevalent aeroallergens were Lepidoglyphus 86 (50.60%), Dermatophagoides pteronyssinus 85 (50%), Dermatophagoides farina 82 (48.20%), Thyrophagus 50 (29.40%), Blomia 46 (27.10%), Acarus 43 (25.30%), cat dander 26 (15.30%), dog dander 24 (14.10%), cow and buffalo dander 20 (11.8%), ragweed 20 (11.8%), grass pollen 18 (10.60%) and mugwort 17 (10%). CONCLUSIONS: This study highlights that the frequency of aeroallergens based on skin prick test in patients presenting to a tertiary care hospital which showed the dominance of house dust mites, dog and cat hair, pollen, and grasses. Reduced exposure and training of patients about protection against these agents will possibly help in controlling the severity of allergic rhinitis in this region.

Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba.

Plastid genomes (plastomes) of photosynthetic angiosperms are for the most part highly conserved in their organization, mode of inheritance and rates of nucleotide substitution. A small number of distantly related lineages share a syndrome of features that deviate from this general pattern, including extensive genomic rearrangements, accelerated rates of nucleotide substitution, biparental inheritance and plastome-genome incompatibility. Previous studies of plastomes in Passiflora with limited taxon sampling suggested that the genus exhibits this syndrome. To examine this phenomenon further, 15 new plastomes from Passiflora were sequenced and combined with previously published data to examine the phylogenetic relationships, genome organization and evolutionary rates across all five subgenera and the sister genus Adenia. Phylogenomic analyses using 68 protein-coding genes shared by Passiflora generated a fully resolved and strongly supported tree that is congruent with previous phylogenies based on a few plastid and nuclear loci. This phylogeny was used to examine the distribution of plastome rearrangements across Passiflora. Multiple gene and intron losses and inversions were identified in Passiflora with some occurring in parallel and others that extended across the Passifloraceae. Furthermore, extensive expansions and contractions of the inverted repeat (IR) were uncovered and in some cases this resulted in exclusion of all ribosomal RNA genes from the IR. The most highly rearranged lineage was subgenus Decaloba, which experienced extensive IR expansion that incorporated up to 25 protein-coding genes usually located in large single copy region. Nucleotide substitution rate analyses of 68 protein-coding genes across the genus showed lineage- and locus-specific acceleration. Significant increase in dS, dN and dN/dS was detected for clpP across the genus and for ycf4 in certain lineages. Significant increases in dN and dN/dS for ribosomal subunits and plastid-encoded RNA polymerase genes were detected in the branch leading to the expanded IR-clade in subgenus Decaloba. This subgenus displays the syndrome of unusual features, making it an ideal system to investigate the dynamic evolution of angiosperm plastomes.

Plastome based phylogenetics and younger crown node age in Pelargonium.

The predominantly South-African plant genus Pelargonium L'Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7th largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43% taxon coverage for Pelargonium. We also performed a dating analysis to examine the timing of the major radiations in the genus. Phylogenetic analyses of nucleotide, amino acid, and ITS alignments confirmed the previously-documented subgeneric split into five main clades ((C1,C2),(B(A1,A2))) although clade only A1 received low bootstrap support. Using calibration evidence from a range of sources the Pelargonium crown age was estimated to be 9.7 My old, much younger than previous estimates for the genus but similar to recent studies of other Cape Floristic lineages that are part of both Fynbos and Succulent Karoo biomes.

Caffeine citrate - Is it a silver bullet in neonatology?

Caffeine citrate is one of the most prescribed drug in the present day NICU for apnea. Its efficacy, tolerability, wide therapeutic index and safety margin has made it the drug of choice among the methylxanthines. Its therapeutic uses in apnea of prematurity, mechanical ventilation, bronchopulmonary dysplasia has made it a "silver bullet" in neonatology. However, there are still controversies surrounding this drug. This review is aimed to update the reader about the basic pharmacology, current therapeutic uses, adverse effects, controversies as well as present and future research of caffeine.

Post-delivery mycobacterium tuberculosis infection misdiagnosed as systemic lupus erythematosus.

Tuberculosis is a common infectious mycobacterial disease having a wide range of clinical and serological manifestations that are similar to rheumatic disease. Differential diagnosis is a crucial aspect in any rheumatic disease as many other infectious diseases portray clinical similarities and autoantibody positivity. Our case report illustrates of a young woman just after the delivery of a child presented an unusual case of extrapulmonary tuberculosis infection initially misdiagnosed as systemic lupus erythematosus (SLE).

Effects of maternal epidural analgesia on the neonate--a prospective cohort study.

BACKGROUND: Epidural analgesia is one of the most popular modes of analgesia for child birth. There are controversies regarding adverse effects and safety of epidural analgesia. This study was conducted to study the immediate effects of the maternal epidural analgesia on the neonate during early neonatal phase. METHODS: A prospective cohort study of 100 neonates born to mothers administered epidural analgesia were compared with 100 neonates born to mothers not administered epidural analgesia in terms of passage of urine, initiation of breast feeding, birth asphyxia and incidence of instrumentation. RESULTS: There was significant difference among the two groups in the passage of urine (P value 0.002) and incidence of instrumentation (P value 0.010) but there was no significant difference in regards to initiation of breast feeding and birth asphyxia. CONCLUSIONS: Epidural analgesia does not have any effect on the newborns in regards to breast feeding and birth asphyxia but did have effects like delayed passage of urine and increased incidence of instrumentation.

Scleredema--an uncommon cause of swelling in a child--a case report and review of the literature.

BACKGROUND: Body swelling in a child is a common symptom. Apart from systemic causes like renal, hepatic, and cardiac, rarely such a swelling may be caused by dermatologic conditions. CASE PRESENTATION: A child presented with swelling of the body which was subsequently diagnosed as scleredema, a rare and benign dermatologic condition. Scleredema can be confused with similar sounding terms like scleroderma and scleromyxedema. CONCLUSIONS: The case is presented to highlight scleredema as a rare cause of body swelling in paediatrics and to differentiate it from similar sounding rare terms like scleroderma and scleromyxedema.

Gaucher's disease: rare presentation of a rare disease.

Gaucher's disease is a rare lysosymal storage disorder characterized by deposition of glucocerebroside in cells of the macrophage monocyte system. Gaucher's disease has 3 types-non-neuronopathic (type I), acute neuronopathic (type II), and chronic neuronopathic (type III). It generally presents with delayed milestones, seizures, bony deformities, or massive organomegaly. The acute neuronoapthic variety is the rarer type that predominantly presents with neurological features. The authors present a case of the acute neuronopathic variety of Gaucher's disease where the child presented with only abnormal head position.