Number Of Sequences Research Articles

Mitochondrial genome data provide insights into the phylogenetic relationships within Triplophysadalaica (Kessler, 1876) (Cypriniformes, Nemacheilidae).

Due to the detrimental effect of formaldehyde on DNA, ethanol has replaced formalin as the primary preservative for animal specimens. However, short-term formalin fixation of specimens might be applied during field collection. In an increasing number of studies, DNA extraction and sequencing have been successfully conducted from formalin-fixed specimens. Here the DNA from five specimens of Triplophysadalaica (Kessler, 1876) were extracted and performed high-throughput sequencing. Four of the specimens underwent short-term fixation with formalin and were subsequently transferred to ethanol. One was continuously stored in ethanol. No significant difference of DNA quality and amount were observed among these samples. Followed by assembly and annotation, five mitochondrial genomes ranging in length from 16,569 to 16,572 bp were obtained. Additionally, previously published data of other individuals or species were included to perform phylogenetic analyses. In the reconstructed trees, all eight individuals of T.dalaica form a monophyletic group within the Triplophysa branch. The group is divided into three clades: (1) samples from the Yellow River, (2) those from the Yangtze River, and (3) those from the Haihe River, and the Lake Dali Nur. This study sheds initial light on the phylogeographic relationships among different populations of T.dalaica, and will support the research about its evolutionary history in the future.

Annotation of 2,507 Saccharomyces cerevisiae genomes.

Saccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Currently, a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain. However, these genomes are distributed at different websites and a large number of them are released without annotation information. To provide one complete annotated genome data resource, we collected 2,507 Saccharomyces cerevisiae genome assemblies and re-annotated 2,506 assemblies using a custom annotation pipeline, producing a total of 15,407,164 protein-coding gene models. With a custom pipeline, all these gene sequences were clustered into families. A total of 1,506 single-copy genes were selected as marker genes, which were then used to evaluate the genome completeness and base qualities of all assemblies. Pangenomic analyses were performed based on a selected subset of 847 medium-high-quality genomes. Statistical comparisons revealed a number of gene families showing copy number variations among different organism sources. To the authors' knowledge, this study represents the largest genome annotation project of S. cerevisiae so far, providing rich genomic resources for the future studies of the model organism S. cerevisiae and its relatives.IMPORTANCESaccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Though a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain, these genomes are distributed at different websites and most are released without annotation, hindering the efficient reuse of these genome resources. Here, we collected 2,507 genomes for Saccharomyces cerevisiae, performed genome annotation, and evaluated the genome qualities. All the obtained data have been deposited at public repositories and are freely accessible to the community. This study represents the largest genome annotation project of S. cerevisiae so far, providing one complete annotated genome data set for S. cerevisiae, an important workhorse for fundamental biology, biotechnology, and industry.

Reducing Airway Occlusion Time Without Losing Accuracy to Predict Successful Mechanical Ventilator Liberation During the Measurement of the Timed Inspiratory Effort Index.

In 2013, a new predictor of successful mechanical ventilation liberation named timed inspiratory effort (TIE) index was devised with the normalization of the maximum inspiratory pressure (obtained within 60 s of unidirectional airway occlusion) with the time at which the value was reached. The aim of this study was to verify whether the presence of a sequence of a certain number of inspiratory effort values between 30-60 s > 1.0 cm H2O/s could predict weaning success in a performance comparable to the TIE index. This was a retrospective observational study using 4 databases of previous studies on the TIE index. All patients receiving mechanical ventilation for ≤ 24 h were eligible. Liberation from mechanical ventilation-extubation decisions was made based on performance with spontaneous breathing trials. P < .05 was considered significant. The performance of the TIE index was evaluated by calculating the area under the receiver operating characteristics (AUROC) curve. From 349 eligible patients, 165 subjects were selected for analysis. The AUROC for the TIE index in the studied sample was 0.92 (95% CI 0.87-0.97, P < .001). A sequence of ≤ 4 inspiratory efforts > 1.0 cm H2O/s was found in 51.5% of the subjects, with successful ventilatory liberation occurring in 95.3%. The highest specificity values belonged to the sequence of ≤ 4 and ≤ 5 inspiratory efforts > 1.0 cm H2O/s; the highest positive predictive value and positive likelihood ratio belonged to the sequence of ≤ 4 inspiratory efforts > 1.0 cm H2O/s. The mean time that could have been spared if the procedure were interrupted after the first sequence of 4 inspiratory efforts > 1.0 cm H2O/s was 23 ± 3 s. The presence of a sequence of ≤ 4 inspiratory efforts > 1.0 cm H2O/s during the TIE index measurement was a reliable predictor of weaning success, which could allow timely interruption of the procedure and entail a substantial reduction in airway occlusion time.

Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution.

Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.

Clinical phenotype of a Kallmann syndrome patient with IL17RD and CPEB4 variants.

This study aimed to characterize the clinical phenotype and genetic variations in patients with Kallmann syndrome (KS). This study involved the collection and analysis of clinical data from an individual with sporadic KS. Following this, peripheral blood samples were obtained from the patient and his parents. Genomic deoxyribonucleic acid was extracted and subjected to whole-exome sequencing and genomic copy number variation (CNV) detection. Finally, Sanger sequencing was performed to validate the suspected pathogenic variants. Whole-exome sequencing confirmed that the child carried both the IL17RD variant (c.2101G>A, p.Gly701Ser) inherited from the mother and the new CPEB4 variant (c.1414C>T, p.Arg472*). No pathogenic CNVs were identified in CNV testing. Bioinformatics analysis shows that the IL17RD protein undergoing Gly701Ser mutation and is speculated to be phosphorylated and modified, thereby disrupting fibroblast growth factor signaling. This study also suggested that the CPEB4 might play a crucial role in the key signaling process affecting olfactory bulb morphogenesis. Overall, the findings of this study broaden the gene expression profile of KS-related pathogenic genes. This offers a new avenue for exploring the pathogenic mechanism of KS and provides valuable insights for precise clinical diagnosis and treatment strategies for this condition.

Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant

BackgroundPrimulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.ResultsIn this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.ConclusionsThis study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.

(1232) - Characterizing the Impact of Donor Sequence Number on Outcomes Following Heart Transplantation

(1232) - Characterizing the Impact of Donor Sequence Number on Outcomes Following Heart Transplantation

(941) - High Donor Sequence Number and Outcomes Following Lung Transplantation in the United States

(941) - High Donor Sequence Number and Outcomes Following Lung Transplantation in the United States

(351) - Higher Donor Sequence Numbers are Not Associated with Worse Lung Transplant Outcomes

(351) - Higher Donor Sequence Numbers are Not Associated with Worse Lung Transplant Outcomes

ROUGH LACUNARY STATISTICAL ANALYSIS OF ORDER OF η OF TRIPLE DIFFERENCE SEQUENCE SPACES

We generalized the concepts in the probability of rough lacunary statistical analysis of order η by introducing the difference operator Δ_γ^α of fractional order, where α is a proper fraction and γ=(γ_mnk ) is any fixed sequence of nonzero real or complex numbers. We study some properties of this operator involving lacunary sequence θ and arbitrary sequence p=(p_rst ) of strictly positive real numbers and investigate the topological structures of related with triple difference sequence spaces. The main focus of the present paper is to generalize rough lacunary statistical analysis of order η of triple difference sequence spaces and give the relations between statistical analysis and lacunary statistical analysis of order η.

Performance of tri-tubular conical energy absorber under axial compression

Quasi static axial compression loading on tri-tubular cone (TC) has been carried out using LS-DYNA finite element analysis method. Tri-tubular cones of three arrangements; the first arrangement (model TC-1) consists of cone heights of 50 mm, 75 mm and 100 mm where the inner cone is the maximum height. The second arrangement (model TC-2) consists of cone heights of 100 mm, 75 mm, and 50 mm where the outer cone is the maximum height. The third arrangement (model TC-3) consists of three cones of the same height of 100 mm. Cone semi vertex angle of 20o was maintained for all tri-tubular cones tested. Materials used for this research are glass, jute and jute-glass/epoxy. Crashworthiness analyses were performed to investigate the effect of material used, and tri-tubular cone arrangement on peak load. Crush efficiency, and absorbed energy were drawn and discussed. Failure mechanism of the fractured specimens was also discussed. Effect of number of layers and fiber stacking sequence were also investigated. Results show that the cone arrangement TC-3 gives better performance than the cone arrangement TC-2 followed by the cone arrangement TC-1. Maximum load obtained by tri-tubular cone type TC-3 was found higher 7.09% and 14.96% than TC-2 and TC-1 respectively for glass/epoxy. Material saving was achieved by using tri-tubular cones of different heights under compression. Material used has significant influence on the absorbed energy. Failure mode of tri-tubular conical energy absorber was presented and discussed.

Blood-inspired random bit generation using microfluidics system

The development of random number generators (RNGs) using speckle patterns is pivotal for secure encryption key generation, drawing from the recent statistical properties identified in speckle-based imaging. Speckle-based RNG systems generate a sequence of random numbers through the unpredictable and reproducible nature of speckle patterns, ensuring a source of randomness that is independent of algorithms. However, to guarantee their effectiveness and reliability, these systems demand a meticulous and rigorous approach. In this study, we present a blood-inspired RNG system with a microfluidics device, designed to generate random numbers at a rate of 5.5 MHz and a high-speed of 1250 fps. This process is achieved by directing a laser beam through a volumetric scattering medium to procure speckle patterns. Additionally, designed microfluidic device requires only a minimal blood sample of 5 µl to capture these speckle patterns effectively. After implementing the two-pass tuple-output von Neumann debiasing algorithm to counteract statistical biases, we utilized the randomness statistical test suite from the National Institute of Standards and Technology for validation. The generated numbers successfully passed these tests, ensuring their randomness and unpredictability. Our blood-inspired RNG, utilizing whole blood, offers a pathway for affordable, high-output applications in fields like encryption, computer security, and data protection.

Tiling Rectangles and the Plane Using Squares of Integral Sides

We study the problem of perfect tiling in the plane and explore the possibility of tiling a rectangle using integral distinct squares. Assume a set of distinguishable squares (or equivalently a set of distinct natural numbers) is given, and one has to decide whether it can tile the plane or a rectangle or not. Previously, it has been proved that tiling the plane is not feasible using a set of odd numbers or an infinite sequence of natural numbers including exactly two odd numbers. The problem is open for different situations in which the number of odd numbers is arbitrary. In addition to providing a solution to this special case, we discuss some open problems to tile the plane and rectangles in this paper.

Writing productivity development in elementary school: A systematic review

The ability to produce fluent and coherent written text impacts learning and attainments. Valid and reliable assessments of writing are needed to monitor progression, develop goals for writing and identify struggling writers. In order to inform practice and research a systematic review was conducted to investigate which writing productivity measures captured writing development and identified struggling writers in elementary school. Sixty-seven empirical studies were identified for inclusion, appraised, and their data extracted under the themes of writing genre, duration of writing task, use of priming of topic knowledge prior to the writing assessment, use of planning time, writing modality, gender, age of participants and learning difficulties. Total Number of Words and Correct Word Sequences were the most common means of measuring productivity. Productivity varied significantly between genres and durations of writing tasks and was higher in girls than boys. Students with learning difficulties scored significantly lower in writing productivity when compared to typically developing peers. Insufficient research was available to draw conclusions regarding the effects of priming of topic knowledge, planning and modality on writing productivity. Study limitations, links to the assessment of writing and recommended further research are discussed.

A general-purpose code for correlated sampling using batch statistics with MCNP6 for fixed-source problems

Background Correlated sampling can be applied with batch statistics using MCNP6’s tally fluctuation chart (TFC) to reduce the uncertainty of a difference of tallies between a base case and a perturbed case without modifying the source code. The cases are correlated if they are run with the same random number sequence. Equations implemented Equations used to apply correlated sampling to the difference of two tallies are summarized from previous work. Equations used to apply correlated sampling to a ratio of two tallies, to the difference of two tallies divided by a third tally, and to other combinations of ratios are presented. New computer code A general-purpose, command-line-driven computer program, COSUBS (Correlated Sampling Using Batch Statistics), is presented that reads MCNP6 TFCs from output files and applies these equations. The user specifies the input relative perturbation, if desired, and any normalization tally, if desired. Example problems show how to run COSUBS and interpret the output.

Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing

Objective Investigate the performance of real-time 16S PCR and third-generation 16S sequencing in the diagnosis of external ventricular drain related infections (EVDRI). Methods Subjects with suspected EVDRI were prospectively included at Uppsala University Hospital. Subjects were included into three groups: subjects with negative CSF culture with and without antibiotic treatment and subjects with positive CSF culture, respectively. CSF was analysed with real-time 16S PCR and third-generation 16S sequencing. Real-time 16S PCR positivity/negativity and number of 16S sequence reads were compared between groups. For culture positive subjects, species identification in third-generation sequencing and routine culture was compared. Results 84 subjects were included. There were 18, 44 and 22 subjects in the three groups. Real-time PCR was positive in 17 of 22 subjects in the culture positive group and negative in 61 of the 62 subjects in the two culture negative groups. The sensitivity and specificity for real-time 16S PCR compared to culture was estimated to 77% and 98%, respectively. Species identification in 16S sequencing and culture was concordant in 20 of 22 subjects. The number of 16S sequence reads were significantly higher in the culture positive group than in both culture negative groups (p < 0.001). There was no significant difference in number of 16S sequences between the two culture negative groups. Conclusions Real-time 16S PCR predict culture results with sufficient reliability. Third-generation 16S sequencing could enhance sensitivity and species identification in diagnostics of EVD-related infections. False negative culture results appear to be uncommon in patients with suspected EVDRI.

Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2.

SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.

Systematic methodologies to surveil and evaluate the early imperceptible thermal degradation of EPDM composite

Without knowledge and resultful surveillance of the early degradation of polymers, it is challenging to realize the high reliability of high-end equipment and the screening and grading of waste plastics. Their reliability evaluation and lifetime prediction are also unfulfillable for a lack of sensitive characterization techniques. This work, taking commercial ethylene propylene diene monomer (EPDM) composite as an example, explores a variety of multi-scale evaluation methods to identify its early thermal aging behaviors and molecular mechanisms, including various spectroscopic technology, swelling-equilibrium tests, scanning electron microscope (SEM), thermal analysis, contact angle tests and mechanical properties. Only some methods can give the perceptible indicators of the slight thermal degraded EPDM, namely fluorescent probe technology, infrared spectroscopy for gas mixtures, swelling-equilibrium tests and specific mechanical properties. Other methods are inferior in early aging identification. Both fluorescent probe technology and infrared spectroscopy for gas mixtures can recognize the thermal degradation induced products within 5 h at a temperature lower than 120 °C, while elongation at break can reflect the damage of EPDM within 5 h at 60 °C. Based on the time-temperature superposition principle, the master curve of the thermal aged EPDM is constructed using the data of elongation at break, which predicts that 50% retention of elongation at break occurs after 10.5 years at 30 °C. We further propose a new aging evaluation methodology to reflect the aging degree comprehensively, which is based on the standardized sequence numbers obtained from the above sensitive characterization methods.

Repeated Fair Allocation of Indivisible Items

The problem of fairly allocating a set of indivisible items is a well-known challenge in the field of (computational) social choice. In this scenario, there is a fundamental incompatibility between notions of fairness (such as envy-freeness and proportionality) and economic efficiency (such as Pareto-optimality). However, in the real world, items are not always allocated once and for all, but often repeatedly. For example, the items may be recurring chores to distribute in a household. Motivated by this, we initiate the study of the repeated fair division of indivisible goods and chores, and propose a formal model for this scenario. In this paper, we show that, if the number of repetitions is a multiple of the number of agents, there always exists a sequence of allocations that is proportional and Pareto-optimal. On the other hand, irrespective of the number of repetitions, an envy-free and Pareto-optimal sequence of allocations may not exist. For the case of two agents, we show that if the number of repetitions is even, it is always possible to find a sequence of allocations that is overall envy-free and Pareto-optimal. We then prove even stronger fairness guarantees, showing that every allocation in such a sequence satisfies some relaxation of envy-freeness. Finally, in case that the number of repetitions can be chosen freely, we show that envy-free and Pareto-optimal allocations are achievable for any number of agents.

Genomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in the cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 8 severe de novo pdSNVs in genes not previously implicated in ASD (AGPAT3, IRX5, MGAT5B, RAB8B, RAP1A, RASAL2, SLC9A1, YME1L1) highlighted promising candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, although this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in ASD/NDD candidate genes not yet established. In conclusion, our study highlights promising ASD candidate genes and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.