Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges.

Background: The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference genome (reads alignment). The presence of repeats extends the technical ambiguity, making the algorithm unable to distinguish the reads resulting in misassembly and affecting the assembly approach accuracy. On the other hand, the massive number of reads causes a big assembly performance challenge. Method: The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization. Results: Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach. Conclusion: We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.

Epidemiological investigation of norovirus infections in Punjab, Pakistan, through the One Health approach.

Introduction: Norovirus, mainly associated with acute gastroenteritis, is very contagious and can affect a vast range of species ranging from cattle, pigs, dogs, mice, cats, sheep, and lions to humans. It is a foodborne pathogen that mainly transmits through the fecal-oral route. Methods: This is the first-ever study conducted in Lahore and Sheikhupura districts of Punjab, Pakistan, to investigate noroviruses through the One Health approach. From January 2020 to September 2021, 200 fecal samples were collected from clinical cases of hospitalized patients and 200 fecal samples from sick animals at veterinary hospitals and local farms. In addition, 500 food and beverage samples were collected from street vendors and retail stores. A predesigned questionnaire was used to assess the risk factors and clinical characteristics of sick people and animals. Results and discussion: Overall, 14% of the human clinical samples were positive by RT-PCR for genogroup GII. All bovine samples were negative. Food and beverage samples were tested in pools, resulting in sugarcane juice samples positive for genogroup GII. Previous contact with acute gastroenteritis patients, sex, and presence of vomiting were found to be significant risk factors (p ≤ 0.05). The substantial number of diarrhea cases associated with noroviruses calls for additional studies to investigate the epidemiology and transmission and to improve surveillance.

Acetochlor Affects Bighead Carp (Aristichthys Nobilis) by Producing Oxidative Stress, Lowering Tissue Proteins, and Inducing Genotoxicity.

Acetochlor is persistently used in the agroproduction sector to control broadleaf weeds. Due to frequent and continuous applications, this herbicide can reach nearby water bodies and may induce deleterious changes in aquatic life. Therefore, investigation of harmful impacts of different environmental pollutants, including herbicides, is vital to knowing the mechanisms of toxicity and devising control strategies. The current experiment included bighead carp (n = 80) to estimate adverse impacts. Fish were randomly placed in 4 different experimental groups (T0-T3) and were treated for 36 days with acetochlor at 0, 300, 400, and 500 µg/L. Fresh blood without any anticoagulant was obtained and processed for nuclear and morphological changes in erythrocytes. At the same time, various visceral organs, including the gills, liver, brain, and kidneys, were removed and processed on days 12, 24, and 36 to determine oxidative stress and various antioxidant biomarkers. Comet assays revealed significantly increased DNA damage in isolated cells of the liver, kidneys, brain, and gills of treated fish. We recorded increased morphological and nuclear changes (P ≤ 0.05) in the erythrocyte of treated fish. The results on oxidative stress showed a higher quantity of oxidative biomarkers and a significantly (P ≤ 0.05) low concentration of cellular proteins in the gills, liver, brain, and kidneys of treated fish compared to unexposed fish. Our research findings concluded that acetochlor renders oxidative stress in bighead carp.

Atomistic and machine learning studies of solute segregation in metastable grain boundaries.

The interaction of alloying elements with grain boundaries (GBs) influences many phenomena, such as microstructural evolution and transport. While GB solute segregation has been the subject of active research in recent years, most studies focus on ground-state GB structures, i.e., lowest energy GBs. The impact of GB metastability on solute segregation remains poorly understood. Herein, we leverage atomistic simulations to generate metastable structures for a series of [001] and [110] symmetric tilt GBs in a model Al-Mg system and quantify Mg segregation to individual sites within these boundaries. Our results show large variations in the atomic Voronoi volume due to GB metastability, which are found to influence the segregation energy. The atomistic data are then used to train a Gaussian Process machine learning model, which provides a probabilistic description of the GB segregation energy in terms of the local atomic environment. In broad terms, our approach extends existing GB segregation models by accounting for variability due to GB metastability, where the segregation energy is treated as a distribution rather than a single-valued quantity.

The role of grain boundary character in solute segregation and thermal stability of nanocrystalline Pt-Au.

Nanocrystalline (NC) metals suffer from an intrinsic thermal instability; their crystalline grains undergo rapid coarsening during processing treatments or under service conditions. Grain boundary (GB) solute segregation has been proposed to mitigate grain growth and thermally stabilize the grain structures of NC metals. However, the role of GB character in solute segregation and thermal stability of NC metals remains poorly understood. Herein, we employ high resolution microscopy techniques, atomistic simulations, and theoretical analysis to investigate and characterize the impact of GB character on segregation behavior and thermal stability in a model NC Pt-Au alloy. High resolution electron microscopy along with X-ray energy dispersive spectroscopy and automated crystallographic orientation mapping is used to obtain spatially correlated Pt crystal orientation, GB misorientation, and Au solute concentration data. Atomistic simulations of polycrystalline Pt-Au systems are used to reveal the plethora of GB segregation profiles as a function of GB misorientation and the corresponding impact on grain growth processes. With the aid of theoretical models of interface segregation, the experimental data for GB concentration profiles are used to extract GB segregation energies, which are then used to elucidate the impact of GB character on solute drag effects. Our results highlight the paramount role of GB character in solute segregation behavior. In broad terms, our approach provides future avenues to employ GB segregation as a microstructure design strategy to develop NC metallic alloys with tailored microstructures.

Vitamin D Status and Its Associated Risk Factors among Adults in the Southwest Region of Cameroon.

BACKGROUND: Vitamin D has been shown to exert its actions on the musculoskeletal, gastrointestinal, prostate, renal, endocrine, immune, and cardiovascular systems. Current reported data of hypovitaminosis D reveals a global pandemic, with an estimated one billion people worldwide presenting with hypovitaminosis D. OBJECTIVE: This study aimed at investigating the vitamin D status and its associated risk factors in Cameroonians from the South West Region. METHOD: The study was a community- and hospital-based prospective longitudinal study. It was carried out during the dry and rainy seasons between the months of July and December 2015 in the South West Region of Cameroon involving 372 participants aged 35 years and above. After obtaining informed consent, a structured questionnaire was used to capture demographic data and risk factors of vitamin D deficiency. Blood samples were collected from the volunteer participants in the peak months of the rainy season and dry season, and the serum used to analyse for vitamin D by ELISA and calcium by spectrophotometry. 25(OH)D levels ≥75 nmol/L (≥30 ng/mL) were considered sufficient while levels <75 nmol/L were considered as hypovitaminosis D (insufficiency/deficiency). RESULTS: Hypovitaminosis D (deficiency/insufficiency) was prevalent in 25.8% (96) of the study population, with only 3.2% (12) deficiency and 22.6% (84) insufficiency. There was a significant inverse relationship (r=-0.119, p=0.02) between age and 25(OH)D levels; however, this relationship was not significant when controlled for gender, number of hours spent outdoors, and percentage of body covered. Gender, ethnic origin, percentage of body covered, time spent outdoors, and season did not influence serum vitamin D levels. CONCLUSION: Results of this study suggest that the prevalence of hypovitaminosis D is relatively low in this study population and only age is a risk factor of vitamin D deficiency.