PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information.

The dynamic evolution of the severe acute respiratory syndrome coronavirus 2 virus is primarily driven by mutations in its genetic sequence, culminating in the emergence of variants with increased capability to evade host immune responses. Accurate prediction of such mutations is fundamental in mitigating pandemic spread and developing effective control measures. This study introduces a robust and interpretable deep-learning approach called PRIEST. This innovative model leverages time-series viral sequences to foresee potential viral mutations. Our comprehensive experimental evaluations underscore PRIEST's proficiency in accurately predicting immune-evading mutations. Our work represents a substantial step in utilizing deep-learning methodologies for anticipatory viral mutation analysis and pandemic response.

Performance evaluation of deep learning based stream nitrate concentration prediction model to fill stream nitrate data gaps at low-frequency nitrate monitoring basins.

Accurate and frequent nitrate estimates can provide valuable information on the nitrate transport dynamics. The study aimed to develop a data-driven modeling framework to estimate daily nitrate concentrations at low-frequency nitrate monitoring sites using the daily nitrate concentration and stream discharge information of a neighboring high-frequency nitrate monitoring site. A Long Short-Term Memory (LSTM) based deep learning (DL) modeling framework was developed to predict daily nitrate concentrations. The DL modeling framework performance was compared with two well-established statistical models, including LOADEST and WRTDS-Kalman, in three selected basins in Iowa, USA: Des Moines, Iowa, and Cedar River. The developed DL model performed well with NSE >0.70 and KGE >0.70 for 67% and 79% nitrate monitoring sites, respectively. DL and WRTDS-Kalman models performed better than the LOADEST in nitrate concentration and load estimation for all low-frequency sites. The average NSE performance of the DL model in daily nitrate estimation is 20% higher than that of the WRTDS-Kalman model at 18 out of 24 sites (75%). The WRTDS-Kalman model showed unrealistic fluctuations in the estimated daily nitrate time series when the model received limited observed nitrate data (less than 50) for simulation. The DL model indicated superior performance in winter months' nitrate prediction (60% of cases) compared to WRTDS-Kalman models (33% of cases). The DL model also better represented the exceedance days from the USEPA maximum contamination level (MCL). Both the DL and WRTDS-Kalman models demonstrated similar performance in annual stream nitrate load estimation, and estimated values are close to actual nitrate loads.

Direct Shoot From Root and True-to-Type Micropropagation of Limonium "Misty Blue" in Partially Immersed Culture on an Aluminum Mesh Raft.

Commercial plant tissue culture now primarily serves the ornamental horticulture industry. The main pillars of the commercial tissue culture business are scalability of production, cost reduction, limited labor involvement, high quality, and genetic homogeneity of propagated plants. Based on these requirements, the current protocol employs a partially immersed liquid culture medium supported by a flexible aluminum mesh raft with a wire stand to facilitate shoot organogenesis from the horizontally placed root explants and hold the plants upright for shoot multiplication and rooting of Limonium Misty Blue. It is a florist crop that is in high demand as both dried and fresh flower fillers in various floral decorations. The majority of cultivated Limonium or statice cultivars are heterozygous in nature and propagate commercially through in vitro propagation to cater to the huge demand for planting materials needed for flower production. This is the first protocol to describe direct shoot organogenesis from the roots in a liquid half-component of Murashige and Skoog's (1962) (MS) basal medium supplemented with 1.6 µM NAA and 1.1 µM BA. The regenerated shoots are multiplied and rooted at the same time on the raft in a MS-based liquid culture medium that included 0.44 µM BA and 1.07 µM NAA. In comparison to agar-gelled medium, plants cultured in liquid medium grow more quickly without any signs of hyperhydricity. In liquid medium, a clump of 4-5 shoots is formed from a single shoot explant within 4 weeks and are rooted simultaneously within 6 weeks. On average, seven explants may fit on each raft, so on average, 25 healthy plants are produced from a single bottle. The regenerated plants are easily hardened in the greenhouse, and using ISSR-based molecular markers, the genetic homogeneity of the randomly selected hardened plants can be determined.

Service life assessment of yttria stabilized zirconia (YSZ) based thermal barrier coating through wear behaviour.

Countless research has suggested Yttria-stabilized Zirconia (YSZ) to be a top candidate for being implemented as thermal barrier coatings (TBC). However, when exposed to prolonged service, temperature and stress variations succeed in initiating a catastrophic phase transformation from tetragonal to monoclinic structure in Zirconia. Hence, the estimation of endurance for YSZ-based TBC is necessary to minimize failure in such situations. The main purpose of this research was to determine the relationship between tribological investigations and the estimated lifespan of YSZ coatings accurately. The study used various methods such as wear resistance testing, optical profilometry, specific wear rate, and coefficient of friction to estimate the maximum durability of TBCs. The research also provided insights into the composition and microstructure of the TBC system and found the optimized concentration of Yttrium doping to be 3.5 wt %. The study discovered that erosion was the main cause of roughness depreciation from SN to S1000. The estimation of the service life was primarily made based on optical profilometry, specific wear rate (SWR), coefficient of friction (COF) and wear resistance values which were further supported by the results of chemical characterization of the samples through electron dispersive spectroscopy (EDS), wavelength dispersive spectroscopy (WDS) and X-Ray Diffraction (XRD) analysis. The results were reliable and accurate and suggested future areas of investigation, such as 3D profilometry for surface roughness and thermal conductivity evaluation using laser-assisted infrared thermometers.

A deep learning-based novel approach to generate continuous daily stream nitrate concentration for nitrate data-sparse watersheds.

High-frequency stream nitrate concentration provides critical insights into nutrient dynamics and can help to improve the effectiveness of management decisions to maintain a sustainable ecosystem. However, nitrate monitoring is conventionally conducted through lab analysis using in situ water samples and is typically at coarse temporal resolution. In the last decade, many agencies started collecting high-frequency (5-60 min intervals) nitrate data using optical sensors. The hypothesis of the study is that the data-driven models can learn the trend and temporal variability in nitrate concentration from high-frequency sensor-based nitrate data in the region and generate continuous nitrate data for unavailable data periods and data-limited locations. A Long Short-Term Memory (LSTM) model-based framework was developed to estimate continuous daily stream nitrate for dozens of gauge locations in Iowa, USA. The promising results supported the hypothesis; the LSTM model demonstrated median test-period Nash-Sutcliffe efficiency (NSE) = 0.75 and RMSE = 1.53 mg/L for estimating continuous daily nitrate concentration in 42 sites, which are unprecedented performance levels. Twenty-one sites (50 % of all sites) and thirty-four sites (76 % of all sites) demonstrated NSE > 0.75 and 0.50, respectively. The average nitrate concentration of neighboring sites was identified as a crucial determinant of continuous daily nitrate concentration. Seasonal model performance evaluation showed that the model performed effectively in the summer and fall seasons. About 26 sites showed correlations >0.60 between estimated nitrate concentration and discharge. The concentration-discharge (c-Q) relationship analysis showed that the study watersheds had four dominant nitrate transport patterns from landscapes to streams with increasing discharge, including the flushing pattern being the most dominant one. Stream nitrate estimation impedes due to data inadequacy. The modeling framework can be used to generate temporally continuous nitrate at nitrate data-limited regions with a nearby sensor-based nitrate gauge. Watershed planners and policymakers could utilize the continuous nitrate data to gain more information on the regional nitrate status and design conservation practices accordingly.

Evaluating water quality benefits of manureshed management in the Susquehanna River Basin.

Manureshed management guides the sustainable use of manure resources by matching areas of crop demand (nutrient sinks) with areas generating livestock manure (nutrient sources). A better understanding of the impacts of manureshed management on water quality within sensitive watersheds is needed. We quantified the potential water quality benefits of manureshed-oriented management through scenario-based analyses in the Susquehanna River Basin (SRB) using the Soil and Water Assessment Tool. Five manureshed management scenarios were developed and compared with a baseline "business-as-usual" scenario. The baseline assumes manure is less transportable, which means some locations have manure application in excess of crop demand. The "watershed nutrient balance" scenarios assume excess manure from surplus locations is transportable and that manure is applied around the SRB based on crop nutrient demand. The "watershed nutrient balance avoiding runoff prone areas" scenarios assume manure is transportable but not applied in vulnerable landscapes of the SRB. Each scenario was evaluated under two application rates considering crop nitrogen demand (N-based) and phosphorus demand (P-based). Phosphorus-based manureshed management was more effective in water quality improvements than N-based management. Phosphorus-based nutrient balance scenarios simulated 3 and 25% reduction in total N (TN) and total P (TP), respectively, from the baseline scenario at the watershed outlet. The N- and P-based scenarios avoiding runoff prone areas simulated 3 and 6% reduction in TN loss and 4 and 25.2% reduction in TP loss, respectively, from the baseline. Overall, the manureshed management scenarios were more effective in improving the quality of local streams in livestock-intensive regions than at the watershed outlet.

Shared Autonomy to Reduce Sedentary Behavior Among Sit-Stand Desk Users in the United States and India: Web-Based Study.

BACKGROUND: Fitness technologies such as wearables and sit-stand desks are increasingly being used to fight sedentary lifestyles by encouraging physical activity. However, adherence to such technologies decreases over time because of apathy and increased dismissal of behavioral nudges. OBJECTIVE: To address this problem, we introduced shared autonomy in the context of sit-stand desks, where user input is integrated with robot autonomy to control the desk and reduce sedentary behavior and investigated user reactions and preferences for levels of automation with a sit-stand desk. As demographics affect user acceptance of robotic technology, we also studied how perceptions of nonvolitional behavior change differ across cultures (United States and India), sex, familiarity, dispositional factors, and health priming messages. METHODS: We conducted a web-based vignette study in the United States and India where a total of 279 participants watched video vignettes of a person interacting with sit-stand desks of various levels of automation and answered questions about their perceptions of the desks such as ranking of the different levels of automation. RESULTS: Participants generally preferred either manual or semiautonomous desks over the fully autonomous option (P<.001). However, participants in India were generally more amenable to the idea of nonvolitional interventions from the desk than participants in the United States (P<.001). Male participants had a stronger desire for having control over the desk than female participants (P=.01). Participants who were more familiar with sit-stand desks were more likely to adopt autonomous sit-stand desks (P=.001). No effects of health priming messages were observed. We estimated the projected health outcome by combining ranking data and hazard ratios from previous work and found that the semiautonomous desk led to the highest projected health outcome. CONCLUSIONS: These results suggest that the shared autonomy desk is the optimal level of automation in terms of both user preferences and estimated projected health outcomes. Demographics such as culture and sex had significant effects on how receptive users were to autonomous intervention. As familiarity improves the likelihood of adoption, we propose a gradual behavior change intervention to increase acceptance and adherence, especially for populations with a high desire for control.

Somatic Embryogenesis of Anthurium andraeanum Linden., -A Tropical Florists' Plant.

The global floriculture market is expected to reach US$41.1 billion by 2027 at a CAGR of 5% over the analysis period 2020-2027; on the year 2020, the recorded market value in this trade was US$29.2 billion. The florists mainly use Anthurium andraeanum flowers in fashionable bouquets and floral arrangements because of their beautiful, attractive bright colored eye-catching spathe, candle-like spadix, prolonged vase life, etc. The cut flower industry always seeks elite cultivars and new hybrids of A. andraeanum, that in turn depend on the availability of large numbers of clonal planting propagules. In vitro somatic embryogenesis is an important technique for large-scale clonal propagation, development of transgenic plants, creation of new variety by somaclonal variation, mutagenesis on in vitro plants, and germplasm preservation for future use. Here, we describe the protocol of somatic embryogenesis of Anthurium andraeanum cv. Cancan, an important commercial cultivated variety. The protocol has been optimized by using 4 different types of culture media which are used during embryogenic callus induction, multiplication of callus, induction of somatic embryogenesis, and maturation plus conversion of embryos into plantlets. The protocol outlines the detailed methods from mother plant procurement to hardening of micro plants that is ready to transfer in the field and it can be used for large-scale commercial propagation.

A novel hotspot and rare somatic mutation p.A138V, at TP53 is associated with poor survival of pancreatic ductal and periampullary adenocarcinoma patients.

BACKGROUND: Pancreatic Ductal Adenocarcinoma (PDAC) is a cancer of the exocrine pancreas and 5-year survival rates remain constant at 7%. Along with PDAC, Periampullary Adenocarcinoma (PAC) accounts for 0.5-2% of all gastrointestinal malignancies. Genomic observations were well concluded for PDAC and PACs in western countries but no reports are available from India till now. METHODS: Targeted Next Generation Sequencing were performed in 8 (5 PDAC and 3 PAC) tumour normal pairs, using a panel of 412 cancer related genes. Primary findings were replicated in 85 tumour samples (31 PDAC and 54 PAC) using the Sanger sequencing. Mutations were also validated by ASPCR, RFLP, and Ion Torrent sequencing. IHC along with molecular dynamics and docking studies were performed for the p.A138V mutant of TP53. Key polymorphisms at TP53 and its associated genes were genotyped by PCR-RFLP method and association with somatic mutations were evaluated. All survival analysis was done using the Kaplan-Meier survival method which revealed that the survival rates varied significantly depending on the somatic mutations the patients harboured. RESULTS: Among the total 114 detected somatic mutations, TP53 was the most frequently mutated (41%) gene, followed by KRAS, SMAD4, CTNNB1, and ERBB3. We identified a novel hotspot TP53 mutation (p.A138V, in 17% of all patients). Low frequency of KRAS mutation (33%) was detected in these samples compared to patients from Western counties. Molecular Dynamics (MD) simulation and DNA-protein docking analysis predicted p.A138V to have oncogenic characteristics. Patients with p.A138V mutation showed poorer overall survival (p = 0.01). So, our finding highlights elevated prevalence of the p53p.A138V somatic mutation in PDAC and pancreatobiliary PAC patients. CONCLUSION: Detection of p.A138V somatic variant in TP53 might serve as a prognostic marker to classify patients. It might also have a role in determining treatment regimes. In addition, low frequency of KRAS hotspot mutation mostly in Indian PDAC patient cohort indicates presence of other early drivers in malignant transformation.

Genetic Alterations of Periampullary and Pancreatic Ductal Adenocarcinoma: An Overview.

Pancreatic Ductal AdenoCarcinoma (PDAC) is one of the most lethal malignancies of all solid cancers. Precancerous lesions for PDAC include PanIN, IPMNs and MCNs. PDAC has a poor prognosis with a 5-year survival of approximately 6%. Whereas Periampulary AdenoCarcinoma (PAC) having four anatomic subtypes, pancreatic, Common Bile Duct (CBD), ampullary and duodenum shows relative better prognosis. The highest incidence of PDAC has been reported with black with respect to white population. Similarly, incidence rate of PAC also differs with different ethnic populations. Several lifestyle, environmental and occupational exposures including long-term diabetes, obesity, and smoking, have been linked to PDAC, however, for PAC the causal risk factors were poorly described. It is now clear that PDAC and PAC are a multi-stage process resulting from the accumulation of genomic alterations in the somatic DNA of normal cells as well as inherited mutations. Approximately 10% of PDAC have a familial inheritance. Germline mutations in CDKN2A, BRCA2, STK11, PALB2, PRSS1, etc., as well as certain syndromes have been well associated with predisposition to PDAC. KRAS, CDKN2A, TP53 and SMAD4 are the 4 "mountains" (high-frequency driver genes) which have been known to earliest somatic alterations for PDAC while relatively less frequent in PAC. Our understanding of the molecular carcinogenesis has improved in the last few years due to extensive research on PDAC which was not well explored in case of PAC. The genetic alterations that have been identified in PDAC and different subgroups of PAC are important implications for the development of genetic screening test, early diagnosis, and prognostic genetic markers. The present review will provide a brief overview of the incidence and prevalence of PDAC and PAC, mainly, increased risk in India, the several kinds of risk factors associated with the diseases as well as required genetic alterations for disease initiation and progression.