Use of Dermal Substitute Matrices for Coverage of Exposed Limb Vascular Repairs: A Literature Review.

Background: Prompt coverage of vascular repairs in the extremities is needed to protect from desiccation and trauma. In the absence of local soft tissues to provide early coverage pending demarcation of the tissues and the zone of injury, there is no clear data in the literature on the ideal coverage method. This article is the first to review the use of dermal substitutes for temporary coverage of extremity vascular repairs pending definitive coverage. Methods: We conducted a review of the literature to identify previous articles indexed in PubMed and Ovid using these search terms: [(skin) OR (artificial skin) OR (Integra) OR (dermal substitute) OR (dermal substitute matrix) OR (dermal regeneration) OR (dermal regeneration matrix) OR (dermal regeneration template)] AND [(bypass) OR (graft) OR (vascular surgery) OR (revascularization) OR (salvage) OR (limb salvage) OR (vascular repair) OR (artery repair) OR (arterial repair)] AND [(limb) OR (extremity) OR (leg) OR (arm) OR (vascular injury) OR (amputation)]. Results: Of the 32 articles retrieved for initial review, five case reports with six patients of dermal substitute use for direct coverage of extremity repairs were identified. In all cases, the dermal substitute was able to provide stable coverage pending definitive coverage or was allowed to heal secondarily. Conclusions: Dermal substitute matrices are a potential means of temporary coverage of exposed extremity vascular repairs when there is a paucity of local soft tissues pending more definitive coverage.

Anomalous trends in global ocean carbon concentrations following the 2022 eruptions of Hunga Tonga-Hunga Ha'apai.

We report on observed trend anomalies in climate-relevant global ocean biogeochemical properties, as derived from satellite ocean color measurements, that show a substantial decline in phytoplankton carbon concentrations following eruptions of the submarine volcano Hunga Tonga-Hunga Ha'apai in January 2022. The anomalies are seen in remotely-sensed ocean color data sets from multiple satellite missions, but not in situ observations, thus suggesting that the observed anomalies are a result of ocean color retrieval errors rather than indicators of a major shift in phytoplankton carbon concentrations. The enhanced concentration of aerosols in the stratosphere following the eruptions results in a violation of some fundamental assumptions in the processing algorithms used to obtain marine biogeochemical properties from satellite radiometric observations, and it is demonstrated through radiative transfer simulations that this is the likely cause of the anomalous trends. We note that any future stratospheric aerosol disturbances, either natural or geoengineered, may lead to similar artifacts in satellite ocean color and other remote-sensing measurements of the marine environment, thus confounding our ability to track the impact of such events on ocean ecosystems.

Spectral correlation in MODIS water-leaving reflectance retrieval uncertainty.

Spectral remote sensing reflectance, Rrs(λ) (sr-1), is the fundamental quantity used to derive a host of bio-optical and biogeochemical properties of the water column from satellite ocean color measurements. Estimation of uncertainty in those derived geophysical products is therefore dependent on knowledge of the uncertainty in satellite-retrieved Rrs. Furthermore, since the associated algorithms require Rrs at multiple spectral bands, the spectral (i.e., band-to-band) error covariance in Rrs is needed to accurately estimate the uncertainty in those derived properties. This study establishes a derivative-based approach for propagating instrument random noise, instrument systematic uncertainty, and forward model uncertainty into Rrs, as retrieved using NASA's multiple-scattering epsilon (MSEPS) atmospheric correction algorithm, to generate pixel-level error covariance in Rrs. The approach is applied to measurements from Moderate Resolution Imaging Spectroradiometer (MODIS) on the Aqua satellite and verified using Monte Carlo (MC) analysis. We also make use of this full spectral error covariance in Rrs to calculate uncertainty in phytoplankton pigment chlorophyll-a concentration (chla, mg/m3) and diffuse attenuation coefficient of downwelling irradiance at 490 nm (Kd(490), m-1). Accounting for the error covariance in Rrs generally reduces the estimated relative uncertainty in chla by ∼1-2% (absolute value) in waters with chla < 0.25 mg/m3 where the color index (CI) algorithm is used. The reduction is ∼5-10% in waters with chla > 0.35 mg/m3 where the blue-green ratio (OCX) algorithm is used. Such reduction can be higher than 30% in some regions. For Kd(490), the reduction by error covariance is generally ∼2%, but can be higher than 20% in some regions. The error covariance in Rrs is further verified through forward-calculating chla from MODIS-retrieved and in situ Rrs and comparing estimated uncertainty with observed differences. An 8-day global composite of propagated uncertainty shows that the goal of 35% uncertainty in chla can be achieved over deep ocean waters (chla ≤ 0.1 mg/m3). While the derivative-based approach generates reasonable error covariance in Rrs, some assumptions should be updated as our knowledge improves. These include the inter-band error correlation in top-of-atmosphere reflectance, and uncertainties in the calibration of MODIS 869 nm band, in ancillary data, and in the in situ data used for system vicarious calibration.

Splenogonadal fusion: a case report.

BACKGROUND: Accessory splenic tissue is a commonly encountered phenomenon in medical literature. Typically, these accessory spleens are found in close proximity to the main spleen, either in the hilum or within the surrounding ligaments. Nevertheless, it is noteworthy that they can also be located in unusual sites such as the jejunum wall, mesentery, pelvis, and, exceptionally rarely, the scrotum. The first documented case of accessory splenic tissue in the scrotum was reported by Sneath in 1913 and is associated with a rare congenital anomaly called splenogonadal fusion. This report describes an infant who presented with a scrotal mass noted by his mother and after examination, investigations, and surgical exploration, it was revealed to be splenogonadal fusion. CASE DESCRIPTION: An 8-month-old Caucasian male patient presented with a mass in the left testicle and bluish discoloration of the scrotum, which had been incidentally noticed in the previous 2 months. The general physical examination was unremarkable. Other than a palpable scrotal mass that was related to the upper pole of the testis, the rest of examination was unremarkable. Imaging revealed that this mass originated from the tail of the epididymis without infiltrating the testis and tumor markers were normal. On inguinal exploration, a reddish brown 2 × 2 cm mass was found attached to the upper pole and was completely excised without causing any harm to the testis, vessels, or epididymis. Histopathological evaluation confirmed the presence of intratesticular ectopic splenic tissue. CONCLUSION: Although uncommon, splenogonadal fusion can be included in the differential diagnosis of a testicular swelling. Accurate diagnosis allows for appropriate treatment planning which helps to avoid unnecessary radical orchiectomy, which can have a significant impact on the patient's reproductive and psychological wellbeing.

Determination of Appropriate Umbilicus Position during Abdominoplasty in Male Patients.

Background: Abdominoplasty techniques are well documented. The ideal position of the umbilicus has, however, received limited attention. Unfortunately, umbilicus position is not universally agreed upon in male cosmetic abdominoplasty. This study was conducted to determine the ideal umbilicus anthropometric measurements in young men, and the relationships between umbilical position and anterior trunk and torso reference points that may be applicable to intraoperative positioning. It is aimed also at investigating whether umbilicus position would be more accurately determined by considering nipple position instead of the abdominal crease, as recently proposed. Methods: Several anthropometric measurements of various anterior abdominal and thoracic landmarks were conducted on 60 young and middle-aged male volunteers and 30 cadavers at São Paulo city. All statistical analysis was completed using Stata software. Results: Of all the measured reference points, a much stronger correlation (0.513) was demonstrated between umbilicus-anterior axillary fold (U-AX) and inter-nipple (N-N) distances with a constant golden number ratio relationship (N-N = U-AX × 0.618) compared with the weak correlation of 0.034 between umbilicus-xiphisternum and umbilicus-abdominal crease. In 75% of volunteers, the calculated U-AX was within ±3 cm of actual measurement, and in 33.33% within ±1 cm. Conclusions: U-AX = 1.618 × N-N equation is more predictive of adequate umbilicus repositioning during abdominoplasty in male patients. Chest and abdomen of men are a single aesthetic unit. Proper positioning of the nipples and umbilicus, as well as harmonious abdominal and torso proportions are critical for an optimal final aesthetic outcome.

Assessing vulnerability of densely populated areas to air pollution using Sentinel-5P imageries: a case study of the Nile Delta, Egypt.

Air pollution represents one of the major environmental stressors with serious implications on human health and ecosystem health. Recently remote sensing imageries; as an alternative cost and time-effective method compared with regular monitoring techniques, were used for provision of appropriate data concerning air quality over large areas. In this context, Sentinel-5P satellite provides high-resolution images of atmospheric pollutants including nitrogen dioxide, ozone, carbon monoxide (CO) and particulate matter (PM). The current work aims to delineate vulnerability of densely populated areas in Northern-Egypt to air pollution through retrieving CO and PM2.5 from Sentinel-5P images and validate the retrieved data through simultaneous In-Situ measurements. For this purpose, our approach comprised four-step methodology; data acquisition on study area, data manipulation, validation of retrieved air quality data and mapping the vulnerability to air pollution. Based on the data retrieved from the imagery, a composite vulnerability index for each CO and PM2.5 value was developed delineating the most vulnerable areas to air pollution in the Northern Nile Delta region. Such results revealed that Sentinel-5P imagery can serve as a valuable tool for monitoring air quality and assessing vulnerability of densely populated areas to air pollution. Accordingly, it can be concluded that the applied Sentinel-5P based model can be applied effectively for other air pollutants and can be extrapolated to other areas with similar and/or different environmental settings.

Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States.

The presence or absence of awns-whether wheat heads are 'bearded' or 'smooth' - is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data for wheat (Triticum aestivum) to estimate the yield effects of awns under different environmental conditions over a 12-year period in the southeastern USA. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.

Optimizing retrieval spaces of bio-optical models for remote sensing of ocean color.

We investigated the optimal number of independent parameters required to accurately represent spectral remote sensing reflectances (R rs) by performing principal component analysis on quality controlled in situ and synthetic R rs data. We found that retrieval algorithms should be able to retrieve no more than four free parameters from R rs spectra for most ocean waters. In addition, we evaluated the performance of five different bio-optical models with different numbers of free parameters for the direct inversion of in-water inherent optical properties (IOPs) from in situ and synthetic R rs data. The multi-parameter models showed similar performances regardless of the number of parameters. Considering the computational cost associated with larger parameter spaces, we recommend bio-optical models with three free parameters for the use of IOP or joint retrieval algorithms.

Hydroxy proline and gamma-aminobutyric acid: markers of susceptibility to vine decline disease caused by the fungus Monosporascus cannonballus in melons (Cucumis melo L.).

Background: Vine decline disease caused by the fungus Monosporascus cannonballus, is a threat to melon production (Cucumis melo L.) worldwide. Nonetheless, little is known about the metabolites produced during the host pathogen interaction. Thus, the objective of this study was to measure quantities of amino acids produced over time during such an interaction. Methods: Two melon genotypes named TAM-Uvalde (susceptible) and USDA PI 124104 (resistant) were grown and inoculated with M. cannonballus. The metabolites previously stated were measured before inoculation (0 hours) and 24, 48 and 72 hours after inoculation, using high performance liquid chromatography analysis. Results: The production of some amino acids during the interaction of the resistant and susceptible melon genotypes with the fungus M. cannonballus was different regarding quantities over time. Interestingly, hydroxy proline was always up-regulated in higher quantities in response to pathogen infection in the genotype TAM-Uvalde. Also, the up-regulation in higher quantities of gamma-aminobutyric acid in the genotype TAM-Uvalde 48 and 72 hours after inoculation, suggests more penetration of the pathogen in its roots. Hence, taken together, hydroxy proline and gamma-aminobutyric acid levels could be used as markers of susceptibility to vine decline disease caused by M. cannonballus, which could be useful in developing resistant varieties.

Expanding horizons of reconstructive microsurgery in Lebanon: Reconstruction of complex traumatic wounds with anterolateral thigh perforator flaps in paediatrics patients less than 10 years of age.

Paediatric complex wounds pose a challenge to the reconstructive surgeon due to the intricacy of reconstructive options required. Developments in microsurgery and microsurgical technique have brought free tissue transfer ever closer to the comfort zone of the reconstructive surgeon for reconstruction of paediatric traumatic complex wounds. We present our experience of microsurgical reconstruction in Lebanon for complex traumatic wounds in paediatric patients under the age of 10 years using the free anterolateral thigh (ALT) flap. The ALT flap has proven its value as a safe, adaptable, and aesthetically acceptable reconstructive option in paediatric complex trauma.

Predictors of surgical site infection following reconstructive flap surgery: A multi-institutional analysis of 37,177 patients.

Purpose: Rates of surgical site infection (SSI) following reconstructive flap surgeries (RFS) vary according to flap recipient site, potentially leading to flap failure. This is the largest study to determine predictors of SSI following RFS across recipient sites. Methods: The National Surgical Quality Improvement Program database was queried for patients undergoing any flap procedure from years 2005 to 2020. RFS involving grafts, skin flaps, or flaps with unknown recipient site were excluded. Patients were stratified according to recipient site: breast, trunk, head and neck (H&N), upper and lower extremities (UE&LE). The primary outcome was the incidence of SSI within 30 days following surgery. Descriptive statistics were calculated. Bivariate analysis and multivariate logistic regression were performed to determine predictors of SSI following RFS. Results: 37,177 patients underwent RFS, of whom 7.5% (n = 2,776) developed SSI. A significantly greater proportion of patients who underwent LE (n = 318, 10.7%) and trunk (n = 1,091, 10.4%) reconstruction developed SSI compared to those who underwent breast (n = 1,201, 6.3%), UE (n = 32, 4.4%), and H&N (n = 100, 4.2%) reconstruction (p < .001). Longer operating times were significant predictors of SSI following RFS across all sites. The strongest predictors of SSI were presence of open wound following trunk and H&N reconstruction [adjusted odds ratio (aOR) 95% confidence interval (CI) 1.82 (1.57-2.11) and 1.75 (1.57-1.95)], disseminated cancer following LE reconstruction [aOR (CI) 3.58 (2.324-5.53)], and history of cardiovascular accident or stroke following breast reconstruction [aOR (CI) 16.97 (2.72-105.82)]. Conclusion: Longer operating time was a significant predictor of SSI regardless of reconstruction site. Reducing operating times through proper surgical planning might help mitigate the risk of SSI following RFS. Our findings should be used to guide patient selection, counseling, and surgical planning prior to RFS.

QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster.

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

Estimating pixel-level uncertainty in ocean color retrievals from MODIS.

The spectral distribution of marine remote sensing reflectance, Rrs, is the fundamental measurement of ocean color science, from which a host of bio-optical and biogeochemical properties of the water column can be derived. Estimation of uncertainty in these derived properties is thus dependent on knowledge of the uncertainty in satellite-retrieved Rrs (uc(Rrs)) at each pixel. Uncertainty in Rrs, in turn, is dependent on the propagation of various uncertainty sources through the Rrs retrieval process, namely the atmospheric correction (AC). A derivative-based method for uncertainty propagation is established here to calculate the pixel-level uncertainty in Rrs, as retrieved using NASA's multiple-scattering epsilon (MSEPS) AC algorithm and verified using Monte Carlo (MC) analysis. The approach is then applied to measurements from the Moderate Resolution Imaging Spectroradiometer (MODIS) on the Aqua satellite, with uncertainty sources including instrument random noise, instrument systematic uncertainty, and forward model uncertainty. The uc(Rrs) is verified by comparison with statistical analysis of coincident retrievals from MODIS and in situ Rrs measurements, and our approach performs well in most cases. Based on analysis of an example 8-day global products, we also show that relative uncertainty in Rrs at blue bands has a similar spatial pattern to the derived concentration of the phytoplankton pigment chlorophyll-a (chl-a), and around 7.3%, 17.0%, and 35.2% of all clear water pixels (chl-a ≤ 0.1 mg/m3) with valid uc(Rrs) have a relative uncertainty ≤ 5% at bands 412 nm, 443 nm, and 488 nm respectively, which is a common goal of ocean color retrievals for clear waters. While the analysis shows that uc(Rrs) calculated from our derivative-based method is reasonable, some issues need further investigation, including improved knowledge of forward model uncertainty and systematic uncertainty in instrument calibration.

Optimal estimation framework for ocean color atmospheric correction and pixel-level uncertainty quantification.

Ocean color (OC) remote sensing requires compensation for atmospheric scattering and absorption (aerosol, Rayleigh, and trace gases), referred to as atmospheric correction (AC). AC allows inference of parameters such as spectrally resolved remote sensing reflectance (Rrs(λ);sr-1) at the ocean surface from the top-of-atmosphere reflectance. Often the uncertainty of this process is not fully explored. Bayesian inference techniques provide a simultaneous AC and uncertainty assessment via a full posterior distribution of the relevant variables, given the prior distribution of those variables and the radiative transfer (RT) likelihood function. Given uncertainties in the algorithm inputs, the Bayesian framework enables better constraints on the AC process by using the complete spectral information compared to traditional approaches that use only a subset of bands for AC. This paper investigates a Bayesian inference research method (optimal estimation [OE]) for OC AC by simultaneously retrieving atmospheric and ocean properties using all visible and near-infrared spectral bands. The OE algorithm analytically approximates the posterior distribution of parameters based on normality assumptions and provides a potentially viable operational algorithm with a reduced computational expense. We developed a neural network RT forward model look-up table-based emulator to increase algorithm efficiency further and thus speed up the likelihood computations. We then applied the OE algorithm to synthetic data and observations from the moderate resolution imaging spectroradiometer (MODIS) on NASA's Aqua spacecraft. We compared the Rrs(λ) retrieval and its uncertainty estimates from the OE method with in-situ validation data from the SeaWiFS bio-optical archive and storage system (SeaBASS) and aerosol robotic network for ocean color (AERONET-OC) datasets. The OE algorithm improved Rrs(λ) estimates relative to the NASA standard operational algorithm by improving all statistical metrics at 443, 555, and 667 nm. Unphysical negative Rrs(λ), which often appears in complex water conditions, was reduced by a factor of 3. The OE-derived pixel-level Rrs(λ) uncertainty estimates were also assessed relative to in-situ data and were shown to have skill.

Capturing Wheat Phenotypes at the Genome Level.

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Descriptive epidemiology of soft tissue and bone sarcomas in Lebanon.

OBJECTIVES: Most epidemiologic studies on soft tissue sarcomas (STS) and bone sarcomas (BS) are performed in western countries, with few in the Middle East and North Africa region. We describe the epidemiology of sarcomas in Lebanon using the medical records database at the American University of Beirut Medical Center (AUBMC). METHODS: This single-center retrospective cohort study included patients with sarcomas registered in the database between 2015 and 2019. Their charts were reviewed for baseline characteristics, tumor biology and location, treatment modalities, recurrence, metastasis, and death. RESULTS: The cohort included 234 patients with STS and 99 patients with BS. Most tumors were <10 cm in size. The most common subtypes were liposarcoma for STS and osteosarcoma for BS. The most common location of STS was the thigh. The most frequent sites of STS metastasis were the lungs. Histological subtype, smoking status, and tumor size and grade were significant for progression-free survival (PFS) in patients with STS. By multivariable analysis, smoking was significantly associated with poorer PFS in STS. For BS, only tumor grade was significant for PFS. CONCLUSION: The epidemiology of sarcomas at AUBMC is similar to that previously reported. Smoking history was associated with poorer survival in patients with STS.

A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding.

Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a training population to develop prediction models for grain yield selection. An imbalanced set of yield data collected from 102 environments (year-by-location) over 10 years, through testing yield in 40-66 lines each year at 6-14 locations with 38-41 lines repeated in the test in any two consecutive years, was used. Based on correlations among data from different environments within two adjacent years and heritability estimated in each environment, yield data from 87 environments were selected and assigned to two correlation-based groups. The yield best linear unbiased estimation (BLUE) from each group, along with reaction to greenbug and Hessian fly in each line, was used for GWAS to reveal genomic regions associated with yield and insect resistance. A total of 74 genomic regions were associated with grain yield and two of them were commonly detected in both correlation-based groups. Greenbug resistance in TXE lines was mainly controlled by Gb3 on chromosome 7DL in addition to two novel regions on 3DL and 6DS, and Hessian fly resistance was conferred by the region on 1AS. Genomic prediction models developed in two correlation-based groups were validated using a set of 105 new advanced breeding lines and the model from correlation-based group G2 was more reliable for prediction. This research not only identified genomic regions associated with yield and insect resistance but also established the method of using historical imbalanced breeding data to develop a genomic prediction model for crop improvement. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01287-8.

Development of the Wheat Practical Haplotype Graph database as a resource for genotyping data storage and genotype imputation.

To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10-14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.

Antimicrobial and cytotoxic activity of electrosprayed chitosan nanoparticles against endodontic pathogens and Balb/c 3T3 fibroblast cells.

The aims of this study were to synthesize highly positively charged chitosan nanoparticles (Ch-Np) using the electrospraying technique, and to test their antimicrobial activity against endodontic pathogens, and cytotoxicity against fibroblast cells. Ch-Np were synthesized from low molecular weight chitosan (LMW-Ch) using the electrospraying technique, and characterized. The antimicrobial activity was evaluated against Streptococcus mutans, Enterococcus faecalis, and Candida albicans in their planktonic state using a Time-Kill Test performed by using broth micro-dilution technique, and against biofilm biomass using a microtiter plate biofilm assay. The cytotoxicity was evaluated using Balb/c 3T3 fibroblast cells with the standard MTT assay. Electrospraying of LMW-Ch produced Ch-Np with an average size of 200 nm, and a surface charge of 51.7 mV. Ch-Np completely eradicated S. mutans and E. faecalis in the planktonic state and showed fungistatic activity against C. albicans. Furthermore, it significantly reduced the biofilm biomass for all the tested microbial species [S. mutans (p = 0.006), E. faecalis (p < 0.0001), and C. albicans (p = 0.004)]. When tested for cytotoxicity using 3T3 cells, Ch-Np showed no cytotoxicity. In conclusion, the highly positively charged, colloidal dispersion of Ch-Np are effective as a biocompatible endodontic antimicrobial agent.

Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments.

Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross 'TAM 112'/'TAM 111' was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m-2 and increased test weight by 2.14 and 3.47 kg m-3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits.