Development and optimization of expected cross value for mate selection problems.

In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.

Efficient genomics-based 'end-to-end' selective tree breeding framework.

Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an "end-to-end" selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals' breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits' correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method's superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.

Exploring Bismuth Coordination Complexes as Visible-Light Absorbers: Synthesis, Characterization, and Photophysical Properties.

Bismuth-based coordination complexes are advantageous over other metal complexes, as bismuth is the heaviest nontoxic element with high spin-orbit coupling and potential optoelectronics applications. Herein, four bismuth halide-based coordination complexes [Bi2Cl6(phen-thio)2] (1), [Bi2Br6(phen-thio)2] (2), [Bi2I6(phen-thio)2] (3), and [Bi2I6(phen-Me)2] (4) were synthesized, characterized, and subjected to detailed photophysical studies. The complexes were characterized by single-crystal X-ray diffraction, powder X-ray diffraction, and NMR studies. Spectroscopic analyses of 1-4 in solutions of different polarities were performed to understand the role of the organic and inorganic components in determining the ground- and excited-state properties of the complexes. The photophysical properties of the complexes were characterized by ground-state absorption, steady-state photoluminescence, microsecond time-resolved photoluminescence, and absorption spectroscopy. Periodic density functional theory (DFT) calculations were performed on the solid-state structures to understand the role of the organic and inorganic parts of the complexes. The studies showed that changing the ancillary ligand from chlorine (Cl) and bromine (Br) to iodine (I) bathochromically shifts the absorption band along with enhancing the absorption coefficient. Also, changing the halides (Cl, Br to I) affects the photoluminescent quantum yields of the ligand-centered (LC) emissive state without markedly affecting the lifetimes. The combined results confirmed that ground-state properties are strongly influenced by the inorganic part, and the lower-energy excited state is LC. This study paves the way to design novel bismuth coordination complexes for optoelectronic applications by rigorously choosing the ligands and bismuth salt.

Spatial extent as a sensitive amyloid-PET metric in preclinical Alzheimer's disease.

INTRODUCTION: Spatial extent-based measures of how far amyloid beta (Aß) has spread throughout the neocortex may be more sensitive than traditional Aß-positron emission tomography (PET) measures of Aß level for detecting early Aß deposits in preclinical Alzheimer's disease (AD) and improve understanding of Aß's association with tau proliferation and cognitive decline. METHODS: Pittsburgh Compound-B (PIB)-PET scans from 261 cognitively unimpaired older adults from the Harvard Aging Brain Study were used to measure Aß level (LVL; neocortical PIB DVR) and spatial extent (EXT), calculated as the proportion of the neocortex that is PIB+. RESULTS: EXT enabled earlier detection of Aß deposits longitudinally confirmed to reach a traditional LVL-based threshold for Aß+ within 5 years. EXT improved prediction of cognitive decline (Preclinical Alzheimer Cognitive Composite) and tau proliferation (flortaucipir-PET) over LVL. DISCUSSION: These findings indicate EXT may be more sensitive to Aß's role in preclinical AD than level and improve targeting of individuals for AD prevention trials. HIGHLIGHTS: Aß spatial extent (EXT) was measured as the percentage of the neocortex with elevated Pittsburgh Compound-B. Aß EXT improved detection of Aß below traditional PET thresholds. Early regional Aß deposits were spatially heterogeneous. Cognition and tau were more closely tied to Aß EXT than Aß level. Neocortical tau onset aligned with reaching widespread neocortical Aß.

Presenilin-1 mutation position influences amyloidosis, small vessel disease, and dementia with disease stage.

INTRODUCTION: Amyloidosis, including cerebral amyloid angiopathy, and markers of small vessel disease (SVD) vary across dominantly inherited Alzheimer's disease (DIAD) presenilin-1 (PSEN1) mutation carriers. We investigated how mutation position relative to codon 200 (pre-/postcodon 200) influences these pathologic features and dementia at different stages. METHODS: Individuals from families with known PSEN1 mutations (n = 393) underwent neuroimaging and clinical assessments. We cross-sectionally evaluated regional Pittsburgh compound B-positron emission tomography uptake, magnetic resonance imaging markers of SVD (diffusion tensor imaging-based white matter injury, white matter hyperintensity volumes, and microhemorrhages), and cognition. RESULTS: Postcodon 200 carriers had lower amyloid burden in all regions but worse markers of SVD and worse Clinical Dementia Rating® scores compared to precodon 200 carriers as a function of estimated years to symptom onset. Markers of SVD partially mediated the mutation position effects on clinical measures. DISCUSSION: We demonstrated the genotypic variability behind spatiotemporal amyloidosis, SVD, and clinical presentation in DIAD, which may inform patient prognosis and clinical trials. HIGHLIGHTS: Mutation position influences Aß burden, SVD, and dementia. PSEN1 pre-200 group had stronger associations between Aß burden and disease stage. PSEN1 post-200 group had stronger associations between SVD markers and disease stage. PSEN1 post-200 group had worse dementia score than pre-200 in late disease stage. Diffusion tensor imaging-based SVD markers mediated mutation position effects on dementia in the late stage.

Efficacy, safety, and immunogenicity of an inactivated, adjuvanted enterovirus 71 vaccine in infants and children: a multiregion, double-blind, randomised, placebo-controlled, phase 3 trial.

BACKGROUND: Children are susceptible to severe or fatal enterovirus 71 (EV71) infections. We aimed to evaluate the efficacy, safety, and immunogenicity of EV71vac, an aluminium phosphate-adjuvanted inactivated EV71 vaccine in children aged 2-71 months. METHODS: We did a randomised, double-blinded, placebo-controlled, phase 3 trial at five hospitals in Taiwan and two in Vietnam. Children aged 2-71 months were stratified by country and age, and randomly assigned (1:1) to receive two doses of EV71vac or placebo via intramuscular injection 56 days apart. Children aged 2-23 months received a third booster dose on day 366. The primary endpoint was the clinical efficacy of the total vaccinated cohort against EV71-associated diseases during the follow-up period, from 14 days after the second dose to when 15 cases of EV71 infections were confirmed in the per-protocol population. Our safety analysis included all participants who received at least one dose of EV71vac. This trial is registered with ClinicalTrials.gov, NCT03865238, and is complete. FINDINGS: Between April 23 and Dec 25, 2019, of 3663 children assessed, 3061 were randomly assigned, of whom 3049 were vaccinated: 1521 children in the EV71vac group and 1528 in the placebo group. By May 20, 2021, our primary efficacy analysis included 2959 children, with 1476 children in the EV71vac group and 1483 children in the placebo group. The vaccine efficacy of EV71vac was 96·8% (95% CI 85·5-100) against EV71 associated diseases (p<0·0001). The percentage of participants who reported solicited adverse events were similar in both groups: 865 (56·9%) in the EV71vac group and 852 (55·8%) in the placebo group. Almost all reported solicited adverse events were mild and self-limited. INTERPRETATION: EV71vac is safe, well-tolerated, and highly effective in preventing EV71 associated diseases in children aged 2-71 months. FUNDING: Medigen Vaccine Biologics and A+ Industrial Innovative R&D Program of the Ministry of Economic Affairs, Taiwan.

Amyloid-Related Imaging Abnormalities in the DIAN-TU-001 Trial of Gantenerumab and Solanezumab: Lessons from a Trial in Dominantly Inherited Alzheimer Disease.

OBJECTIVE: To determine the characteristics of participants with amyloid-related imaging abnormalities (ARIA) in a trial of gantenerumab or solanezumab in dominantly inherited Alzheimer disease (DIAD). METHODS: 142 DIAD mutation carriers received either gantenerumab SC (n = 52), solanezumab IV (n = 50), or placebo (n = 40). Participants underwent assessments with the Clinical Dementia Rating® (CDR®), neuropsychological testing, CSF biomarkers, ß-amyloid positron emission tomography (PET), and magnetic resonance imaging (MRI) to monitor ARIA. Cross-sectional and longitudinal analyses evaluated potential ARIA-related risk factors. RESULTS: Eleven participants developed ARIA-E, including 3 with mild symptoms. No ARIA-E was reported under solanezumab while gantenerumab was associated with ARIA-E compared to placebo (odds ratio [OR] = 9.1, confidence interval [CI][1.2, 412.3]; p = 0.021). Under gantenerumab, APOE-ɛ4 carriers were more likely to develop ARIA-E (OR = 5.0, CI[1.0, 30.4]; p = 0.055), as were individuals with microhemorrhage at baseline (OR = 13.7, CI[1.2, 163.2]; p = 0.039). No ARIA-E was observed at the initial 225 mg/month gantenerumab dose, and most cases were observed at doses >675 mg. At first ARIA-E occurrence, all ARIA-E participants were amyloid-PET+, 60% were CDR >0, 60% were past their estimated year to symptom onset, and 60% had also incident ARIA-H. Most ARIA-E radiologically resolved after dose adjustment and developing ARIA-E did not significantly increase odds of trial discontinuation. ARIA-E was more frequently observed in the occipital lobe (90%). ARIA-E severity was associated with age at time of ARIA-E. INTERPRETATION: In DIAD, solanezumab was not associated with ARIA. Gantenerumab dose over 225 mg increased ARIA-E risk, with additional risk for individuals APOE-ɛ4(+) or with microhemorrhage. ARIA-E was reversible on MRI in most cases, generally asymptomatic, without additional risk for trial discontinuation. ANN NEUROL 2022;92:729-744.

Longitudinal head-to-head comparison of 11C-PiB and 18F-florbetapir PET in a Phase 2/3 clinical trial of anti-amyloid-ß monoclonal antibodies in dominantly inherited Alzheimer's disease.

PURPOSE: Pittsburgh Compound-B (11C-PiB) and 18F-florbetapir are amyloid-ß (Aß) positron emission tomography (PET) radiotracers that have been used as endpoints in Alzheimer's disease (AD) clinical trials to evaluate the efficacy of anti-Aß monoclonal antibodies. However, comparing drug effects between and within trials may become complicated if different Aß radiotracers were used. To study the consequences of using different Aß radiotracers to measure Aß clearance, we performed a head-to-head comparison of 11C-PiB and 18F-florbetapir in a Phase 2/3 clinical trial of anti-Aß monoclonal antibodies. METHODS: Sixty-six mutation-positive participants enrolled in the gantenerumab and placebo arms of the first Dominantly Inherited Alzheimer Network Trials Unit clinical trial (DIAN-TU-001) underwent both 11C-PiB and 18F-florbetapir PET imaging at baseline and during at least one follow-up visit. For each PET scan, regional standardized uptake value ratios (SUVRs), regional Centiloids, a global cortical SUVR, and a global cortical Centiloid value were calculated. Longitudinal changes in SUVRs and Centiloids were estimated using linear mixed models. Differences in longitudinal change between PET radiotracers and between drug arms were estimated using paired and Welch two sample t-tests, respectively. Simulated clinical trials were conducted to evaluate the consequences of some research sites using 11C-PiB while other sites use 18F-florbetapir for Aß PET imaging. RESULTS: In the placebo arm, the absolute rate of longitudinal change measured by global cortical 11C-PiB SUVRs did not differ from that of global cortical 18F-florbetapir SUVRs. In the gantenerumab arm, global cortical 11C-PiB SUVRs decreased more rapidly than global cortical 18F-florbetapir SUVRs. Drug effects were statistically significant across both Aß radiotracers. In contrast, the rates of longitudinal change measured in global cortical Centiloids did not differ between Aß radiotracers in either the placebo or gantenerumab arms, and drug effects remained statistically significant. Regional analyses largely recapitulated these global cortical analyses. Across simulated clinical trials, type I error was higher in trials where both Aß radiotracers were used versus trials where only one Aß radiotracer was used. Power was lower in trials where 18F-florbetapir was primarily used versus trials where 11C-PiB was primarily used. CONCLUSION: Gantenerumab treatment induces longitudinal changes in Aß PET, and the absolute rates of these longitudinal changes differ significantly between Aß radiotracers. These differences were not seen in the placebo arm, suggesting that Aß-clearing treatments may pose unique challenges when attempting to compare longitudinal results across different Aß radiotracers. Our results suggest converting Aß PET SUVR measurements to Centiloids (both globally and regionally) can harmonize these differences without losing sensitivity to drug effects. Nonetheless, until consensus is achieved on how to harmonize drug effects across radiotracers, and since using multiple radiotracers in the same trial may increase type I error, multisite studies should consider potential variability due to different radiotracers when interpreting Aß PET biomarker data and, if feasible, use a single radiotracer for the best results. TRIAL REGISTRATION: ClinicalTrials.gov NCT01760005. Registered 31 December 2012. Retrospectively registered.

Weighted kernels improve multi-environment genomic prediction.

Crucial to variety improvement programs is the reliable and accurate prediction of genotype's performance across environments. However, due to the impactful presence of genotype by environment (G×E) interaction that dictates how changes in expression and function of genes influence target traits in different environments, prediction performance of genomic selection (GS) using single-environment models often falls short. Furthermore, despite the successes of genome-wide association studies (GWAS), the genetic insights derived from genome-to-phenome mapping have not yet been incorporated in predictive analytics, making GS models that use Gaussian kernel primarily an estimator of genomic similarity, instead of the underlying genetics characteristics of the populations. Here, we developed a GS framework that, in addition to capturing the overall genomic relationship, can capitalize on the signal of genetic associations of the phenotypic variation as well as the genetic characteristics of the populations. The capacity of predicting the performance of populations across environments was demonstrated by an overall gain in predictability up to 31% for the winter wheat DH population. Compared to Gaussian kernels, we showed that our multi-environment weighted kernels could better leverage the significance of genetic associations and yielded a marked improvement of 4-33% in prediction accuracy for half-sib families. Furthermore, the flexibility incorporated in our Bayesian implementation provides the generalizable capacity required for predicting multiple highly genetic heterogeneous populations across environments, allowing reliable GS for genetic improvement programs that have no access to genetically uniform material.

Nutritional and feeding challenges in aerodigestive patients.

PURPOSE OF REVIEW: Aerodigestive disorders encompass conditions that affect both the airway and gastrointestinal tract. These include conditions such as acquired and congenital defects of the airway and esophagus as well as neuromuscular disorders. Patients often suffer from dysphagia, aspiration, and respiratory disorders. This article will provide a review of current practices in the management of feeding disorders, oropharyngeal dysphagia, and nutritional support in the aerodigestive population. RECENT FINDINGS: Oral aversion, aspiration, and feeding-tube dependence are all commonly encountered problems in the aerodigestive population. Intensive inpatient and outpatient programs along with use of appetite stimulants and psychotropic medications may help to improve feeding-related disorders. Aspiration affects many patients and requires close monitoring of clinical symptoms along with routine assessment with video fluoroscopy. Developments in blenderized feeds and formula supplementation have also provided new options for patients with feeding intolerance. SUMMARY: Patients with aerodigestive disorders require complex medical care, and multidisciplinary teams are the most effective in addressing their medical needs. Advances in feeding, occupational, and pharmacologic therapy have allowed healthcare providers to better address the needs of these patients.

Factors Associated with Preferences for Long-Acting Injectable Antiretroviral Therapy Among Adolescents and Young People Living with HIV in South Africa.

Long-acting injectable anti-retroviral therapy (LAART) may overcome barriers to long-term adherence and improve the survival of adolescents and young people living with HIV (AYLHIV). Research on the acceptability of LAART for this age-group is limited. We asked 953 AYLHIV about their preferred (theoretical) ART mode of delivery (pill, injectable, or other) in 2017-2018, before LAART was available or known to AYLHIV in South Africa. One in eight (12%) AYLHIV preferred LAART over single or multiple pill regimens. In multivariate analyses, six factors were associated with LAART preference: medication stock-outs (aOR = 2.56, 95% CI 1.40-4.68, p = 0.002), experiencing side-effects (aOR = 1.84, 95% CI 1.15-2.97, p = 0.012), pill-burden (aOR = 1.88, 95% CI 1.20-2.94, p = 0.006), past-year treatment changes (aOR = 1.63, 95% CI 1.06-2.51, p = 0.025), any HIV stigma (aOR = 2.22, 95% CI 1.39-3.53, p ≤ 0.001) and recent ART initiation (aOR = 2.02, 95% CI 1.09-3.74, p = 0.025). In marginal effects modelling, 66% of adolescents who experienced all factors were likely to prefer LAART, highlighting the potential high acceptability of LAART among adolescents and young people living with HIV struggling to adhere and have good HIV treatment outcomes. Adolescent boys who reported high ART pill burden were more likely to prefer LAART than their female peers in moderation analyses, suggesting that LAART may be particularly important to improve treatment outcomes among male AYLHIV as they become older. Adding LAART to existing treatment options for AYLHIV, particularly higher risk groups, would support AYLHIV to attain and sustain viral suppression-the third 95, and reduce their risk of AIDS-related mortality.

RESUMEN: La terapia antirretroviral inyectable de acción prolongada (TAR LA) puede superar las barreras a la adherencia y mejorar la supervivencia de los adolescentes y jóvenes que viven con el VIH (AJVVIH). La investigación sobre la aceptabilidad del TAR LA para este grupo de edad es limitada. Preguntamos a 953 AJVVIH sobre su modo preferido (teórico) de administración de ART (píldora, inyectable u otro) en 2017­2018, antes de que TAR LA estuviera disponible o fuera conocido por los AJVVIH en Sudáfrica. Uno de cada ocho (12%) AJVVIH prefirió TAR LA sobre los regímenes de píldoras simples o múltiples. En los análisis multivariantes, seis factores se asociaron con la preferencia de TAR LA: agotamiento de la medicación (odd ratio ajustada [ORa] = 2,56, IC95% 1,40­4,68 p = 0,002), experimentar efectos secundarios (ORa = 1,84, IC95% 1,15­2,97 p = 0,012), carga de píldoras (ORa = 1. 88, IC95% 1,20­2,94 p = 0,006), cambios de tratamiento en el último año (ORa = 1,63, IC95% 1,06­2,51 p = 0,025), cualquier estigma del VIH (ORa = 2,22, IC95% 1,39­3,53 p ≤ 0,001) y el inicio reciente del TAR (ORa = 2,02, IC95% 1,09­3,74 p = 0,025). En la modelización de efectos marginales, el 66% de los adolescentes que experimentaron todos los factores eran propensos a preferir la TAR LA, lo que pone de relieve la alta aceptabilidad potencial de la TAR LA entre los adolescentes y los jóvenes que viven con el VIH que luchan por adherirse y tener buenos resultados en el tratamiento del VIH. Los adolescentes varones que informaron de una alta carga de píldoras para el tratamiento antirretroviral eran más propensos a preferir la TAR LA que sus pares mujeres en los análisis de moderación, lo que sugiere que la TAR LA puede ser particularmente importante para mejorar los resultados del tratamiento entre los hombres que viven con el VIH a medida que crecen. La adición de la TAR LA a las opciones de tratamiento existentes para las personas que viven con el VIH, en particular los grupos de mayor riesgo, ayudaría a las personas que viven con el VIH a alcanzar y mantener la supresión vírica -el tercer 95- y a reducir el riesgo de mortalidad relacionada con el sida.

Development of membrane-active peptide therapeutics in oncology.

Membrane-active peptides play an essential role in many living organisms and their immune systems and counter many infectious diseases. Many have dual or multiple mechanisms and can synergize with other molecules, like peptides, proteins, and small molecules. Although membrane-active peptides have been intensively studied in the past decades and more than 3500 sequences have been identified, only a few received approvals from the US Food and Drug Administration. In this review, we investigated all the peptide therapeutics that have entered the market or were subjected to preclinical and clinical studies to understand how they succeeded. With technological advancement (e.g., chemical modifications and pharmaceutical formulations) and a better understanding of the mechanism of action and the potential targets, we found at least five membrane-active peptide drugs that have entered preclinical/clinical phases and show promising results for cancer treatment. We summarized our findings in this review and provided insights into membrane-active anticancer peptide therapeutics.

Immunogenicity and safety of heterologous mRNA-1273/MVC-COV1901 vaccination versus homologous mRNA1273 vaccination: A randomized, double-blind controlled study.

BACKGROUND/PURPOSE: MVC-COV1901 is a protein vaccine based on the same SARS-CoV-2 strain used in mRNA vaccine mRNA-1273. Data are lacking on immunogenicity and safety of MVC-COV1901 as heterologous boost for people already received one dose of mRNA-1273. METHODS: This is a randomized, double-blind trial that recruited adults aged 20-70 years who previously received a single dose of mRNA-1273 vaccine and were randomly assigned in a 1:1 ratio to receive a second dose with the homologous vaccine or protein-based MVC-COV1901 8-12 weeks after the first dose. The primary outcome was neutralizing antibody titers in terms of the geometric mean titer (GMT) 14 days after the second dose. Safety was assessed in all participants who received a dose of the study vaccine. The study is registered with ClinicalTrials.gov (NCT05079633). RESULTS: From September 30 to November 5, 2021, 144 participants were enrolled and randomly assigned to the MVC-COV1901 boost group (n = 72) or the mRNA-1273 boost group (n = 72). The neutralizing antibodies on Day 15 and the anti-SARS-CoV-2 IgG titers on Day 15 and 29 of homologous mRNA-1273 were significantly higher than those of heterologous mRNA-1273/MVC-COV1901. Cellular immune responses were comparable in both groups. However, adverse events were much more frequent after the mRNA-1273 boost than after the MVC-COV1901 boost. CONCLUSION: Our results show that heterologous boost with MVC-COV1901 yielded an inferior immunogenicity but significantly fewer adverse events, compared with homologous boost with mRNA-1273. In people experienced severe adverse events after prime dose of mRNA-1273, as well as in periods when the supply of mRNA-1273 is limited, MVC-COV1901 could serve as an acceptable alternative heterologous boost.

Exploring the cognitive development of children born to adolescent mothers in South Africa.

This study explores the cognitive development of children born to adolescent mothers within South Africa compared to existing reference data, and explores development by child age bands to examine relative levels of development. Cross-sectional analyses present data from 954 adolescents (10-19 years) and their first-born children (0-68 months). All adolescents completed questionnaires relating to themselves and their children, and standardized child cognitive assessments (Mullen Scales of Early Learning) were undertaken. Cognitive development scores of the sample were lower than USA reference population scores and relative performance compared to the reference population was found to decline with increasing child age. When compared to children born to adult mothers in the sub-Saharan African region, children born to adolescent mothers (human immunodeficiency virus [HIV] unexposed; n = 724) were found to have lower cognitive development scores. Findings identify critical periods of development where intervention may be required to bolster outcomes for children born to adolescent mothers. Highlights: An exploration of the cognitive development of children born to adolescent mothers within South Africa utilizing the Mullen Scales of Early Learning.Cognitive development scores of children born to adolescent mothers within South Africa were lower compared to USA norm reference data and declined with child age.Previous studies utilizing the Mullen Scales of Early Learning within sub-Saharan Africa were summarized, and comparisons were made with the current sample.Findings highlight a potential risk of developmental delay among children born to adolescent mothers compared to children of adult mothers in the sub-Saharan African region.

Hamsters Protected from SARS-CoV-2 Delta Variant Challenge after Two Doses of Adjuvanted SARS-CoV-2 Recombinant Spike Protein (S-2P) and One Dose of Beta S-2P.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern negatively impact the effectiveness of vaccines. In this study, we challenge hamsters with the delta variant after 2- or 3-dose inoculations with SARS-CoV-2 vaccines constructed from stabilized prefusion spike proteins (S-2P) of Wuhan (W) and beta (B) variants. Compared to 3 doses of W S-2P, 2 doses of W S-2P followed by a third dose of B S-2P induced the highest neutralizing antibody titer against live SARS-CoV-2 virus and enhanced neutralization of omicron variant pseudovirus. Reduced lung live virus titer and pathology suggested that all vaccination regimens protect hamsters from SARS-CoV-2 delta variant challenge.

Evaluating the Neutralizing Ability of a CpG-Adjuvanted S-2P Subunit Vaccine Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern.

BACKGROUND: Variants of concern (VoCs) have the potential to diminish the neutralizing capacity of antibodies elicited by vaccines. MVC-COV1901 is a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine consisting of recombinant prefusion stabilized spike protein S-2P adjuvanted with CpG 1018 and aluminum hydroxide. We explored the effectiveness of MVC-COV1901 against the VoCs. METHODS: Serum samples were taken from rats and phase 1 clinical trial human subjects immunized with a low, medium, or high dose of MVC-COV1901. The neutralizing titers of serum antibodies were assayed with pseudoviruses coated with the SARS-CoV-2 spike protein of the wild-type (WT), D614G, Alpha, or Beta variants. RESULTS: Rats vaccinated twice with vaccine containing high doses of antigen retained high levels of neutralization activity against the Beta variant, albeit with a slight reduction compared to WT. After the third dose, neutralizing titers against the Beta variant were noticeably enhanced regardless of the amount of antigen used for immunization. In humans, vaccinated phase 1 subjects still showed appreciable neutralization abilities against the D614G, Alpha, and Beta variants, although neutralizing titers were significantly reduced against the Beta variant. CONCLUSIONS: Two doses of MVC-COV1901 were able to elicit neutralizing antibodies against SARS-CoV-2 variants with an overall tendency of inducing higher immune response at a higher dose level. The neutralizing titers to the Beta variant in rats and humans were lower than those for WT and the Alpha variant. An additional third dose in rats was able to partially compensate for the reduction in neutralization against the Beta variant. We have demonstrated that immunization with MVC-COV1901 was effective against VoCs.

GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated Peanut (Arachis hypogaea L.).

BACKGROUND: Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety's adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. The objective of this study was to map the quantitative trait locus (QTL) associated with peanut growth habit-related traits by combining the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods. RESULTS: GWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, the 90 suggestive and significant SNPs associated with lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT) were identified. These SNPs were distributed among 15 chromosomes. A total of 597 associated candidate genes may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the linkage disequilibrium (LD) decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467-144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The expression levels of Araip.E64SW detected by qRT-PCR showed significant difference between 'Jihua 5' and 'M130'. CONCLUSIONS: In this study, the SNP (AX-147,251,085 and AX-144,353,467) associated with LBA by GWAS was overlapped with the results in BSA-seq through combined analysis of GWAS and BSA-seq. Based on LD decay distance, the genome range related to LBA on B05 was shortened to 144,193,467-144,513,467. Three candidate genes related to F-box family proteins (Araip.E64SW, Araip.YG1LK, and Araip.JJ6RA) and one candidate gene related to PPP family proteins (Araip.YU281) may be involved in plant growth and development in this genome region. The expression analysis revealed that Araip.E64SW was involved in peanut growth habits. These candidate genes will provide molecular targets in marker-assisted selection for peanut growth habits.

Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine.

BACKGROUND: Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias. RESULTS: MT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP. CONCLUSIONS: The power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.

Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations.

While droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e. height growth, drought avoidance based on water-use efficiency inferred from δ13C and pest resistance based on defence traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ13C and increased the evolutionary potential of height growth and δ13C across populations. We found, however, no pronounced gradient in defences and their evolutionary potential along populations or test sites. Response to selection was weak in defences across test sites, but high for height growth particularly at warm test sites. Response to the selection of δ13C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with a limited evolutionary influence from pest (biotic) pressures.

Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP.

Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918-1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits' heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.