Yield prediction in a peanut breeding program using remote sensing data and machine learning algorithms.

Peanut is a critical food crop worldwide, and the development of high-throughput phenotyping techniques is essential for enhancing the crop's genetic gain rate. Given the obvious challenges of directly estimating peanut yields through remote sensing, an approach that utilizes above-ground phenotypes to estimate underground yield is necessary. To that end, this study leveraged unmanned aerial vehicles (UAVs) for high-throughput phenotyping of surface traits in peanut. Using a diverse set of peanut germplasm planted in 2021 and 2022, UAV flight missions were repeatedly conducted to capture image data that were used to construct high-resolution multitemporal sigmoidal growth curves based on apparent characteristics, such as canopy cover and canopy height. Latent phenotypes extracted from these growth curves and their first derivatives informed the development of advanced machine learning models, specifically random forest and eXtreme Gradient Boosting (XGBoost), to estimate yield in the peanut plots. The random forest model exhibited exceptional predictive accuracy (R2 = 0.93), while XGBoost was also reasonably effective (R2 = 0.88). When using confusion matrices to evaluate the classification abilities of each model, the two models proved valuable in a breeding pipeline, particularly for filtering out underperforming genotypes. In addition, the random forest model excelled in identifying top-performing material while minimizing Type I and Type II errors. Overall, these findings underscore the potential of machine learning models, especially random forests and XGBoost, in predicting peanut yield and improving the efficiency of peanut breeding programs.

Novel genes and alleles of the BTB/POZ protein family in Oryza rufipogon.

The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O. rufipogon as outcomes of tandem duplication events. Phylogenetic grouping of duplicated OrBTB genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The O. rufipogon genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant, O. sativa ssp. japonica. Comparative sequence analysis and structure comparisons of novel OrBTB genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.

Increased Presentation of Diabetic Ketoacidosis and Changes in Age and Month of Type 1 Diabetes at Onset during the COVID-19 Pandemic in Spain.

Objective: To assess the impact of the COVID-19 pandemic and lockdown measures on the presenting characteristics (age at diagnosis, severity, monthly distribution) of newly diagnosed type 1 diabetes in Spanish children. Research Design and Methods: An ambispective observational multicenter study was conducted in nine Spanish tertiary-level hospitals between January 2015 and March 2021. Inclusion criteria: new cases of type 1 diabetes in children (0-14 years) recording age, sex, date of diagnosis, presence of diabetic ketoacidosis (DKA) at onset, and severity of DKA. Data were compared before and during the pandemic. Results: We registered 1444 new cases of type 1 diabetes in children: 1085 in the pre-pandemic period (2015-2019) and 359 during the pandemic (2020-March 2021). There was a significant increase in the group aged ≤4 years in the pandemic period (chi-squared = 10.986, df 2, p = 0.0041). In 2020-2021, cases of DKA increased significantly by 12% (95% CI: 7.2-20.4%), with a higher percentage of moderate and severe DKA, although this increase was not significant. In 2020, there was a sharp decrease in the number of cases in March, with a progressive increase from May through November, higher than in the same months of the period 2015-2019, highlighting the increase in the number of cases in June, September, and November. The first three months of 2021 showed a different trend to that observed both in the years 2015-2019 and in 2020, with a marked increase in the number of cases. Conclusions: A change in monthly distribution was described, with an increase in DKA at onset of type 1 diabetes. No differences were found in severity, although there were differences in the age distribution, with an increase in the number of cases in children under 4 years of age.

DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds.

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.

Mutations in HID1 Cause Syndromic Infantile Encephalopathy and Hypopituitarism.

OBJECTIVE: Precursors of peptide hormones undergo posttranslational modifications within the trans-Golgi network (TGN). Dysfunction of proteins involved at different steps of this process cause several complex syndromes affecting the central nervous system (CNS). We aimed to clarify the genetic cause in a group of patients characterized by hypopituitarism in combination with brain atrophy, thin corpus callosum, severe developmental delay, visual impairment, and epilepsy. METHODS: Whole exome sequencing was performed in seven individuals of six unrelated families with these features. Postmortem histopathological and HID1 expression analysis of brain tissue and pituitary gland were conducted in one patient. Functional consequences of the homozygous HID1 variant p.R433W were investigated by Seahorse XF Assay in fibroblasts of two patients. RESULTS: Bi-allelic variants in the gene HID1 domain-containing protein 1 (HID1) were identified in all patients. Postmortem examination confirmed cerebral atrophy with enlarged lateral ventricles. Markedly reduced expression of pituitary hormones was found in pituitary gland tissue. Colocalization of HID1 protein with the TGN was not altered in fibroblasts of patients compared to controls, while the extracellular acidification rate upon stimulation with potassium chloride was significantly reduced in patient fibroblasts compared to controls. INTERPRETATION: Our findings indicate that mutations in HID1 cause an early infantile encephalopathy with hypopituitarism as the leading presentation, and expand the list of syndromic CNS diseases caused by interference of TGN function. ANN NEUROL 2021;90:149-164.

Seed-to-seed early-season cold resiliency in sorghum.

Early planted sorghum usually experiences cooler day/night temperatures, which may result in delayed growth, floral initiation, and infertile pollen, limiting productivity in high altitudes and temperate regions. Genetic variability for cold tolerance in sorghum has been evaluated by characterizing germination, emergence, vigor, and seedling growth under sub-optimal temperatures. However, the compounded effect of early season cold on plant growth and development and subsequent variability in potential grain yield losses has not been evaluated. Agro-morphological and physiological responses of sorghum grown under early-, mid-, and standard planting dates in West Texas were characterized from seed-to-seed. A set of diverse lines and hybrids with two major sources of tolerance, and previously selected for seedling cold tolerance were used. These were evaluated with a standard commercial hybrid known for its seedling cold tolerance and some cold susceptible breeding lines as checks. Variabilities in assessed parameters at seedling, early vegetative, and maturity stages were observed across planting dates for genotypes and sources of cold tolerance. Panicle initiation was delayed, and panicle size reduced, resulting in decreased grain yields under early and mid-planting dates. Coupled with final germination percent, panicle width and area were significant unique predictors of yield under early and mid-planting dates. Significant variability in performance was observed not only between cold tolerant and susceptible checks, but noticeably between sources of cold tolerance, with the Ethiopian highland sources having lesser yield penalties than their Chinese counterparts. Thus, screening for cold tolerance should not be limited to early seedling characterization but should also consider agronomic traits that may affect yield penalties depending on the sources of tolerance.

Adherence and long-term outcomes of growth hormone therapy with easypod™ in pediatric subjects: Spanish ECOS study.

BACKGROUND: Non-adherence to r-hGH treatments occurs in a variable percentage of subjects. One problem found when evaluating adherence is the great variability in methods of detection and definitions utilized in studies. This study assessed the level of adherence in subjects receiving r-hGH with the easypod™ electronic device. METHODS: National, multicenter, prospective and observational study involving 238 subjects (144 with GH deficiency (GHD), and 86 with small for gestational age (SGA), 8 with Turner Syndrome), who received r-hGH with easypod™ for at least 3 months before inclusion. The follow-up period was 4 years. RESULTS: Overall adherence was 94.5%; 97.5% after 6 months, 95.3% after 1 year, 93.7% after 2, 94.4% after 3 and 95.5% after 4 years of treatment. No differences in adherence were observed between prepubertal and pubertal groups and GHD and SGA groups. Change in height after 1 and 2 years, change in height SDS after 1 and 2 years, HV after 1 year, HV SDS after at 1 and 4 years, change in BMI after 1 year and change in BMI SDS at 1 and 2 years showed significant correlation with adherence. No significant differences in adherence according to IGF-I levels were found in follow-up visits or between groups. CONCLUSIONS: The easypod™ electronic device, apart from being a precise and objective measure of adherence to r-hGH treatment, allows high compliance rates to be achieved over long periods of time. Adherence significantly impacts growth outcomes associated with r-hGH treatment.

Safety Outcomes During Pediatric GH Therapy: Final Results From the Prospective GeNeSIS Observational Program.

Context: Safety concerns have been raised regarding premature mortality, diabetes, neoplasia, and cerebrovascular disease in association with GH therapy. Objective: To assess incidence of key safety outcomes. Design: Prospective, multinational, observational study (1999 to 2015). Setting: A total of 22,311 GH-treated children from 827 investigative sites in 30 countries. Patients: Children with growth disorders. Interventions: GH treatment. Main outcome measures: Standardized mortality ratio (SMR) and standardized incidence ratio (SIR) with 95% CIs for mortality, diabetes, and primary cancer using general population registries. Results: Predominant short stature diagnoses were GH deficiency (63%), idiopathic short stature (13%), and Turner syndrome (8%), with mean ± SD follow-up of 4.2 ± 3.2 years (∼92,000 person-years [PY]). Forty-two deaths occurred in patients with follow-up, with an SMR (95% CI) of 0.61 (0.44, 0.82); the SMR was elevated for patients with cancer-related organic GH deficiency [5.87 (3.21, 9.85)]. Based on 18 cases, type 2 diabetes mellitus (T2DM) risk was elevated [SIR: 3.77 (2.24, 5.96)], but 72% had risk factors. In patients without cancer history, 14 primary cancers were observed [SIR: 0.71 (0.39, 1.20)]. Second neoplasms occurred in 31 of 622 cancer survivors [5.0%; 10.7 (7.5, 15.2) cases/1000 PY] and intracranial tumor recurrences in 67 of 823 tumor survivors [8.1%; 16.9 (13.3, 21.5) cases/1000 PY]. All three hemorrhagic stroke cases had risk factors. Conclusions: GeNeSIS (Genetics and Neuroendocrinology of Short Stature International Study) data support the favorable safety profile of pediatric GH treatment. Overall risk of death or primary cancer was not elevated in GH-treated children, and no hemorrhagic strokes occurred in patients without risk factors. T2DM incidence was elevated compared with the general population, but most cases had diabetes risk factors.

Sinus graft with safescraper: 5-year results.

PURPOSE: In the procedure of sinus floor elevation, autogenous bone, allogenic grafts, and several other bone substitutes are used. However, autogenous bone is still considered the gold standard. Donor sites for autogenous bone are generally the iliac crest, oral cavity, calvarium bone, and tibia. In this work the experience with the use of a Safescraper device for harvesting of autogenous bone is reported and a decision-making algorithm for grafting in sinus floor elevation procedures is proposed. MATERIALS AND METHODS: Forty sinus augmentation procedures were performed in 34 patients. All sinuses were filled with a mixture of autogenous bone and bovine hydroxyapatite. A Safescraper device was used to harvest autologous bone from the maxillary area. Platelet-rich plasma was used to sustain bone placement. Sixty-five dental implants were placed at 4 months with a flapless procedure. A clinical and radiological 5-year retrospective case series of a cohort is reported. RESULTS: In all cases new bone formation was confirmed radiologically and implant placement was performed successfully. Analysis of samples obtained by biopsy with histology and microcomputed tomography showed the presence of mature bone. Healing problems were observed in only 1 case. CONCLUSIONS: Sinus augmentation with bone grafts obtained from oral cavity with a bone scraper device has the advantage of providing autogenous bone without the need for an extra surgical approach. This procedure yields satisfactory results in bone formation, implant survival, and patient satisfaction. When combined with a flapless approach for implant placement, a decrease in the morbidity of the entire process is achieved.

Weight loss in prepubertal obese children is associated with a decrease in adipocyte fatty-acid-binding protein without changes in lipocalin-2: a 2-year longitudinal study.

CONTEXT: Lipocalin-2 and adipocyte fatty-acid-binding protein (A-FABP or FABP4) are adipokines potentially involved in the pathophysiology of obesity and metabolic syndrome in adults. In children, they have been scarcely studied. OBJECTIVE: To analyze lipocalin-2 and A-FABP circulating levels before and after 2 years of a dieting and lifestyle intervention in a prepubertal obese cohort. DESIGN AND SETTING: Case-control study with a prospective follow-up of cases for 2 years in our referral pediatric endocrine outpatient center. PATIENTS AND METHODS: Seventy-three prepubertal obese children, 8.03 ± 1.08-years old, and 47 age- and gender-matched lean controls were studied. Anthropometric parameters, blood pressure, fasting oral glucose tolerance test, homeostatic model insulin resistance index (HOMA-IR), lipid profile, lipocalin-2, and A-FABP were evaluated. Weight loss was considered if z-score body mass index (BMI) decreased at least 0.5 s.d. RESULTS: At baseline, lipocalin-2 and A-FABP were higher in prepubertal obese children than those in lean controls (P<0.001). A-FABP showed a gradual increase, according to the obesity degree (r(2)=0.632; P<0.001). After 2 years, obese patients who lost weight showed a decrease in A-FABP (a mean 2% reduction in BMI was associated with a mean 29% decrease in A-FABP (P<0.001)) without changes in lipocalin-2 levels. Regression model analysis adjusted by age, sex, BMI, and HOMA showed that A-FABP was lower in males (ß=-5.77 (CI 95%: -9.7; -1.84)) and was modified by BMI (ß=2.7 (CI 95%: 1.77-3.62), r(2)=0.659). Lipocalin-2 was not modified by any of these variables. CONCLUSIONS: Prepubertal obese children show high plasma lipocalin-2 and A-FABP levels, but only A-FABP is influenced by weight loss.