Mixed modeling for fiber yield genetic selection in sugarcane

The current demand for clean and renewable energy has provoked considerable changes in the production system of agroindustrial companies. The generation of bioelectricity through the burning of sugarcane bagasse has considerably risen in the recent years. This work aimed to focus on the sugarcane genotypes selection for fiber productivity. The experiment was outlined in randomized blocks with four repetitions, and sixteen genotypes were evaluated. The evaluated traits were: cane tons per hectare, sucrose tons per hectare, fiber tons per hectare, fiber content and apparent sucrose content. To the selection, the mixed linear models methodology was used. The heritability coefficients suggest a significant genetic gain and the harmonic means of relative performances of predicted genotypic values allowed the identification of stable genotypes related to the traits evaluated in four harvest cycles. Considering the current average demand of sugarcane agroindustry for varieties with fiber content between 12% and 17% and sucrose content near 13%, for energy generation and sugar production, the genotypes EECAC 06, EECAC 03, EECAC 04 and EECAC 07 are presented as commercial cultivation options. Highlights - Mixed models constitute an efficient tool for sugarcane selection focused onto fiber and sucrose production. - This methodology provides significant genetic gains based on predicted genetic values free from interaction with harvest cycles. - The evaluated genotypes present high fiber and sucrose productivity, genotypic adaptability and stability throughout harvest cycles, indicating longevity in the sugarcane crop.

The Complex Role of Utterance Length on Grammaticality: Multivariate Multilevel Analysis of English and Spanish Utterances of First-Grade English Learners

Purpose: This study examined the relationship between utterance length, syntactic complexity, and the probability of making an error at the utterance level. Method: The participants in this study included 830 Spanish-speaking first graders who were learning English at school. Story retells in both Spanish and English were collected from all children. Generalized mixed linear models were used to examine within-child and between-children effects of utterance length and subordination on the probability of making an error at the utterance level. Results: The relationship between utterance length and grammaticality was found to differ by error type (omission vs. commission), language (Spanish vs. English), and level of analysis (within-child vs. between-children). For errors of commission, the probability of making an error increased as a child produced utterances that were longer relative to their average utterance length (within-child effect). Contrastively, for errors of omission, the probability of making an error decreased when a child produced utterances that were longer relative to their average utterance length (within-child effect). In English, a child who produced utterances that were, on average, longer than the average utterance length for all children produced more errors of commission and fewer errors of omission (between-children effect). This between-children effect was similar in Spanish for errors of commission but nonsignificant for errors of omission. For both error types, the within-child effects of utterance length were moderated by the use of subordination. Conclusion: The relationship between utterance length and grammaticality is complex and varies by error type, language, and whether the frame of reference is the child's own language (within-child effect) or the language of other children (between-children effect). Supplemental Material https://doi.org/10.23641/asha.17035916

Stool and ruminal microbiome components associated with methane emission and feed efficiency in Nelore beef cattle.

Background: The impact of extreme changes in weather patterns in the economy and human welfare are some of the biggest challenges that our civilization is facing. From the anthropogenic activities that contribute to climate change, reducing the impact of farming activities is a priority, since it is responsible for up to 18% of greenhouse gases linked to such activities. To this end, we tested if the ruminal and fecal microbiome components of 52 Brazilian Nelore bulls, belonging to two treatment groups based on the feed intervention, conventional and by-products based diet, could be used in the future as biomarkers for methane emission and feed efficiency in bovine.Results: We identified a total of 5,693 Amplicon Sequence Variants (ASVs) in the Nelore bulls microbiomes. Differential abundance (DA) analysis with the ANCOM approach identified 30 bacterial and 15 archaea ASVs as DA among treatment groups. Association analysis using Maaslin2 and Mixed Linear Models indicated that bacterial ASVs are linked to the residual methane emission (RCH4) and Residual Feed Intake (RFI) phenotypes, contributing to the host’s phenotypic variation, suggesting their potential as targets for interventions and/or biomarkers.Conclusion: Feed composition induced significant differences in abundance and richness of ruminal and fecal microbial populations. The diet based on industrial byproducts applied to our treatment groups influenced the microbiome diversity of bacteria and archaea, but not of protozoa. Different ASVs were associated with RCH4 emission and RFI in both ruminal and fecal microbiomes. While ruminal ASVs are expected to directly influence RCH4 emission and RFI, the relation of fecal taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits might also be associated with host health due to their link to anti-inflammatory compounds, and these have the potential to be used as accessible biomarkers for these complex phenotypes.

Effects of Receiving Two Initial Feedings of Colostrum on the Average Daily Gain and Health of Pre-Weaning Group Housed Holstein Heifer Calves

We studied the effect on average daily gain (ADG) and health of an additional colostrum feeding to Holstein dairy heifers 12–16 h after the first colostrum feeding, provided within 2 h of birth. Calves (n = 190) with an average birth weight of 38.8 kg (29.5–52.6 kg) were randomly enrolled in blocks to either the control (CON) or colostrum (COL). The CON received 3 L of acidified pasteurized whole milk, and the COL received 3 L of pasteurized colostrum [average: 25.5 (24.7–26.4)% Brix]. Calves were group-housed, weighed, withers height measured weekly. Serum was obtained and analyzed with a% Brix refractometer. Mixed linear models were used to assess the differences in ADG, body weight, and height between the treatment and control. There was no difference in ADG between the COL and CON. However, serum % Brix was higher in the COL group (9.7%) than in the CON group (9.2%). Calves in the COL had more antibiotic treatments for respiratory diseases but fewer antibiotic treatments for otitis than the CON. In conclusion, providing an extra feeding of colostrum did not contribute to ADG of Holstein heifers during the pre-weaning period but did provide them with a higher total serum protein concentration.

Pharmacological impacts on schizophrenia functional analysis: a postmortem proteome study.

Schizophrenia (SCZ) is a severe and debilitating mental illness. Antipsychotic drugs (APDs) are used to treat both positive and negative SCZ symptoms, by influencing the cellular, subcellular-synaptic, and molecular processes. We posit that these effects influence our understanding of SCZ. To address this, we analyzed postmortem dorsolateral prefrontal cortex grey matter samples from control and SCZ subjects (n=10/group) using liquid-chromatography mass-spectrometry-based proteomics. We retrieved SCZ-altered and APD-influenced proteome-sets using linear and mixed linear models, respectively, and validated them experimentally using independent cohorts and insilico using published datasets. Functional analysis of proteome-sets was contrasted at the biological pathway, cell-type, subcellular-synaptic, and drug-target levels. The SCZ-altered proteome was conserved across several studies from DLPFC and other brain areas and was dependent on drug effect. At the pathway level, we observed an aberrant extracellular event and, except for homeostasis, signal-transduction, cytoskeleton, and dendrites associated downregulated changes, the APDs compensated for the majority of the SCZ-altered pathways. At the cell-type level, the up-and down-regulated SCZ-altered events were associated with two different subsets of striatum projecting layer-5 pyramidal-neurons regulating dopaminergic secretion. At the subcellular synaptic level, compensatory pre- and post-synaptic events were observed. At the drug target level, dopaminergic processes influence the SCZ-altered up-regulated proteome, whereas non-dopaminergic and a diverse array of non-neuromodulatory mechanisms influence the SCZ-altered down-regulated proteome. While these findings are dependent on pharmacological effects, they are also consistent with previous SCZ studies, implying the need to re-evaluate previous results. We discuss our findings in the context of cortico-striatal influence in SCZ-pathology.

Identification of functional features underlying heat stress response in Sprague-Dawley rats using mixed linear models

Since global temperature is expected to rise by 2℃ in 2050 heat stress may become the most severe environmental factor. In the study, we illustrate the application of mixed linear models for the analysis of whole transcriptome expression in livers and adrenal tissues of Sprague-Dawley rats obtained by a heat stress experiment. By applying those models, we considered four sources of variation in transcript expression, comprising transcripts (1), genes (2), Gene Ontology terms (3), and Reactome pathways (4) and focussed on accounting for the similarity within each source, which was expressed as a covariance matrix. Models based on transcripts or genes levels explained a larger proportion of log2 fold change than models fitting the functional components of Gene Ontology terms or Reactome pathways. In the liver, among the most significant genes were PNKD and TRIP12. In the adrenal tissue, one transcript of the SUCO gene was expressed more strongly in the control group than in the heat-stress group. PLEC had two transcripts, which were significantly overexpressed in the heat-stress group. PER3 was significant only on gene level. Moving to the functional scale, five Gene Ontologies and one Reactome pathway were significant in the liver. They can be grouped into ontologies related to DNA repair, histone ubiquitination, the regulation of embryonic development and cytoplasmic translation. Linear mixed models are valuable tools for the analysis of high-throughput biological data. Their main advantages are the possibility to incorporate information on covariance between observations and circumventing the problem of multiple testing.

Quantitative Anatomic Comparison of Microsurgical Transcranial, Endoscopic Endonasal, and Transorbital Approaches to the Spheno-Orbital Region

BACKGROUND The spheno-orbital region (SOR) is a complex anatomic area that can be accessed with different surgical approaches. OBJECTIVE To quantitatively compare, in a preclinical setting, microsurgical transcranial approaches (MTAs), endoscopic endonasal transpterygoid approach (EEA), and endoscopic transorbital approaches (ETOAs) to the SOR. METHODS These approaches were performed in 5 specimens: EEA, ETOAs (superior eyelid and inferolateral), anterolateral MTAs (supraorbital, minipterional, pterional, pterional-transzygomatic, and frontotemporal-orbitozygomatic), and lateral MTAs (subtemporal and subtemporal transzygomatic). All specimens underwent high-resolution computed tomography; an optic neuronavigation system with dedicated software was used to quantify working volume and exposed area for each approach. Mixed linear models with random intercepts were used for statistical analyses. RESULTS Anterolateral MTAs offer a direct route to the greater wings (GWs) and lesser wings (LWs); only they guarantee exposure of the anterior clinoid. Lateral MTAs provide access to a large area corresponding to the GW, up to the superior orbital fissure (SOF) anteriorly and the foramen rotundum medially. ETOAs also access the GW, close to the lateral portion of SOF, but with a different angle of view as compared to lateral MTAs. Access to deep and medial structures, such as the lamina papyracea and the medial SOF, is offered only by EEA, which exposes the LW and GW only to a limited extent. CONCLUSION This is the first study that offers a quantitative comparison of the most used approaches to SOR. A detailed knowledge of their advantages and limitations is paramount to choose the ideal one, or their combination, in the clinical setting.

Reliability of mechanical ventilation during continuous chest compressions: a crossover study of transport ventilators in a human cadaver model of CPR

Background Previous studies have stated that hyperventilation often occurs in cardiopulmonary resuscitation (CPR) mainly due to excessive ventilation frequencies, especially when a manual valve bag is used. Transport ventilators may provide mandatory ventilation with predetermined tidal volumes and without the risk of hyperventilation. Nonetheless, interactions between chest compressions and ventilations are likely to occur. We investigated whether transport ventilators can provide adequate alveolar ventilation during continuous chest compression in adult CPR. Methods A three-period crossover study with three common transport ventilators in a cadaver model of CPR was carried out. The three ventilators ‘MEDUMAT Standard²’, ‘Oxylog 3000 plus’, and ‘Monnal T60’ represent three different interventions, providing volume-controlled continuous mandatory ventilation (VC-CMV) via an endotracheal tube with a tidal volume of 6 mL/kg predicted body weight. Proximal airflow was measured, and the net tidal volume was derived for each respiratory cycle. The deviation from the predetermined tidal volume was calculated and analysed. Several mixed linear models were calculated with the cadaver as a random factor and ventilator, height, sex, crossover period and incremental number of each ventilation within the period as covariates to evaluate differences between ventilators. Results Overall median deviation of net tidal volume from predetermined tidal volume was − 21.2 % (IQR: 19.6, range: [− 87.9 %; 25.8 %]) corresponding to a tidal volume of 4.75 mL/kg predicted body weight (IQR: 1.2, range: [0.7; 7.6]). In a mixed linear model, the ventilator model, the crossover period, and the cadaver’s height were significant factors for decreased tidal volume. The estimated effects of tidal volume deviation for each ventilator were − 14.5 % [95 %-CI: −22.5; −6.5] (p = 0.0004) for ‘Monnal T60’, − 30.6 % [95 %-CI: −38.6; −22.6] (p < 0.0001) for ‘Oxylog 3000 plus’ and − 31.0 % [95 %-CI: −38.9; −23.0] (p < 0.0001) for ‘MEDUMAT Standard²’. Conclusions All investigated transport ventilators were able to provide alveolar ventilation even though chest compressions considerably decreased tidal volumes. Our results support the concept of using ventilators to avoid excessive ventilatory rates in CPR. This experimental study suggests that healthcare professionals should carefully monitor actual tidal volumes to recognise the occurrence of hypoventilation during continuous chest compressions.

Voice Quality of Children With Cerebral Palsy

Purpose Many children with cerebral palsy (CP) are described as having altered vocal quality. The current study utilizes psychoacoustic measures, namely, low-amplitude (H1*–H2*) and high-amplitude (H1*–A2*) spectral tilt and cepstral peak prominence (CPP), to identify the vocal fold articulation characteristics in this population. Method Eight children with CP and eight typically developing (TD) peers produced vowel singletons [i, ɑ, u] and a story retell task with the same vowels in the words “beets, Bobby, boots.” H1*–H2*, H1*–A2*, and CPP were extracted from each vowel. Results were analyzed with mixed linear models to identify the effect of Group (CP, TD), Task (vowel singleton, story retell), and Vowel [i, ɑ, u] on the dependent variables. Results Children with CP have lower spectral tilt values (H1*–H2* and H1*–A2*) and lower CPP values than their TD peers. For both groups, vowel singletons were associated with lower CPP values as compared to story retell. Finally, the vowel [ɑ] was associated with higher spectral tilt and higher CPP values as compared to [i, u]. Conclusions Children with CP have more constricted and creaky vocal quality due to lower spectral tilt and greater noise. Unlike adults, children demonstrate poorer vocal fold articulation when producing vowel singletons as compared to story retell. Finally, low vowels like [ɑ] seem to be produced with less constriction and noise as compared to high vowels.

AFEchidna is a R package for genetic evaluation of plant and animal breeding datasets

Progeny tests play important roles in plant and animal breeding programs, and mixed linear models are usually performed to estimate variance components of random effects, estimate the fixed effects (Best Linear Unbiased Estimates, BLUEs) and predict the random effects (Best Linear Unbiased Predictions, BLUPs) via restricted maximum likehood (REML) methods in progeny test datasets. The current pioneer software for genetic assessment is ASReml, but it is commercial and expensive. Although there is free software such as Echidna or the R package sommer, the Echidna syntax is complex and the R package functionality is limited. Therefore, this study aims to develop a R package named AFEchidna based on Echidna software. The mixed linear models are conveniently implemented for users through the AFEchidna package to solve variance components, genetic parameters and the BLUP values of random effects, and the batch analysis of multiple traits, multiple variance structures and multiple genetic parameters can be also performed, as well as comparison between different models and genomic BLUP analysis. The AFEchidna package is free, please email us ([email protected]) to get a copy if one is interested for it. The AFEchidna package is developed to expand free genetic assessment software with the expectation that its efficiency could be close to the commercial software.