Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling amino acid requirements of poultry

Abstract Poultry nutritionists should constantly evaluate their feeds and feeding programs in view of the changes that continue to be made to the potential growth rate of broilers and egg production in laying hens with the objective of providing the birds with the optimum economic level of nutrients at all times. In this review, the models generated at Universidade Estadual Paulista (UNESP) Jaboticabal, to estimate the optimum intake of amino acids (AA) for broilers and laying hens are presented. These models were used to estimate the variation in AA intake within a broiler population making use of coefficients of variation that represent the real situation in a commercial broiler operation. The range of AA intakes obtained was compared to some commonly applied feeding programs and recommendations. Based on results of our developed models and other feeding programs, feeds were formulated and growth was predicted using a growth simulation model (Avinesp). The prediction of growth showed that these models are reliable and useful tools to assist the nutritionists in decision making. In a study with laying hens, the Reading model (RM) was used to establish optimum economic AA intakes in a flock of hens. The input variables were the means and standard deviations of egg output and BW, and the relationship between the marginal cost of the AA and the marginal revenue for eggs. Based on this model, the optimum intake of each AA can vary with each of the variables considered. The models proposed in our study enable important decisions to be made regarding AA intakes to be used to obtain optimum economic performance from a population of broilers and laying hens.
Inclusion of limited amounts of extruded legumes plus cereal mixes in normocaloric or obesogenic diets for rats: II. Effects on intestinal microbiota composition.

BACKGROUND Differences in the composition of the intestinal microbiota and energetic metabolism between lean and obese population have been described. Legume consumption has been reported to modulate intestinal microbiota composition. However, to the best of our knowledge no information can be found in the literature on the effects of consumption of diets containing extruded legume plus cereal mixes on the intestinal microbiota composition of rats. Our purpose was to evaluate the effects on lipids profile (accompanying paper) and intestinal microbiota composition (current paper) of incorporating this new food ingredient in normocaloric and obesogenic diets. RESULTS Intestinal and fecal qPCR-based microbial composition of rats fed the extruded legumes plus cereal mixes differed (P < 0.05) from controls. Obesogenic diets did not affect bacterial counts. However, the inclusion of the extruded mixes reduced (P < 0.05) log10 counts in some bacterial groups and increased (P < 0.05) counts of Lactobacilli, while others remained unaffected. PCoA at the Genus level grouped together Lactobacillus reuteri, Akkermansia miciniphila and species from Parabacteroides, Prevotella, Rikenellaceae, and Lactobacillus with extruded legume plus cereal diets. Extruded legumes plus cereal mixes feeding was associated with increased mRNA expression of the cytokines IL6 and TNF-α and decreased expression of TLR4. CONCLUSIONS Our results show that the inclusion in the diet of limited amounts (closer to practical human eating behaviour) of an extruded legumes plus cereal mix did modulate the intestinal microbiota composition. Taken together, these results point to protective, health promoting properties of extruded legume plus cereal mixes. This article is protected by copyright. All rights reserved.
Seed dormancy and germination traits of 89 arid zone species targeted for mine-site restoration in the Pilbara region of Western Australia

29 INTRODUCTION . 30 METHODS . 34 Study location . 34 Seed collection . 37 Seed viability . 41 Seed characteristics . 41 Germination experiments . 42 Seed dormancy classification . 43 ‘Germination signature’ assignment and classification tree analysis . 44 RESULTS . 47
Expression of cannabinoid CB1R–GPR55 heteromers in neuronal subtypes of the Macaca fascicularis striatum

The cannabinoid CB1 receptor (CB1R) is the most abundant G protein–coupled receptor in the central nervous system, consistent with the important role of endocannabinoids as neuromodulators. Cannabinoids also modulate the function of G protein–coupled receptor 55 (GPR55), which forms heteroreceptor complexes with the CB1R in the striatum. The aim was to characterize cannabinoid CB1R–GPR55 heteromers (CB1R/GPR55Hets) in the basal ganglia input nuclei of nonhuman primates, Macaca fascicularis, both in projection neurons and interneurons, by the in situ proximity ligation assay. Striatal projecting neurons were identified by the retrograde neuroanatomical tracer, biotinylated dextran amine (BDA), injected into external or internal subdivisions of the globus pallidus. Triple immunofluorescent stains were carried out to visualize (1) BDA‐labeled neurons, (2) CB1R/GPR55Hets, and (3) striatal interneurons positive for choline acetyltransferase, parvalbumin, calretinin, or nitric oxide synthase. CB1R/GPR55Hets were identified within both types of projection neurons as well as all interneurons except those that are cholinergic. Moreover, CB1R/GPR55Hets were found specifically in the neuronal cell surface, and also in intracellular membranes. Further research efforts will be needed to confirm the intracellular occurrence of heteromers and their potential as therapeutic targets in diseases related to motor control imbalances, particularly within a parkinsonian context (with or without levodopa‐induced dyskinesia).
Aerial movements of mites in almonds: implications for pest management

Not available – first paragraph follows: Spider mites and predatory mites can live all year on deciduous trees and vines. During the growing season they colonize the foliage, and during winter they overwinter under bark and in crevices in a state of dormancy (diapause). Spider mites and predatory mites can move from plant to plant by walking or they can be accidentally transferred by other organisms. Spider mites are also known to disperse aerially, and clusters of spider mite females can sometimes be seen on the tips of branches before their dispersal. Some spider mite species drop from leaves on thin silk strands and are picked up by the wind.
Identification and Characterization of Three Novel β1,3-N-Acetylglucosaminyltransferases Structurally Related to the β1,3-Galactosyltransferase Family*

We have isolated three types of cDNAs encoding novel β1,3-N-acetylglucosaminyltransferases (designated β3Gn-T2, -T3, and -T4) from human gastric mucosa and the neuroblastoma cell line SK-N-MC. These enzymes are predicted to be type 2 transmembrane proteins of 397, 372, and 378 amino acids, respectively. They share motifs conserved among members of the β1,3-galactosyltransferase family and a β1,3-N-acetylglucosaminyltransferase (designated β3Gn-T1), but show no structural similarity to another type of β1,3-N-acetylglucosaminyltransferase (iGnT). Each of the enzymes expressed by insect cells as a secreted protein fused to the FLAG peptide showed β1,3-N-acetylglucosaminyltransferase activity for type 2 oligosaccharides but not β1,3-galactosyltransferase activity. These enzymes exhibited different substrate specificity. Transfection of Namalwa KJM-1 cells with β3Gn-T2, -T3, or -T4 cDNA led to an increase in poly-N-acetyllactosamines recognized by an anti-i-antigen antibody or specific lectins. The expression profiles of these β3Gn-Ts were different among 35 human tissues. β3Gn-T2 was ubiquitously expressed, whereas expression of β3Gn-T3 and -T4 was relatively restricted. β3Gn-T3 was expressed in colon, jejunum, stomach, esophagus, placenta, and trachea. β3Gn-T4 was mainly expressed in brain. These results have revealed that several β1,3-N-acetylglucosaminyltransferases form a family with structural similarity to the β1,3-galactosyltransferase family. Considering the differences in substrate specificity and distribution, each β1,3-N-acetylglucosaminyltransferase may play different roles.
Proximate Composition of Edible Palaemonid Prawn Macrobrachium idea (Heller, 1862)

In the present study, proximate composition (protein, carbohydrate, lipid, ash and moisture) and fatty acids were studied in different size groups and sexes of Macrobrachium idae. In general, the protein content was higher in younger ones than in adults. The total values of saturated fatty acids were maximum in females (21.84%) than in males (12.82%). Among various saturated fatty acids recorded, the amount of oleic acid in both sexes was more. As in saturated fatty acids the total amount of monounsaturated fatty acid also shows maximum in males rather than females. The total amount of polyunsaturated fatty acids of M. idae is minimum than monounsaturated fatty acids and saturated fatty acids. The present study clearly indicated that the nutritive value of M. idae is very well comparable to the edible species of decapod crustaceans already studied (shrimps, prawns and lobsters). Considering the above results from the nutritional point of view, M. idae can be very well used as food and perhaps as a candidate species in future for culture.
Practice effects in mild cognitive impairment: A validation of Calamia et al. (2012)

Abstract Objective In a meta-analysis examining practice effects on repeated neuropsychological testing, Calamia et al. (2012) provided information to predict practice effects in healthy and clinical samples across a range of cognitive domains. However, these estimates have not been validated. Method This study used these prediction estimate calculations to predict follow-up scores across one year on a brief battery of neuropsychological tests in a sample of 93 older adults with amnestic mild cognitive impairment. The predicted follow-up scores were compared to observed follow-up scores. Results Using Calamia et al. model’s intercept, age, retest interval, clinical status, and specific cognitive tests, three of the seven observed follow-up scores in this cognitive battery were significantly lower than the Calamia et al. predicted follow-up scores. Differences between individual participants’ observed and predicted follow-up scores were more striking. For example, on Delayed Recall of the Hopkins Verbal Learning Test – Revised, 40% of the sample had Calamia et al. predicted scores that were one or more standard deviations above their observed scores. These differences were most notable on tests that were not in Calamia et al.’s cognitive battery, suggesting the meta-analysis results may not generalize as well to other tests. Conclusions Although Calamia et al. provided a method for predicting practice effects and follow-up scores, these results raise caution when using them in MCI, especially on cognitive tests that were not in their meta-analysis.
Predicting Human Microbe-Drug Associations via Graph Convolutional Network with Conditional Random Field

Abstract Motivation Human microbes play critical roles in drug development and precision medicine. How to systematically understand the complex interaction mechanism between human microbes and drugs remains a challenge nowadays. Identifying microbe-drug associations can not only provide great insights into understanding the mechanism, but also boost the development of drug discovery and repurposing. Considering the high cost and risk of biological experiments, the computational approach is an alternative choice. However, at present, few computational approaches have been developed to tackle this task. Results In this work, we leveraged rich biological information to construct a heterogeneous network for drugs and microbes, including a microbe similarity network, a drug similarity network, and a microbe-drug interaction network. We then proposed a novel Graph Convolutional Network (GCN) based framework for predicting human Microbe-Drug Associations, named GCNMDA. In the hidden layer of GCN, we further exploited the Conditional Random Field (CRF), which can ensure that similar nodes (i.e., microbes or drugs) have similar representations. To more accurately aggregate representations of neighborhoods, an attention mechanism was designed in the CRF layer. Moreover, we performed a random walk with restart (RWR) based scheme on both drug and microbe similarity networks to learn valuable features for drugs and microbes respectively. Experimental results on three different datasets showed that our GCNMDA model consistently achieved better performance than seven state-of-the-art methods. Case studies for three microbes including SARS-CoV-2 and two antimicrobial drugs (i.e., Ciprofloxacin and Moxifloxacin) further confirmed the effectiveness of GCNMDA in identifying potential microbe-drug associations. Availability Python codes and dataset are available at: https://github.com/longyahui/GCNMDA. Supplementary informationbtaa598_SupplementaryMaterials Click here for additional data file. Supplementary data are available at Bioinformatics online.
The effect of perceptual decision-making on the interpretation of twin fetal heart rate tracings

Abstract Objective Decision-making is an integrative process during which multiple sources of available evidence are combined into a singular response. Importantly, subconscious processes occur in perceptual decisions that may influence interpretations of visually displayed data such as fetal heart rate tracings (FHRT), which are typically presented together for twins. To examine the potential impact of subconscious perceptual influences on fetal well-being, differences in assessments of FHRTs for twin gestations presented singly or paired were evaluated for baseline fetal heart rate, variability, accelerations, decelerations, and overall concern. Study design Obstetrical nurses (N = 27) assessed FHRTs from 20 twin gestations (each of which had at least one live birth with a 5-min Apgar <7) presented either on the same tracing or as singletons on separate tracings. Nurses were naïve to the fact that the fetal heart rate tracings presented in the unpaired condition were the same as those presented in the paired condition. Assessments were then compared between the two conditions. Results Each nurse participant completed ratings on five metrics for each of 20 twin gestations across two conditions (80 FHRT assessments, 400 metrics total per participant). The intraobserver impact of visual context was calculated as the frequency of changed opinions regarding an individual metric (e.g. variability) between the paired and unpaired contexts for each individual fetal heart rate. Assessments of variability (average Kappa = 0.59), decelerations (average Kappa = 0.34), and overall level of concern (average Kappa = 0.33) were moderately to heavily impacted by viewing condition (unpaired vs. paired FHRT). Analysis of interobserver agreement using intraclass correlations (two-way random effect, absolute agreement) indicates poor agreement on unpaired assessments for both accelerations (ICC = 0.01, 95% CI −0.01–0.04) and decelerations (ICC = 0.22, 95% CI 0.15–0.33). These results are mirrored in poor agreement on paired assessments for both accelerations (ICC = 0.00, 95% CI −0.01–0.03) and decelerations (ICC = 0.27, 95% CI 0.19–0.39). There was moderate agreement on overall level of concern for unpaired assessments (ICC = 0.55, 95% CI 0.44–0.67) and near moderate agreement for the paired condition (ICC = 0.45, 95% CI 0.34–0.58). Conclusions The simultaneous presentation of fetal heart rate tracings in twin gestations introduces both intraobserver and interobserver variances in the interpretation of variability, accelerations, and decelerations, likely due to the influence of subconscious perceptual decision-making. This may theoretically affect outcomes in cases in which visual information is nuanced. More research is necessary to determine whether the standard protocol of simultaneous assessment of FHRT in twins is subliminally affected by perceptual decision-making.
A theoretical morphologic analysis of convergently evolved erect helical colony form in the Bryozoa

Abstract Exploration of the theoretical morphospace of erect helical colony form in Bryozoa, created by McKinney and Raup (1982), reveals that only a small volume of the three-dimensional space of hypothetical form is occupied by actual colonies of the Paleozoic fenestrates (Class Stenolaemata) Archimedes and Helicopora, helical species of the cheilostome (Class Gymnolaemata) Bugula, and the cyclostome (Class Stenolaemata) Crisidmonea archimediformis. Actual helical-colony bryozoans are not found in regions of the morphospace characterized by colony geometries that possess the largest surface areas of filtration sheet. Examination of computer-simulated colonies in the theoretical morphospace reveals that, although possessing high surface areas, colonies in the empty region of high-surface-area morphospace possess other aspects of geometry that are unrealistic as filter-feeding geometries: the filtration-sheet whorls are held at small acute angles to the central colony axis and are deeply nested within one another, both of which are disadvantageous conditions for the system of filter feeding used by the extant cheilostome Bugula, and presumably by extinct helical-colony bryozoans as well. Even though actual bryozoans are found only in the low to intermediate surface-area regions of the theoretical morphospace, surface area of filtration sheet is a major determinant of form in these helical colonies, as is evidenced by a negative correlation in values of the parameters BWANG and ELEV exhibited by the colony data. Minimum values of BWANG are even further constrained by the apparent need of the Archimedes colonies to maintain filtration-sheet branching densities within the range of 20 to 50.
Does financial inclusion predict a lower risk of loneliness in later life? Evidence from the AgeHeaPsyWel-HeaSeeB study 2016–2017

Abstract Objective For many older people, loneliness represents a common source of impaired quality of life particularly in the context of poor access to financial services. This article examines the association between financial inclusion and loneliness in older adults and explores the moderating effects of gender and physical activity in this association. Methods One thousand two-hundred participants completed the Short Form Revised UCLA Loneliness Scale assessing loneliness during 2016–2017 Aging, Health, Psychological Well-being and Health-seeking Behavior (AgeHeaPsyWel-HeaSeeB) Study. Financial inclusion was assessed using an 8-item Financial Instrument Scale. Results Multiple ordinary least squares (OLS) regressions showed that increases in financial inclusion were associated with decreases in loneliness in the total sample (β = −0.679, p < 0.001) and in women (β = −0.787, p < 0.001) but not in men (β = −0.594, p = 0.084). The negative effect of financial inclusion on loneliness was pronounced among those who engaged in physical activity (β = −0.646, p < 0.042). Conclusions Findings underscore the importance of financial inclusion for loneliness in later life particularly among older women and those who engage in physical activity. Encouraging and strengthening financial inclusion may crucially improve psychological health and emotional well-being among aging adults.
Home Telehealth Technologies for Heart Failure: An Examination of Adherence Among Veterans.

The current retrospective cohort study uses Department of Veterans Affairs (VA) clinical and facility data of Veterans with heart failure enrolled in the VA Home Tele-health (HT) Program. General estimating equations with facility as a covariate were used to model percent average adherence at 1, 3, 6, and 12 months post-enrollment. Most HT patients were White, male, and of older age (mean = 71 years). Average adherence increased the longer patients remained in the HT program. Number of weekly reports of HT use, not having depression, and being of older age were all associated with higher adherence. Compared to White Veterans, Black and other non-White Veterans had lower adherence. These findings identify subgroups of patients (e.g., those with depression, of younger age, non-White) that may benefit from additional efforts to improve adherence to HT technologies. [Journal of Gerontological Nursing, 46(7), 26-34. ].
What determines the population density and reproductive success of rough-legged buzzards, Buteo lagopus, in the Siberian tundra?

The annual variability of the breeding performance of rodentivorous birds of prey has traditionally been explained in terms of annual fluctuations in rodent abundance. This paper presents data from the Siberian tundra showing that this relationship may not be so simple as generally thought. The data consist of parameters of small mammal population fluctuations (small mammal density (SMD), average body weight, species diversity and rate of change of species diversity), inter-specific competition and meteorological factors (mean temperature and snow melt date) during every stage of the breeding cycle of the rough-legged buzzard (Buteo lagopus). The density of breeding pairs was found to be correlated with the SMD, whereas the total number of territorial pairs including non-breeding ones could be most accurately predicted by a model incorporating both the SMD and the population density of a larger competitor, the snowy owl (Nyctea scandiaca). Clutch size showed no correlation with the SMD. The best-fit multiple regression model to predict clutch size includes only small mammal diversity and its rate of change as predictive factors. Number of nestlings and egg losses did not show any correlation with any of the prey-related or weather parameters. Although the total number of rough-legged buzzard fledglings produced per unit area showed a significant positive correlation with the SMD in a single-factor regression, the most accurate multiple regression model to predict overall reproductive output included only the rate of change of the small mammal species diversity. The number of offspring produced by the buzzards in a given area fluctuated synchronously with the SMD, but the cycle was significantly more consistent in amplitude in the predator as compared to the prey.
PATTERNS OF KARYOTYPIC MEGAEVOLUTION IN REITHRODONTOMYS: EVIDENCE FROM A CYTOCHROME-b PHYLOGENETIC HYPOTHESIS

Abstract Phylogenetic relationships among 7 species of Reithrodontomys were examined using the complete mitochondrial cytochrome-b gene. DNA-sequence data were analyzed using parsimony (weighted and unweighted) and genetic distance methods. In all analyses, R. sumichrasti, R. megalotis, and R. zacatecae formed a monophyletic clade. Likewise, R. montanus and R. raviventris were depicted as sister taxa in all analyses. Our study supports recognition of R. zacatecae as a species distinct from R. megalotis and recognition of R. raviventris as distinct from R. montanus. Patterns of chromosomal evolution were examined using differential staining as resolved by 3 DNA probes and fluorescent in situ hybridization. Using the phylogeny based on DNA sequences, we concluded that there has been extensive chromosomal repatterning (in most cases karyotypic megaevolution) in the evolution of R. zacatecae, R. megalotis, R. sumichrasti, R. montanus, R. raviventris, and R. humulis.