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With its unique geographic location at the northern end of the Central American isthmus, Honduras straddles the boundaries of two distinct cultural regions—the Mesoamerican and the Istmo-Colombian. In this context, we briefly discuss the progress of population genetics studies conducted within Honduras. The text underscores the importance of conducting fieldwork to improve our understanding of the genetic history, population dynamics, and emergence of diseases among the Indigenous communities of this country. Among the seven distinct Indigenous populations currently under genetic investigation, we highlight the case of the Garifuna people. We explore their origins, patterns of migration, genetic differentiation, and the prevalence of Hypertrophic Cardiomyopathy (HCM), which may be linked to founder effects. Our research endeavors in Honduras emphasize the value of an interdisciplinary approach in the study of local human populations that have been instrumental in shaping our evolving comprehension of the genetic landscapes within this unique geographical and cultural setting.

Purpose: To investigate the use of super-resolution imaging techniques to enable telepathology using low-cost commercial cameras. Design: Experimental study. Participants: A total of 139 ophthalmic pathology slides obtained from the Ophthalmic Pathology service at the University of California, Irvine. Methods: Denoising Diffusion Probabilistic Model (DDPM) was developed to predict super-resolution pathology slide images from low-resolution inputs. The model was pretrained using 150 000 images randomly sampled from the ImageNet dataset. Patch aggregation was used to generate large images with DDPM. The performance of DDPM was evaluated against that of generative adversarial networks (GANs) and Robust UNet, which were also trained on the same dataset. Main Outcome Measures: The performance of models trained to generate super-resolution output images from low-resolution input images can be evaluated by using the mean squared error (MSE) and Structural Similarity Index Measure (SSIM), as well as subjective grades provided by expert pathologist graders. Results: In total, our study included 110 training images, 9 validation images, and 20 testing images. The objective performance scores were averaged over patches generated from 20 test images. The DDPM-based approach with pretraining produced the best results, with an MSE score of 1.35e-5 and an SSIM score of 0.8987. A qualitative analysis of super-resolution images was conducted by expert 3 pathologists and 1 expert ophthalmic microscopist, and the average accuracy of identifying the correct ground truth images ranged from 25% to 70% (with an average accuracy of 46.5%) for widefield images and 25% to 60% (with an average accuracy of 38.25%) for individual patches. Conclusions: The DDPM-based approach with pretraining is assessed to be effective at super-resolution prediction for ophthalmic pathology slides both in terms of objective and subjective measures. The proposed methodology is expected to decrease the reliance on costly slide scanners for acquiring high-quality pathology slide images, while also streamlining clinical workflow and expanding the scope of ophthalmic telepathology. Financial Disclosure(s): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Introduction: When visualizing complex data, the layout method chosen can greatly affect the ability to identify outliers, spot incorrect modeling assumptions, or recognize unexpected patterns. Additionally, visual layout can play a crucial role in communicating results to peers.Methods: In this paper, we compared the effectiveness of three visual layouts—the adjacency matrix, a half-matrix layout, and a circular layout—for visualizing spatial connectivity data, e.g., contacts derived from chromatin conformation capture experiments. To assess these visual layouts, we conducted a study comprising 150 participants from Amazon’s Mechanical Turk, as well as a second expert study comprising 30 biomedical research scientists.Results: The Mechanical Turk study found that the circular layout was the most accurate and intuitive, while the expert study found that the circular and half-matrix layouts were more accurate than the matrix layout.Discussion: We concluded that the circular layout may be a good default choice for visualizing smaller datasets with relatively few spatial contacts, while, for larger datasets, the half- matrix layout may be a better choice. Our results also demonstrated how crowdsourcing methods could be used to determine which visual layouts are best for addressing specific data challenges in bioinformatics.

Humans perceive light in the visible spectrum (400-700 nm). Some night vision systems use infrared light that is not perceptible to humans and the images rendered are transposed to a digital display presenting a monochromatic image in the visible spectrum. We sought to develop an imaging algorithm powered by optimized deep learning architectures whereby infrared spectral illumination of a scene could be used to predict a visible spectrum rendering of the scene as if it were perceived by a human with visible spectrum light. This would make it possible to digitally render a visible spectrum scene to humans when they are otherwise in complete "darkness" and only illuminated with infrared light. To achieve this goal, we used a monochromatic camera sensitive to visible and near infrared light to acquire an image dataset of printed images of faces under multispectral illumination spanning standard visible red (604 nm), green (529 nm) and blue (447 nm) as well as infrared wavelengths (718, 777, and 807 nm). We then optimized a convolutional neural network with a U-Net-like architecture to predict visible spectrum images from only near-infrared images. This study serves as a first step towards predicting human visible spectrum scenes from imperceptible near-infrared illumination. Further work can profoundly contribute to a variety of applications including night vision and studies of biological samples sensitive to visible light.

The research has shown the interesting contributions of shearing in mid-gestation on the performance of lambs from birth to weaning. Other studies have reported that shearing at early pregnancy influences the development of the placenta and lamb live weight at birth. However, there was a lack of information on the effect of early-prepartum shearing on the behavior of the offspring from weaning onward. This study evaluated the effect of shearing ewes at 50 days of gestation on the growth, reproductive behavior and response to a gastrointestinal parasite challenge in the female offspring from weaning to 18 months old. Fifty-seven Polwarth female lambs were used, 22 being singles and 35 twins born to ewes either shorn at 50 days of pregnancy (PS, n = 23) or shorn at 62 days postpartum (U, control, n = 34) resulting in four subgroups: single lambs born to PS ewes (n = 8), born to U ewes (n = 14), twin lambs born to PS ewes (n = 15) or born to U ewes (n = 20). All progeny were managed together under improved pasture with a minimum forage allowance of 6% live weight on dry basis. Body weight, body condition score and fecal eggs count were recorded every 14 days from weaning to 18 months of age. Concentrations of progesterone were measured weekly (from 4 to 10 months of age and from 14 to 18 months of age) to establish the onset of puberty. Ovulation rate at an induced and a natural heat (545 ± 1.0 and 562 ± 1.0 day old) was recorded. Prepartum shearing did not affect the age at puberty or the ovulation rate of female offspring, but those born as singles were more precocious ( P = 0.03) and heavier ( P = 0.02) at puberty than twin born lambs. Both the average value of parasite egg count ( P = 0.0 7) and the Famacha index ( P = 0.02) for the entire study period were lower in lambs born to prepartum shorn ewes than those born to postpartum shorn ewes. In conclusion, shearing at 50 days of gestation did not affect the growth or the reproductive behavior of female offspring. However, female lambs born from ewe shorn during gestation showed a better response to the parasitic challenge, and further research is required to confirm this.

There is a growing interest to improve feed efficiency (FE) traits in cattle. The genomic selection was proposed to improve these traits since they are difficult and expensive to measure. Up to date, there are scarce studies about the implementation of genomic selection for FE traits in indicine cattle under different scenarios of pseudo-phenotypes, models, and validation strategies on a commercial large scale. Thus, the aim was to evaluate the feasibility of genomic selection implementation for FE traits in Nelore cattle applying different models and pseudo-phenotypes under validation strategies. Phenotypic and genotypic information from 4 329 and 3 467 animals were used, respectively, which were tested for residual feed intake, DM intake, feed efficiency, feed conversion ratio, residual BW gain, and residual intake and BW gain. Six prediction methods were used: single-step genomic best linear unbiased prediction, Bayes A, Bayes B, Bayes Cπ, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayes R. Phenotypes adjusted for fixed effects (Y*), estimated breeding value (EBV), and EBV deregressed (DEBV) were used as pseudo-phenotypes. The validation approaches used were: (1) random: the data was randomly divided into ten subsets and the validation was done in each subset at a time; (2) age: the partition into training and testing sets was based on year of birth and testing animals were born after 2016; and (3) EBV accuracy: the data was split into two groups, being animals with accuracy above 0.45 the training set; and below 0.45 the validation set. In the analyses that used the Y* as pseudo-phenotype, prediction ability (PA) was obtained by dividing the correlation between pseudo-phenotype and genomic EBV (GEBV) by the square root of the heritability of the trait. When EBV and DEBV were used as the pseudo-phenotype, the simple correlation of this quantity with the GEBV was considered as PA. The prediction methods show similar results for PA and bias. The random cross-validation presented higher PA (0.17) than EBV accuracy (0.14) and age (0.13). The PA was higher for Y* than for EBV and DEBV (30.0 and 34.3%, respectively). Random validation presented the highest PA, being indicated for use in populations composed mainly of young animals and traits with few generations of data recording. For high heritability traits, the validation can be done by age, enabling the prediction of the next-generation genetic merit. These results would support breeders to identify genomic approaches that are more viable for genomic prediction for FE-related traits.

The relationships between ovulation rate and nutrition remain confused, probably because of uncontrolled variation in experimental conditions. To help resolve the problem, we analyzed data from 20 experiments conducted between 2002 and 2016, in Uruguay with grazing ewes. All experiments were carried out by a single laboratory under comparable conditions of experimental design and measured variables. The studies used a total of 3 720 ewes, of purebred Corriedale, Polwarth, or East Friesian x Polwarth genotypes. In all experiments, a control group grazed native pastures and extra nutrition was provided to the treatment groups using either improved pastures or supplements. Ovulation rate was measured by counting corpora lutea using laparoscopy or rectal ultrasound or by counting foetuses at ultrasound on day 45 of gestation. For statistical analysis, data were grouped according to nutritional treatment (control or supplemented) and, within these groups, type of supplement to provide energy or protein (protected or not from rumen degradation). Across all experiments, 92–99% of the ewes ovulated and the effects of diet, length of supplementation, and initial live weight and genotype are reported. Within diets, ovulation was most affected by overall energy intake during supplementation (P

Several methods have been used for genome-enabled prediction (or genomic selection) of complex traits, for example, multiple regression models describing a target trait with a linear function of a set of genetic markers. Genomic selection studies have been focused mostly on single-trait analyses. However, most profitability traits are genetically correlated, and an increase in prediction accuracy of genomic breeding values for genetically correlated traits is expected when using multiple-trait models. Thus, this study was carried out to assess the accuracy of genomic prediction for carcass and meat quality traits in Nelore cattle, using single- and multiple-trait approaches. The study considered 15 780, 15 784, 15 742 and 526 records of rib eye area (REA, cm2), back fat thickness (BF, mm), rump fat (RF, mm) and Warner–Bratzler shear force (WBSF, kg), respectively, in Nelore cattle, from the Nelore Brazil Breeding Program. Animals were genotyped with a low-density single nucleotide polymorphism (SNP) panel and subsequently imputed to arrays with 54 and 777 k SNPs. Four Bayesian specifications of genomic regression models, namely, Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression; blending methods, BLUP; and single-step genomic best linear unbiased prediction (ssGBLUP) methods were compared in terms of prediction accuracy using a fivefold cross-validation. Estimates of heritability ranged from 0.20 to 0.35 and from 0.21 to 0.46 for RF and WBSF on single- and multiple-trait analyses, respectively. Prediction accuracies for REA, BF, RF and WBSF were all similar using the different specifications of regression models. In addition, this study has shown the impact of genomic information upon genetic evaluations in beef cattle using the multiple-trait model, which was also advantageous compared to the single-trait model because it accounted for the selection process using multiple traits at the same time. The advantage of multi-trait analyses is attributed to the consideration of correlations and genetic influences between the traits, in addition to the non-random association of alleles.

Novel visualization methods and strategies are necessary to cope with the deluge of datasets present in any scientific field to make discoveries and find answers to previously unanswered questions. These methods and strategies should not only present scientific findings as images in a concise way but also need to be effective and expressive, which often remain untested. Here, we present Versus, a tool to enable easy image quality assessment and image ranking, utilizing a two-alternative forced choice methodology (2AFC) and an efficient ranking algorithm based on a binary search. The tool provides a systematic way of setting up evaluation experiments via the web without the necessity to install any additional software or require any programming skills. Furthermore, Versus can easily interface with crowdsourcing platforms, such as Amazon’s Mechanical Turk, or can be used as a stand-alone system to carry out evaluations with experts. We demonstrate the use of Versus by means of an image evaluation study, aiming to determine if hue, saturation, brightness, and texture are good indicators of uncertainty in three-dimensional protein structures. Drawing from the power of crowdsourcing, we argue that there is demand and also great potential for this tool to become a standard for simple and fast image evaluations, with the aim to test the effectiveness and expressiveness of scientific visualizations. Keywords: Evaluation, Visualization, Visual analytics, Image comparison, Crowdsourcing, Evaluation methods, 2AFC, Image evaluation, Tool, Visualization evaluation

The objective of this study was to evaluate the effects of the energy restriction of gestation of adult ewes from day 45 to day 115 on lamb live performance parameters, carcass and meat traits. In experiment I, dietary energy was restricted at 70% of the metabolizable energy (ME) requirements, after which ewes were re-fed ad libitum until lambing. In experiment II, dietary energy was restricted at 60% of the ME requirements, and ewes were re-fed to ME requirements until lambing. All ewes grazed together from the end of the restriction periods to weaning. Lambs were weaned and lot fed until slaughter. Feed intake, weight gain and feed efficiency were recorded, and body fat thickness and ribeye area (REA) were measured in the longissimus thoracis muscle. After slaughter, carcass weight and yield, fat depth, carcass and leg length, and frenched rack and leg weights and yields were determined. Muscle fiber type composition, Warner-Bratzler shear force, pH and color were determined in the longissimus lumborum muscle. In experiment I, energy restriction followed by ad libitum feeding affected lamb birth weight (P0.05) were observed on later BW, REA, BF or carcass traits. Lambs born to non-restricted-fed ewes had higher (P

The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology. The analyses were processed with the BLUPF90 family of programs. When applied to a genome-wide association studies, the single-step GBLUP methodology is an iterative process that estimates weights for the SNPs. The weights of SNPs were included in all analyses by iteratively applying the single-step GBLUP methodology and repeated twice so that the effect of the SNP and the effect of the animal were recalculated in order to increase the weight of SNPs with large effects and to reduce the weight of those with small effects. The genome-wide association results are reported based on the proportion of variance explained by windows of 50 adjacent SNPs. Considering the two iterations, only windows with an additive genetic variance >1.5% were presented in the results. Associations were observed with birth weight on BTA 14, with weight gain from birth to weaning on BTA 5 and 29, with weight gain from weaning to yearling on BTA 11, and with yearling height on BTA 8, showing the genes TMEM68 (transmembrane protein 8B) associated with birth weight and yearling height, XKR4 (XK, Kell blood group complex subunit-related family, member 4) associated with birth weight, NPR2 (natriuretic peptide receptor B) associated with yearling height, and REG3G (regenerating islet-derived 3-gamma) associated with weight gain from weaning to yearling. These genes play an important role in feed intake, weight gain and the regulation of skeletal growth.

The objective of this study was to estimate (co)variance components using random regression on B-spline functions to weight records obtained from birth to adulthood. A total of 82 064 weight records of 8145 females obtained from the data bank of the Nellore Breeding Program (PMGRN/Nellore Brazil) which started in 1987, were used. The models included direct additive and maternal genetic effects and animal and maternal permanent environmental effects as random. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of age (cubic regression) were considered as random covariate. The random effects were modeled using B-spline functions considering linear, quadratic and cubic polynomials for each individual segment. Residual variances were grouped in five age classes. Direct additive genetic and animal permanent environmental effects were modeled using up to seven knots (six segments). A single segment with two knots at the end points of the curve was used for the estimation of maternal genetic and maternal permanent environmental effects. A total of 15 models were studied, with the number of parameters ranging from 17 to 81. The models that used B-splines were compared with multi-trait analyses with nine weight traits and to a random regression model that used orthogonal Legendre polynomials. A model fitting quadratic B-splines, with four knots or three segments for direct additive genetic effect and animal permanent environmental effect and two knots for maternal additive genetic effect and maternal permanent environmental effect, was the most appropriate and parsimonious model to describe the covariance structure of the data. Selection for higher weight, such as at young ages, should be performed taking into account an increase in mature cow weight. Particularly, this is important in most of Nellore beef cattle production systems, where the cow herd is maintained on range conditions. There is limited modification of the growth curve of Nellore cattle with respect to the aim of selecting them for rapid growth at young ages while maintaining constant adult weight.

Hand joint involvement in rheumatic diseases is often precocious and predominant as compared to other skeletomuscular regions. Clinical examination not always allows for easy detection of fluid outpouring and synovial involvement, and undoubtedly does not allow to diagnose pathognomonic bone alterations of several rheumatic conditions. Articular ultrasonography is an innocuous methodology, easily reproducible and directly applied by a rheumatologist. The aim of this vignette is to present ultrasonography elementary lesions of the hand for a prompt diagnosis.

Objective: To assess the efficacy of Cellfood®’s therapy in the treatment of fibromyalgia. Methods: This study was a single-blind, cross-over, randomized placebo-controlled trial. Fourty female were selected from 320 cases investigated in the period 2003-2005 of june. To be included in this study, it was required that the diagnosis of fibromyalgia was made by a specialist in according to the ACR classification criteria of 1990. The patient’s age was between 35-47 years, the choice of criteria were the absence of improvements with the conventional therapy and the normality of medical check-up. The patients were divided into two different-groups of thirty-one and nine subjects, each-one (group A) treated with Cellfood® for six months in according to the Eurodream’s scheme, and each-other (group B) treated with placebo for three months and successively with Cellfood® for three months.Besides we have estimated the tender points with algometer and the health status of women with the Fibromyalgia Impact Questionnaire (FIQ) at the baseline (T0) and at three (T1) and six month (T2). Result: The group A had an appreciable improvement of the parameters at T1 statistically significant compared to the group B, while we observed a stability of they at T2 on the group A and an improvementof the parameters of the group B statistically non significant compared to each-one. Conclusion: Our result suggest that the Cellfood®’s therapy improve fibromyalgia symptoms and health-related quality of life.

Bisphosphonates (BPs) are pharmacological compounds widely used in the treatment of a variety of bone-related diseases, particularly where the bone-turnover is skewed in favour of osteolysis. The mechanisms by which BPs reduce bone-resorption directly acting on osteoclasts (OCs) are now largely clarified even at molecular level. The researches concerning the BPs effects on osteoblasts (OBs) have instead shown variable results. Objectives: We have investigated the efficacy of neridronate (NER), an amino-BP, as anabolic agent on human OBs. Moreover, we have tried to verify if NER is able to negatively modulate the production of IL-6 on OBs stimulated or not by the pro-inflammatory cytokine Il-1b. Methods: We have tested if different concentrations of NER (from 10-11M to 10-3M), added to primary human OB cultures, could affect the cells number, the endogenous cellular alkaline phosphatase (ALP) activity, the collagen I (COLI) synthesis, the formation of mineralized nodules and the IL-6 production. Our experimental approach was performed testing a wide range of NER concentrations because, under physiological conditions, OBs seems to be exposed to variable and transient levels of the drug. Results: Our results show that NER doesn’t negatively affect in vitro the viability, proliferation and cellular activity of human OBs, even after 20 days of exposure to concentrations ²10-5 M (therapeutic dose). In addition, NER seems to enhance the differentiation of cultured OBs in mature bone-forming cells. A maximum increase of COL-I synthesis (+25% after 4 days; p

Nutrition and suckling are largely recognised as the most important factors affecting the postpartum period and consequently the reproductive efficiency of beef cattle. The aim of this study was to evaluate the effects of body condition score (BCS) and suckling restriction with and without the presence of the calf on milk production, reproductive efficiency and calf performance. Sixty-three crossbred (Angus × Hereford) multiparous cows were managed to maintain different BCS at calving and thereafter (low vs moderate; L, n= 31 and M, n= 32). Within each group of BCS (L and M) at week 9 postpartum (66 ± 0.88 days postpartum) cows were assigned to three suckling treatments (ST): (i) suckling ad libitum(S, n= 20); (ii) calves fitted with nose plates during 14 days remaining with their dams (NP, n= 22); and (iii) calves were completely removed from their dams for 14 days, and thereafter returned (CR, n= 21). Milk production was assessed by milking procedure at Day 65 (the day before onset of ST) and every 20–22 days until the end of the experiment. Cows were bled via jugular venipuncture every 28 days from Day –98 (Day 0 = calving) until Day 66. From Day 66 cows were bled every 7 days until the end of the mating period (Day 128). Concentrations of progesterone, non-esterified fatty acids and β-hydroxybutyrate acid and insulin were measured. Presence of corpus luteum (CL) was recorded and maximum follicle diameter was measured in all cows from the onset of the ST (Day 66) and during the following 4 weeks (until Day 94) in a weekly frequency. At Day 94, more cows (P< 0.001) in NP and in CR had CL compared with S cows (68, 57 and 21% for NP, CR and S, respectively). At that time, more cows in M-BCS presented CL than cows in L-BCS (77 vs 25; P< 0.0001). Within M-BCS, there were no differences in milk production between ST groups, while L-BCS cows with NP or CR produced less milk than S cows. Calf liveweight at weaning was 159.3 ± 3.1, 150.1 ± 2.9 and 147.0 ± 3.1 kg for S, NP and CR, respectively (P< 0.001). Suckling restriction with and without the presence of the calf had similar effects on reproductive performance, milk production and calf growth, while BCS interacted with ST to influence milk production. These results indicate that temporary suckling restriction could be an excellent management tool to increase reproductive performance of cows in moderate condition. [ABSTRACT FROM AUTHOR]