Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivariate analysis of body morphometric traits in conjunction with performance of reproduction and milk traits in crossbred progeny of Murrah × Jafarabadi buffalo (Bubalus bubalis) in North-Eastern Brazil

We studied the relationship between body morphometric traits, and their underlying association with milk production (MP), lactation length (LL), first calving interval (FCI) and subsequent calving interval (CI) of crossbred progeny of Murrah × Jafarabadi buffalo aiming to assist in selection programs. We carried out principal component analysis (PCA) of the body morphometric traits, which include breast width (BW), thigh width (THW), hip width (HW), rump width (RW), rump length (RL), body depth (BD), body length (BL), height withers (HEW), rear height (RH), shoulder width (SW), thorax width (TW), loin width (LW), distance from the head to ischium (DHI), and thoracic perimeter (TP). We determined the association of morphometric traits with milk/reproduction traits using canonical correlation analysis (CCA). The analysis revealed that the first six PCA accounted for 82.14% of the total observed variation, and the traits THW, HW, TW, LW, RW, HEW, TP, RH, and BW, accounted for almost half (48.00%) of the total variance indicating a higher contribution in body structural conformation. The first canonical function was significant (p<0.05), accounted for 72.46% of the total variance, and the canonical correlation was 0.56, indicating the dependence between both groups of traits. Higher canonical loadings were obtained for LL (0.49), FCI (0.46), BW (-0.71), BL (-0.56), DHI (-0.34), HEW, (-0.38) and TP (-0.50). These traits were most important for the derivation of canonical statistical variables, and presented a higher canonical correlations (r) between the dependent (LL/FCI) and independent (BW, BL, DHI, HEW and TP) groups. The results could suggest that the body morphometric traits THW, HW, TW, LW, RW, HEW, BD, TP, RH, and BW could play important role in body structural composition, indicating a suitable functional type, and aid designing of selection programs for buffalo breeding.
The ratio of circulating endothelin-1:endothelin-3 associated with TIMI risk and dynamic TIMI risk score in ST elevation acute myocardial infarction.

In ST segment elevation acute myocardial infarction (STEMI), the endothelin (ET) system imbalance, reflected by circulating ET-1:ET-3 ratio has not been investigated. This study primary objective was to measure the circulating ET-1:ET-3 ratio and correlated it with the risk stratification for 1-year mortality of STEMI, based on TIMI score. On admission TIMI risk score and at discharge dynamic TIMI risk score were calculated in 68 consecutive subjects with STEMI. Subjects with high TIMI risk score associated with higher mean ET-1 level and ET-1:ET-3 ratio. The ET-1:ET-3 ratio more accurately predicted the high TIMI risk score than ET-1 level. Subjects with high dynamic TIMI risk score associated with higher mean ET-1 level and ET-1:ET-3 ratio. The ET-1:ET-3 ratio more accurately predicted the high dynamic TIMI risk score than ET-1 level. From multivariable analysis, the ET-1:ET-3 ratio did not independently associated with high on admission TIMI risk score but independently predicted high at discharge dynamic TIMI risk score (OR 9.186, p value 0.018). In conclusion, combining the ET-1 and ET-3 levels into the ET-1:ET-3 ratio provided a prognostic value by independently predicting the increased risk to 1-year mortality as indicated by at discharge dynamic TIMI risk score in patients with STEMI.
Randomized and Controlled Clinical Trial of Bone Healing After Alveolar Ridge Preservation Using Xenografts and Allografts Versus Plasma Rich in Growth Factors

The aim of this study was to compare bone regeneration in the anterior maxilla between bone substitutes and autologous platelet concentrate in alveolar ridge preservation. Forty patients requiring tooth extraction in the anterior maxilla were randomly allocated to the following 4 treatment modalities: spontaneous healing (control), natural bovine bone mineral covered with resorbable native collagen membrane (BBM/CM), freeze-dried bone allograft covered with resorbable native collagen membrane (FDBA/CM), and plasma rich in growth factors (PRGF) alone. Bone biopsies and histomorphometrical analysis were performed after 3 months of healing. The following parameters were assessed: newly formed mineralized tissue, newly formed nonmineralized tissue, and residual bone-grafting material (if applicable). Statistical analysis was performed to provide descriptive analysis and to compare the parameters of the bone regeneration between the study groups. Histomorphometrical analysis revealed the highest new mineralized tissue formation in the PRGF group. Statistically significant differences in new mineralized tissue formation were found between control/PRGF (46.4% ± 15.2% vs 75.5% ± 16.3%), control/(BBM/CM) (46.4% ± 15.2% vs 20.3% ± 21.9%), control/(FDBA/CM) (46.4% ± 15.2% vs 7.2% ± 8.6%), PRGF/(BBM/CM) (75.5% ± 16.3% vs 20.3% ± 21.9%), and PRGF/(FDBA/CM) (75.5% ± 16.3% vs 7.2% ± 8.6%) groups. The new mineralized tissue formation was in the following order: PRGF > control > BBM > FDBA. Alveolar ridge preservation in the esthetic zone with PRGF was the most effective for bone regeneration of the alveolar ridge.
Microbial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee Colonies

The pollen stores of bumble bees host diverse microbiota that influence overall colony fitness. Yet, the taxonomic identity of these symbiotic microbes is relatively unknown. In this descriptive study, we characterized the microbial community of pollen provisions within captive-bred bumble bee hives obtained from two commercial suppliers located in North America. Findings from 16S rRNA and ITS gene-based analyses revealed that pollen provisions from the captive-bred hives shared several microbial taxa that have been previously detected among wild populations. While diverse microbes across phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Ascomycota were detected in all commercial hives, significant differences were detected at finer-scale taxonomic resolution based on the supplier source. The causative agent of chalkbrood disease in honey bees, Ascosphaera apis, was detected in all hives obtained from one supplier source, although none of the hives showed symptoms of infection. The shared core microbiota across both commercial supplier sources consisted of two ubiquitous bee-associated groups, Lactobacillus and Wickerhamiella/Starmerella clade yeasts that potentially contribute to the beneficial function of the microbiome of bumble bee pollen provisions.
Heterogeneity of Stemlike Circulating Tumor Cells in Invasive Breast Cancer

The presence of stem and epithelial–mesenchymal-transition (EMT) features in circulating tumor cells (CTCs) determines their invasiveness, adaptability to the microenvironment, and resistance to proapoptotic signals and chemotherapy. It also allows them to fulfil the role of metastatic “seeds”. We evaluated the heterogeneity of stem CTCs by their CD44, ALDH1, and CD133 expression depending on N-cadherin expression in breast-cancer patients. A total of 38 female patients were selected for this study. CTC phenotypes were determined by flow cytometry before any type of treatment. Multiplex immunofluorescence was used for the evaluation of tumor-cell heterogeneity in primary lesions. In patients who had CD44-CD24- CTCs, a subset of cells with the expression of other stem-cell markers (CD133 and ALDH1) were detected. Expression of CD133 and/or ALDH1 may be associated with expression of N-cadherin: all populations of N-cadherin+ CTCs demonstrate stem features; in the absence of N-cadherin expression, true nonstem (CD44-CD24-CD133-ALDH1-) cells are found. The heterogeneity of stem marker expression in CTCs was observed regardless of N-cadherin expression. In our study, stromal cell-derived factor-1 (SDF-1) receptor expression in CTCs did not depend on stemlike traits, but was instead associated with N-cadherin expression. Subpopulations of tumor cells, detected both in tumors and blood, were identified. Breast cancer was characterized by pronounced interpersonal and intrapersonal heterogeneity of CTCs by the presence and combination of various stem features and N-cadherin expression. To complete the characterization of stemlike features of CTCs, we suggest the simultaneous use of the three stem markers.
Inhibition of myostatin prevents microgravity-induced loss of skeletal muscle mass and strength

The microgravity conditions of prolonged spaceflight are known to result in skeletal muscle atrophy that leads to diminished functional performance. To assess if inhibition of the growth factor myostatin has potential to reverse these effects, mice were treated with a myostatin antibody while housed on the International Space Station. Grip strength of ground control mice increased 3.1% compared to baseline values over the 6 weeks of the study, whereas grip strength measured for the first time in space showed flight animals to be -7.8% decreased in strength compared to baseline values. Control mice in space exhibited, compared to ground-based controls, a smaller increase in DEXA-measured muscle mass (+3.9% vs +5.6% respectively) although the difference was not significant. All individual flight limb muscles analyzed (except for the EDL) weighed significantly less than their ground counterparts at the study end (range -4.4% to -28.4%). Treatment with myostatin antibody YN41 was able to prevent many of these space-induced muscle changes. YN41 was able to block the reduction in muscle grip strength caused by spaceflight and was able to significantly increase the weight of all muscles of flight mice (apart from the EDL). Muscles of YN41-treated flight mice weighed as much as muscles from Ground IgG mice, with the exception of the soleus, demonstrating the ability to prevent spaceflight-induced atrophy. Muscle gene expression analysis demonstrated significant effects of microgravity and myostatin inhibition on many genes. Gamt and Actc1 gene expression was modulated by microgravity and YN41 in opposing directions. Myostatin inhibition did not overcome the significant reduction of microgravity on femoral BMD nor did it increase femoral or vertebral BMD in ground control mice. In summary, myostatin inhibition may be an effective countermeasure to detrimental consequences of skeletal muscle under microgravity conditions.
Non‐memory subjective cognitive concerns predict incident motoric cognitive risk syndrome

Motoric cognitive risk syndrome (MCR) is a predementia condition that combines slow gait and subjective cognitive concerns. As the earliest markers of MCR are relatively unknown, the role of subjective cognitive concerns was investigated to predict incident MCR in a well‐characterized prospective cohort of non‐demented older adults.
Acute Effects of the Consumption of Passiflora setacea Juice on Metabolic Risk Factors and Gene Expression Profile in Humans

Background: Passiflora setacea (PS) is a passionfruit variety of the Brazilian savannah and is a rich source of plant food bioactives with potential anti-inflammatory activity. This study aimed to investigate the effect of an acute intake of PS juice upon inflammation, metabolic parameters, and gene expression on circulating immune cells in humans. Methods: Overweight male volunteers (n = 12) were enrolled in two double-blind placebo-controlled studies. Blood samples were collected from fasting volunteers 3 h after the consumption of 250 mL of PS juice or placebo (PB). Metabolic parameters (insulin, glucose, total cholesterol, high-density lipoprotein (LDL), high-density lipoprotein (HDL), and total triglycerides) and circulating cytokines were evaluated (study 1). Peripheral blood mononuclear cell (PBMC) from the same subjects were isolated and RNA was extracted for transcriptomic analyses using microarrays (study 2). Results: Insulin and homeostatic model assessment for insulin resistance (HOMA-IR) levels decreased statistically after the PS juice intake, whereas HDL level increased significantly. Interleukin (IL)-17A level increased after placebo consumption, whereas its level remained unchanged after PS juice consumption. Nutrigenomic analyses revealed 1327 differentially expressed genes after PS consumption, with modulated genes involved in processes such as inflammation, cell adhesion, or cytokine–cytokine receptor. Conclusion: Taken together, these clinical results support the hypothesis that PS consumption may help the prevention of cardiometabolic diseases.
Male Infertility is a Women’s Health Issue—Research and Clinical Evaluation of Male Infertility Is Needed

Infertility is a devastating experience for both partners as they try to conceive. Historically, when a couple could not conceive, the woman has carried the stigma of infertility; however, men and women are just as likely to contribute to the couple’s infertility. With the development of assisted reproductive technology (ART), the treatment burden for male and unexplained infertility has fallen mainly on women. Equalizing this burden requires reviving research on male infertility to both improve treatment options and enable natural conception. Despite many scientific efforts, infertility in men due to sperm dysfunction is mainly diagnosed by a semen analysis. The semen analysis is limited as it only examines general sperm properties such as concentration, motility, and morphology. A diagnosis of male infertility rarely includes an assessment of internal sperm components such as DNA, which is well documented to have an impact on infertility, or other components such as RNA and centrioles, which are beginning to be adopted. Assessment of these components is not typically included in current diagnostic testing because available treatments are limited. Recent research has expanded our understanding of sperm biology and suggests that these components may also contribute to the failure to achieve pregnancy. Understanding the sperm’s internal components, and how they contribute to male infertility, would provide avenues for new therapies that are based on treating men directly for male infertility, which may enable less invasive treatments and even natural conception.
Identifying Genetic Lesions in Ocular Adnexal Extranodal Marginal Zone Lymphomas of the MALT Subtype by Whole Genome, Whole Exome and Targeted Sequencing

The pathogenesis of ocular adnexal marginal zone lymphomas of mucosa-associated lymphatic tissue-type (OAML) is not fully understood. We performed whole genome sequencing (WGS) and/or whole exome sequencing (WES) for 13 cases of OAML and sequenced 38 genes selected from this analysis in a large cohort of 82 OAML. Besides confirmation of frequent mutations in the genes transducin beta like 1 X-linked receptor 1 (TBL1XR1) and cAMP response element binding protein (CREBBP), we newly identifed JAK3 as a frequently mutated gene in OAML (11% of cases). In our retrospective cohort, JAK3 mutant cases had a shorter progression-free survival compared with unmutated cases. Other newly identified genes recurrently mutated in 5–10% of cases included members of the collagen family (collagen type XII alpha 1/2 (COL12A1, COL1A2)) and DOCK8. Evaluation of the WGS data of six OAML did not reveal translocations or a current infection of the lymphoma cells by viruses. Evaluation of the WGS data for copy number aberrations confirmed frequent loss of TNFAIP3, and revealed recurrent gains of the NOTCH target HES4, and of members of the CEBP transcription factor family. Overall, we identified several novel genes recurrently affected by point mutations or copy number alterations, but our study also indicated that the landscape of frequently (>10% of cases) mutated protein-coding genes in OAML is now largely known.
Infectious laryngotracheitis: Etiology, epidemiology, pathobiology, and advances in diagnosis and control – a comprehensive review

Abstract Infectious laryngotracheitis (ILT) is a highly contagious upper respiratory tract disease of chicken caused by a Gallid herpesvirus 1 (GaHV-1) belonging to the genus Iltovirus, and subfamily Alphaherpesvirinae within Herpesviridae family. The disease is characterized by conjunctivitis, sinusitis, oculo-nasal discharge, respiratory distress, bloody mucus, swollen orbital sinuses, high morbidity, considerable mortality and decreased egg production. It is well established in highly dense poultry producing areas of the world due to characteristic latency and carrier status of the virus. Co-infections with other respiratory pathogens and environmental factors adversely affect the respiratory system and prolong the course of the disease. Latently infected chickens are the primary source of ILT virus (ILTV) outbreaks irrespective of vaccination. Apart from conventional diagnostic methods including isolation and identification of ILTV, serological detection, advanced biotechnological tools such as PCR, quantitative real-time PCR, next generation sequencing, and others are being used in accurate diagnosis and epidemiological studies of ILTV. Vaccination is followed with the use of conventional vaccines including modified live attenuated ILTV vaccines, and advanced recombinant vector vaccines expressing different ILTV glycoproteins, but still these candidates frequently fail to reduce challenge virus shedding. Some herbal components have proved to be beneficial in reducing the severity of the clinical disease. The present review discusses ILT with respect to its current status, virus characteristics, epidemiology, transmission, pathobiology, and advances in diagnosis, vaccination and control strategies to counter this important disease of poultry.
Successful treatment of Sapho syndrome and hidradenitis suppurativa: A therapeutic challenge

The SAPHO (synovitis, acne, pustulosis, hyperostosis, osteitis) syndrome is a rare, chronic, autoinflammatory, debilitating disease. The average age of onset is between 30 and 40 years. The etiology is multifactorial, including environmental, genetic, immunological, or infectious causes like Propionibacterium acnes. SAPHO syndrome can be associated with other neutrophilic disorders. Hidradenitis suppurativa (HS), or acne inversa, is a chronic, inflammatory, recurrent, debilitating skin disease of the hair follicle. It usually presents after puberty with painful, deep-seated, inflamed lesions in the apocrine gland-bearing areas of the body. A few cases of concomitant SAPHO and HS have been described. Some of these cases presented occasional ocular involvement, including bilateral keratitis, acute anterior uveitis, persistent proteinuria, and tumors. The quality of life of patients affected by both SAPHO and HS could be very compromised and, often, treatment of both diseases could be challenging. We report the case of a 22-year old man who came to our attention for severe acne of the trunk and neck, and multiple nodules, abscesses, and tunnels localized in the armpit, groin, back, and chest (Figure 1 and 2, A-C), arisen 2 years earlier, and compatible with the diagnosis of HS. For this condition the patient was previously treated with various antibiotics (ie, penicillin, tetracycline, clindamycin and rifampicin), and several drainages of the cutaneous lesions, with scarce improvement. Six years earlier, he had received the diagnosis of acne fulminans and he was treated for 6 months with methylprednisolone 25 mg/day and isotretinoin 30 mg/day, with resolution of the disease, while a mild acne persisted on the face. One year later, the patient was diagnosed with SAPHO syndrome, during a rheumatology consultation, due to diffuse arthralgia. MRI (Figure 3A,B) showed osteitis and hyperostosis of the sternoclavicular joints, and bone scintigraphy (Figure 3C) revealed intense hyperactivity of the sternoclavicular and sacroiliac joints and of the C4 soma. For the SAPHO syndrome, he was previously treated in different periods with cyclosporine 200 mg/day for 2 months, Adalimumab 40 mg weekly for 2 months, and then with Infliximab 5 mg/kg for 3 months, with mild improvement of the disease. When he came to our attention, besides SAPHO syndrome and HS, the patient had no comorbidities. In that time, he was treated with Adalimumab 80 mg weekly, Methotrexate 10 mg weekly, metformin 1 g/day, and prednisone 5 mg/day. Considering the good control of the rheumatic disease, but given the flare-ups of the HS, mainly localized on the armpit, we decided to inject the inflamed lesions of this region with triamcinolone 40 mg plus lincomycin 600 mg diluted in saline solution for a total volume of 20 mL, three times at 2-week intervals. A stark improvement was
A Novel Approach to Atomistic Molecular Dynamics Simulation of Phenolic Resins Using Symthons

Materials science is beginning to adopt computational simulation to eliminate laboratory trial and error campaigns—much like the pharmaceutical industry of 40 years ago. To further computational materials discovery, new methodology must be developed that enables rapid and accurate testing on accessible computational hardware. To this end, the authors utilise a novel methodology concept of intermediate molecules as a starting point, for which they propose the term ‘symthon’ (The term ‘Symthon’ is being used as a simulation equivalent of the synthon, popularised by Dr Stuart Warren in ‘Organic Synthesis: The Disconnection Approach’, OUP: Oxford, 1983.) rather than conventional monomers. The use of symthons eliminates the initial monomer bonding phase, reducing the number of iterations required in the simulation, thereby reducing the runtime. A novel approach to molecular dynamics, with an NVT (Canonical) ensemble and variable unit cell geometry, was used to generate structures with differing physical and thermal properties. Additional script methods were designed and tested, which enabled a high degree of cure in all sampled structures. This simulation has been trialled on large-scale atomistic models of phenolic resins, based on a range of stoichiometric ratios of formaldehyde and phenol. Density and glass transition temperature values were produced, and found to be in good agreement with empirical data and other simulated values in the literature. The runtime of the simulation was a key consideration in script design; cured models can be produced in under 24 h on modest hardware. The use of symthons has been shown as a viable methodology to reduce simulation runtime whilst generating accurate models.
Quantum-Mechanical Assessment of the Energetics of Silver Decahedron Nanoparticles

We present a quantum-mechanical study of silver decahedral nanoclusters and nanoparticles containing from 1 to 181 atoms in their static atomic configurations corresponding to the minimum of the ab initio computed total energies. Our thermodynamic analysis compares T = 0 K excess energies (without any excitations) obtained from a phenomenological approach, which mostly uses bulk-related properties, with excess energies from ab initio calculations of actual nanoclusters/nanoparticles. The phenomenological thermodynamic modeling employs (i) the bulk reference energy, (ii) surface energies obtained for infinite planar (bulk-related) surfaces and (iii) the bulk atomic volume. We show that it can predict the excess energy (per atom) of nanoclusters/nanoparticles containing as few as 7 atoms with the error lower than 3%. The only information related to the nanoclusters/nanoparticles of interest, which enters the phenomenological modeling, is the number of atoms in the nanocluster/nanoparticle, the shape and the crystallographic orientation(s) of facets. The agreement between both approaches is conditioned by computing the bulk-related properties with the same computational parameters as in the case of the nanoclusters/nanoparticles but, importantly, the phenomenological approach is much less computationally demanding. Our work thus indicates that it is possible to substantially reduce computational demands when computing excess energies of nanoclusters and nanoparticles by ab initio methods.