Miracle-dz/UniFAR-FTUs huggingface dataset:
Welfare and Performance of Three Turkey Breeds—Comparison between Infrared Beak Treatment and Natural Beak Abrasion by Pecking on a Screed Grinding Wheel

Simple Summary Beak trimming of turkeys is an animal welfare issue. It can result in acute pain, potential chronic pain, and a change in feeding, drinking, and pecking ability and general behavior. It is still permitted by law in Germany when the intervention is necessary to protect turkeys from feather pecking and cannibalism. In the present study, an alternative method using grinding wheels (blunting disks) that were fitted in the feed pans when the turkeys were six weeks old was tested. The disks were expected to blunt the beak tips during feeding and reduce the severity of pecking injuries. Six hundred male turkeys of three breeds (B.U.T. 6, B.U.T. Premium, Auburn) were housed separately in 24 groups. The birds in 12 groups were beak trimmed, those in the other 12 were not, but received the blunting disk. The results showed a noticeable beak abrasion in birds provided with blunting disk. Injuries and plumage conditions were equivalent between the treatments. Summarized, the blunting method may be an alternative to infrared beak treatment, but its effectiveness should be confirmed under commercial conditions. The blunting method could potentially result in improved animal welfare of turkeys by minimizing acute pain, chronic pain, and injurious pecking. Abstract Feather pecking and cannibalism are behavioral disorders that cause animal-welfare-relevant and economic problems. To mitigate these problems, the beaks of conventionally reared turkeys are usually already trimmed in the hatcheries. To find an alternative to beak trimming, we conducted this study with male turkeys of three breeds: B.U. T. 6, B.U. T. Premium and, Auburn (200 turkeys per breed). Half of the birds had infrared-trimmed beaks; the other half had intact beaks. For each treatment combination (breed, beak status), 25 turkeys were housed in one section. A screed grinding wheel was installed in each feed pan of the non-beak-trimmed turkeys as of week six to facilitate natural beak abrasion until slaughter. Eight randomly selected turkeys per section were regularly examined to record injuries, plumage condition, and beak dimensions. In addition, 96 beaks from randomly slaughtered birds were examined macroscopically and histologically. The results concerning injuries and plumage condition showed in most cases no differences between the beak-trimmed turkeys and the ones provided with the blunting disks. The histological examinations revealed alterations in only the beak-trimmed birds. We can conclude that the blunting method smoothens the beak during feeding and thus may be a possible alternative to beak trimming.
Childhood Obesity-Related Mechanisms: MicroRNome and Transcriptome Changes in a Nested Case-Control Study

Childhood obesity could contribute to adulthood obesity, leading to adverse health outcomes in adults. However, the mechanisms for how obesity is developed are still unclear. To determine the epigenome-wide and genome-wide expression changes related with childhood obesity, we compared microRNome and transcriptome levels as well as leptin protein levels in whole bloods of 12 obese and 24 normal children aged 6 years. miR-328-3p, miR-1301-3p, miR-4685-3p, and miR-6803-3p were negatively associated with all obesity indicators. The four miRNAs were also associated with 3948 mRNAs, and separate 475 mRNAs (185 among 3948 mRNAs) were associated with all obesity indicators. The 2533 mRNAs (64.2%) among the 3948 mRNAs and 286 mRNAs (60.2%) among the 475 mRNAs were confirmed as targets of the four miRNAs in public databases through miRWalk 2.0. Leptin protein was associated with miR-6803-3p negatively and all obesity indicators positively. Using DAVID bioinformatics resources 6.8, top three pathways for obesity-related gene set were metabolic pathways, pathways in cancer, and PI3K-Akt signaling pathway. The top three obesity-related disease classes were metabolic, cardiovascular, and chemdependency. Our results support that childhood obesity could be developed through miRNAs-related epigenetic mechanism and, further, these obesity-related epigenetic changes could control the pathways related with the development of various diseases.
Oxidative Stress Biomarkers in the Relationship between Type 2 Diabetes and Air Pollution

The incidence and prevalence of type 2 diabetes have increased in the last decades and are expected to further grow in the coming years. Chronic hyperglycemia triggers free radical generation and causes increased oxidative stress, affecting a number of molecular mechanisms and cellular pathways, including the generation of advanced glycation end products, proinflammatory and procoagulant effects, induction of apoptosis, vascular smooth-muscle cell proliferation, endothelial and mitochondrial dysfunction, reduction of nitric oxide release, and activation of protein kinase C. Among type 2 diabetes determinants, many data have documented the adverse effects of environmental factors (e.g., air pollutants) through multiple exposure-induced mechanisms (e.g., systemic inflammation and oxidative stress, hypercoagulability, and endothelial and immune responses). Therefore, here we discuss the role of air pollution in oxidative stress-related damage to glycemic metabolism homeostasis, with a particular focus on its impact on health. In this context, the improvement of new advanced tools (e.g., omic techniques and the study of epigenetic changes) may provide a substantial contribution, helping in the evaluation of the individual in his biological totality, and offer a comprehensive assessment of the molecular, clinical, environmental, and epidemiological aspects.
Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017–2019

Acinetobacter baumannii is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and to rapidly acquire the resistance to a broad spectrum of antibiotics. Thus, the epidemiological surveillance of A. baumannii within a particular hospital, region, and across the world is an important healthcare task that currently usually includes performing whole-genome sequencing (WGS) of representative isolates. During the past years, the dissemination of A. baumannii across the world was mainly driven by the strains belonging to two major groups called the global clones or international clones (ICs) of high risk (IC1 and IC2). However, currently nine ICs are already considered. Although some clones were previously thought to spread in particular regions of the world, in recent years this is usually not the case. In this study, we determined five ICs, as well as three isolates not belonging to the major ICs, in one multidisciplinary medical center within the period 2017–2019. We performed WGS using both short- and long-read sequencing technologies of nine representative clinical A. baumannii isolates, which allowed us to determine the antibiotic resistance and virulence genomic determinants, reveal the CRISPR/Cas systems, and obtain the plasmid structures. The phenotypic and genotypic antibiotic resistance profiles are compared, and the possible ways of isolate and resistance spreading are discussed. We believe that the data obtained will provide a better understanding of the spreading and resistance acquisition of the ICs of A. baumannii and further stress the necessity for continuous genomic epidemiology surveillance of this problem-causing bacterial species.
Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa

Findings from previous comparative genomics studies of the Mycobacterium tuberculosis complex (MTBC) suggest genomic variation among the genotypes may have phenotypic implications. We investigated the diversity in the phenotypic profiles of the main prevalent MTBC genotypes in West Africa. Thirty-six whole genome sequenced drug susceptible MTBC isolates belonging to lineages 4, 5 and 6 were included in this study. The isolates were phenotypically characterized for urease activity, tween hydrolysis, Thiophen-2-Carboxylic Acid Hydrazide (TCH) susceptibility, nitric oxide production, and growth rate in both liquid (7H9) and solid media (7H11 and Löwenstein–Jensen (L-J)). Lineage 4 isolates showed the highest growth rate in both liquid (p = 0.0003) and on solid (L-J) media supplemented with glycerol (p<0.001) or pyruvate (p = 0.005). L6 isolates optimally utilized pyruvate compared to glycerol (p<0.001), whereas L5 isolates grew similarly on both media (p = 0.05). Lineage 4 isolates showed the lowest average time to positivity (TTP) (p = 0.01; Average TTP: L4 = 15days, L5 = 16.7days, L6 = 29.7days) and the highest logCFU/mL (p = 0.04; average logCFU/mL L4 = 5.9, L5 = 5.0, L6 = 4.4) on 7H11 supplemented with glycerol, but there was no significant difference in growth on 7H11 supplemented with pyruvate (p = 0.23). The highest release of nitrite was recorded for L5 isolates, followed by L4 and L6 isolates. However, the reverse was observed in the urease activity for the lineages. All isolates tested were resistant to TCH except for one L6 isolate. Comparative genomic analyses revealed several mutations that might explain the diverse phenotypic profiles of these isolates. Our findings showed significant phenotypic diversity among the MTBC lineages used for this study.
Determination of Annual Plasma Hormone Levels Associated with Reproduction in Long-Day Breeding Domestic Geese

Simple Summary In domestic birds, breeding practices and optimisation of the microenviroment and nutrition ensure egg production throughout the entire year. However, domestic geese experience an annual cycle of reproductive quiescence and recrudescence. Thus, patterns of reproductive hormones related to the initiation and termination of the breeding–laying period between the sexes seems to be especially important. This paper presents annual patterns of prolactin (PRL), triiodothyronine (T3), thyroxine (T4), testosterone (T), progesterone (P4), and estradiol (E2) in ganders and female geese. Long-day breeding Zatorska geese kept in controlled commercial conditions experienced periods with elevated plasma PRL levels in both sexes post-breeding and during the second half of the breeding–laying period. Increased plasma PRL levels by the end of the breeding–laying period were detected earlier in ganders than in female geese. Annual patterns of thyroid hormones (THs) were partially in agreement with existing theories on the specific role of THs in termination of breeding, which is permissive rather than causal. It may be suggested that ganders terminate their breeding–laying period one month earlier than female geese. These results may be useful in the manipulation of the endocrine axis to extend the duration of seasonal hatching egg production. Abstract This paper examines the dynamics of circulating hormone changes connected with reproduction in geese during the annual period related to gonad morphometry. One hundred geese were examined. The levels of prolactin (PRL), triiodothyronine (T3), thyroxine (T4), testosterone (T), progesterone (P4) and estradiol (E2) were estimated. In both sexes, PRL level patterns fit a quadratic trend with elevations in the post-breeding and the second half of the breeding–laying periods. During these periods, differences in the PRL level between sexes were noted. In ganders, increased PRL levels during the laying period occurred earlier compared to in female geese. Cubic trends for T and E2 in ganders and quadratic for T, P4, and E2 in female geese were observed. PRL was negatively correlated with T in both sexes and with P4 and E2 in female geese. A higher level of T3 and variation in T4 in ganders with a quartic trend in ganders vs. a quadratic in female geese were noted. Patterns of PRL, T, and E2 suggested that the breeding–laying period in ganders may be shorter than in female geese. These findings will be used to explore experimental manipulations of the endocrine axis to increase synchronisation of both sexes.
Synergistic AHR Binding Pathway with EMT Effects on Serous Ovarian Tumors Recognized by Multidisciplinary Integrated Analysis

Epithelial ovarian cancers (EOCs) are fatal and obstinate among gynecological malignancies in advanced stage or relapsed status, with serous carcinomas accounting for the vast majority. Unlike EOCs, borderline ovarian tumors (BOTs), including serous BOTs, maintain a semimalignant appearance. Using gene ontology (GO)-based integrative analysis, we analyzed gene set databases of serous BOTs and serous ovarian carcinomas for dysregulated GO terms and pathways and identified multiple differentially expressed genes (DEGs) in various aspects. The SRC (SRC proto-oncogene, non-receptor tyrosine kinase) gene and dysfunctional aryl hydrocarbon receptor (AHR) binding pathway consistently influenced progression-free survival and overall survival, and immunohistochemical staining revealed elevated expression of related biomarkers (SRC, ARNT, and TBP) in serous BOT and ovarian carcinoma samples. Epithelial–mesenchymal transition (EMT) is important during tumorigenesis, and we confirmed the SNAI2 (Snail family transcriptional repressor 2, SLUG) gene showing significantly high performance by immunohistochemistry. During serous ovarian tumor formation, activated AHR in the cytoplasm could cooperate with SRC, enter cell nuclei, bind to AHR nuclear translocator (ARNT) together with TATA-Box Binding Protein (TBP), and act on DNA to initiate AHR-responsive genes to cause tumor or cancer initiation. Additionally, SNAI2 in the tumor microenvironment can facilitate EMT accompanied by tumorigenesis. Although it has not been possible to classify serous BOTs and serous ovarian carcinomas as the same EOC subtype, the key determinants of relevant DEGs (SRC, ARNT, TBP, and SNAI2) found here had a crucial role in the pathogenetic mechanism of both tumor types, implying gradual evolutionary tendencies from serous BOTs to ovarian carcinomas. In the future, targeted therapy could focus on these revealed targets together with precise detection to improve therapeutic effects and patient survival rates.
Clinical Outcome Prediction in COVID-19 Patients by Lymphocyte Subsets Analysis and Monocytes’ iTNF-α Expression

Simple Summary Several studies have explored the role of the inflammatory cells and cytokines involved in the protection or pathogenesis of coronavirus disease 2019. Unfortunately, the results have been controversial, and further studies are needed to better understand not only the roles but also the balance of these parameters, which are crucial data to improve prevention and treatment. As COVID-19 has a well-determined phasic progression and rapidly deteriorates approximately seven days after the onset of symptoms, it is extremely necessary to detect the clinical signs that are predictive of the outcome as early as possible. To this end, in this preliminary study, we evaluated the data relating to the monocyte intracellular TNF-α expression and lymphocyte subpopulations in peripheral blood collected from patients at admission and every day of hospitalization until day 7. Our findings point to a modulation of the different cellular mediators of the immune system, which probably play a key role in the outcome of the coronavirus disease 2019. Abstract In December 2019, a novel coronavirus, “SARS-CoV-2”, was recognized as the cause of coronavirus disease 2019 (COVID-19). Several studies have explored the changes and the role of inflammatory cells and cytokines in the immunopathogenesis of the disease, but until today, the results have been controversial. Based on these premises, we conducted a retrospective assessment of monocyte intracellular TNF-α expression (iTNF-α) and on the frequencies of lymphocyte sub-populations in twenty-five patients with moderate/severe COVID-19. We found lymphopenia in all COVID-19 infected subjects compared to healthy subjects. On initial observation, in patients with favorable outcomes, we detected a high absolute eosinophil count and a high CD4+/CD8+ T lymphocytes ratio, while in the Exitus Group, we observed high neutrophil and CD8+ T lymphocyte counts. During infection, in patients with favorable outcomes, we observed a rise in the lymphocyte count, in the monocyte and in Treg lymphocyte counts, and in the CD4+ and in CD8+ T lymphocytes count but a reduction in the CD4+/CD8+ T lymphocyte ratio. Instead, in the Exitus Group, we observed a reduction in the Treg lymphocyte counts and a decrease in iTNF-α expression. Our preliminary findings point to a modulation of the different cellular mediators of the immune system, which probably play a key role in the outcomes of COVID-19.
Effect of Inulin Source and a Probiotic Supplement in Pig Diets on Carcass Traits, Meat Quality and Fatty Acid Composition in Finishing Pigs

Simple Summary Fructooligosaccharides, including inulin, are prebiotics involved in the regulation of bacterial flora, intestinal health, and metabolism in animals. Oligosaccharides and inulin-containing plants are the subject of numerous studies around the world. Inulin is an important oligosaccharide, considered a prebiotic in the diet of humans and animals. In this study, we examined the effect of the supplementation of probiotic bacteria in the diet with inulin or dried Jerusalem artichoke tubers on the performance, pig meat quality, and fatty acid profile of meat and backfat, which provided novel information on the use of these additives in livestock production. An improvement in the antioxidant status of meat and in the water-holding capacity, as well as a reduction in the shear force after the addition of both prebiotics can be mentioned as the pertinent results. However, the meat sensory traits were unchanged by supplementation with the prebiotics and probiotics. This study forms part of the current global work on feed additives that support animals’ health and concurrently allow the use of antibiotic treatments to be limited. Therefore, the results of this experiment are of great practical importance and can be proposed for use in pig farming as part of the intensive work which is underway across the EU to reduce the use of antibiotics. In addition, meat with higher quality and a longer shelf life derived from pigs fed with feed containing additives of natural origin are sought by consumers who value healthy and safe food. Abstract In this experiment, we investigated the effect of the supplementation of probiotic bacteria in the diet with inulin or dried Jerusalem artichoke tubers on the performance, meat quality, and fatty acid composition in the meat and backfat of fatteners. One hundred and forty-four crossbred pigs (PIC × Penarlan P76) were divided into six groups and fattened from 30 to 114 kg. The meat proximate composition, pH, color, texture, shear force, water-holding capacity, sensory attributes, and thiobarbituric-acid-reactive substances were measured. Normal post-mortem meat glycolysis was demonstrated and no meat defects were present. The chemical constituents in muscle tissues were similar, except for intramuscular fat (IMF). The addition of the prebiotics resulted in a higher IMF level, whereas a significantly lower content was found after the probiotic supplementation. Meat from both prebiotic groups was lighter, less red, and more yellow and showed a higher hue angle. The addition of both prebiotics significantly improved the antioxidant status of meat (by approximately 16% and 18%) and the water-holding capacity (less free water and higher M/T ratios), but reduced shear force (by 17%, p ≤ 0.05) and hardness (by 39% and 35%, respectively, p ≤ 0.05). The addition of the prebiotics and probiotics had no effect on any of the evaluated sensory attributes.
Investigation of the factors influencing surgical treatment of duodenal gastrointestinal stromal tumors

BACKGROUND Duodenal gastrointestinal stromal tumor (DGIST) is a rare tumor with a specific anatomic site and biological characteristics. As the incidence of lymph node metastasis is very low, the main treatment method is surgery. Two main surgical techniques (local resection and Whipple) are performed in patients with DGISTs. The critical question is which surgical technique to choose. AIM To identify factors influencing the choice of surgery for DGISTs. METHODS The clinicopathological data of patients with DGISTs who underwent surgery between January 1999 and January 2021 were analyzed. We used the Student’s t-test or Mann-Whitney U-test and the χ2 test or Fisher’s exact test to determine the differences between the two groups of patients. Furthermore, we used logistic analysis to identify the relevant factors and independent factors related to the type of surgery. The Kaplan-Meier method was used to analyze the patient’s survival information and Cox regression analysis was performed to determine prognostic risk factors. RESULTS Overall, 86 patients were analyzed, including 43 men (50%) and 43 women (50%). We divided the patients into two groups based on surgical technique (local resection or Whipple surgery). There were no differences in the age, mitotic figures, and complications between the two groups; however, the tumor size, tumor location, risk grade, postoperative hospital stay, and abdominal drainage time were significantly different. Based on univariate logistic analysis, the Whipple procedure was chosen if the tumor size was ≥ 5.0 cm, the tumor was located in the descending part of the duodenum, or the risk grade was medium or high. In our research, the five-year overall survival rate of patients was more than 90%. We also describe two DGIST patients with liver metastases at first diagnosis and analyzed their management in order to provide advice on complicated cases. CONCLUSION The Whipple procedure was performed if the primary tumor was in the descending part of the duodenum, tumor size was ≥ 5.0 cm, or the tumor risk grade was medium or high.
An autonomous framework for interpretation of 3D objects geometric data using 2D images for application in additive manufacturing

Additive manufacturing, artificial intelligence and cloud manufacturing are three pillars of the emerging digitized industrial revolution, considered in industry 4.0. The literature shows that in industry 4.0, intelligent cloud based additive manufacturing plays a crucial role. Considering this, few studies have accomplished an integration of the intelligent additive manufacturing and the service oriented manufacturing paradigms. This is due to the lack of prerequisite frameworks to enable this integration. These frameworks should create an autonomous platform for cloud based service composition for additive manufacturing based on customer demands. One of the most important requirements of customer processing in autonomous manufacturing platforms is the interpretation of the product shape; as a result, accurate and automated shape interpretation plays an important role in this integration. Unfortunately despite this fact, accurate shape interpretation has not been a subject of research studies in the additive manufacturing, except limited studies aiming machine level production process. This paper has proposed a framework to interpret shapes, or their informative two dimensional pictures, automatically by decomposing them into simpler shapes which can be categorized easily based on provided training data. To do this, two algorithms which apply a Recurrent Neural Network and a two dimensional Convolutional Neural Network as decomposition and recognition tools respectively are proposed. These two algorithms are integrated and case studies are designed to demonstrate the capabilities of the proposed platform. The results suggest that considering the complex objects which can be decomposed with planes perpendicular to one axis of Cartesian coordination system and parallel withother two, the decomposition algorithm can even give results using an informative 2D image of the object.