Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA-Seq-Based Analysis of Cortisol-Induced Differential Gene Expression Associated with Piscirickettsia salmonis Infection in Rainbow Trout (Oncorhynchus mykiss) Myotubes

Simple Summary Skeletal muscle is the most abundant tissue in fish and the main product of the Chilean salmonid aquaculture industry. Intensive farming conditions generate stress and increased susceptibility to infectious diseases, such as salmonid rickettsial septicemia (SRS), that directly affect this tissue. However, the immunocompetence of skeletal muscle during infection is poorly understood. To further explore the interplay between pathogen infection and stress on this tissue, we analyze the transcriptional profile of isolated rainbow trout (Oncorhynchus mykiss) muscle cells pretreated with 3 h of the stress hormone cortisol, and then infected with the SRS etiologic agent Piscirickettsia salmonis for 8 h, using RNA sequencing technology. For the first time, the obtained data reveals the biological processes related to programmed cell death, negative regulation of cell proliferation, and innate immune response. These results are validated by real-time qPCR. Furthermore, cortisol pretreatment significantly stimulated bacterial gene expression compared to infected cells. These data demonstrated that fish skeletal muscle can activate an intrinsic immune-like response against P. salmonis that is differentially regulated by cortisol. The information provided here will help us to understand the molecular mechanisms of fish muscle cells respond to infection, which could prevent P. salmonis outbreaks in skeletal muscle under stress conditions. Abstract Salmonid rickettsial septicemia (SRS) is the major infectious disease of the Chilean salmonid aquaculture industry caused by Piscirickettsia salmonis. Intensive farming conditions generate stress and increased susceptibility to diseases, being skeletal muscle mainly affected. However, the interplay between pathogen infection and stress in muscle is poorly understood. In this study, we perform an RNA-seq analysis on rainbow trout myotubes that are pretreated for 3 h with cortisol (100 ng/mL) and then infected with P. salmonis strain LF-89 for 8 h (MOI 50). Twelve libraries are constructed from RNA samples (n = 3 per group) and sequenced on Illumina HiSeq 4000. A total of 704,979,454 high-quality reads are obtained, with 70.25% mapped against the reference genome. In silico DETs include 175 total genes—124 are upregulated and 51 are downregulated. GO enrichment analysis reveals highly impacted biological processes related to apoptosis, negative regulation of cell proliferation, and innate immune response. These results are validated by RT-qPCR of nine candidate transcripts. Furthermore, cortisol pretreatment significantly stimulated bacterial gene expression of ahpC and 23s compared to infection. In conclusion, for the first time, we describe a transcriptomic response of trout myotubes infected with P. salmonis by inducing apoptosis, downregulating cell proliferation, and intrinsic immune-like response that is differentially regulated by cortisol.
Egg Incubation Mechanics of Giant Birds

Simple Summary Extinct giant birds have been a source of imagination, and knowledge of their incubation mechanics is crucial to our understanding of the evolution of avian reproduction. Despite the extensive studies on avian eggs, our understanding of the eggshell mechanics of giant birds, particularly the extinct ones, remains incomplete—most of these prior works were based on empirical or allometric relationships with limited quantitative analysis. In the present study, with the help of advanced three-dimensional computer simulation using data from published fossil records, we obtain more comprehensive quantitative analysis to answer important questions related to contact incubation of giant birds. Specifically, how much safety margin does the reversed sexual size dimorphism (RSSD) of moas provide? What is the theoretical upper limit of body mass for contact incubation? Is the Williams’ egg, or the putative Genyornis oological material (PGOM), really the egg of the extinct giant bird Genyornis newtoni, as commonly accepted since its discovery in 1981? Abstract Finite element analysis (FEA) was used to conduct mechanical analyses on eggshells of giant birds, and relate this to the evolution and reproductive behavior of avian species. We aim to (1) investigate mechanical characteristics of eggshell structures of various ratite species, enabling comparisons between species with or without reversed sexual size dimorphism (RSSD); (2) quantify the safety margin provided by RSSD; (3) determine whether the Williams’ egg can have been incubated by an extinct giant bird Genyornis newtoni; (4) determine the theoretical maximum body mass for contact incubation. We use a dimensionless number C to quantify relative shell stiffness with respect to the egg size, allowing for comparison across wide body masses. We find that RSSD in moas significantly increases the safety margin of contact incubation by the lighter males. However, their safety margins are still smaller than those of the moa species without RSSD. Two different strategies were adopted by giant birds—one is RSSD and thinner shells, represented by some moa species; the other is no RSSD and regular shells, represented by the giant elephant bird. Finally, we predicted that the upper limit of body mass for contact incubation was 2000 kg.
Cannabis Extract Has a Positive–Immunostimulating Effect through Proteolytic System and Metabolic Compounds of Honey Bee (Apis mellifera) Workers

Simple Summary The aim of our study was to test the immunostimulating effect of a diet with hemp extract on the resistance of the honey bee (Apis mellifera). The experiment compared the effect of supplementation between the bees receiving the extract in the form of a mixture with sugar syrup and on the strip with the extract, compared to the bees that had no contact with substance. In order to determine this effect, the biochemical indicators were analyzed: the proteolytic system (proteases, protease inhibitors, total protein concentration) responsible for the fight against pathogens/parasites, biomarkers (ALT, AST, ALP), and the basic components of metabolism (glucose and urea concentrations). Parameters were determined in the hemolymph of 2- and 7-day-old workers. Hemp extracts caused an increase in the protein concentrations. Regardless of the method of administration, proteases decreased. Protease inhibitors increased, except supplementation on strips where the activity decreased. The biomarker activities increased in the control group and workers feeding extract in syrup and decreased in workers supplemented with the extract on strips. The results of the metabolic component were as follows: glucose and urea concentrations indicate that the extract will not adversely affect metabolic changes in the insect’s organism. Hemp extract improves the natural immunity of bees. Abstract In the study, we assessed the effect of hemp extract on activities of resistance parameters and the metabolic compound concentration in adult workers’ hemolymph. Bees were divided into the following groups: (1) control group fed with mixture of sugar and water-glycerine solution, (2) experimental group with pure sugar syrup and inside with cotton strips soaked with hemp extract, (3) experimental group with a mixture of sugar syrup with hemp extract. Hemp extracts caused an increase in the protein concentrations and reduced the protease activities regardless of the administration method. The protease inhibitor activities were decreased only in the group that received hemp extract on the strips. The biomarker activities (ALP, ALT, AST) increased from the control group and workers feeding extract in syrup and decreased in workers supplemented with the extract on strips. In young, 2-day-old workers, the glucose concentration was higher in the groups feeding with the extract than in the control. Hemp extract influenced an increase in urea concentrations in workers’ hemolymph in comparison with the control. The hemp supplementation positively influences the immune system of workers, and the appropriate method of administration may be adapted to the health problems of bees.
Horizontal Ridge Augmentation: A Comparison between Khoury and Urban Technique

Simple Summary With the emergence of novelty regeneration techniques in the implant dentistry field, the professional may have some queries about which one to use in their daily practice. No systematic review, to date, analyzes the horizontal gains achievable with the two main procedures for bone regeneration: the Khoury technique, which uses split blocks obtained from the patient himself, or the Urban technique, which employs membranes to contain the biomaterials. Regarding this paper, the reader will be able to decide if any of these options is adequate for the indication required. Abstract Purpose. The objective of this systematic review was to evaluate and compare the clinical efficacy of horizontal alveolar ridge augmentation techniques described by Khoury and Urban. Methods. A systematic electronic search in the MEDLINE databases, SCOPUS, WOS, and the Cochrane Central Register of Controlled Trials (CENTRAL) as well as a manual search, were conducted independently by two reviewers up to July 2021. Results. Six studies met the pre-established inclusion criteria and were included in the descriptive analysis. Due to the heterogeneity found across the included studies, meta-analysis could not be performed. Horizontal bone gain was between 3.93 ± 0.9 mm and 5.02 ± 0.8 mm with the Khoury technique and between 3.9 ± 0.9 mm and 5.68 ± 1.42 mm with the Urban technique. Similar complication rates were reported in both groups: infection (7%), in the Khoury technique, and membrane exposure (3.2–13.6%), in the Urban technique, being the most frequent events. Conclusions. Both techniques were found to be effective, in terms of clinical bone gain, for horizontal alveolar ridge gain. Nevertheless, available literature is limited, and there is a lack of comparative studies to better evaluate the results.
Evaluation of C-Reactive Protein and Associated Factors Among Patients Suffering from Rheumatoid Arthritis at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia

Background Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder, which is associated with increased pro-inflammatory mediators to induce an elevation in acute-phase response, migration of immune cells and swelling of synovial joints. Evaluation of the level of C-reactive protein and associated risk factors in RA patients was the main aim of this study. Identifying the association between disease activity of RA (hsCRP) and socio-demographic characteristics was another aim of the study. Methods Institution-based cross-sectional study was conducted at the Rheumatology Clinic of Tikur Anbessa Specialized Hospital. In this study, the level of hsCRP was measured in both case and control groups. Simple descriptive statistics, multivariate analysis, independent sample t-test were utilized for statistical analysis. The strength of association between different risk factors and hsCRP was measured using odds ratio and 95% confidence interval. P-value < 0.05 was considered as statistically significant. Result The result of this study showed that the hsCRP level was significantly higher among RA patients as compared to the control groups (P-value = 0.004). There was an association between smoking and high disease activity status (AOR= 20.03, p= 0.40). Low economic status had a statistically significant association with high hsCRP level (AOR = 12.79, p=0.00). In this study, 42 RA patients had >3mg/l hsCRP level with different occupational exposures. On the other hand, 31 RA patients had <3mg/l hsCRP level among different exposures. Although there was no statistically significant association, the association between associated risk factors (oil consumption, physical exercise, educational status) and disease activity was computed in this study. Conclusion The inflammatory marker, hsCRP was significantly higher among patients as compared to controls. The higher hsCRP showed a high grade of systemic inflammation in RA patients. C-reactive protein was elevated in rheumatoid factor positive patients and patients with high BMI value. Additionally, the result of our study showed that different socio-economic factors had an association with disease activity of RA.
The Quality, Intake, and Digestibility of Virginia Fanpetals (Sida hermaphrodita L. Rusby) Silage Produced under Different Technologies and Its Effect on the Performance of Young Cattle

Simple Summary Competition for high-quality arable land has prompted a search for alternative forage crops. For example, Virginia fanpetals is a high-yielding perennial plant with low soil requirements. Due to its chemical composition, it can be a valuable component of ruminant diets. Previous research has shown that it cannot be used for hay production, and the natural moisture content of silage was unsatisfactory. Laboratory analyses suggest that the quality and feed value of Virginia fanpetals silage may be affected by harvesting and preservation methods. However, to date, most studies have focused on the nutritional value of Virginia fanpetals silage and its inclusion in animal diets. Therefore, the present study investigated different harvesting and preservation methods, such as direct-cut harvesting with a forage harvester, and harvesting after field wilting with a forage harvester or a round baler. The quality parameters, intake and digestibility of silage, and the performance of growing bulls, fed the experimental silage, as the sole forage was evaluated. It was discovered that the highest-quality silage was produced when herbage was harvested with a forage harvester after field wilting. Abstract Different harvesting and preservation methods of Virginia fanpetals herbage were evaluated, based on the chemical composition and digestible organic matter (OM) content (D-value) of silage fed to adult sheep, the intake and digestibility of silage, and the performance of young cattle. The following harvesting methods were compared: direct-cut harvesting with a precision-cut forage harvester (DC), harvesting after field wilting with a precision-cut forage harvester (WC) or a round baler (WRB). The silage was fed for 81 days to 24 Polish Holstein Friesian (HF) bulls, as the sole forage supplemented with 3.0 kg of concentrate/head/day. Harvesting methods affected the density (p < 0.001) and water-soluble carbohydrate (WSC) content (p = 0.047). Differences were found among the groups in the digestibility coefficients of OM (DC-73.7, WC-78.9, WRB-79.9%) (p = 0.007), and crude protein (CP) (69.8%, 77.1%, 78.5%, respectively) (p < 0.001). Dry matter intake (DMI) reached 8.38 kg (DC), 8.74 kg (WC) and 7.21 kg (WRB). Live weight gain (LWG) differed (p < 0.001) among groups (0.939, 1.033, 0.813 kg/day, respectively). The feed conversion ratio (FCR) tended to improve in WC (8.66 kg DMI/kg LWG) (p = 0.08). The highest-quality silage was produced in group WC, and it could be successfully fed to growing bulls as the sole forage.
Trends in Outpatient Prescribing Patterns for Ocular Topical Anti-Infectives in Six Major Areas of China, 2013–2019

Topical anti-infectives are important in the management of ocular infections, but little is known about their current status and trends in their use in China. Thus, we carried out a prescription-based, cross-sectional study using the database of Hospital Prescription Analysis Projection of China, and aimed to analyze the trend in the use of ocular topical anti-infectives for outpatients of the ophthalmology department from 2013 to 2019. A total of 2,341,719 prescriptions from 61 hospitals located in six major areas written by ophthalmologists for outpatients were identified, and 1,002,254 of the prescriptions contained at least one anti-infective. The yearly anti-infective prescriptions increased continuously from 126,828 prescriptions in 2013 to 163,434 prescriptions in 2019. The cost also increased from 4,503,711 Chinese Yuan (CNY) in 2013 to CNY 5,860,945 in 2019. However, the use rate of anti-infectives decreased slightly from 46.5% in 2013 to 41.1% in 2019. Patients aged between 19 and 45 years old had the highest anti-infective use rate. Levofloxacin was the most frequently used anti-infective and kept on increasing among all age groups, occupying 67.1% of the total cost at the end of the study. Tobramycin was more frequently used in pediatric patients than in adults, but the use still decreased. Ganciclovir was the preferred anti-viral drug over acyclovir. In conclusion, the prescriptions and cost of ocular topical anti-infectives for outpatients both increased progressively. The increasingly widespread use of levofloxacin raised concerns regarding safety in pediatrics and resistance development. The observed trends can lead to the more efficient management of ocular anti-topical anti-infectives in China.
Analysis of Carotenoids in Haloarchaea Species from Atacama Saline Lakes by High Resolution UHPLC-Q-Orbitrap-Mass Spectrometry: Antioxidant Potential and Biological Effect on Cell Viability

Haloarchaea are extreme halophilic microorganisms belonging to the domain Archaea, phylum Euryarchaeota, and are producers of interesting antioxidant carotenoid compounds. In this study, four new strains of Haloarcula sp. , isolated from saline lakes of the Atacama Desert, are reported and studied by high-resolution mass spectrometry (UHPLC-Q-Orbitrap-MS/MS) for the first time. In addition, determination of the carotenoid pigment profile from the new strains of Haloarcula sp. , plus two strains of Halorubrum tebenquichense, and their antioxidant activity by means of several methods is reported. The effect of biomass on cellular viability in skin cell lines was also evaluated by MTT assay. The cholinesterase inhibition capacity of six haloarchaea (Haloarcula sp. ALT-23; Haloarcula sp. TeSe-41; Haloarcula sp. TeSe-51; Haloarcula sp. Te Se-89 and Halorubrum tebenquichense strains TeSe-85 and Te Se-86) is also reported for the first time. AChE inhibition IC50 was 2.96 ± 0.08 μg/mL and BuChE inhibition IC50 was 2.39 ± 0.09 μg/mL for the most active strain, Halorubrum tebenquichense Te Se-85, respectively, which is more active in BuCHe than that of the standard galantamine. Docking calculation showed that carotenoids can exert their inhibitory activity fitting into the enzyme pocket by their halves, in the presence of cholinesterase dimers.
Release of Iron-Loaded Ferritin in Sodium Iodate-Induced Model of Age Related Macular Degeneration: An In-Vitro and In-Vivo Study

To evaluate the role of iron in sodium iodate (NaIO3)-induced model of age-related macular degeneration (AMD) in ARPE-19 cells in-vitro and in mouse models in-vivo. ARPE-19 cells, a human retinal pigment epithelial cell line, was exposed to 10 mM NaIO3 for 24 h, and the expression and localization of major iron modulating proteins was evaluated by Western blotting (WB) and immunostaining. Synthesis and maturation of cathepsin-D (cat-D), a lysosomal enzyme, was evaluated by quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) and WB, respectively. For in-vivo studies, C57BL/6 mice were injected with 40 mg/kg mouse body weight of NaIO3 intraperitoneally, and their retina was evaluated after 3 weeks as above. NaIO3 induced a 10-fold increase in ferritin in ARPE-19 cells, which co-localized with LC3II, an autophagosomal marker, and LAMP-1, a lysosomal marker. A similar increase in ferritin was noted in retinal lysates and retinal sections of NaIO3-injected mice by WB and immunostaining. Impaired synthesis and maturation of cat-D was also noted. Accumulated ferritin was loaded with iron, and released from retinal pigmented epithelial (RPE) cells in Perls’ and LAMP-1 positive vesicles. NaIO3 impairs lysosomal degradation of ferritin by decreasing the transcription and maturation of cat-D in RPE cells. Iron-loaded ferritin accumulates in lysosomes and is released in lysosomal membrane-enclosed vesicles to the extracellular milieu. Accumulation of ferritin in RPE cells and fusion of ferritin-containing vesicles with adjacent photoreceptor cells is likely to create an iron overload, compromising their viability. Moreover, reduced activity of cat-D is likely to promote accumulation of other cellular debris in lysosomal vesicles, contributing to AMD-like pathology.
Hybrid rule-based botnet detection approach using machine learning for analysing DNS traffic

Botnets can simultaneously control millions of Internet-connected devices to launch damaging cyber-attacks that pose significant threats to the Internet. In a botnet, bot-masters communicate with the command and control server using various communication protocols. One of the widely used communication protocols is the ‘Domain Name System’ (DNS) service, an essential Internet service. Bot-masters utilise Domain Generation Algorithms (DGA) and fast-flux techniques to avoid static blacklists and reverse engineering while remaining flexible. However, botnet’s DNS communication generates anomalous DNS traffic throughout the botnet life cycle, and such anomaly is considered an indicator of DNS-based botnets presence in the network. Despite several approaches proposed to detect botnets based on DNS traffic analysis; however, the problem still exists and is challenging due to several reasons, such as not considering significant features and rules that contribute to the detection of DNS-based botnet. Therefore, this paper examines the abnormality of DNS traffic during the botnet lifecycle to extract significant enriched features. These features are further analysed using two machine learning algorithms. The union of the output of two algorithms proposes a novel hybrid rule detection model approach. Two benchmark datasets are used to evaluate the performance of the proposed approach in terms of detection accuracy and false-positive rate. The experimental results show that the proposed approach has a 99.96% accuracy and a 1.6% false-positive rate, outperforming other state-of-the-art DNS-based botnet detection approaches.