Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Maternal Genetic Background of Two Hungarian Autochthonous Sheep Breeds Coming from Different Geographical Directions

Simple Summary By the 19th century, adequately producing, independent domestic animal breeds had developed in many regions around the globe. However, from the middle of the 20th century they have largely been replaced by high-performing, specialized, single-purpose cosmopolitan breeds. Breed maintenance is an activity aimed at rescuing old breeds from the threat of extinction. This process includes recording the valuable traits of a rare breed, specific diversity conservation selection, and utilization in the original production environment. Additionally, it deals with the history of breeds and the study of their genetic makeup. The aim of this paper is to evaluate the maternal genetic background of two autochthonous sheep breeds in Hungary. Abstract The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (KST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background.
Effect of pH on the structure and function of cyclin-dependent kinase 6

Cyclin-dependent kinase 6 (CDK6) is an important protein kinase that regulates cell growth, development, cell metabolism, inflammation, and apoptosis. Its overexpression is associated with reprogramming glucose metabolism through alternative pathways and apoptosis, which ultimately plays a significant role in cancer development. In the present study, we have investigated the structural and conformational changes in CDK6 at varying pH employing a multi-spectroscopic approach. Circular dichroism (CD) spectroscopy revealed at extremely acidic conditions (pH 2.0–4.0), the secondary structure of CDK6 got significantly disrupted, leading to aggregates formation. These aggregates were further characterized by employing Thioflavin T (ThT) fluorescence. No significant secondary structural changes were observed over the alkaline pH range (pH 7.0–11.0). Further, fluorescence and UV spectroscopy revealed that the tertiary structure of CDK6 was disrupted under extremely acidic conditions, with slight alteration occurring in mild acidic conditions. The tertiary structure remains intact over the entire alkaline range. Additionally, enzyme assay provided an insight into the functional aspect of CDK at varying pH; CDK6 activity was optimal in the pH range of 7.0–8.0. This study will provide a platform that provides newer insights into the pH-dependent dynamics and functional behavior of CDK6 in different CDK6 directed diseased conditions, viz. different types of cancers where changes in pH contribute to cancer development.
Assessment of colon cancer molecular mechanism: a system biology approach

Aim: The current study aimed to assess and compare colon cancer dysregulated genes from the GEO and STRING databases. Background: Colorectal cancer is known as the third most common kind of cancer and the second most important reason for global cancer-related mortality rates. There have been many studies on the molecular mechanism of colon cancer Methods: From the STRING database, 100 differentially expressed proteins related to colon cancers were retrieved and analyzed by network analysis. The central nodes of the network were assessed by gene ontology. The findings were compared with a GSE from GEO. Results: Based on data from the STRING database, TP53, EGFR, HRAS, MYC, AKT1, GAPDH, KRAS, ERBB2, PTEN, and VEGFA were identified as central genes. The central nodes were not included in the significant DEGs of the analyzed GSE. Conclusion: A combination of different database sources in system biology investigations provides useful information about the studied diseases.
Investigating the Association between Unhealthy Dietary Habits and Obesity among Libyan Adults

Background: Although an increasing number of studies have reported on nutrition transition and unhealthy eating habits (UEHs) worldwide, there is a paucity of studies on UEHs in the Arab region, particularly in Libya. Aim: This study investigated the associations between obesity among Libyan adults and UEHs. Methods: A cross-sectional survey was conducted at the five major districts in Benghazi, Libya. A multistage cluster sampling strategy was implemented to choose and recruit Libyan adults. Anthropometric measurements were gathered by highly qualified nurses, using the Segmental Body Composition Monitor and a portable Stadiometer. The study used and adapted the two Self-administered questionnaires: the WHO STEPS Instrument and eating behaviors linked with obesity questionnaire. Results: Among a total of 401 participants who were successfully recruited in this study, 253 (63%) were female (aged 20–65 years), the response rate achieved was 78%. The prevalence of obesity amongst Libyan adults was estimated to be 42.4%. The results revealed the presence of a significant association between obesity (BMI ≥ 30 kg/m2) and five UEHs for Libyan men and six UEHs for Libyan women. For Libyan men, an association was found between obesity and the following five explanatory factors: fast food intake in a day and a week, which were (OR: 2.52, 95% CI: 4.04–12.32) and (OR: 4.65, 95% CI: 1.04–9.46), respectively; large food portion sizes consumed at one sitting (OR: 19.54, 95% CI: 1.41–27.74); a high frequency of skipping breakfast either in a typical day or a week, which were (OR: 0.02, 95% CI: 0.01–0.77) and (OR: 0.03, 95% CI: 0.01–0.24), respectively. For Libyan women, a significant association was found between obesity and the following six explanatory factors: fast food intake in a day and a week, which were (OR: 2.14, 95% CI: 3.32–11.12) and (OR: 5.5, 95% CI: 1.88–16.11), respectively; intake of sugar-sweetened beverages in a typical week (OR: 4.02, 95% CI: 1.35–11.99); and large food portion sizes consumed at one sitting at one sitting (OR: 3.40, 95% CI: 1.18–9.84); and a high frequency of skipping breakfast either in a typical day or a week, which were (OR: 0.11, 95% CI: 0.03–0.43) and (OR: 0.12, 95% CI: 0.08–0.63), respectively. Conclusions: The findings of the study reveal areas of action for Libyan researchers, clinicians, policymakers, and government officials about UEHs in the Libyan context. This could inform establishing and developing new interventions for preventing and controlling the obesity epidemic through food system improvements.
The Alchemy System for Statistical Relational AI: User Manual

The Alchemy package provides a series of algorithms for statistical relational learning and probabilistic logic inference, based on the Markov logic representation. If you are not already familiar with Markov logic, we recommend that you read the papers Markov Logic Networks [7], Discriminative Training of Markov Logic Networks [9], Learning the Structure of Markov Logic Networks [3], Memory-Efficient Inference in Relational Domains [10] and Sound and Efficient Inference with Probabilistic and Deterministic Dependencies [6] (mln.pdf, dtmln.pdf, lsmln.pdf, lazysat.pdf and mcsat.pdf in the papers/ directory) before reading this manual. We welcome your feedback on any aspect of the Alchemy package. Please email us at alchemy@cs.washington. edu to let us know what you find easy or hard to use, what results you have obtained with Alchemy, the features you wish to have but are not currently provided, and any bugs that you encounter. Please cite Kok et al. (2005) [4] if you use the Alchemy system.
X-ray scintillator lens-coupled with CMOS camera for pre-clinical cardiac vascular imaging—A feasibility study

We present the design and characterization of an X-ray imaging system consisting of an off-the-shelf CMOS sensor optically coupled to a CsI scintillator. The camera can perform both high-resolution and functional cardiac imaging. High-resolution 3D imaging requires microfocus X-ray tubes and expensive detectors, while pre-clinical functional cardiac imaging requires high flux pulsed (clinical) X-ray tubes and high-end cameras. Our work describes an X-ray camera, namely an “optically coupled X-ray(OCX) detector,” used for both the aforementioned applications with no change in the specifications. We constructed the imaging detector with two different CMOS optical imaging cameras called CMOS sensors, 1.A monochrome CMOS sensor coupled with an f1.4 lens and 2.an RGB CMOS sensor coupled with an f0.95 prime lens. The imaging system consisted of our X-ray camera, micro-focus X-ray source (50kVp and 1mA), and a rotary stage controlled from a personal computer (PC) and LabVIEW interface. The detective quantum efficiency (DQE) of the imaging system(monochrome) estimated using a cascaded linear model was 17% at 10 lp/mm. The system modulation transfer function (MTF) and the noise power spectrum (NPS) were inputs to the DQE estimation. Because of the RGB camera’s low quantum efficiency (QE), the OCX detector DQE was 19% at 5 lp/mm. The contrast to noise ratio (CNR) at different frame rates was studied using the capillary tubes filled with various dilutions of iodinated contrast agents. In-vivo cardiac angiography demonstrated that blood vessels of the order of 100 microns or above were visible at 40 frames per second despite the low X-ray flux. For high-resolution 3D imaging, the system was characterized by imaging a cylindrical micro-CT contrast phantom and comparing it against images from a commercial scanner.
Decreased Expression of Estrogen Receptors Is Associated with Tumorigenesis in Papillary Thyroid Carcinoma

Papillary thyroid carcinomas (PTC), which is derived from thyroid follicular cells, is the most commonly differentiated thyroid cancer with sex disparity. However, the role of estrogen receptors (ERs) in the pathogenesis of PTC remains unclear. The present study aimed to determine the association of ER mRNA expression levels with clinicopathologic features in PTC. To that aim, the mRNA levels of ESR1 (ERα66), ESR1 (ERα36), ESR2, and G-protein-coupled estrogen receptor 1 (GPER1) in snap-frozen tissue samples from PTCs and adjacent normal thyroid tissues were determined using quantitative reverse transcription polymerase chain reaction (RT-qPCR), and the correlation between ER mRNA expression levels and clinicopathologic features was analyzed. The expression of ERα66, ERα36, ERβ, and GPER1 was lower in PTC specimens than in adjacent normal thyroid tissues. Moreover, low GPER1 expression was associated with extrathyroidal extension. There was no obvious difference in expression of ERs between PTC specimens from male and female patients. In conclusion, our findings highlight the importance of ERs in PTC tumorigenesis.
A Possibility for Quantitative Detection of Mechanically-Induced Invisible Damage by Thermal Property Measurement via Entropy Generation for a Polymer Material

Entropy generation from a mechanical and thermal perspective are quantitatively compared via molecular dynamic (MD) simulations and mechanical and thermal experiments. The entropy generation values regarding mechanical tensile loading—which causes invisible damage—of the Polyamide 6 (PA6) material are discussed in this study. The entropy values measured mechanically and thermally in the MD simulation were similar. To verify this consistency, mechanical and thermal experiments for measuring entropy generation were conducted. The experimentally obtained mechanical entropy was slightly less than that calculated by MD simulation. The thermal capacity is estimated based on the specific heat capacity measured by differential scanning calorimetry (DSC), applying the assumed extrapolation methods. The estimated entropy generation was higher than the aforementioned values. There is a possibility that the entropy-estimating method used in this study was inappropriate, resulting in overestimations. In any case, it is verified that entropy increases with mechanical loading and material invisible damage can be qualitatively detected via thermal property measurements.
Multifaceted Analyses of Isolated Mitochondria Establish the Anticancer Drug 2-Hydroxyoleic Acid as an Inhibitor of Substrate Oxidation and an Activator of Complex IV-Dependent State 3 Respiration

The synthetic fatty acid 2-hydroxyoleic acid (2OHOA) has been extensively investigated as a cancer therapy mainly based on its regulation of membrane lipid composition and structure, activating various cell fate pathways. We discovered, additionally, that 2OHOA can uncouple oxidative phosphorylation, but this has never been demonstrated mechanistically. Here, we explored the effect of 2OHOA on mitochondria isolated by ultracentrifugation from U118MG glioblastoma cells. Mitochondria were analyzed by shotgun lipidomics, molecular dynamic simulations, spectrophotometric assays for determining respiratory complex activity, mass spectrometry for assessing beta oxidation and Seahorse technology for bioenergetic profiling. We showed that the main impact of 2OHOA on mitochondrial lipids is their hydroxylation, demonstrated by simulations to decrease co-enzyme Q diffusion in the liquid disordered membranes embedding respiratory complexes. This decreased co-enzyme Q diffusion can explain the inhibition of disjointly measured complexes I–III activity. However, it doesn’t explain how 2OHOA increases complex IV and state 3 respiration in intact mitochondria. This increased respiration probably allows mitochondrial oxidative phosphorylation to maintain ATP production against the 2OHOA-mediated inhibition of glycolytic ATP production. This work correlates 2OHOA function with its modulation of mitochondrial lipid composition, reflecting both 2OHOA anticancer activity and adaptation to it by enhancement of state 3 respiration.
Stem Cell Transplantation and Cell-Free Treatment for Periodontal Regeneration

Increasing attention has been paid to cell-based medicines. Many in vivo and in vitro studies have demonstrated the efficacy of stem cell transplantation for the regeneration of periodontal tissues over the past 20 years. Although positive evidence has accumulated regarding periodontal regeneration using stem cells, the exact mechanism of tissue regeneration is still largely unknown. This review outlines the practicality and emerging problems of stem cell transplantation therapy for periodontal regeneration. In addition, possible solutions to these problems and cell-free treatment are discussed.
Cellular and Gene Expression Response to the Combination of Genistein and Kaempferol in the Treatment of Mucopolysaccharidosis Type I

Flavonoids are investigated as therapeutics for mucopolysaccharidosis, a metabolic disorder with impaired glycosaminoglycan degradation. Here we determined the effects of genistein and kaempferol, used alone or in combination, on cellular response and gene expression in a mucopolysaccharidosis type I model. We assessed the cell cycle, viability, proliferation, subcellular localization of the translocation factor EB (TFEB), number and distribution of lysosomes, and glycosaminoglycan synthesis after exposure to flavonoids. Global gene expression was analysed using DNA microarray and quantitative PCR. The type and degree of flavonoid interaction were determined based on the combination and dose reduction indexes. The combination of both flavonoids synergistically inhibits glycosaminoglycan synthesis, modulates TFEB localization, lysosomal number, and distribution. Genistein and kaempferol in a 1:1 ratio regulate the expression of 52% of glycosaminoglycan metabolism genes. Flavonoids show synergy, additivity, or slight antagonism in all analysed parameters, and the type of interaction depends on the concentration and component ratios. With the simultaneous use of genistein and kaempferol in a ratio of 4:1, even a 10-fold reduction in the concentration of kaempferol is possible. Flavonoid mixtures, used as the treatment of mucopolysaccharidosis, are effective in reducing glycosaminoglycan production and storage and show a slight cytotoxic effect compared to single-flavonoid usage.
A Review and Analysis of the National Dog Population Management Program in Chile

Simple Summary Free-roaming dogs are a worldwide problem that cause a wide array of issues in society. In Chile, a law protecting companion animals, and describing the role of responsible owners, was promulgated in 2017, followed by a national program aimed at mitigating dog-related problems throughout the country. The aim of this review is to explain and discuss certain components of the program and to provide suggestions for future changes. A simple model was created to assist managers in Chilean municipalities to more closely estimate the local dog population. The recommendations include the collection of baseline data and a dog population size estimate prior to implementing interventions, as well as the development of clear objectives, achievable goals and indicators, and the investment of public funds in long-term sustainable strategies such as education and enforcement rather than offering free veterinary services. Abstract Free-roaming dogs are a worldwide problem, with Chile having some of the highest human-to-dog ratios in the world. In 2017, Law 21.020 was promulgated and the federal government developed a national responsible pet ownership program. The objectives of this article are to describe and discuss the dog-related components of the program, to design a tool for determining human-to-dog ratios in Chile, and to make recommendations to managers to improve the program outcomes. The overarching goal of the program was to mitigate the conflict between humans and dogs, but many of the interventions were animal-focused and the indicators did not consider the perception of the Chilean public. Using human density data and known dog populations, we found that as the human density increased, there were fewer dogs per person. Veterinary services and sterilizations were the mainstay of the program and were offered for free to citizens. Education was offered to all ages through public events, as well as municipality and organization activities. The identification of dogs was obligatory for dog owners. Enforcement was not included in the program. The recommendations are to conduct preintervention baseline data collections and to tailor interventions and indicators appropriately; to use dog population size estimates determined at the local level rather than a country-wide estimate; to replace free veterinary services with low-cost sterilization campaigns; to create sustainable plans for education; and to create enforcement teams in communities.
The Impact of Career Plateau on Job Burnout in the COVID-19 Pandemic: A Moderating Role of Regulatory Focus

This study reviewed the mental health problems experienced by office workers exposed to new kinds of work stress, career plateau, and job burnout, due to no-contact teleworking during the COVID-19 pandemic. Human beings tend to evaluate their own qualities to determine their own superiority by comparing themselves with others. Appropriate social comparison helps to promote self-understanding and boost self-esteem. However, in the case of no-contact remote working, where the amount of time spent alone is drastically increased, the information obtained from such social comparisons is naturally insufficient, resulting in the perception of reaching a career plateau. Prolonged anxiety and a sense of helplessness have been shown to cause job burnout; however, so far, few studies have examined career plateau as an antecedent factor for job burnout. This study also considered the moderating effect of regulatory focus in order to closely examine the effect of career plateau on job burnout. According to the regulatory focus theory, differences appear in various psychological processes, such as human choices, judgments, motivations, and attitudes, determined by whether individuals adopt a promotion focus or a prevention focus. This study aimed to verify whether regulatory focus operates in a conditional context, in the process of job burnout following career plateau, to change the magnitude and direction of the influence of career plateau. To this end, a hierarchical regression analysis was performed by collecting data from 202 people working for three Korean companies. As a result of the analysis, it was found that the career plateau had a significant effect on job burnout. This direct effect was still significant even after considering the interaction with regulatory focus. In addition, promotion focus was found to have a negative moderating effect, while prevention focus had no effect on the influence of career plateau on job burnout. This study demonstrated that the negative effects of career plateau, which have been presented in various ways in academia, lead to job burnout under the non-face-to-face teleworking systems implemented due to the COVID-19 pandemic, and suggested that promotion focus can play a positive role in alleviating this dynamic.
Impact of Androgen Receptor Activity on Prostate-Specific Membrane Antigen Expression in Prostate Cancer Cells

Prostate-specific membrane antigen (PSMA) is an essential molecular regulator of prostate cancer (PCa) progression coded by the FOLH1 gene. The PSMA protein has become an important factor in metastatic PCa diagnosis and radioligand therapy. However, low PSMA expression is suggested to be a resistance mechanism to PSMA-based imaging and therapy. Clinical studies revealed that androgen receptor (AR) inhibition increases PSMA expression. The mechanism has not yet been elucidated. Therefore, this study investigated the effect of activation and inhibition of androgen signaling on PSMA expression levels in vitro and compared these findings with PSMA levels in PCa patients receiving systemic therapy. To this end, LAPC4, LNCaP, and C4-2 PCa cells were treated with various concentrations of the synthetic androgen R1881 and antiandrogens. Changes in FOLH1 mRNA were determined using qPCR. Open access databases were used for ChIP-Seq and tissue expression analysis. Changes in PSMA protein were determined using western blot. For PSMA staining in patients’ specimens, immunohistochemistry (IHC) was performed. Results revealed that treatment with the synthetic androgen R1881 led to decreased FOLH1 mRNA and PSMA protein. This effect was partially reversed by antiandrogen treatment. However, AR ChIP-Seq analysis revealed no canonical AR binding sites in the regulatory elements of the FOLH1 gene. IHC analysis indicated that androgen deprivation only resulted in increased PSMA expression in patients with low PSMA levels. The data demonstrate that AR activation and inhibition affects PSMA protein levels via a possible non-canonical mechanism. Moreover, analysis of PCa tissue reveals that low PSMA expression rates may be mandatory to increase PSMA by androgen deprivation.