Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomics alterations in chicken jejunum caused by 24 h fasting

The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
Perceived Correspondence of Health Effects as a New Determinant Influencing Purchase Intention for Functional Food

This study has revealed the role of a new factor, perceived correspondence of health effects, in consumer acceptance of functional foods. Using a web survey of 1016 people, we hypothesized and verified the following: when an ingredient does not occur naturally in the carrier but the consumer assigns the same health effect to it as to the carrier, the product’s acceptance will be more positive than it would be if an identical health effect was not associated with the carrier and the functional ingredient. Factors influencing consumer acceptance were examined via binary logistic regression models. According to the results, if a functional food developer fortifies the carrier with an ingredient that does not occur naturally in the carrier, the product can expect higher acceptance if the health effects perceived by consumers are properly matched. In general, it has been found that expected taste and awareness of the product were decisive in all demographic and income groups, whereas perceived correspondence of health effects had a lesser, but still positive influence on acceptance.
miR-1306 Mediates the Feedback Regulation of the TGF-β/SMAD Signaling Pathway in Granulosa Cells

Transforming growth factor-β receptor II (TGFBR2), the type II receptor of the TGF-β/SMA- and MAD-related protein (SMAD) signaling pathway, plays a crucial role in TGF-β signal transduction and is regulated by multiple factors. Nevertheless, the modulation of the non-coding RNA involved in the process of TGFBR2 expression in ovaries is not well studied. In our study, we isolated and characterized the 3′-untranslated region (UTR) of the porcine TGFBR2 gene and microRNA-1306 (miR-1306) was identified as the functional miRNA that targets TGFBR2 in porcine granulosa cells (GCs). Functional analysis showed that miR-1306 promotes apoptosis of GCs as well as attenuating the TGF-β/SMAD signaling pathway targeting and impairing TGFBR2 in GCs. Moreover, we identified the miR-1306 core promoter and found three potential SMAD4-binding elements (SBEs). Luciferase and chromatin immunoprecipitation (ChIP) assays revealed that the transcription factor SMAD4 directly binds to the miR-1306 core promoter and inhibits its transcriptional activity. Furthermore, the TGF-β/SMAD signaling pathway is modulated by SMAD4 positive feedback via inhibition of miR-1306 expression in GCs. Collectively, our findings provide evidence of an epigenetic mechanism that modulates as well as mediates the feedback regulation of the classical TGF-β/SMAD signaling pathway in GCs from porcine ovaries.
The Eukaryotic Translation Initiation Factor 4F Complex Restricts Rotavirus Infection via Regulating the Expression of IRF1 and IRF7

The eIF4F complex is a translation initiation factor that closely regulates translation in response to a multitude of environmental conditions including viral infection. How translation initiation factors regulate rotavirus infection remains poorly understood. In this study, the knockdown of the components of the eIF4F complex using shRNA and CRISPR/Cas9 were performed, respectively. We have demonstrated that loss-of-function of the three components of eIF4F, including eIF4A, eIF4E and eIF4G, remarkably promotes the levels of rotavirus genomic RNA and viral protein VP4. Consistently, knockdown of the negative regulator of eIF4F and programmed cell death protein 4 (PDCD4) inhibits the expression of viral mRNA and the VP4 protein. Mechanically, we confirmed that the silence of the eIF4F complex suppressed the protein level of IRF1 and IRF7 that exert potent antiviral effects against rotavirus infection. Thus, these results demonstrate that the eIF4F complex is an essential host factor restricting rotavirus replication, revealing new targets for the development of new antiviral strategies against rotavirus infection.
Topological electronic structure and Rashba effect in Bi thin layers: theoretical predictions and experiments

The goal of the present review is to cross-compare theoretical predictions with selected experimental results on bismuth thin films exhibiting topological properties and a strong Rashba effect. The theoretical prediction that a single free-standing Bi(1 1 1) bilayer is a topological insulator has triggered a large series of studies of ultrathin Bi(1 1 1) films grown on various substrates. Using selected examples we review theoretical predictions of atomic and electronic structure of Bi thin films exhibiting topological properties due to interaction with a substrate. We also survey experimental signatures of topological surface states and Rashba effect, as obtained mostly by angle- and spin-resolved photoelectron spectroscopy.
Unique Gene Expression Signatures in the Intestinal Mucosa and Organoids Derived from Germ-Free and Monoassociated Mice

Commensal microbiota contribute to gut homeostasis by inducing transcription of mucosal genes. Analysis of the impact of various microbiota on intestinal tissue provides an important insight into the function of this organ. We used cDNA microarrays to determine the gene expression signature of mucosa isolated from the small intestine and colon of germ-free (GF) mice and animals monoassociated with two E. coli strains. The results were compared to the expression data obtained in conventionally reared (CR) mice. In addition, we analyzed gene expression in colon organoids derived from CR, GF, and monoassociated animals. The analysis revealed that the complete absence of intestinal microbiota mainly affected the mucosal immune system, which was not restored upon monoassociation. The most important expression changes observed in the colon mucosa indicated alterations in adipose tissue and lipid metabolism. In the comparison of differentially expressed genes in the mucosa or organoids obtained from GF and CR mice, only six genes were common for both types of samples. The results show that the increased expression of the angiopoietin-like 4 (Angptl4) gene encoding a secreted regulator of lipid metabolism indicates the GF status.
Influence of Porosity on the Mechanical Behavior during Uniaxial Compressive Testing on Voronoi-Based Open-Cell Aluminium Foam

We have studied an application of the Voronoi tessellation method in the modeling of open-cell aluminium foam under uniaxial compressive loading. The Voronoi code was merged with computer-aided design (CAD) for converting the polyhedral model into an irregular open-cell cellular structure to create porous samples for compression testing simulations. Numerical simulations of the uniaxial compression uniformly over the upper surface of the sample in the z-axis direction at a constant 20 N load was realised. Samples with three different porosities (30%, 60% and 80%) were studied. A nonlinear elasto-plastic material model with perfect plasticity, without hardening, based on the von Mises yield criterion was applied below 10% strain. Corresponding stress–strain curves were observed and the influence of porosity on deformation mechanism was discussed. Samples with higher porosity exhibited significantly higher normal stress under the same load, and increased stress plateaus. An increase of porosity produced an increase of both compressive and tensile stresses and struts exhibited complex stress fields. Voronoi-based modeling was in accordance with experimental results in the literature in the case of the quasi-static condition and linear elastic region (below 1% strain). Further study is necessary to enable the simulation of real dynamic behaviour under all deformation regimes by using the Voronoi tessellation method.
Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency

Phosphorothioate (PT) modifications of the DNA backbone, widespread in prokaryotes, are first identified in bacterial enteropathogens Escherichia coli B7A more than a decade ago. However, methods for high resolution mapping of PT modification level are still lacking. Here, we developed the PT-IC-seq technique, based on iodine-induced selective cleavage at PT sites and high-throughput next generation sequencing, as a mean to quantitatively characterizing the genomic landscape of PT modifications. Using PT-IC-seq we foud that most PT sites are partially modified at a lower PT frequency (< 5%) in E. coli B7A and Salmonella enterica serovar Cerro 87, and both show a heterogeneity pattern of PT modification similar to those of the typical methylation modification. Combining the iodine-induced cleavage and absolute quantification by droplet digital PCR, we developed the PT-IC-ddPCR technique to further measure the PT modification level. Consistent with the PT-IC-seq measurements, PT-IC-ddPCR analysis confirmed the lower PT frequency in E. coli B7A. Our study has demonstrated the heterogeneity of PT modification in the bacterial population and we also established general tools for rigorous mapping and characterization of PT modification events at whole genome level. We describe to our knowledge the first genome-wide quantitative characterization of PT landscape and provides appropriate strategies for further functional studies of PT modification.
Securing the Future: Transformative Justice and Children ‘Born of War’

Children born as the result of conflict related sexual violence often embody painful memories of war-affected communities. As a result, children ‘born of war’ experience abuse and neglect, social isolation and a sense of never-belonging. Existing scholarship grapples with the challenges of seeking justice for children ‘born of war’ given the complex ways their suffering is entangled with that of so many other victims. In post-conflict northern Uganda, a community-based organization composed of survivors of forced marriage and motherhood collectively seeks justice for their children in a process locally referred to as child tracing. The Women’s Advocacy Network brings together differently affected victim groups to help identify the paternal relatives of their children, mediate conflict and transform fractious relationships in order to secure a future for their children. Through this process, children who once divided communities, propel a collective reach towards justice.
Characteristics and Potentiality of Human Adipose-Derived Stem Cells (hASCs) Obtained from Enzymatic Digestion of Fat Graft

Human adipose-derived stem cells localize in the stromal-vascular portion, and can be ex vivo isolated using a combination of washing steps and enzymatic digestion. For this study, we undertook a histological evaluation of traditional fat graft compared with fat graft enriched with stromal vascular fraction cells isolated by the Celution™ system to assess the interactions between cells and adipose tissue before the breast injection. In addition, we reported on histological analyses of biopsies derived from fat grafted (traditional or enriched with SVFs) in the breast in order to assess the quality of the adipose tissue, fibrosis and vessels. The hASCs derived from enzymatic digestion were systematically characterized for growth features, phenotype and multi-potent differentiation potential. They fulfill the definition of mesenchymal stem cells, albeit with a higher neural phenotype profile. These cells also express genes that constitute the core circuitry of self-renewal such as OCT4, SOX2, NANOG and neurogenic lineage genes such as NEUROD1, PAX6 and SOX3. Such findings support the hypothesis that hASCs may have a potential usefulness in neurodegenerative conditions. These data can be helpful for the development of new therapeutic approaches in personalized medicine to assess safety and efficacy of the breast reconstruction.
Developing a Course on Security and Intelligence with Spy Novels: An Extension of the Science Education Initiative into International Relations

Abstract This study brings together insights from the Science Education Initiative with a new course, “Spy Novel Diplomacy: Propaganda and International Relations,” which has been taught as a General Education Seminar for first year students. The class will continue on an annual basis from the spring semester of 2020 onward. Thus what follows is a combination of the Science Education Initiative with innovative teaching that incorporates literature. After an overview, work proceeds in five additional sections. The first section summarizes the Science Education Initiative and considers its potential for more expansive implementation. Ideas from that venture are identified for adoption in the new course on Spy Novel Diplomacy. The second section explores the potential value from works of fiction and visualization in the International Relations classroom. Section three introduces the new course on Spy Novel Diplomacy, connecting at a general level with innovative teaching techniques. Section four applies insights from the Science Education Initiative to the class in specific ways. The fifth and final section reflects on the Spy Novel Diplomacy course in relation to the Science Education Initiative, along with future directions in pedagogy.
Reduction of cadmium toxicity in wheat through plasma technology

Cadmium (Cd) contamination in plant-derived food is a big concern. This study examines whether and how Ar/O2 and Ar/Air plasma techniques lead to Cd detoxification in wheat. Treatment with Ar/O2 and Ar/Air changed the seed surface and decreased the pH of seeds as well as the cultivation media. Generally, plants subjected to Cd treatment from seeds treated with Ar/O2and Ar/Air plasma showed considerable progress in morphology and total chlorophyll synthesis compared to Cd-treated wheat, suggesting that plasma technology is effective for Cd detoxification. Furthermore, Ar/O2 and Ar/Air plasma treated plants showed a significant decrease in root and shoot Cd concentration, which is consistent with the reduced expression of Cd transporters in the root (TaLCT1 and TaHMA2) compared with the plants not treated with plasma in response to Cd stress. This Cd inhibition is possibly accomplished by the decrease of pH reducing the bioavailability of Cd in the rhizosphere. These observations are in line with maintenance of total soluble protein along with reduced electrolyte leakage and cell death (%) in root and shoot due to Ar/O2 and Ar/Air treatments. Further, Cd-induced elevated H2O2 or oxidative damage in tissues was mainly diminished through the upregulation of antioxidant enzymes (SOD and CAT) and their corresponding genes (TaSOD and TaCAT) induced by Ar/O2 and Ar/Air plasma. Grafting results suggest that root originating nitric oxide signal possibly drives the mechanisms of Cd detoxification due to plasma treatment in wheat. These findings provide a novel and eco-friendly use of plasma technology for the mitigation of Cd toxicity in wheat plants.
Assessment of Ozone Sensitivity in Three Wheat Cultivars Using Ethylenediurea

Three wheat (Triticum aestivum L.) cultivars [HD 2987 (ozone (O3) sensitive), PBW 502 (intermediately sensitive) and Kharchiya 65 (O3 tolerant)] with known sensitivity to O3 were re-evaluated using ethylenediurea (EDU; 400 ppm) to ascertain the use of EDU in determiningO3 sensitivity under highly O3-polluted tropical environments. EDU treatment helped in improving the growth, biomass, photosynthetic pigments and the antioxidative defense system of all the wheat cultivars. Under EDU treatment, PBW 502 retained more biomass, while HD 2987 showed better performance and ultimately the greatest increment in yield. Cultivar Kharchiya 65 also showed a positive response to EDU as manifested with an increase in pigment contents, total biomass and enzymatic antioxidants; however, this increment was comparatively lower compared to the other two cultivars. The results indicated that EDU did not have many physiological effects on cultivars but helped in counteracting O3 primarily by scavenging reactive oxygen species and enhancing the antioxidative defense system where superoxide dismutase emerged as the major responsive biochemical parameter against ambient O3. The observed results clearly indicated that differential O3 sensitivity in three wheat cultivars established by the previous study is in accordance with the present study using EDU as a sensitivity tool, which is an easy and efficient technology in comparison to chamber and Free-Air Carbon dioxide Enrichment (FACE) experiments although its mechanistic understanding needs to be further validated.
The Contributions of Prostate Cancer Stem Cells in Prostate Cancer Initiation and Metastasis

Research in the last decade has clearly revealed a critical role of prostate cancer stem cells (PCSCs) in prostate cancer (PC). Prostate stem cells (PSCs) reside in both basal and luminal layers, and are the target cells of oncogenic transformation, suggesting a role of PCSCs in PC initiation. Mutations in PTEN, TP53, and RB1 commonly occur in PC, particularly in metastasis and castration-resistant PC. The loss of PTEN together with Ras activation induces partial epithelial–mesenchymal transition (EMT), which is a major mechanism that confers plasticity to cancer stem cells (CSCs) and PCSCs, which contributes to metastasis. While PTEN inactivation leads to PC, it is not sufficient for metastasis, the loss of PTEN concurrently with the inactivation of both TP53 and RB1 empower lineage plasticity in PC cells, which substantially promotes PC metastasis and the conversion to PC adenocarcinoma to neuroendocrine PC (NEPC), demonstrating the essential function of TP53 and RB1 in the suppression of PCSCs. TP53 and RB1 suppress lineage plasticity through the inhibition of SOX2 expression. In this review, we will discuss the current evidence supporting a major role of PCSCs in PC initiation and metastasis, as well as the underlying mechanisms regulating PCSCs. These discussions will be developed along with the cancer stem cell (CSC) knowledge in other cancer types.
Facial reanimation with masseter nerve–innervated free gracilis muscle transfer in established facial palsy patients

Background The masseter nerve is a useful donor nerve for reconstruction in patients with established facial palsy, with numerous advantages including low morbidity, a strong motor impulse, high reliability, and fast reinnervation. In this study, we assessed the results of masseter nerve–innervated free gracilis muscle transfer in established facial palsy patients. Methods Ten patients with facial palsy who received treatment from January 2015 to January 2017 were enrolled in this study. Three patients received masseter nerve–only free gracilis transfer, and seven received double-innervated free gracilis transfer (masseter nerve and a cross-face nerve graft). Patients were evaluated using the Facial Assessment by Computer Evaluation software (FACEgram) to quantify oral commissure excursion and symmetry at rest and when smiling after muscle transfer. Results The mean time between surgery and initial movement was roughly 167.7 days. A statistically significant increase in excursion at rest and when smiling was seen after muscle transfer. There was a significant increase in the distance of oral commissure excursion at rest and when smiling. A statistically significant increase was observed in symmetry when smiling. Terzis’ functional and aesthetic grading scores showed significant improvements postoperatively. Conclusions Masseter nerve innervation is a good option with many uses in in established facial palsy patients. For some conditions, it is the first-line treatment. Free gracilis muscle transfer using the masseter nerve has excellent results with good symmetry and an effective degree of recovery.
The contribution of Chinese-educated physicians to health care in the United States

Background Migration of physicians has been a cause for global concern. In China, reforms of the higher education and healthcare systems have led to a shortage of postgraduate training positions relative to the number of medical graduates. Medical graduates opt for non-clinical roles or move abroad to pursue further training and practice opportunities. The impact of this physician migration is not known. This study quantifies where Chinese migrant physicians to the U.S. were educated, where they went to practice, and how these trends have changed over time. Methods We combined data on physician characteristics from the 2008 and 2017 American Medical Association Physician Masterfiles with demographic information from the Educational Commission for Foreign Medical Graduates. Using a repeated cross-sectional approach, we reviewed the available data, including citizenship at entry to medical school, medical school attended, practice specialty, and practice location. Results The number of Chinese-educated physicians (CEPs) to the United States (US) has increased over the past 10 years, from 3,878 in 2008 to 5,355 in 2017 (+38.1%). The majority held Chinese citizenship at entry to medical school (98.4% vs 97.1%) with the remainder being citizens of other East Asian nations. Of the Chinese citizens identified in 2008, 913 (19.3%) attended medical school outside of China; in 2017, 376 (6.7%) attended medical school outside of China, representing a decrease of 58.8%. Overall, in 2017, four Chinese medical schools provided 32.1% of all Chinese-educated physicians in the US. Over 50% of the CEPs were practicing in Internal Medicine, Anatomic/ Clinical Pathology, Anesthesiology, Family Medicine or Neurology. Compared with all IMGs, CEPs are more likely to be Anatomic/ Clinical Pathologists and Anesthesiologists. CEPs were concentrated in several states, including New York, California and Massachusetts. In 2017, a lower proportion of CEPs in the US healthcare workforce were in residency training, compared to 2008 (13.2% vs 22.8%). Conclusions Unlike trends from some other South Asian countries, the number of CEPs in the US has increased over the past 10 years. Migration trends may vary depending on citizenship and country of medical school training. The majority of Chinese-educated graduates come to the US from relatively few medical schools. Fewer CEPs currently in residency training might indicate lower success rates in securing GME training in the US.