Miracle-dz/UniFAR-FTUs huggingface dataset:
Fecal Microbiota Transplantation Alters the Outcome of Hepatitis B Virus Infection in Mice

The susceptibility of mice to hepatitis B virus (HBV) infection depends on their genetic background. The gut microbiota modulates the antiviral immune response in the liver and plays a protective role against HBV infection. However, whether HBV infection outcomes depend on the gut microbiota remains unclear. In this study, we assessed the gut microbiota composition in naïve BALB/c and C57BL/6 mice using 16S rRNA gene sequencing. The gut microbiota in BALB/c mice was depleted using broad-spectrum antibiotics (ABX) and then reconstituted with fecal microbiota from naïve BALB/c or C57BL/6 mice to evaluate the effect of fecal microbiota transplantation (FMT) on the outcomes of and immune response to HBV infection. We found that HBV infection outcomes and the gut microbiota composition differed between BALB/c and C57BL/6 mice. Commensal bacteria from the fecal microbiota selectively colonized the guts of ABX-treated BALB/c mice. Mice receiving fecal microbiota from BALB/c or C57BL/6 mice displayed different HBV infection outcomes. The fecal microbiota from C57BL/6 mice induced immune tolerance in the liver and prolonged HBV infection. In conclusion, HBV infection outcomes in mice are determined by the host genetic background and gut microbiota composition. Reconstitution of the gut microbiota by FMT can alter the susceptibility to HBV infection in mice.
Enhancing HR Frequency for Precise Genome Editing in Plants

Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
Impact of the COVID-19 Restrictive Measures on Urban Traffic-Related Air Pollution in Serbia

This study has analyzed the traffic-related change in atmospheric pollutants levels (PM2.5, PM10, CO, NO2, SO2, and O3) caused by the COVID-19 restrictive measures, based on traffic ground-based stations data in urban areas in Serbia. The possible influence of several meteorological factors (temperature, wind, pressure, and humidity), and mobility on the pollutants’ levels were also considered. The obtained results showed a positive correlation of daily NO2 concentrations with mobility and its significant reduction during restrictive measures at all selected monitoring stations. The reduction of NO2 was higher than in other countries (71.1–111.5% for measured, and 49.3–92.6% for “deweathered” data), indicating a high traffic impact on NO2 levels in Serbia. The PM, CO, and SO2 showed a weak correlation with mobility during the period with restrictive measures, which, besides traffic, indicates the significant influence of other sources of their concentration. The O3 concentrations were increased at all measuring stations and are negatively correlated to mobility. Comparison of pollutant concentrations during restriction with the equivalent period in preceding years showed reductions in NO2 and SO2 concentrations. However, compared to previous years, the concentrations of PM2.5, PM10, and CO increased in the period with restrictive measures, indicating lower sensitivity to population mobility and higher dependence on other emission sources. The findings suggest the justification for the use of traffic reduction strategies to improve air quality.
Developing Problem-Solving Expertise for Word Problems

Studying worked examples impose relatively low cognitive load because learners’ attention is directed to learn the schema, which is embedded in the worked examples. That schema encompasses both conceptual knowledge and procedural knowledge. It is well-documented that worked examples are effective in facilitating the acquisition of problem-solving skills. However, the use of worked examples to develop problem-solving expertise is less known. Typically, experts demonstrate an efficient way to solve problems that is quicker, faster, and having fewer solution steps. We reviewed five studies to validate the benefit of worked examples to develop problem-solving expertise for word problems. Overall, a diagram portrays the problem structure, coupled with either study worked examples or complete multiple example–problem pairs, facilitates the formation of an equation to solve words problems efficiently. Hence, an in-depth understanding of conceptual knowledge (i.e., problem structure) might contribute to superior performance of procedural knowledge manifested in the reduced solution steps.
Shifting Rice Cropping Systems Mitigates Ecological Footprints and Enhances Grain Yield in Central China

Intensive cereal production has brought about increasingly serious environmental threats, including global warming, environmental acidification, and water shortage. As an important grain producer in the world, the rice cultivation system in central China has undergone excessive changes in the past few decades. However, few articles focused on the environmental impacts of these shifts from the perspective of ecological footprints. In this study, a 2-year field trial was carried out in Hubei province, China, to gain insight into carbon footprint (CF), nitrogen footprint (NF), and water footprint (WF) performance. The three treatments were, namely, double-rice system (DR), ratoon rice system (RR), and rice-wheat system (RW). Results demonstrated that RR significantly increased the grain yield by 10.22–15.09% compared with DR, while there was no significant difference in the grain yield between RW and DR in 2018–2019. All of the calculation results by three footprint approaches followed the order: RR < RW < DR; meanwhile, RR was always significantly lower than DR. Methane and NH3 field emissions were the hotspots of CF and NF, respectively. Blue WF accounts for 40.90–42.71% of DR, which was significantly higher than that of RR and RW, primarily because DR needs a lot of irrigation water in both seasons. The gray WF of RW was higher than those of DR and RR, mainly due to the higher application rate of N fertilizer. In conclusion, RR possesses the characteristics of low agricultural inputs and high grain yield and can reduce CF, NF, and WF, considering the future conditions of rural societal developments and rapid demographic changes; we highlighted that the RR could be a cleaner and sustainable approach to grain production.
Association of Proton Pump Inhibitor and Infection and Major Adverse Clinical Events in Patients With ST-Elevation Myocardial Infarction: A Propensity Score Matching Analysis

Background Infections are not common but important in patients with acute myocardial infarction, and are associated with worse outcomes. Infection was proved to be associated with the use of proton pump inhibitor (PPI) in several cohorts. It remains unclear whether PPI usage affects infection in patients with acute myocardial infarction. Methods We consecutively enrolled patients with ST-elevation myocardial infarction (STEMI) undergoing percutaneous coronary intervention (PCI) from January 2010 to June 2018. All patients were divided into the PPI group and non-PPI group according to whether the PPI was used. The primary endpoint was the development of infection during hospitalization. Results A total of 3027 patients were finally enrolled, with a mean age of 62.2 ± 12.6 years. 310 (10.2%) patients were developed infection during hospitalization. Baseline characteristics were similar between the PPI and non-PPI groups (n = 584 for each group) after propensity score analysis. PPI usage was significantly associated with infection based on the propensity score matching analysis (adjusted OR = 1.62, 95% CI = 1.02-2.57, P = 0.041). Comparing to patients with non-PPI usage, PPI administration was positively associated with higher risk of in-hospital all-cause mortality (adjusted OR = 3.25, 95% CI = 1.06-9.97, P = 0.039) and in-hospital major adverse clinical events (adjusted OR = 3.71, 95% CI = 1.61-8.56, P = 0.002). Subgroup analysis demonstrated that the impact of PPI on infection was not significantly different among patients with or without diabetes and patients with age ≥65 years or age <65 years. Conclusion PPI usage was related to a higher incidence of infection during hospitalization, in-hospital all-cause mortality, and in-hospital major adverse clinical events (MACE) in STEMI patients.
Effect of Dietary Zinc Methionine Supplementation on Growth Performance, Immune Function and Intestinal Health of Cherry Valley Ducks Challenged With Avian Pathogenic Escherichia coli

This study was carried out to evaluate the effects of supplemental zinc methionine (Zn–Met) on growth performance, immune function, and intestinal health of meat ducks challenged with avian pathogenic Escherichia coli (APEC). A total of 480 1-day-old Cherry Valley male ducks were randomly assigned to 8 treatments with 10 replicates, each replicate containing 10 ducks. A 4 × 2 factor design was used with four dietary zinc levels (0, 30, 60, 120 mg Zn/kg in the form Zn–Met was added to the corn–soybean basal diet) and challenged with or without APEC at 8-days-old ducks. The trial lasted for 14 days. The results showed that a dietary Zn–Met supplementation significantly increased body weight (BW) of 14 days and BW gain, and decreased mortality during 7–14-days-old ducks (p < 0.05). Furthermore, dietary 30, 60, 120 mg/kg Zn–Met supplementation noticeably increased the thymus index at 2 days post-infection (2 DPI) and 8 DPI (p < 0.05), and 120 mg/kg Zn–Met enhanced the serum IgA at 2 DPI and IgA, IgG, IgM, C3 at 8 DPI (p < 0.05). In addition, dietary 120 mg/kg Zn–Met supplementation dramatically increased villus height and villus height/crypt depth (V/C) of jejunum at 2 DPI and 8 DPI (p < 0.05). The TNF-α and IFN-γ mRNA expression were downregulated after supplemented with 120 mg/kg Zn–Met in jejunum at 8 DPI (p < 0.05). Moreover, dietary 120 mg/kg Zn–Met supplementation stimulated ZO-3, OCLN mRNA expression at 2 DPI and ZO-2 mRNA expression in jejunum at 8 DPI (p < 0.05), and improved the MUC2 concentration in jejunum at 2 DPI and 8 DPI (p < 0.05). At the same time, the cecal Bifidobacterium and Lactobacillus counts were increased (p < 0.05), and Escherichia coli counts were decreased (p < 0.05) after supplemented with Zn–Met. In conclusion, inclusion of 120 mg/kg Zn–Met minimizes the adverse effects of APEC challenge on meat ducks by improving growth performance and enhancing immune function and intestinal health.
Associations of DNA Base Excision Repair and Antioxidant Enzyme Genetic Risk Scores with Biomarker of Systemic Inflammation

Background: Inflammation is implicated in the etiology of various aging-related diseases. Numerous dietary and lifestyle factors contribute to chronic systemic inflammation; genetic variation may too. However, despite biological plausibility, little is known about associations of antioxidant enzyme (AE) and DNA base excision repair (BER) genotypes with human systemic inflammation. Methods: We genotyped 22 single nucleotide polymorphisms (SNPs) in 3 AE genes, and 79 SNPs in 14 BER genes to develop inflammation-specific AE and BER genetic risk scores (GRS) in two pooled cross-sectional studies (n = 333) of 30–74-year-old White adults without inflammatory bowel disease, familial adenomatous polyposis, or a history of cancer or colorectal adenoma. Of the genotypes, based on their associations with a biomarker of systemic inflammation, circulating high sensitivity C-reactive protein (hsCRP) concentrations, we selected 2 SNPs of 2 genes (CAT and MnSoD) for an AE GRS, and 7 SNPs of 5 genes (MUTYH, SMUG1, TDG, UNG, and XRCC1) for a BER GRS. A higher GRS indicates a higher balance of variant alleles directly associated with hsCRP relative to variant alleles inversely associated with hsCRP. We also calculated previously-reported, validated, questionnaire-based dietary (DIS) and lifestyle (LIS) inflammation scores. We used multivariable general linear regression to compare mean hsCRP concentrations across AE and BER GRS categories, individually and jointly with the DIS and LIS. Results: The mean hsCRP concentrations among those in the highest relative to the lowest AE and BER GRS categories were, proportionately, 13.9% (p = 0.30) and 57.4% (p = 0.009) higher. Neither GRS clearly appeared to modify the associations of the DIS or LIS with hsCRP. Conclusion: Our findings suggest that genotypes of DNA BER genes collectively may be associated with systemic inflammation in humans.
Long Term Survivals in Aggressive Primary Brain Malignancies Treated With an Adjuvant Ketogenic Diet

Aggressive primary brain tumors (APBT) glioblastoma multiforme and grade IV astrocytoma are treated with multimodality treatments that include surgery to remove as much tumor as possible without sacrificing neurological function followed by radiation therapy and chemotherapy usually temozolomide. Survivals in adults are in the range of 8–16 months. The addition of a ketogenic diet (KD) to rodents with transplanted brain tumors increased survival in nine of 11 animals to over 299 days compared to survival in untreated controls of 33 days and radiation only controls of 38 days. We treated humans with APBT with standard of care neurosurgery immediately followed by 6 weeks of an adjuvant ketogenic diet concurrent with radiation therapy and temozolomide. Twice daily measurements of blood ketones and glucose were recorded and the patients' diet was modified toward the goal of maintaining blood ketone levels approaching 3 mM. Of the nine patients who completed the protocol three younger patients age 32, 28, and 22 at enrollment are alive and employed with clinically stable disease and brain images 74, 58, and 52 months since diagnosis. All the six older patients mean age 55 have died with disease progression detected on average 8 months after Dx. In conclusion: 1. It is possible to implement and maintain dietary induced ketosis in patients with APBT; 2. The longer survivals observed in younger patients treated with KD need to be confirmed in larger studies that should be focused on younger patients possibly under age 40.
Berberine and Oligomeric Proanthocyanidins Exhibit Synergistic Efficacy Through Regulation of PI3K-Akt Signaling Pathway in Colorectal Cancer

Background Naturally occurring dietary botanicals offer time-tested safety and anti-cancer efficacy, and a combination of certain compounds has shown to overcome the elusive chemotherapeutic resistance, which is of great significance for improving the mortality of patients with colorectal cancer (CRC). Accordingly, herein, we hypothesized that berberine (BBR) and oligomeric proanthocyanidins (OPCs) might regulate synergistically multiple oncogenic pathways to exert a superior anti-cancer activity in CRC. Methods We performed a series of cell culture studies, followed by their interrogation in patient-derived organoids to evaluate the synergistic effect of BBR and OPCs against CRC. In addition, by performing whole genome transcriptomic profiling we identified the key targeted genes and pathways regulated by the combined treatment. Results We first demonstrated that OPCs facilitated enhanced cellular uptake of BBR in CRC cells by measuring the fluorescent signal of BBR in cells treated individually or their combination. The synergism between BBR and OPCs were investigated in terms of their anti-tumorigenic effect on cell viability, clonogenicity, migration, and invasion. Furthermore, the combination treatment potentiated the cellular apoptosis in an Annexin V binding assay. Transcriptomic profiling identified oncogene MYB in PI3K-AKT signaling pathway might be critically involved in the anti-tumorigenic properties of the combined treatment. Finally, we successfully validated these findings in patient-derived CRC tumor organoids. Conclusions Collectively, we for the first time demonstrate that a combined treatment of BBR and OPCs synergistically promote the anti-tumorigenic properties in CRC possibly through the regulation of cellular apoptosis and oncogene MYB in the PI3K-Akt signaling pathway.
Serial Mediation Roles of Alexithymia and Loneliness in the Association Between Family Function and Internet Addiction Among Chinese College Students

A lot of previous research has highlighted the negative consequences of Internet addiction. However, relatively few is known about the underlying mechanism for Internet addiction among college students in relation to family function. The present study explored the relationship between family function and Internet addiction among college students, as well as the mediating effects of alexithymia and loneliness. A sample of 783 Chinese college students were administered a number of psychometric scales including the “General Function” subscale of the Chinese version of the Family Assessment Device, Toronto Alexithymia Scale, UCLA Loneliness Scale, and Revised Chinese Internet Addiction Scale. The results showed that family function was negatively associated with Internet addiction; the association was significantly mediated by alexithymia; the association was significantly mediated by loneliness; and alexithymia and loneliness sequentially mediated the association. The total mediating effect was 63.96%. The results of the present study are of great significance to the prevention and intervention of Internet addiction among college students.
Assessing the Quality of Argumentative Texts: Examining the General Agreement Between Different Rating Procedures and Exploring Inferences of (Dis)agreement Cases

Assessing argumentative writing skills is not a straightforward task, as multiple elements need to be considered. In function of providing feedback to students and keeping track of their progress, evaluating argumentative texts in a suitable, valid and efficient way is important. In this state-of-the-art exploratory study, 130 argumentative texts written by eleventh graders were assessed by means of three different rating procedures (i.e., absolute holistic rating, comparative holistic rating, and absolute analytic rating). The main aim of this study is twofold. First, we aim to examine the correlations between the three rating procedures and to study the extent to which these procedures differ in assigning scores. In doing so, the more innovative approach of pairwise comparisons is compared to more established assessment methods of absolute holistic and analytic rating. Second, we aim to identify key characteristics that determine the quality of an argumentative text, independent of the rating procedure used. Furthermore, key elements of mid-range, weak and strong argumentative texts were studied in detail. The results reveal low to moderate agreement between the different procedures, indicating that all procedures are suitable to assess the quality of an argumentative text; each procedure, however, has its own qualities and applicability.
Controlling the Stage: A High-Level Control System for Virtual Audiences in Virtual Reality

This article presents a novel method for controlling a virtual audience system (VAS) in Virtual Reality (VR) application, called STAGE, which has been originally designed for supervised public speaking training in university seminars dedicated to the preparation and delivery of scientific talks. We are interested in creating pedagogical narratives: narratives encompass affective phenomenon and rather than organizing events changing the course of a training scenario, pedagogical plans using our system focus on organizing the affects it arouses for the trainees. Efficiently controlling a virtual audience towards a specific training objective while evaluating the speaker’s performance presents a challenge for a seminar instructor: the high level of cognitive and physical demands required to be able to control the virtual audience, whilst evaluating speaker’s performance, adjusting and allowing it to quickly react to the user’s behaviors and interactions. It is indeed a critical limitation of a number of existing systems that they rely on a Wizard of Oz approach, where the tutor drives the audience in reaction to the user’s performance. We address this problem by integrating with a VAS a high-level control component for tutors, which allows using predefined audience behavior rules, defining custom ones, as well as intervening during run-time for finer control of the unfolding of the pedagogical plan. At its core, this component offers a tool to program, select, modify and monitor interactive training narratives using a high-level representation. The STAGE offers the following features: i) a high-level API to program pedagogical narratives focusing on a specific public speaking situation and training objectives, ii) an interactive visualization interface iii) computation and visualization of user metrics, iv) a semi-autonomous virtual audience composed of virtual spectators with automatic reactions to the speaker and surrounding spectators while following the pedagogical plan V) and the possibility for the instructor to embody a virtual spectator to ask questions or guide the speaker from within the Virtual Environment. We present here the design, and implementation of the tutoring system and its integration in STAGE, and discuss its reception by end-users.
Novel Machine-Learning Based Framework Using Electroretinography Data for the Detection of Early-Stage Glaucoma

Purpose Early-stage glaucoma diagnosis has been a challenging problem in ophthalmology. The current state-of-the-art glaucoma diagnosis techniques do not completely leverage the functional measures' such as electroretinogram's immense potential; instead, focus is on structural measures like optical coherence tomography. The current study aims to take a foundational step toward the development of a novel and reliable predictive framework for early detection of glaucoma using machine-learning-based algorithm capable of leveraging medically relevant information that ERG signals contain. Methods ERG signals from 60 eyes of DBA/2 mice were grouped for binary classification based on age. The signals were also grouped based on intraocular pressure (IOP) for multiclass classification. Statistical and wavelet-based features were engineered and extracted. Important predictors (ERG tests and features) were determined, and the performance of five machine learning-based methods were evaluated. Results Random forest (bagged trees) ensemble classifier provided the best performance in both binary and multiclass classification of ERG signals. An accuracy of 91.7 and 80% was achieved for binary and multiclass classification, respectively, suggesting that machine-learning-based models can detect subtle changes in ERG signals if trained using advanced features such as those based on wavelet analyses. Conclusions The present study describes a novel, machine-learning-based method to analyze ERG signals providing additional information that may be used to detect early-stage glaucoma. Based on promising performance metrics obtained using the proposed machine-learning-based framework leveraging an established ERG data set, we conclude that the novel framework allows for detection of functional deficits of early/various stages of glaucoma in mice.