Miracle-dz/UniFAR-FTUs huggingface dataset:
Burrowing by translocated boodie (Bettongia lesueur) populations alters soils but has limited effects on vegetation

Abstract Digging and burrowing mammals modify soil resources, creating shelter for other animals and influencing vegetation and soil biota. The use of conservation translocations to reinstate the ecosystem functions of digging and burrowing mammals is becoming more common. However, in an increasingly altered world, the roles of translocated populations, and their importance for other species, may be different. Boodies (Bettongia lesueur), a commonly translocated species in Australia, construct extensive warrens, but how their warrens affect soil properties and vegetation communities is unknown. We investigated soil properties, vegetation communities, and novel ecosystem elements (specifically non‐native flora and fauna) on boodie warrens at three translocation sites widely distributed across the species’ former range. We found that soil moisture and most soil nutrients were higher, and soil compaction was lower, on warrens in all sites and habitat types. In contrast, there were few substantial changes to vegetation species richness, cover, composition, or productivity. In one habitat type, the cover of shrubs less than 1 m tall was greater on warrens than control plots. At the two sites where non‐native plants were present, their cover was greater, and they were more commonly found on boodie warrens compared to control plots. Fourteen species of native mammals and reptiles were recorded using the warrens, but, where they occurred, the scat of the non‐native rabbit (Oryctolagus cuniculus) was also more abundant on the warrens. Together, our results suggest that translocated boodie populations may be benefiting both native and non‐native flora and fauna. Translocated boodies, through the construction of their warrens, substantially alter the sites where they are released, but this does not always reflect their historic ecosystem roles.
Agent‐based modeling of the effects of forest dynamics, selective logging, and fragment size on epiphyte communities

Abstract Forest canopies play a crucial role in structuring communities of vascular epiphytes by providing substrate for colonization, by locally varying microclimate, and by causing epiphyte mortality due to branch or tree fall. However, as field studies in the three‐dimensional habitat of epiphytes are generally challenging, our understanding of how forest structure and dynamics influence the structure and dynamics of epiphyte communities is scarce. Mechanistic models can improve our understanding of epiphyte community dynamics. We present such a model that couples dispersal, growth, and mortality of individual epiphytes with substrate dynamics, obtained from a three‐dimensional functional–structural forest model, allowing the study of forest–epiphyte interactions. After validating the epiphyte model with independent field data, we performed several theoretical simulation experiments to assess how (a) differences in natural forest dynamics, (b) selective logging, and (c) forest fragmentation could influence the long‐term dynamics of epiphyte communities. The proportion of arboreal substrate occupied by epiphytes (i.e., saturation level) was tightly linked with forest dynamics and increased with decreasing forest turnover rates. While species richness was, in general, negatively correlated with forest turnover rates, low species numbers in forests with very‐low‐turnover rates were due to competitive exclusion when epiphyte communities became saturated. Logging had a negative impact on epiphyte communities, potentially leading to a near‐complete extirpation of epiphytes when the simulated target diameters fell below a threshold. Fragment size had no effect on epiphyte abundance and saturation level but correlated positively with species numbers. Synthesis: The presented model is a first step toward studying the dynamic forest–epiphyte interactions in an agent‐based modeling framework. Our study suggests forest dynamics as key factor in controlling epiphyte communities. Thus, both natural and human‐induced changes in forest dynamics, for example, increased mortality rates or the loss of large trees, pose challenges for epiphyte conservation.
miR-93-5p promotes insulin resistance to regulate type 2 diabetes progression in HepG2 cells by targeting HGF

Insulin resistance is a common feature of type 2 diabetes mellitus (T2DM). However, the mechanisms underlying insulin resistance are not completely understood. The present study aimed to investigate the effect of microRNA (miR)-93-5p on insulin resistance in T2DM cells. Human hepatocellular carcinoma (HCC; HepG2) cells were cultured in medium with high glucose content (30 mM glucose) to establish an in vitro insulin-resistant cell model (IR group). Glucose consumption and glycogen synthesis assays were performed to assess glucose consumption and glycogen synthesis, respectively. By performing immunoprecipitation assays, the abundance of the Met-insulin receptor complex was detected in HepG2 cells. miR-93-5p and hepatocyte growth factor (HGF) mRNA expression levels were measured via reverse transcription-quantitative PCR, and HGF protein expression levels were measured via western blotting. A dual-luciferase reporter assay was conducted to investigate the interaction between miR-93-5p and HGF. Cell Counting Kit-8, BrdU and caspase-3 activity assays were performed to evaluate cell viability, proliferation and apoptosis, respectively, in insulin-resistant HepG2 cells following transfection with small interfering RNA-HGF, HGF overexpression vector, miR-93-5p mimic or miR-93-5p inhibitor. The results demonstrated that miR-93-5p expression was significantly increased and HGF expression was significantly decreased in HCC tissues isolated from patients with or without T2DM compared with adjacent healthy tissues isolated from patients without T2DM. Compared with the IR group, miR-93-5p overexpression significantly increased cell proliferation, glucose consumption and glycogen synthesis, but significantly inhibited apoptosis in insulin-resistant HepG2 cells. By contrast, compared with the IR group, HGF overexpression significantly inhibited cell proliferation, glucose consumption and glycogen synthesis, but significantly enhanced cell apoptosis in insulin-resistant HepG2 cells. Following co-transfection with HGF overexpression vector and miR-93-5p mimic, miR-93-5p mimic-mediated induction of HepG2 cell proliferation, glucose consumption and glycogen synthesis in insulin-resistant HepG2 cells was inhibited. Collectively, the results of the present study indicated that miR-93-5p enhanced insulin resistance to regulate T2DM progression in HepG2 cells by targeting HGF.
The role of miRNAs in COVID-19 disease

Nowadays, the SARS Coronavirus 2 (SARS-CoV-2) infection is recognized as the primary cause of mortality in humans. SARS-CoV-2 is transmitted through human-to-human contact and is asymptomatic in most patients. In addition to approved vaccines against SARS-CoV-2 infection, miRNAs may also be promising options against this new virus. miRNAs are small and noncoding RNAs 18–25 nucleotides in length that target the mRNAs to degrade them or obstruct their translation miRNAs act as an observer in cells. This study reviewed the literature on the potential role of cellular miRNAs in the SARS-CoV-2-host interplay as a therapeutic option in COVID-19 patients.
Microstructure, optical, and electrical properties of p-type SnO thin films

SnO thin films were fabricated by electron beam evaporation on (100) Si and c- and r-plane Al2O3 substrates. The films grown at 25 °C are nanocrystalline, while the films grown at 600 °C are epitaxial on r-plane Al2O3 and (001) textured on Si and c-plane Al2O3. The SnO films have an optical band gap of 2.82–2.97 eV and p-type conductivity, according to Hall measurements, with resistivities of 0.5–110 Ω cm, hole concentrations of 1017–1019 cm−3, and Hall mobilities of 0.1–2.6 cm2/Vs. The p-type conductivity, which appears to correlate with VSn, can be enhanced via Y- and Sb-doping. Defect complexes of SbSn−2VSn are suggested to be the acceptors in Sb-(or Y-) doped SnO films.
Variations Of Lipid Peroxidation And Superoxide Dismutase Activity Due To Haemodialysis In Gorgan

Background: Free radicals are formed in all living organisms during normal cell metabolism. Patients with chronic renal failure who are regularly dialyzed are candidates for free radical damage. The aim of this study was to evaluate the variations of lipid peroxidation and erythrocyte superoxide dismutase due to haemodialysis in Gorgan. Method : The sampling procedure was the purposive sampling of22 patients (age 43.54±9.21 years of old ) with chronic renal failure (CRF) disease who were haemodialysed at the 5 th Azar hospital of the Gorgan dialysis center (from September 2007 to February 2008) and 22 age and sex matched healthy controls (43.77±9.33 years of old ) were recruited for this study. This study was a clinical trial. Results : Plasma lipid peroxidation levels showed significant differences between the predialysis and the control group (P<0.001). They were found to be increased in the post-dialysis group when compared with the predialysis and the control groups(P<0.001). Erythrocyte superoxide dismutase levels were found to be decreased in the post-dialysis group when compared with the predialysis and the control groups (P<0.001). There was also significant difference between it’s levels in the control and the predialysis groups (P<0.001). Erythrocyte superoxide dismutase levels were lower in the dialysis group than in the control group. (P<0.001). Conclusions : The significant differences of the erythrocyte superoxide dismutase levels between the pre- and post-dialysis groups may be related to the loss of this antioxidant through membranes during the dialysis process and the decreased superoxide dismutase levels may also be related to the increase of lipid peroxidation in haemodialysed patients. This situation may play an important role in the development of atherosclerosis in these groups.
The absence of islet autoantibodies in clinically diagnosed older-adult onset type 1 diabetes suggests an alternative pathology, advocating for routine testing in this age group.

Objective Islet autoantibodies at diagnosis are not well studied in older-adult onset (>30years) type 1 diabetes due to difficulties of accurate diagnosis. We used a type 1 diabetes genetic risk score (T1DGRS) to identify type 1 diabetes aiming to evaluate the prevalence and pattern of autoantibodies in older-adult onset type 1 diabetes. Methods We used a 30 variant T1DGRS in 1866 white-European individuals to genetically confirm a clinical diagnosis of new onset type 1 diabetes. We then assessed the prevalence and pattern of GADA, IA2A and ZnT8A within genetically consistent type 1 diabetes across three age groups (<18years (n=702), 18-30years (n=524) and >30years (n=588)). Findings In autoantibody positive cases T1DGRS was consistent with 100% type 1 diabetes in each age group. Conversely in autoantibody negative cases, T1DGRS was consistent with 93%(56/60) of <18years, 55%(37/67) of 18-30years and just 23%(34/151) of >30years having type 1 diabetes. Restricting analysis to genetically consistent type 1 diabetes showed similar proportions of positive autoantibodies across age groups (92% <18years, 92% 18-30years, 93% >30years)[p=0.87]. GADA was the most common autoantibody in older-adult onset type 1 diabetes, identifying 95% of autoantibody positive cases versus 72% in those <18years. Interpretation Older adult-onset type 1 diabetes has identical rates but different patterns of positive autoantibodies to childhood onset. In clinically suspected type 1 diabetes in older-adults, absence of autoantibodies strongly suggests non-autoimmune diabetes. Our findings suggest the need to change guidelines from measuring islet autoantibodies where there is diagnostic uncertainty to measuring at least GADA in all suspected adult type 1 diabetes cases.
Improvement of the tunnel oxide quality by a low thermal budget dual oxidation for flash memories

The high-quality ultrathin tunnel oxide using a low thermal budget dual oxidation has been developed. Due mainly to the reduction of imperfect chemical bonds and interface roughness, the tunnel and gate oxide quality in the fabrication of flash memory such as stress-induced leakage current (SILC), effective electron mobility, and cycling endurance characteristics, were improved compared to the pure dry oxides.
Stakeholder interactions with the federal government related to Bill S-228 and marketing to kids in Canada: a quantitative descriptive study

Background: Canadian federal restrictions on food marketing to children (children’s marketing) were proposed in 2016 as Bill S-228, the Child Health Protection Act, which subsequently died on the parliamentary table. This study quantified the interactions (meetings, correspondence and lobbying) related to Bill S-228 and children’s marketing by different stakeholders with the federal government. Methods: Interactions between all stakeholders and government related to children’s marketing and Bill S-228 (Sept. 1, 2016–Sept. 30, 2019) were analyzed. These included the “Meetings and correspondence on healthy eating” database, detailing interactions between stakeholders and Health Canada related to nutrition policies; and Canada’s Registry of Lobbyists, reporting activities of paid lobbyists. We categorized the interactions by stakeholder type (industry, nonindustry and mixed), and analyzed the number and type of interactions with different government offices. Results: We analyzed 139 meetings, 65 lobbying registrants, 215 lobbying registrations and 3418 communications related to children’s marketing and Bill S-228. Most interactions were from industry stakeholders, including 84.2% of meetings (117/139), 81.5% of lobbying registrants (53/65), 83.3% of lobbying registrations (179/215) and 83.9% of communications (2866/3418). Most interactions (> 80%) in the highest-ranking government offices were by industry. Interpretation: Industry stakeholders interacted with government more often, more broadly and with higher ranking offices than nonindustry stakeholders on subjects related to children’s marketing and Bill S-228. Although further research is needed to analyze the nature of the discourse around children’s marketing, it is apparent that industry viewpoints were more prominent than those of nonindustry stakeholders.
Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug‐Resistance Plasmids

Abstract The persistence of plasmids in bacterial populations represents a puzzling evolutionary problem with serious clinical implications due to their role in the ongoing antibiotic resistance crisis. Recently, major advancements have been made toward resolving this “plasmid paradox” but mainly in a nonclinical context. Here, we propose an additional explanation for the maintenance of multidrug‐resistance plasmids in clinical Escherichia coli strains. After coevolving two multidrug‐resistance plasmids encoding resistance to last resort carbapenems with an extraintestinal pathogenic E. coli strain, we observed that chromosomal media adaptive mutations in the global regulatory systems CCR (carbon catabolite repression) and ArcAB (aerobic respiration control) pleiotropically improved the maintenance of both plasmids. Mechanistically, a net downregulation of plasmid gene expression reduced the fitness cost. Our results suggest that global chromosomal transcriptional rewiring during bacterial niche adaptation may facilitate plasmid maintenance.
The impact of positioning on bottle-feeding in preterm infants (≤34 GA). A comparative study of the semi-elevated and the side-lying position - A pilot study.

OBJECTIVE The aim of the study was to compare the advantages of semi-elevated and side-lying positioning during bottle-feeding of preterm infants ≤34 weeks gestational age (34+0/7). MATERIAL AND METHODS The study included six neonates (n=6) bom ≤34 weeks gestational age who reached the age ≥32 weeks of postmenstrual age on the day when the study began and were hospitalized in the neonatology ward. Four bottle-feeding sessions were tested in each of the newborns: two in the side-lying and two in the semi-elevated position. The position for the first test was chosen randomly. For each of the positions twelve feeding sessions were examined and each preterm infant hod bottle-feeding sessions analyzed both in the semi-elevated and side-lying positions. The level of saturation and heart rate were measured as the parameters indicative of the newborn's physiological stability. The factors determining the qualitative aspect of feeding included the level of the newborn's alertness and the occurrence of choking episodes. The amount of food consumed and the duration of the feeding were also recorded. RESULTS The side-lying position was more effective with regard to the totol amount of sustenance consumed as compared to the semi-elevated feeding position and the study result was statistically significant (p=0.007). The difference in the number of chokes between the study groups was not statistically significant, although a trend towards a reduced number of choking episodes was observed among infants fed in the side-lying position (p=0.090). There were no significant differences in oxygen saturation, heart rate and level of activity between the study groups. CONCLUSIONS The effects of this pilot study demonstrate the efficacy of the side-lying feeding position regarding the final amount of milk intake. The side-lying position may also reduce the number of choking episodes during the feeding. The results suggest the need to extend the study in order to confirm the potential benefits of using the side-lying position.
Refinement of modulated structures against X-ray powder diffraction data with JANA2000

JANA is a computer program for the refinement and analysis of periodic and aperiodic (incommensurately modulated structures and composite crystals) crystal structures. Here a new module is introduced that allows Rietveld refinements against powder diffraction data. It is shown that JANA2000 provides a state-of-the-art description of the peak profiles. A re-analysis of the low-temperature structure of (CO)xC60 showed that the application of icosahedral symmetry restrictions to the C60 molecule leads to a better description of the electron density and to a corrected position of the CO molecule as compared with a rigid-body refinement. The incommensurately modulated structure of NbTe4 has been successfully refined against X-ray powder diffraction data. The structural parameters are equal to, but less accurate, than the parameters obtained from a single-crystal study.
Nuclear EGFR Expression Is Associated With Poor Survival in Laryngeal Carcinoma

Supplemental Digital Content is available in the text. The membrane EGFR (mEGFR) protein overexpression in the head and neck squamous cell carcinoma (SCC) is considered to cause increased EGFR activity which adds to tumorigenicity and therapy resistance. The mEGFR upon stimulation can translocate to the nucleus nuclear EGFR (nEGFR) where it has been associated with poor prognosis and worse survival in many cancers. The relevance of differentially located EGFR proteins in laryngeal lesions has not been studied enough and remains unclear. Aim of our study was to examine nEGFR and mEGFR protein expression as well as EGFR gene status and cell cycle proliferation markers in the laryngeal polyps, dysplasia, and SCC using immunohistochemistry and in situ hybridization. There was significantly higher frequency of strong nEGFR between SCC, dysplasia, and polyps (P<0.0001), and strong mEGFR in the SCC and laryngeal dysplasia comparing to polyps (P<0.0001). Gene amplification was confirmed only in relatively small number of SCC but not in non-neoplastic lesions. In dysplasia the statistically significant positive correlations between nEGFR, and Ki-67 (P=0.029), p53 (P=0.001), and cyclin D1 (P=0.031) were found. nEGFR and mEGFR expression showed statistically significant inverse correlation in the SCC (P=0.004) as well as nEGFR and cyclin D1 (P=0.032). Univariate statistical analysis showed statistically significant correlation between strong nEGFR protein expression and worse overall survival in laryngeal SCC, alone or in coexpression with strong cyclin D1 and high Ki-67 (P=0.025, P=0.046, P=0.043, respectively). Our data show that nEGFR cellular localization might influence biology of the laryngeal carcinogenesis and is indicator of poor survival.
Molecular pathways to high-level azithromycin resistance in Neisseria gonorrhoeae

Objectives The prevalence of azithromycin resistance in Neisseria gonorrhoeae is increasing in numerous populations worldwide. The aim of this study was to characterize the genetic pathways leading to high-level azithromycin resistance. Methods A customized morbidostat was used to subject two N. gonorrhoeae reference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing. Results Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genes rplD, rplV and rpmH (encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low-to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE-encoded efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA - mainly the well-known A2059G and C2611T mutations, but also at position A2058G. Conclusions This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance in N. gonorrhoeae.
Could Soluble Endothelial Protein C Receptor Levels Recognize SARS-CoV2-Positive Patients Requiring Hospitalization?

Supplemental Digital Content is available in the text ABSTRACT Introduction: The endothelial protein C receptor (EPCR) is a protein that regulates the protein C anticoagulant and anti-inflammatory pathways. A soluble form of EPCR (sEPCR) circulates in plasma and inhibits activated protein C (APC) activities. The clinical impact of sEPCR and its involvement in COVID-19 has not been explored. In this study, we investigated whether sEPCR levels were related to COVID-19 patients’ requirement for hospitalization. Methods: Plasma sEPCR levels were measured on hospital admission in 84 COVID-19 patients, and in 11 non-hospitalized SARS-CoV2-positive patients approximately 6 days after reported manifestation of their symptoms. Multiple logistic regression analysis was performed to identify potential risk factors for hospitalization and receiver operating characteristic (ROC) curves were generated to assess their value. Results: In our cohort, hospitalized patients had considerably higher sEPCR levels upon admission compared with outpatients [107.5 (76.7–156.3) vs. 44.6 (12.1–84.4) ng/mL; P < 0.0001)]. The ROC curve using hospitalization as the classification variable and sEPCR levels as the prognostic variable generated an area under the curve at 0.845 (95% CI = 0.710–0.981, P < 0.001). Additionally, we investigated the predictive value of sEPCR combined with BMI, age, or D-dimers. Conclusions: In our cohort, sEPCR levels in COVID-19 patients upon hospital admission appear considerably elevated compared with outpatients; this could lead to impaired APC activities and might contribute to the pro-coagulant phenotype reported in such patients. sEPCR measurement might be useful as a point-of-care test in SARS-CoV2-positive patients.