Miracle-dz/UniFAR-FTUs huggingface dataset:
Pectin methylesterase modulates aluminium sensitivity in Zea mays and Solanum tuberosum

Cell suspension cultures of Zea mays L. were adapted to grow under conditions of NaCl stress, which increased the cell-wall pectin content of these cells by 31% compared with unadapted cells (controls). Both cultures were treated for 5 or 10 min with pectin methylesterase (PME) and afterwards incubated in the presence of Al for 2 h. The different capabilities of the cells to synthesise callose due to pre-treatment were taken into account by calculating relative Al-induced callose induction (digitonin = 100%). Only in salt-adapted cells with a degree of methylation of cell-wall pectin (DM) decreasing from 34% (control) to 13%, did PME treatment enhance total and BaCl 2 -non-exchangeable Al contents and Al sensitivity as indicated by increased callose formation. In a further step, a wider variation in DM was achieved by subculturing the NaCI-adapted cells for up to 3 weeks without NaCI supply and adapting them to the cellulose-synthesis inhibitor 2,6-dichlorbenzonitrile (DCB). This reduced DM to 26%, while short-term treatment with pectolyase resulted in the lowest DM (12%). After the 2 h Al treatment, there was a close negative relationship between DM and relative callose formation of Al contents, with the exception of pectolyase-treated cells. In addition, intact plants of Solanum tuberosum L. genotypes were characterised for their Al sensitivity in hydroponics using root elongation, Al-induced callose formation and Al contents of root tips as parameters. Based on all three parameters, the transgenic potato mutant overexpressing PME proved to be more Al-sensitive than the wild type, the Al-resistant and even the Al-sensitive potato cultivar. Especially in the root tips (1 cm), Al treatment (2 h, 50 μM) increased the activity of PME more in the Al-sensitive than in the Al-resistant genotypes. The presented data emphasise the importance of the DM of the pectin matrix and the activity of PME for the expression of Al toxicity and Al resistance.
Species distribution models in climate change scenarios are still not useful for informing policy planning: an uncertainty assessment using fuzzy logic

We compared the effect of general circulation models and greenhouse gas emission scenarios on the uncertainty associated with models predicting changes in areas favourable to animal species. Given that mountain species are particularly at risk due to climate warming, we selected one amphibian (Baetic midwife toad), one reptile (Lataste's viper), one bird (Bonelli's eagle), and one mammal (Iberian wild goat) present in Spanish mountains to model their distributional response to climate change during this century. Climate forecasts for the whole century were provided by the Agencia Estatal de Meteorologia (AEMET; National Meteorological Agency) of Spain, which adapted the general circulation models CGCM2 and ECHAM4 and produced expected temperature and precipitation values for Spain according to the A2 and B2 emission scenarios. We constructed separate models of the species response to spatial, topographic, human, and climate variables using current values of the corresponding variables. We predicted future areas favourable to the species by replacing the current climate values with those expected according to each climate change scenario, while keeping spatial, topographic and human variables constant. Fuzzy logic was used to compute the coincidence between predictions for different emission scenarios in the same global circulation model, and the consistency between predictions for the same emission scenario applying different general circulation models. In general, coincidences were higher than consistencies and, thus, discrepancies between predictions were more attributable to uncertainty in global circulation models, i.e. our insufficient knowledge concerning the effect of the oceans and atmosphere on climate, than to the putative effect of different emission scenarios on future climates. Our conclusion is that species distribution models in climate warming scenarios are still not useful for informing emission policy planning, although they have great potential as tools once consistencies become higher than coincidences.
Vaccinia Virus as a Master of Host Shutoff Induction: Targeting Processes of the Central Dogma and Beyond

The synthesis of host cell proteins is adversely inhibited in many virus infections, whereas viral proteins are efficiently synthesized. This phenomenon leads to the accumulation of viral proteins concurrently with a profound decline in global host protein synthesis, a phenomenon often termed “host shutoff”. To induce host shutoff, a virus may target various steps of gene expression, as well as pre- and post-gene expression processes. During infection, vaccinia virus (VACV), the prototype poxvirus, targets all major processes of the central dogma of genetics, as well as pre-transcription and post-translation steps to hinder host cell protein production. In this article, we review the strategies used by VACV to induce host shutoff in the context of strategies employed by other viruses. We elaborate on how VACV induces host shutoff by targeting host cell DNA synthesis, RNA production and processing, mRNA translation, and protein degradation. We emphasize the topics on VACV’s approaches toward modulating mRNA processing, stability, and translation during infection. Finally, we propose avenues for future investigations, which will facilitate our understanding of poxvirus biology, as well as fundamental cellular gene expression and regulation mechanisms.
Carbon isotopic signatures of soil organic matter correlate with leaf area index across woody biomes

Leaf area index (LAI), a measure of canopy density, is a key variable for modelling and understanding primary productivity, and also water use and energy exchange in forest ecosystems. However, LAI varies considerably with phenology and disturbance patterns, so alternative approaches to quantifying stand‐level processes should be considered. The carbon isotope composition of soil organic matter (δ13CSOM) provides a time‐integrated, productivity‐weighted measure of physiological and stand‐level processes, reflecting biomass deposition from seasonal to decadal time scales. Our primary aim was to explore how well LAI correlates with δ13CSOM across biomes. Using a global data set spanning large environmental gradients in tropical, temperate and boreal forest and woodland, we assess the strength of the correlation between LAI and δ13CSOM; we also assess climatic variables derived from the WorldClim database. We found that LAI was strongly correlated with δ13CSOM, but was also correlated with Mean Temperature of the Wettest Quarter, Mean Precipitation of Warmest Quarter and Annual Solar Radiation across and within biomes. Synthesis. Our results demonstrate that δ13CSOM values can provide spatially explicit estimates of leaf area index (LAI) and could therefore serve as a surrogate for productivity and water use. While δ13CSOM has traditionally been used to reconstruct the relative abundance of C3 versus C4 species, the results of this study demonstrate that within stable C3‐ or C4‐dominated biomes, δ13CSOM can provide additional insights. The fact that LAI is strongly correlated to δ13CSOM may allow for a more nuanced interpretation of ecosystem properties of palaeoecosystems based on palaeosol 13C values.
Inflammation-related plasma and CSF biomarkers for multiple sclerosis

Significance Molecular biomarkers for multiple sclerosis have so far mainly been limited to measures in cerebrospinal fluid (CSF). Here, we identified additional biomarkers for multiple sclerosis, 2 in plasma as well as 10 in CSF. Furthermore, we identified 2 biomarkers: eotaxin-1 (CCL11), associated with disease duration and progression in both CSF and plasma, and plasma CCL20 which showed association with disease severity. However, these findings will require further validation. The capability of measuring biomarkers for multiple sclerosis may assist in the monitoring of patients during routine clinical care such as assessing treatment response but may also allow researchers to more accurately characterize pathological processes of inflammation and neurodegeneration in both the CNS and periphery of patients with multiple sclerosis. Effective biomarkers for multiple sclerosis diagnosis, assessment of prognosis, and treatment responses, in particular those measurable in blood, are largely lacking. We have investigated a broad set of protein biomarkers in cerebrospinal fluid (CSF) and plasma using a highly sensitive proteomic immunoassay. Cases from two independent cohorts were compared with healthy controls and patients with other neurological diseases. We identified and replicated 10 cerebrospinal fluid proteins including IL-12B, CD5, MIP-1a, and CXCL9 which had a combined diagnostic efficacy similar to immunoglobulin G (IgG) index and neurofilament light chain (area under the curve [AUC] = 0.95). Two plasma proteins, OSM and HGF, were also associated with multiple sclerosis in comparison to healthy controls. Sensitivity and specificity of combined CSF and plasma markers for multiple sclerosis were 85.7% and 73.5%, respectively. In the discovery cohort, eotaxin-1 (CCL11) was associated with disease duration particularly in patients who had secondary progressive disease (PCSF < 4 × 10−5, Pplasma < 4 × 10−5), and plasma CCL20 was associated with disease severity (P = 4 × 10−5), although both require further validation. Treatment with natalizumab and fingolimod showed different compartmental changes in protein levels of CSF and peripheral blood, respectively, including many disease-associated markers (e.g., IL12B, CD5) showing potential application for both diagnosing disease and monitoring treatment efficacy. We report a number of multiple sclerosis biomarkers in CSF and plasma for early disease detection and potential indicators for disease activity. Of particular importance is the set of markers discovered in blood, where validated biomarkers are lacking.
Disrupting the Behavioral Health Consequences of Racial Discrimination: A Longitudinal Investigation of Racial Identity Profiles and Alcohol-Related Problems

Researchers have documented the negative associations between racial discrimination and alcohol use for young Black people, yet fewer researchers have examined these associations longitudinally and with racial identity as a protective factor. We use data from the Flint Adolescent Study (465 Black/African Americans) to investigate the relationship between discrimination and alcohol-related problems over time, and how that relationship differs with varying trajectories of racial identity (i.e., private and public regard). Among those reporting persistently moderate levels of private regard and high levels of public regard in late adolescence through emerging adulthood, increases in racial discrimination were associated with increases in alcohol-related problems over time. Findings suggest that regard for one’s racial group may function protectively in the health strategies employed in response to discriminatory events. More longitudinal research is needed to delineate how varying racial pride operates with regard to long-term discrimination and behavioral health.
Concise overview of European soil erosion research and evaluation

Abstract Soil loss by erosion is a major threat to European soil resources. It is linked to most other threats to soils and is estimated to incur substantial costs to society. To monitor and evaluate soil erosion comprehensively, measurements and modelled estimates of soil loss by erosion need to integrate water, wind and tillage erosion, as these are common throughout Europe. Tolerable rates of soil erosion (thresholds) in Europe can be set equal to estimated soil formation rates, that is, ~1 t ha−1 yr−1, but defining this threshold will require further research in the context of soil functions. There is a strong need for improving the knowledge base of current erosion rates, especially to develop and validate reliable erosion prediction models. This should include depositional environments (e.g. flood plains) where greater erosion rates than those on hill slopes may be tolerable, depending on the consequent effects on all relevant ecosystem goods and services provided by soil. Moreover, in considering erosion at catchment (watershed) level, the distance between erosion sites and areas of deposition should be taken into account.
Apoptosis in Different Compartments of Antrum and Corpus Mucosa in Chronic Helicobacter pylori Gastritis. An 18-Year Follow-up Study

Background: The association of apoptosis was analysed in three different compartments (foveolar cells- FC, proliferating zone-PZ and glandular part-GP) of antrum and corpus mucosa specimens with development of atrophy and the extent of apoptosis as depending on grade of chronic inflammation, activity of gastritis and Helicobacter pylori colonization at two time points of an 18-year follow-up in an adult population from Saaremaa, Estonia, with a high prevalence of H. pylori infection were compared. Methods: A total of 68 persons (31 men, 37 women; median age, 39 years in 1979) from a primary sample of 304 subjects, endoscoped in 1979 and reinvestigated by endoscopy and biopsy in 1997, were included in the study. The state of the gastric mucosa and the presence of H. pylori in the antrum and corpus mucosa were assessed in accordance with the Sydney system. The dynamics of apoptotic index (AI) between two time points in 1979 and 1997 was evaluated in antrum biopsies of 49 persons and in corpus biopsies of 64 persons. Apoptosis was measured using terminal deoxyuridine nucleotide nick end labelling (TUNEL) histochemistry. Results: The antrum as well as the corpus of 2/68 persons were H. pylori negative at both time points. Atrophy developed in 9/68 persons in the antrum and in 23/68 in the corpus. In PZ and GP of the corpus mucosa as well as in GP of the antrum mucosa, AI decreased significantly during 18 years compared with initial values (P < 0.05), which was not associated with development of atrophy. In all compartments of the antrum and corpus mucosa, studied at the initial and end points of observation, AI did not reveal a difference in persons with and without development of atrophy (P > 0.05). In the samples of 1979 the highest independent effect on the value of AI in the FC compartment for the antrum was exerted by grade of activity of gastritis (P = 0.01) and in GP by degree of chronic inflammation (P = 0.03), while in the samples of 1997 the highest effect was exerted by grade of H. pylori colonization (P = 0.02 and 0.03 in FC and GP, respectively). For the corpus mucosa AI was most strongly affected also by grade of activity of gastritis in FC compartment (P = 0.02) and by degree of chronic inflammation in PZ (P = 0.04), but not by grade of H. pylori colonization. Conclusion: AI was not associated with development of atrophy, but was largely dependent on grade of activity of gastritis and degree of chronic inflammation; in the antrum mucosa AI depended also on grade of H. pylori colonization.
Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO

In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale ex-situ biogas upgrading systems under different temperature (20–70 °C), pH (6.0–8.5), and CO (0–10%, v/v) variables were systematically investigated. High-throughput 16S rRNA gene sequencing was used to identify the microbial consortia, and statistical analyses were conducted to reveal the microbial diversity, the core functional microbes, and their correlative relationships with tested variables. Overall, bacterial community was more complex than the archaea community in all mixed cultures. Hydrogenotrophic methanogens Methanothermobacter, Methanobacterium, and Methanomassiliicoccus, and putative syntrophic acetate-oxidizing bacterium Coprothermobacter and Caldanaerobacter were found to predominate, but the core functional microbes varied under different conditions. Multivariable sensitivity analysis indicated that temperature (p < 0.01) was the crucial variable to determine the microbial consortium structures in hydrogenotrophic methanogenic mixed cultures. pH (0.01 < p < 0.05) significantly interfered with the relative abundance of dominant archaea. Although CO did not affect community (p > 0.1), some potential CO-utilizing syntrophic metabolisms might be enhanced. Understanding of microbial consortia in the hydrogenotrophic methanogenic mixed cultures related to environmental variables was a great advance to reveal the microbial ecology in microbial biogas upgrading process.
Antibodies to Oat Prolamines (Avenins) in Children with Coeliac Disease

Background: The use of oats in a gluten-free diet for children with coeliac disease is presently under investigation. In this study we measured the content of antibodies to oat prolamines (avenin) in sera from coeliac children and reference children. Methods: Crude avenin was prepared by extraction with ethanol and salt-solution and used as antigen in a three-step ELISA. Sera from 81 children, including 34 children with verified coeliac disease, were analysed for both IgA and IgG antibodies to avenin and gliadin. Sera were also incubated with gliadin before exposure to avenin, and vice versa, to assess a possible cross-reaction between the species. Keyhole limpet hemocyanin (KLH) was used as a negative control. Results: Children with coeliac disease on a normal diet had significantly higher levels of antibodies to avenin, both IgG and IgA, than reference children ( P r < r 0.001) and the levels correlated positively with gliadin antibodies, especially of IgA-type ( r r = r 0.798). Both anti-avenin and anti-gliadin antibodies were only absorbed by the corresponding protein. Conclusions: Children with coeliac disease have antibodies to oat proteins at significantly higher levels than reference children. The absorption test did not indicate a cross-reactivity between the prolamines of wheat and oats. The method will be employed for repeated sampling of anti-avenin antibodies during a prospective interventional study with a gluten-free diet supplemented with oats.
Differential ESR1 Promoter Methylation in the Peripheral Blood—Findings from the Women 40+ Healthy Aging Study

Background Estrogen receptor α (ERα) contributes to maintaining biological processes preserving health during aging. DNA methylation changes of ERα gene (ESR1) were established as playing a direct role in the regulation of ERα levels. In this study, we hypothesized decreased DNA methylation of ESR1 associated with postmenopause, lower estradiol (E2) levels, and increased age among healthy middle-aged and older women. Methods We assessed DNA methylation of ESR1 promoter region from dried blood spots (DBSs) and E2 from saliva samples in 130 healthy women aged 40–73 years. Results We found that postmenopause and lower E2 levels were associated with lower DNA methylation of a distal regulatory region, but not with DNA methylation of proximal promoters. Conclusion Our results indicate that decreased methylation of ESR1 cytosine-phosphate-guanine island (CpGI) shore may be associated with conditions of lower E2 in older healthy women.
Detection of Colorectal Tumor and Inflammatory Bowel Disease during Follow-up of Patients with Initial Diagnosis of Irritable Bowel Syndrome

Background: We wanted to estimate the incidence of irritable bowel syndrome (IBS) and functional dyspepsia (FD) in the general population, and the detection of colorectal tumor (CRT) and inflammatory bowel disease (IBD) after the diagnosis of IBS and FD. Methods: Patients aged 20-79 years newly diagnosed with IBS (N = 2956) or FD (N = 9900), together with a comparison cohort randomly sampled from the general source population, were followed-up during a mean time of 3 years. Results: We found an overall incidence of 10.3 per 1000 person-years for FD and 2.6 per 1000 person-years for IBS. There was a greater prevalence of depression, stress, fatigue, and pain disorders among IBS and FD patients than in the general population. During the 1st year after a diagnosis of IBS the cumulative risk of detecting CRT was close to 1% in IBS patients. After the 1st year the risk of CRT in IBS patients was close to that in the general population. We found a significantly increased risk of detecting IBD among patients initially diagnosed as having IBS (relative risk (RR), 16.3; 95% confidence interval (CI), 6.6-40.7), which was constant during all the follow-up period. No association was found between dyspepsia and CRT, or IBD. Conclusion: IBS and FD shared some comorbidity features, yet demographics and incidence rates were different. Unlike the detection of colorectal tumor, the excess risk of IBD after an initial diagnosis of IBS was cumulatively increased during all the follow-up period. The continuously increased risk of IBD detection in IBS patients favors a true association between IBS and IBD.
Sensitivity of total knee replacement wear to variability in motion and load input: A parametric finite element analysis study

Polyethylene wear remains a contributor to long term failure in total knee replacements (TKRs). Advances in materials have improved polyethylene wear rates, therefore further wear reductions require a better understanding of patient‐specific factors that lead to wear. Variability of gait within patients is considerable and could lead to significant variability in wear rates that cannot be predicted by standard testing methods. An in‐silico study was performed to investigate the influence of gait variability on TKR polyethylene wear. Nine characteristic peaks within the load and motion profiles used for TKR wear testing were varied 75% to 125% from baseline (ISO‐14243‐3:2014) to generate 310 unique waveforms. Wear was calculated for 1‐million cycles using a finite element TKR wear model. From the results, a surrogate model was developed using multiple linear regression, and used to predict how wear changes due to dispersion of motion and force peaks within a) ±5%, the maximum allowable input tolerance of ISO, and b) ±25%, more reflective of patient gait inter‐variability. The range of wear within the ±5% tolerance was 0.65 mm3/million cycles and was 3.24 mm3/million cycles within the ±25% variability more in line with the dispersion observed within patients. Although no one kinematic or kinetic peak dominated variability in TKR volumetric wear, variability within flexion/extension peaks were the largest contributor to wear rate variability. Interaction between the peaks of different waveforms was also important. This study, and future studies incorporating patient‐specific data, could help to explain the connection between patient‐specific gait factors and wear rates.