Miracle-dz/UniFAR-FTUs huggingface dataset:
Storage of biodegradable polymers by an enriched microbial community in a sequencing batch reactor operated at high organic load rate

The productionof polyhydroxyalkanoates (PHAs) from organic acids by mixed bacterialcultures using a process based on aerobic enrichment of activated sludge, that selects for mixed microbial cultures able to store PHAs at high rates and yields, is described. Enrichment resulted from the selective pressure established by periodic feeding the carbon source in a sequencing batch reactor (SBR); a mixture of acetic, lactic and propionic acids was fed at high frequency (2 hourly), high dilution rate (1d −1 ), and at high organic load rate (12.75g chemical oxygen demand (COD) L −1 d −1 ). The performance of the SBR was assessed by microbial biomass and PHA production as well as the composition and polymer content of the biomass. A final batch stage was used to increase the polymer concentration of the excess sludge produced in the SBR and in which the behaviour of the biomass was investigated by determining PHA production rates and yields. The microbial biomass selected in the SBR produced PHAs at high rate (278mg PHAs (as COD) g biomass (as COD) −1 h −1 , with a yield of 0.39mg PHAs (as COD) mg removed substrates (as COD) −1 ), reaching a polymer content higher than 50% (on a COD basis). The stored polymer was the copolymer poly(3-hydroxybutyrate/3-hydroxyvalerate) (P(HB/HV)), with an HV fraction of 18% molmol −1 . The microbial community selected in the SBR was analysed by DGGE (denaturing gradient gel electrophoresis). The operating conditions of the SBR were shown to select for a restricted microbial population which appeared quite different in terms of composition with respect to the initial microbial cenosis in the activated sludge used as inoculum. On the basis of the sequencing of the major bands in the DGGE profiles, four main genera were identified: a Methylobacteriaceae bacterium, Flavobacterium sp, Candidatus Meganema perideroedes ,a ndThauera sp. The effects of nitrogen depletion (ie absence of growth) and pH variation were also investigated in the batch stage and compared with the SBR operative mode. Absence of growth did not stimulate higher PHA production, so indicating that the periodic feed regime fully exploited the storage potential of the enriched culture. Polymer production rates remained high between pH 6.5 and 9.5, whereas the HV content in the stored polymer strongly increased as the pH value increased. This study shows that polymer composition in the fi nal batch stage can readily be controlled independently from the feed composition in the SBR.  2005 Society of Chemical Industry
Connecting Upper Limb Functional Stroke Recovery to Global Disability Measures

The modified Rankin Scale (mRS) is the most widely used outcome measure in stroke trials. It is a hierarchical scale, defining categorical outcomes that are assigned numerical values that range from no symptoms (mRS score 0) to death (mRS score 6). 1,2 It is commonly dichotomized into independent recovery (mRS score 0–2) vs death or dependence (mRS score 3–6). The origin of the scale lies not in rigorous clinimetric development but in the pragmatic desire to compare outcomes from different approaches to stroke treatment.3 Its longevity relates partly to chance, being available as an outcome measure in the first generation of acute stroke trials in the 1990s, partly to its brevity and lack of need for specialized training or tools, and partly to its role as a broad measure of global activities limitations (also known as disability) applicable to strokes of all anatomic locations and types. Its near-universal use as an outcome measure in acute stroke trials has led to a high degree of familiarity and acceptance across the spectrum of stroke research, including clinicians, researchers, and regulators.
Widespread bacterial utilization of guanidine as nitrogen source

Guanidine is sensed by at least four different classes of riboswitches that are widespread in bacteria. However, only very few insights into physiological roles of guanidine exist. Genes predominantly regulated by guanidine riboswitches are Gdx transporters exporting the compound from the bacterial cell. In addition, urea/guanidine carboxylases and associated hydrolases and ABC transporters are often found combined in guanidine‐inducible operons. We noted that the associated ABC transporters are configured to function as importers, challenging the current view that riboswitches solely control the detoxification of guanidine in bacteria. We demonstrate that the carboxylase pathway enables utilization of guanidine as sole nitrogen source. We isolated three enterobacteria (Raoultella terrigena, Klebsiella michiganensis, and Erwinia rhapontici) that utilize guanidine efficiently as N‐source. Proteome analyses show that the expression of a carboxylase, associated hydrolases and transport genes is strongly induced by guanidine. Finding two urea/guanidine carboxylase enzymes in E. rhapontici, we demonstrate that the riboswitch‐controlled carboxylase displays specificity toward guanidine, whereas the other enzyme prefers urea. We characterize the distribution of riboswitch‐associated carboxylases and Gdx exporters in bacterial habitats by analyzing available metagenome data. The findings represent a paradigm shift from riboswitch‐controlled detoxification of guanidine to the uptake and assimilation of this enigmatic nitrogen‐rich compound.
Polygenic risk, lifestyle, and cardiovascular mortality: a prospective population-based UK Biobank study

OBJECTIVE: To assess the prognostic ability of polygenic risk scores (PRSs) for coronary artery disease (CAD) and type 2 diabetes mellitus (T2DM) for cardiovascular (CV) mortality, independent of traditional risk factors, and further investigate the additive effect between lifestyle behavior and PRS on CV mortality. DESIGN: Prospective population-based cohort study. SETTING: UK Biobank. PARTICIPANTS: A total 377,909 unrelated participants of white British descent were included in the analyses from the UK Biobank cohort. MAIN OUTCOME MEASURES: Genome-wide PRSs were constructed using >6 million genetic variants. We stratified patients into four PRS risk groups: low (0 to 19th percentile), intermediate (20 to 79th percentile), high (80 to 98th percentile), and very high (99th percentile). We defined a favorable and unfavorable lifestyle with four modifiable lifestyle components, including smoking, obesity, physical activity, and diet. Cox proportional hazard models were used to analyze the relationship between PRS and CV mortality with stratification by age, sex, disease status, and lifestyle behavior. RESULTS: Of 377,909 UK Biobank participants having European ancestry, 3,210 (0.8%) died due to CV disease during a median follow-up of 8.9 years. CV mortality risk was significantly associated with CAD PRS (low vs. very high genetic risk groups, CAD PRS hazard ratio [HR] 2.61 [2.02 to 3.36]) and T2DM PRS (HR 2.08 [1.58 to 2.73]), respectively. These relationships remained significant even after adjustment for a comprehensive range of demographic and clinical factors. In the very high genetic risk group, adherence to an unfavorable lifestyle was further associated with a substantially increased risk of CV mortality (favorable versus unfavorable lifestyle with very high genetic risk for CAD PRS, HR 8.31 [5.12 to 13.49]; T2DM PRS, HR 5.84 [3.39 to 10.04]). Across all genetic risk groups, 32.1% of CV mortality was attributable to lifestyle behavior (population attributable fraction [PAF] 32.1% [95% CI 28.8 to 35.3%]) and 14.1% was attributable to smoking (PAF 14.1% [95% CI 12.4 to 15.7%]). There was no evidence of significant interaction between PRSs and age, sex, or lifestyle behavior in predicting the risk of CV mortality. CONCLUSION: PRSs for CAD or T2DM and lifestyle behaviors are independent predictive factors for future CV mortality in the white, middle-aged population. PRS-based risk assessment could be useful to identify individuals who need intensive behavioral or therapeutic interventions to reduce the risk of CV mortality.
Predicting the Current and Future Distribution of the Invasive Weed Ageratina adenophora in the Chitwan–Annapurna Landscape, Nepal

With increasing globalization, trade, and human movement, the rate of alien species introduction has increased all around the globe. In addition, climate change is thought to exacerbate the situation by allowing range expansion of invasive species into new areas. Predicting the distribution of invasive species under conditions of climate change is important for identifying susceptible areas of invasion and developing strategies for limiting their expansion. We used Maxent modeling to predict the distribution of one of the world's most aggressive invasive weeds, Ageratina adenophora (Sprengel) R. King and H. Robinson, in the Chitwan–Annapurna Landscape (CHAL) of Nepal under current conditions and 3 future climate change trajectories based on 3 representative concentration pathways (RCPs 2.6, 4.5, and 8.5) in 2 different time periods (2050 and 2070) using species occurrence data, and bioclimatic and topographic variables. Minimum temperature in the coldest month was the most important variable affecting the distribution of A. adenophora. About 38% (12,215 km2) of the CHAL area is climatically suitable for A. adenophora, with the Middle Mountain physiographic region being the most suitable one. A predicted increase in current suitable areas ranges from 1 to 2% under future climate scenarios (RCP 2.6 and RCP 8.5). All protected areas and 3 physiographic regions (Siwaliks, High Mountain, High Himalaya) are likely to gain climatically suitable areas in future climate scenarios. The upper elevational distribution limit of the weed is expected to expand by 31–48 m in future climate scenarios, suggesting that the weed will colonize additional areas at higher elevations in the future. In conclusion, our results showed that a vast area of CHAL is climatically suitable for A. adenophora. Expected further range expansion and upslope migration in the future make it essential to initiate effective management measures to prevent further negative impacts of this invasive plant.
Societal Recognition of Ecosystem Service Flows From Red Panda Habitats in Western Nepal

The biologically and culturally diverse mountain habitats of the red panda (Ailurus fulgens) produce numerous ecosystem goods and services of global significance and satisfy the daily sustenance requirements and wellbeing of poor and vulnerable local communities. Most studies of ecosystem services conducted in Nepal have investigated community forest management and protected areas, largely in the lower hills and plains of the country. However, to conserve red pandas and associated biodiversity, knowledge is needed of the services instrumental to the livelihoods and wellbeing of people living in and around their Himalayan mountain habitats. Using case studies of 6 remote villages nearest to known red panda habitats inside and outside a protected area in western Nepal, this study reports on key informant interviews, focus group discussions, informal interactions, and participant observations to identify and categorize the goods and services provided by these habitats. Among the provisioning and cultural ecosystem goods and services obtained from red panda habitats, local people prioritized seasonal grazing in high-altitude pastures, plant materials for medicines and food, wild plants for energy, transhumance culture, and religious interaction with nature. Their dependence on these services varied with season and location, with greater reliance on the services outside the protected areas. Some services used for valuing ecosystems, such as carbon storage and improved air and water quality and biodiversity, were only ever mentioned in a manner that would characterize them as cultural services provided by mountain deities. They only appear to be acknowledged as services with a use value by people from outside the region. This study suggests that understanding the value of the services provided to local communities could allow development of a policy that would also help conserve red pandas, particularly if income can be obtained for providing services to outsiders who have no perceived local economic benefit.
Ligand-independent activity of the ghrelin receptor modulates AMPA receptor trafficking and supports memory formation

Blocking the constitutive activity of the ghrelin receptor impairs spatial and recognition memory. No ligand needed for learning In addition to its role in stimulating appetite, the hormone ghrelin and its receptor GHS-R1a are implicated in cognition. Ribeiro et al. found a role for ghrelin-independent GHS-R1a signaling in learning in mice. The use of inverse agonists and mutants revealed that ligand-independent activity of GHS-R1a maintained the synaptic abundance of AMPA-type glutamate receptors in hippocampal neurons through a phosphorylation-dependent trafficking mechanism in cultured neurons and brain slices, thereby ensuring tonic control of synaptic plasticity. Treating mice with a GHS-R1a inverse agonist impaired spatial and contextual memory formation. Thus, the use of ghrelin receptor–blocking therapies—which have been proposed for treating metabolic disorders, acromegaly, cancer, and alcoholism—may also have cognitive side effects. The biological signals of hunger, satiety, and memory are interconnected. The role of the hormone ghrelin in regulating feeding and memory makes ghrelin receptors attractive targets for associated disorders. We investigated the effects of the high ligand-independent activity of the ghrelin receptor GHS-R1a on the physiology of excitatory synapses in the hippocampus. Blocking this activity produced a decrease in the synaptic content of AMPA receptors in hippocampal neurons and a reduction in GluA1 phosphorylation at Ser845. Reducing the ligand-independent activity of GHS-R1a increased the surface diffusion of AMPA receptors and impaired AMPA receptor–dependent synaptic delivery induced by chemical long-term potentiation. Accordingly, we found that blocking this GHS-R1a activity impaired spatial and recognition memory in mice. These observations support a role for the ligand-independent activity of GHS-R1a in regulating AMPA receptor trafficking under basal conditions and in the context of synaptic plasticity that underlies learning.
Metal‐Free Photocatalytic Aerobic Oxidation of Thiols to Disulfides in Batch and Continuous‐Flow

Disulfides represent significant molecular and structural features in various biologically active compounds and fine chemicals. Therefore, the development of mild, efficient and sustainable methods to access disulfides is of great importance. Here, we describe the development of a mild metal-free photocatalytic aerobic oxidation of thiols to disulfides using Eosin Y and visible-light irradiation. A continuous flow procedure was developed to accelerate the photocatalytic process, enabling the preparation of disulfides with high purity in a time-frame of minutes. The mildness and applicability of our method was exemplified by the flow synthesis of the cyclic peptide hormone, oxytocin, requiring only a 200 s reaction time and an efficient one-pot batch protocol for the preparation of the therapeutic thiuram disulfide, disulfiram.
Fused deposition modeling of poly(ether ether ketone) scaffolds

Abstract In this paper, poly(ether ether ketone) (PEEK) scaffold was manufactured using the fused deposition modeling (FDM) technology with a modified platform. The effect of processing parameters of FDM on the porosity and compressive strength of PEEK scaffold with uniform pores (0.8 mm of diameter) was optimized through Taguchi methodology. With the determined parameters, four kinds of PEEK scaffolds with gradient pores (0.4–0.8 mm, 0.6–1.0 mm, 0.8–1.2 mm, and 1.2–2.0 mm) were manufactured. The scaffolds were investigated using scanning electron microscopy. The results showed that the pores of scaffolds were interconnected with rough surface, which can allow the attachment, migration, and differentiation of cells for bone forming. The tensile strength, compressive max strength, and compressive yield strength of scaffolds were between 18 and 35 MPa, 197.83 and 370.42 MPa, and 26 and 36 MPa, respectively. The mechanical properties of the scaffolds can satisfy the loading requirements of human bones. Therefore, the PEEK scaffolds have a potential to be used in tissue engineering as implants.
Dilution refrigeration with multiple mixing chambers

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Comparison of Commercial near Infrared Transmittance and Reflectance Instruments for Analysis of Whole Grains and Seeds

Near infrared transmittance and reflectance instruments were compared for the determination of protein, oil, moisture and some other constituents and parameters in several grains and seeds of commerce. Both approaches were comparable in accuracy and reproducibility. The importance of optimisation of the wavelength range in whole grain analysis is demonstrated for measurements in both the NIR and visible/NlR wavelength ranges. The RPD statistic, which relates the standard error of prediction to the standard deviation of the original data, is illustrated as a method for the evaluation of calibrations. The concept of monitoring the accuracy of analysis using whole grain calibrations with ground grain calibrations is introduced.
Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

Contact zones between recently-diverged taxa provide opportunities to examine the causes of reproductive isolation and to examine the processes that determine whether two species can coexist over a broad region. The Pacific Wren (Troglodytes pacificus) and the Winter Wren (Troglodytes hiemalis) are two morphologically similar songbird species that started diverging about 4 million years ago, older than most sister species pairs. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct in sympatry. To assess evidence for differentiation, hybridization, and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genomes of the two species. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals from allopatry and sympatry, two first-generation hybrids (i.e., F1’s) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or F2’s or other evidence of recent breeding success of F1 hybrids, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event in the distant past. The sizeable rate of hybridization combined with very low fitness of F1 hybrids is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species. Additionally, we present evidence for a rare duplication of a large chromosomal segment from an autosome to the W chromosome, the female-specific sex chromosome in birds.
Exosomes from COVID-19 patients carry tenascin-C and fibrinogen-β in triggering inflammatory signals in distant organ cells

SARS-CoV-2 infection causes cytokine storm and overshoot immunity in humans; however, it remains to be determined whether genetic material of SARS-CoV-2 and/or virus induced soluble mediators from lung epithelial cells as natural host are carried out by macrophages or other vehicles at distant organs causing tissue damage. We speculated that exosomes as extracellular vesicles are secreted from SARS-CoV-2 infected cells may transport messages to other cells of distant organs leading to pathogenic consequences. For this, we took an unbiased proteomic approach for analyses of exosomes isolated from plasma of healthy volunteers and SARS-CoV-2 infected patients. Our results revealed that tenascin-C (TNC) and fibrinogen-β (FGB) are highly abundant in exosomes from SARS-CoV-2 infected patient’s plasma as compared to that of healthy normal controls. Since TNC and FGB stimulate pro-inflammatory cytokines via NF-κB pathway, we examined the status of TNF-α, IL-6 and CCL5 expression upon exposure of hepatocytes to exosomes from COVID-19 patients and observed significant increase when compared with that from healthy subjects. Together, our results demonstrated that soluble mediators, like TNC and FGB, are transported through plasma exosomes in SARS-CoV-2 infected patients and trigger pro-inflammatory cytokine expression in cells of distant organs in COVID-19 patients. Importance Exosomes play an important role in intercellular communication by inducing physiological changes in recipient cells by transferring bioactive proteins. Little is known about exosomes from SARS-CoV-2 infected cells and their role in pathogenesis. Here, we have carefully examined and analyzed this aspect of SARS-CoV-2 infection. Our results uncovered the potential mechanisms by which SARS-CoV-2 communicates with other cells of distant organs and promotes pathogenesis. We expect to detect whether other factors are modulated in the presence of COVID-19 exosomes. Our exosomes related proteomic experiments prioritize after initial verification to further examine their role in SARS-CoV-2 associated other pathogenic mechanisms to target for therapeutic modalities.
Harmful Algal Bloom-Forming Organism Responds to Nutrient Stress Distinctly From Model Phytoplankton

Resources such as nitrogen (N) and phosphorus (P) play an important role in primary production and constraining phytoplankton bloom dynamics. Models to predict bloom dynamics require mechanistic knowledge of algal metabolic shifts in response to resource limitation. For well-studied model phytoplankton like diatoms, this information is plentiful. However, for less-studied groups such as the raphidophytes, there remain significant gaps in understanding metabolic changes associated with nutrient limitation. Using a novel combination of metabolomics and transcriptomics, we examined how the harmful algal bloom-forming raphidophyte Heterosigma akashiwo shifts its metabolism under N- and P-stress. We chose H. akashiwo because of its ubiquity within estuarine environments worldwide, where bloom dynamics are influenced by N and P availability. Our results show that each stress phenotype is distinct in both the allocation of carbon and the recycling of macromolecules. Further, we identified biomarkers of N- and P-stress that may be applied in situ to help modelers and stakeholders manage, predict, and prevent future blooms. These findings provide a mechanistic foundation to model the metabolic traits and trade-offs associated with N- and P-stress in H. akashiwo, and evaluate the extent to which these metabolic responses can be inferred in other phytoplankton groups.