Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences in plant cover and species composition of semiarid grassland communities of central Mexico and its effects on net ecosystem exchange

Changes in land use across the semiarid grass- lands of northern Mexico have driven a decline of plant cover and alteration of plant species composition. A number of dif- ferent plant communities have resulted from these changes. Their implications, however, on the carbon (C) cycle and regional carbon balance are still poorly understood. Here, we examined the effects of plant cover loss and changes in species composition on net ecosystem CO2 exchange (NEE) and their biotic and abiotic controls. NEE was measured in five representative plant community types within a semiarid grassland by temporarily enclosing the entire aboveground ecosystem using a chamber method (i.e., geodesic dome). Sites included an oat crop (crop), a moderately grazed grass- land (moderate grazing), a 28 yr-old grazing exclosure (ex- closure), an overgrazed site with low perennial grass cover (overgrazed), and an overgrazed site presenting shrub en- croachment (shrub encroachment). For natural vegetation, rates of standardized daytime NEE for sites with a high plant cover (exclosure and moderate grazing) were simi- lar (P > 0.05) as compared to sites with low plant cover (overgrazed and shrub encroachment). However, yearly to- tal nighttime NEE (carbon loss) was more than double (P < 0.05) for sites with high plant cover compared to sites with low cover, resulting to slight C sinks for the low plant cover sites, and neutral or sources for the high plant cover sites as accounted by daytime and nighttime NEE annual bal- ance. Differences in plant cover and its associated biomass defined the sensitivity to environmental controls. Thus, day- time NEE in low plant cover sites reached light compensation points at lower photosynthetic photon flux density than those from high plant cover sites. Differences in species composi- tion did not influence NEE rates even though there were tran- sient or permanent changes in C3 vs. C4 functional groups. Our results allowed the detection of the large variability and contribution of different plant communities to regional C bal- ance in patchy landscapes. Identification of the role of land- scape patches in the regional C balance as either sinks or sources may provide tools allowing land use management strategies that could favor C uptake in patchy landscapes.
Thermomechanical Studies of Yielding and Strain Localization Phenomena of Gum Metal under Tension

This paper presents results of investigation of multifunctional β-Ti alloy Gum Metal subjected to tension at various strain rates. Digital image correlation was used to determine strain distributions and stress-strain curves, while infrared camera allowed for us to obtain the related temperature characteristics of the specimen during deformation. The mechanical curves completed by the temperature changes were applied to analyze the subsequent stages of the alloy loading. Elastic limit, recoverable strain, and development of the strain localization were studied. It was found that the maximal drop in temperature, which corresponds to the yield limit of solid materials, was referred to a significantly lower strain value in the case of Gum Metal in contrast to its large recoverable strain. The temperature increase proves a dissipative character of the process and is related to presence of ω and α″ phases induced during the alloy fabrication and their exothermic phase transformations activated under loading. During plastic deformation, both the strain and temperature distributions demonstrate that strain localization for higher strain rates starts nucleating just after the yield limit leading to specimen necking and rupture. Macroscopically, it is exhibited as softening of the stress-strain curve in contrast to the strain hardening observed at lower strain rates.
Initial Response of Human Bone Marrow–Derived Stem Cells after Contact with Ultrahigh-Molecular-Weight Polyethylene (UHMWPE) Material: An In Vitro Study on Cell Viability and Interleukin-6 Expression

Introduction: Ultrahigh-molecular-weight polyethylene (UHMWPE) is a thermoplastic polymer useful in biomaterial applications, especially in orthopedic field. Yet, little is known concerning its initial effect on human bone marrow stem cells (hBMSCs) after implantation. Materials and Methods: A cytotoxicity analysis was performed with a 3-(4,5-dimethylthiazol 2-yl)-2,5-diphenyltetrazolium assay after 24, 48, and 72h of incubation of hBMSC culture. Expression of interleukin-6 (IL-6) was measured using enzyme-linked immunosorbent assay. Cell viability was measured with Inhibitory concentration 50% (IC50) formula. Results: All treatment groups showed a cell viability of >50% ranging from 78% to >100%. Lower expression of IL-6 of hBMSC compared to control group was found in 48h of incubation period. Conclusion: hBMSC showed high cell viability after initial contact with UHMWPE material. Modulation of IL-6 expression was present at the initial stage as a response to foreign material.
Fibrinogen and fibrin based micro and nano scaffolds incorporated with drugs, proteins, cells and genes for therapeutic biomedical applications

Over the past two decades, many types of natural and synthetic polymer-based micro- and nanocarriers, with exciting properties and applications, have been developed for application in various types of tissue regeneration, including bone, cartilage, nerve, blood vessels, and skin. The development of suitable polymers scaffold designs to aid the repair of specific cell types have created diverse and important potentials in tissue restoration. Fibrinogen (Fbg)- and fibrin (Fbn)-based micro- and nanostructures can provide suitable natural matrix environments. Since these primary materials are abundantly available in blood as the main coagulation proteins, they can easily interact with damaged tissues and cells through native biochemical interactions. Fbg- and Fbn-based micro and nanostructures can also be consecutively furnished/or encapsulated and specifically delivered, with multiple growth factors, proteins, and stem cells, in structures designed to aid in specific phases of the tissue regeneration process. The present review has been carried out to demonstrate the progress made with micro and nanoscaffold applications and features a number of applications of Fbg- and Fbn-based carriers in the field of biomaterials, including the delivery of drugs, active biomolecules, cells, and genes, that have been effectively used in tissue engineering and regenerative medicine.
Progressive Assessment of Ischemic Injury to White Matter Using Diffusion Tensor Imaging: A Preliminary Study of a Macaque Model of Stroke

Background: Previous Diffusion Tensor Imaging (DTI) studies have demonstrated the temporal evolution of stroke injury in grey matter and white matter can be characterized by DTI indices. However, it still remains not fully understood how the DTI indices of white matter are altered progressively during the hyperacute (first 6 hours) and acute stage of stroke (≤ 1 week). In the present study, DTI was employed to characterize the temporal evolution of infarction and white matter injury after stroke insult using a macaque model with permanent ischemic occlusion. Methods and materials: Permanent middle cerebral artery (MCA) occlusion was induced in rhesus monkeys (n=4, 10-21 years old). The brain lesion was examined longitudinally with DTI during the hyperacute phase (2-6 hours, n=4), 48 hours (n=4) and 96 hours (n=3) post-occlusion. Results: Cortical infarction was seen in all animals. The Mean Diffusivity (MD) in lesion regions decreased substantially at the first time point (2 hours post stroke) (35%, p <0.05, compared to the contralateral side) and became pseudo-normalized at 96 hours. In contrast, evident FA reduction was seen at 48 hours (39%, p <0.10) post-stroke. MD reduction in white matter bundles of the lesion area was much less than that in the grey matter during the hyper-acute phase but significant change was observed 4 hours (4.2%, p < 0.05) post stroke . Also, MD pseudonormalisation was seen at 96 hours post stroke. There was a significant correlation between the temporal changes of MD in white matter bundles and those in whole lesion areas during the entire study period. Meanwhile, no obvious fractional anisotropy (FA) changes were seen during the hyper-acute phase in either the entire infarct region or white matter bundles. Significant FA alteration was observed in entire lesion areas and injured white matter bundles 48 and 96 hours post stroke. The stroke lesion in grey matter and white matter was validated by pathological findings. Conclusion: The temporal evolution of ischemic injury to the grey matter and white matter from 2 to 96 hours after stroke onset was characterized using a macaque model and DTI. Progressive MD changes in white matter bundles are seen from hyperacute phase to acute phase after permanent MCA occlusion and temporally correlated with the MD changes in entire infarction regions. MD reduction in white matter bundles is mild in comparison with that in the grey matter but significant and progressive, indicating it may be useful to detect early white matter degeneration after stroke.
Novel approach to heritability detection suggests robustness to paternal genotype in a complex morphological trait

Abstract Heritable variation is essential for evolution by natural selection. In Neotropical army ants, the ecological role of a given species is linked intimately to the morphological variation within the sterile worker caste. Furthermore, the army ant Eciton burchellii is highly polyandrous, presenting a unique opportunity to explore heritability of morphological traits among related workers sharing the same colonial environment. In order to exploit the features of this organismal system, we generated a large genetic and morphological dataset and applied our new method that employs geometric morphometrics (GM) to detect the heritability of complex morphological traits. After validating our approach with an existing dataset of known heritability, we simulated our ability to detect heritable variation given our sampled genotypes, demonstrating the method can robustly recover heritable variation of small effect size. Using this method, we tested for genetic caste determination and heritable morphological variation using genetic and morphological data on 216 individuals of E. burchellii. Results reveal this ant lineage (1) has the highest mating frequency known in ants, (2) demonstrates no paternal genetic caste determination, and (3) suggests a lack of heritable morphological variation in this complex trait associated with paternal genotype. We recommend this method for leveraging the increased resolution of GM data to explore and understand heritable morphological variation in nonmodel organisms.
PIV / PLIF measurements in non-reacting flow of a GT-burner at realistic flow rates

In this work simultaneous velocity field and concentration field measurements at realistic flow-rates conditions (up to 0.5 kg/s air flow and boost pressure) were carried out in a cold flow premixed GT-burner provided by JSC Aviadvigatel. The Reynolds number based on the mean flow rate and nozzle diameter was 300 000. For safety reasons the real fuel (natural gas) was replaced with neon gas to simulate stratification in a strongly swirling flow. Acetone was seeded into the neon flow to provide quantitative fuel concentration measurements based on planar laser-induced fluorescence (PLIF). Velocity measurements were carried out using particle image velocimetry approach (PIV). The air flow was seeded with water-glycerol mixture particles. This paper reports on details of instantaneous combined measurements of concentration and velocity. It was a challenge to make an accurate measurements due to reflections, absorption and compromise between transparence of the combustion chamber walls and required seeding density. However the quality of experimental data and image processing algorithms allowed to measure simultaneous velocity and passive tracer concentration fields.
Epidemiological trends of allergic diseases in adolescents

ABSTRACT Objective: To assess the prevalences of asthma, allergic rhinitis, and allergic rhinoconjunctivitis in adolescents in the city of Belo Horizonte, Brazil, in 2012 by administering the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire, as well as to compare the observed prevalences with those found in studies performed 10 years earlier and employing the same methodology used here. Methods: This was a cross-sectional study conducted between May and December of 2012 and involving adolescents in the 13- to 14-year age bracket. Participants were randomly selected from among adolescents studying at public schools in Belo Horizonte and completed the ISAAC questionnaire. Proportions were calculated in order to assess the prevalences of asthma, allergic rhinitis, and allergic rhinoconjunctivitis in the sample as a whole, and the chi-square goodness-of-fit test was used in order to compare the prevalences observed in 2012 with those found in 2002. Results: The prevalences of symptoms of asthma, allergic rhinitis, and allergic rhinoconjunctivitis in 2012 were 19.8%, 35.3%, and 16.3%, respectively, being significantly higher than those found in 2002 (asthma, p = 0.006; allergic rhinitis, p < 0.01; and allergic rhinoconjunctivitis, p = 0.002). Conclusions: The prevalences of asthma, allergic rhinitis, and allergic rhinoconjunctivitis among adolescents in 2012 were found to be high, having increased in comparison with those found 10 years earlier, despite efforts in prevention, diagnosis, and treatment.
Theranostic liposomes loaded with quantum dots and apomorphine for brain targeting and bioimaging

Quantum dots (QDs) and apomorphine were incorporated into liposomes to eliminate uptake by the liver and enhance brain targeting. We describe the preparation, physicochemical characterization, in vivo bioimaging, and brain endothelial cell uptake of the theranostic liposomes. QDs and the drug were mainly located in the bilayer membrane and inner core of the liposomes, respectively. Spherical vesicles with a mean diameter of ~140 nm were formed. QDs were completely encapsulated by the vesicles. Nearly 80% encapsulation percentage was achieved for apomorphine. A greater fluorescence intensity was observed in mouse brains treated with liposomes compared to free QDs. This result was further confirmed by ex vivo imaging of the organs. QD uptake by the heart and liver was reduced by liposomal incorporation. Apomorphine accumulation in the brain increased by 2.4-fold after this incorporation. According to a hyperspectral imaging analysis, multifunctional liposomes but not the aqueous solution carried QDs into the brain. Liposomes were observed to have been efficiently endocytosed into bEND3 cells. The mechanisms involved in the cellular uptake were clathrin- and caveola-mediated endocytosis, which were energy-dependent. To the best of our knowledge, our group is the first to develop liposomes with a QD-drug hybrid for the aim of imaging and treating brain disorders.
Pichia pastoris Exhibits High Viability and a Low Maintenance Energy Requirement at Near-Zero Specific Growth Rates

ABSTRACT The yeast Pichia pastoris is a widely used host for recombinant protein production. Understanding its physiology at extremely low growth rates is a first step in the direction of decoupling product formation from cellular growth and therefore of biotechnological relevance. Retentostat cultivation is an excellent tool for studying microbes at extremely low specific growth rates but has so far not been implemented for P. pastoris. Retentostat feeding regimes were based on the maintenance energy requirement (mS ) and maximum biomass yield on glucose (YX /S max) estimated from steady-state glucose-limited chemostat cultures. Aerobic retentostat cultivation enabled reproducible, smooth transitions from a specific growth rate (μ) of 0.025 h−1 to near-zero specific growth rates (μ < 0.001 h−1). At these near-zero specific growth rates, viability remained at least 97%. The value of mS at near-zero growth rates was 3.1 ± 0.1 mg glucose per g biomass and h, which was 3-fold lower than the mS estimated from faster-growing chemostat cultures. This difference indicated that P. pastoris reduces its maintenance energy requirement at extremely low μ, a phenomenon not previously observed in eukaryotes. Intracellular levels of glycogen and trehalose increased, while μ progressively declined during retentostat cultivation. Transcriptional reprogramming toward zero growth included the upregulation of many transcription factors as well as stress-related genes and the downregulation of cell cycle genes. This study underlines the relevance of comparative analysis of maintenance energy metabolism, which has an important impact on large-scale industrial processes. IMPORTANCE The yeast Pichia pastoris naturally lives on trees and can utilize different carbon sources, among them glucose, glycerol, and methanol. In biotechnology, it is widely used for the production of recombinant proteins. For both the understanding of life in its natural habitat and optimized production processes, a better understanding of cell physiology at an extremely low growth rate would be of extraordinary value. Therefore, we have grown P. pastoris in a retentostat, which allows the cultivation of metabolically active cells even at zero growth. Here we reached doubling times as long as 38 days and found that P. pastoris decreases its maintenance energy demand 3-fold during very slow growth, which enables it to survive with a much lower substrate supply than baker's yeast.
Effectiveness of Active-Online, an Individually Tailored Physical Activity Intervention, in a Real-Life Setting: Randomized Controlled Trial

Background Effective interventions are needed to reduce the chronic disease epidemic. The Internet has the potential to provide large populations with individual advice at relatively low cost. Objective The focus of the study was the Web-based tailored physical activity intervention Active-online. The main research questions were (1) How effective is Active-online, compared to a nontailored website, in increasing self-reported and objectively measured physical activity levels in the general population when delivered in a real-life setting? (2) Do respondents recruited for the randomized study differ from spontaneous users of Active-online, and how does effectiveness differ between these groups? (3) What is the impact of frequency and duration of use of Active-online on changes in physical activity behavior? Methods Volunteers recruited via different media channels completed a Web-based baseline survey and were randomized to Active-online (intervention group) or a nontailored website (control group). In addition, spontaneous users were recruited directly from the Active-online website. In a subgroup of participants, physical activity was measured objectively using accelerometers. Follow-up assessments took place 6 weeks (FU1), 6 months (FU2), and 13 months (FU3) after baseline. Results A total of 1531 respondents completed the baseline questionnaire (intervention group n = 681, control group n = 688, spontaneous users n = 162); 133 individuals had valid accelerometer data at baseline. Mean age of the total sample was 43.7 years, and 1146 (74.9%) were women. Mixed linear models (adjusted for sex, age, BMI category, and stage of change) showed a significant increase in self-reported mean minutes spent in moderate- and vigorous-intensity activity from baseline to FU1 (coefficient = 0.14, P = .001) and to FU3 (coefficient = 0.19, P < .001) in all participants with no significant differences between groups. A significant increase in the proportion of individuals meeting the HEPA recommendations (self-reported) was observed in all participants between baseline and FU3 (OR = 1.47, P = .03), with a higher increase in spontaneous users compared to the randomized groups (interaction between FU3 and spontaneous users, OR = 2.95, P = .02). There were no increases in physical activity over time in any group for objectively measured physical activity. A significant relation was found between time spent on the tailored intervention and changes in self-reported physical activity between baseline and FU3 (coefficient = 1.13, P = .03, intervention group and spontaneous users combined). However, this association was no longer significant when adjusting for stage of change. Conclusions In a real-life setting, Active-online was not more effective than a nontailored website in increasing physical activity levels in volunteers from the general population. Further research may investigate ways of integrating Web-based physical activity interventions in a wider context, for example, primary care or workplace health promotion.
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance

MOTIVATION Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed. RESULTS We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O(m(3) n(2)), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than approximately 800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.
Regulation of TNF-&alpha expression by serum amyloid A and the effect on renal glomerular cells in diabetic nephropathy patients

Objective: Diabetic nephropathy (DN) has become the second common cause for terminal nephropathy. Serum amyloid A (SAA) is a marker for body inflammation. Previous study showed involvement of SAA in DN onset and pathogenesis. This study aimed to investigate the regulation of inflammatory factor TNF-α and extracellular matrix (ECM) FN by SAA, as well as the effects of SAA on renal glomerular cells in DN patients. Patients and Methods: A total of 188 diabetic patients were divided into pure diabetic, micro-albumin urea and clinical albumin urea groups. ELISA was used to measure the concentration of SAA and TNF- α. Pearson correlation was used to analyze the association of SAA or TNF-α with UAER. RNA interference was used to inhibit SAA expression in glomerular cells, whilst Western blot was performed to measure the SAA and TNF-α expression in cultured cell supernatant after treated with different glucose concentrations. ELISA was then used to evaluate FN expression. Results: Micro-albumin urea and clinical albumin urea groups had significantly higher serum SAA and TNF-α concentrations (p<0.05 compared with pure diabetic group). Their concentrations were positively correlated with UAER (r=0.463, and 0.278, p<0.05). After transfection of anti-SAA, renal glomerular cells showed lower TNF-α and FN levels (p<0.05 compared with control cells cultured under highglucose medium). Conclusions: This study indicated positive correlation between SAA concentration and UAER, indicating the possible involvement of SAA in the onset/progression of DN, which might be possibly via mediating the expression levels of TNF-α and FN.