Miracle-dz/UniFAR-FTUs huggingface dataset:
Is assuming additivity of single‐metal toxicity thresholds a conservative approach to assessing risk of ecotoxicity from elevated soil concentrations of cobalt, copper, and nickel at contaminated sites?

Multiple metal‐impacted soils are often realistic scenarios for risk assessments, but tools to address these are currently lacking. The objective of this work was to evaluate whether assuming concentration addition (CA) of metal mixture effects was conservative for prospective risk assessment of soils that were elevated mainly in Ni and Cu and somewhat with Co, Pb, or As. Observed whole mixture toxicity for field soils with aged metal mixtures was compared to the expected whole mixture toxicity, assuming additivity of prospective single‐metal thresholds (“toxic units”) for the mixture components. Bioavailability‐adjusted single‐metal toxicity thresholds expected for those field soils were the median hazard concentration affecting 5% of species (HC5‐50) from the predicted no‐effect concentration (PNEC) calculator and calculated from the species‐specific dose–response multiple linear relationships (MLRs), all from the European Union Registration, Evaluation, Authorisation and Restriction of Chemicals (EU REACH) dossiers for metals. Generic single‐metal toxicity thresholds were based on Canadian Council of Ministers of the Environment soil quality guidelines (CCME SQGs) for agricultural soils. Observed toxicity thresholds were from the community‐based risk assessments conducted for Port Colborne and Sudbury, Ontario, Canada. Mostly, prospective single‐metal toxicity thresholds were protective relative to the observed toxicity, although that was species or ecological process dependent. The bioavailability‐adjusted single‐metal thresholds were less conservative than the CCME SQG method, even though the former is based on site‐specific EC10 values, and the latter is based on generic EC25 values. When within‐site variability in soil properties was used to calculate the 5th and 95th CI for the HC5 sum of toxic units (∑TUs), CA was conservative for far fewer endpoints. In addition, the prospective ∑TUs were more conservative predictions of the observed whole mixture toxicities for Port Colborne soils than for Sudbury soils. The most appropriate balance of accuracy and conservatism for identifying low‐level risk of the whole mixtures in these soils appeared to be the bioavailability‐adjusted HC5‐50, which was applicable to many endpoints and 2 quite different exposure concentration ratios. Integr Environ Assess Manag 2021;17:753–766. © 2020 SETAC
Genetic structure and asymmetric migration of wheat stripe rust pathogen in western epidemic areas of China.

Puccinia striiformis f. sp tritici (Pst) causes severe global epidemics of wheat stripe rust primarily by airborne urediniospores. Understanding long-distance migration patterns of Pst is critical for disease forecasting and management. Although the western epidemic areas in China have been considered as the source in spreading the inoculum eastward across the country, the migration pathways among different populations within the western epidemic areas are poorly understood. In this study, we investigated the population genetics of 200 Pst isolates from western epidemic areas using AFLP and SSR markers. A coalescent approach was also used to calculate the migration rates among populations. Data analyses with both marker systems indicated high genetic diversity in each regional population. The Mantel test revealed significant positive correlation between genetic and geographic distances. Both DAPC and STRUCTURE analysis supported moderate population structure shaped by seasonality and geography. The calculated migration rates indicated the presence of asymmetric migration between major populations in western epidemic areas, with greater migration rates from high elevation, oversummering areas to low elevation, overwintering areas. Sichuan Basin, one of the low elevation, overwintering areas, sampled in both fall and spring, was inferred as a recipient in fall but a donor in spring. The migration among Pst populations may be partly due to terrace farming and prevailing wind direction in different seasons. Our study has provided a better understanding of fine-scale population structure and the interregional migration pattern of Pst in northwestern China and will inform future rust management.
Infrared measurements of protein conformational dynamics

The topic of how a protein folds has been a major area of research for several decades; however, important details about this process are still undetermined. Experimental limitations in the study of protein folding are a result of no technique possessing both the necessary spatial and temporal resolution. This Thesis presents several studies conducted with the goal of expanding upon the experimentalist's toolbox, involving new methods of interrogating and/or perturbing protein systems of interest. The early chapters of this Thesis describe our efforts using established synthetic methods to extend the utility of infrared spectroscopy in the study of protein folding. Specifically, we show that, using the strategy of cysteine alkylation, we can incorporate novel vibrational probes into proteins in a site-specific manner. We also show that combined sidechain mutagenesis, probing at multiple frequencies, and isotopic labeling to obtain secondary structural resolution in infrared studies of protein folding, in the process uncovering details about the folding mechanism of the Trp-cage miniprotein. Similarly, we illustrated the use of thioamides as site-specific reporters of backbone-backbone hydrogen bonding, and applied this functionalization to the Trpzip2 beta-hairpin system to validate its proposed folding mechanism. Further work involved using Damino acids to interrogate turn regions in proteins, specifically examining Trp-cage folding. The later chapters of this Thesis are focused on the effects of extrinsic molecules on the structural ordering of proteins. Taking advantage of the lack of tertiary structure of intrinsically disordered proteins, we examined the effect that trifluoroethanol has on protein folding, and found evidence that this cosolvent acts as a nanocrowder. We also introduced the idea of using phototriggers to modify the free energy landscape of folding for a given protein, and demonstrated that a peptide that typically folds in an activated (barrier-containing) manner can be made to fold in a downhill fashion upon irradiation. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biochemistry & Molecular Biophysics First Advisor Feng Gai
TEM study of chronic alcoholism effects on early carcinogenesis by probing the nanoscale structural alterations of cell nuclei

Nanoscale structural alteration in the nuclei of cells with the progression of carcinogenesis is due to the rearrangements of the basic building blocks in the cell such as DNA, RNA, lipids, etc. Although epigenetic modifications underlie the development of cancer, exposure to carcinogenic chemicals such as alcohol also enhances the development of cancer. We report the effects of chronic alcoholism on early-carcinogenesis based on changes in the degree of nanoscale structural alterations (L d) in nuclei. For this, transmission electron microscopy (TEM) imaging of the nuclei of colonic cells is performed for the following four mouse models: control mice; chronic alcoholic mice treated with ethanol (i.e., EtOH mice); mice treated with colonic carcinogen azoxymethane (AOM) and dextran sulfate sodium (DSS) that induced colitis (i.e., AOM + DSS mice); and chronic alcoholic or EtOH treated mice, together with AOM and DSS treatment (i.e., AOM + DSS + EtOH mice). The disordered optical lattices are constructed from their respective TEM images of thin colonic cell nuclei and the L d values are calculated using the inverse participation ratio (IPR) technique from the spatially localized eigenfunctions of these lattices. Results show no significant difference in the average L d value of the colon cell nuclei of alcohol treated mice relative to its control [i.e., L d(C) ∼ L d(EtOH)]; however, an increase in the L d value of alcohol treated precancerous cells [i.e., L d(AOM + DSS + EtOH) > L d(AOM + DSS)], indicating that alcohol accelerates the early carcinogenic process.
Induced genetic ablation of Rest leads to the alteration of stimulus‐induced response of the vagal nerve

Rest (RE1‐silencing transcription factor, also called Nrsf) is involved in the maintenance of the undifferentiated state of neuronal stem/progenitor cells by preventing precocious expression of neuronal genes. In order to further investigate the function of Rest in neurons, we generated and examined mice evoking genetic ablation of Rest specifically in neural tissues by generating Rest conditional knockout mice. As the Rest knockout mice are embryonically lethal, we used a Sox1‐Cre allele to excise the floxed Rest gene from the early stage of nerve cell differentiation including neural crest‐derived nerve cells. Using this conditional Rest knockout Sox1‐Cre; Restflox/flox mice, we have revealed the role of Rest in the parasympathetic nervous system in the stomach and heart
Cardioprotective Activity of Selected Polyphenols Based on Epithelial and Aortic Cell Lines. A Review

Polyphenols have recently gained popularity among the general public as products and diets classified as healthy and containing naturally occurring phenols. Many polyphenolic extracts are available on the market as dietary supplements, functional foods, or cosmetics, taking advantage of clients’ desire to live a healthier and longer life. However, due to the difficulty of discovering the in vivo functions of polyphenols, most of the research focuses on in vitro studies. In this review, we focused on the cardioprotective activity of different polyphenols as possible candidates for use in cardiovascular disease therapy and for improving the quality of life of patients. Thus, the studies, which were mainly based on endothelial cells, aortic cells, and some in vivo studies, were analyzed. Based on the reviewed articles, polyphenols have a few points of action, including inhibition of acetylcholinesterase, decrease in reactive oxygen species production and endothelial tube formation, stimulation of acetylcholine-induced endothelium-derived mediator release, and others, which lead to their cardio- and/or vasoprotective effects on endothelial cells. The obtained results suggest positive effects of polyphenols, but more long-term in vivo studies demonstrating effects on mechanism of action, sensitivity, and specificity or efficacy are needed before legal health claims can be made.
The Role of Vitamin C, Vitamin D, and Selenium in Immune System against COVID-19

Low levels of micronutrients have been associated with adverse clinical outcomes during viral infections. Therefore, to maximize the nutritional defense against infections, a daily allowance of vitamins and trace elements for malnourished patients at risk of or diagnosed with coronavirus disease 2019 (COVID-19) may be beneficial. Recent studies on COVID-19 patients have shown that vitamin D and selenium deficiencies are evident in patients with acute respiratory tract infections. Vitamin D improves the physical barrier against viruses and stimulates the production of antimicrobial peptides. It may prevent cytokine storms by decreasing the production of inflammatory cytokines. Selenium enhances the function of cytotoxic effector cells. Furthermore, selenium is important for maintaining T cell maturation and functions, as well as for T cell-dependent antibody production. Vitamin C is considered an antiviral agent as it increases immunity. Administration of vitamin C increased the survival rate of COVID-19 patients by attenuating excessive activation of the immune response. Vitamin C increases antiviral cytokines and free radical formation, decreasing viral yield. It also attenuates excessive inflammatory responses and hyperactivation of immune cells. In this mini-review, the roles of vitamin C, vitamin D, and selenium in the immune system are discussed in relation to COVID-19.
Craniofacial Anthropometry of Healthy Turkish Young Adults: Outer Canthal, Inner Canthal, Palpebral Fissure, and Interpupillary Distances

Supplemental Digital Content is available in the text Abstract This study aims to examine the values of the orbital region in Turkish young adults by the two-dimensional photogrammetry. Anthropometric measurements of the eye and eyelid-related parameters were taken from 100 female and 100 male volunteer Turkish young adults, ranging in age from 18 to 25 years. Endocanthion (en), exocanthion (ex), and pupil (p) were identified on the photograph and the distances between these points were measured with the ImageJ program. The average values of the en-en, ex-en (R), ex-en (L), p-p, and ex-ex were found as 32.92 ± 2.84, 32.48 ± 2.06, 32.22 ± 2.01, 65.32 ± 3.77, and 97.75 ± 5.09 mm, respectively. There were statistically significant differences between the genders in all parameters. Although there are many studies examining these parameters, comprehensive studies are needed in different populations and in many cases. In this study, we believe that the results obtained for Turkish young adults can be used as reference values.
Use of 15N-enriched glycine to estimate vibrissa growth in free-ranging northern elephant seals Mirounga angustirostris

The stable isotope composition of continuously growing but metabolically inert tissues remains unaltered after they are synthesized, providing insights on seasonal and inter-annual variation in the ecology of individuals. In pinnipeds, isotope analysis of sub-sampled vibrissae can provide a longitudinal record of movement, diet, and even physiological state at the individual level. To reliably apply this approach, however, taxon-specific vibrissa growth needs to be estimated, especially for species with complicated annual life cycles that undergo periods of active foraging interspersed with reproduction and/or molting associated with fasting. Here, we intravenously injected 15N-enriched glycine to estimate vibrissa growth in 8 free-ranging adult female northern elephant seals during their (shorter) post-breeding and (longer) post-molting foraging trips; all animals were instrumented with satellite tags to track movements and vibrissae were collected when the animals returned to land. We found a significant positive relationship be tween the maximum δ15N values, representing 15N-glycine injections, and the distance between the origin of the spike and the root of the vibrissa. The δ15N spikes that occurred closest to the root were narrower and had lower δ15N values than those that occurred closer to the tip of the vibrissa, suggesting differential velocities of 15N-glycine absorption and vibrissa growth. A derived von Bertalanffy model yielded mean (±SD) growth of 0.015 ± 0.006 d−1, similar to that previously reported for a single captive northern elephant seal. Vibrissa length is an important consideration for accurately interpreting isotope-based ecological and physiological histories given the non-continuous growth observed in our study.
Conflict within species determines the value of a mutualism between species

Mutually beneficial interactions between species play a key role in maintaining biodiversity and ecosystem function. Nevertheless, such mutualisms can erode into antagonistic interactions. One explanation is that the fitness costs and benefits of interacting with a partner species vary among individuals. However, it is unclear why such variation exists. Here, we demonstrate that social behavior within species plays an important, though hitherto overlooked, role in determining the relative fitness to be gained from interacting with a second species. By combining laboratory experiments with field observations, we report that conflict within burying beetles Nicrophorus vespilloides influences the fitness that can be gained from interacting with the mite Poecilochirus carabi. Beetles transport these mites to carrion, upon which both species breed. We show that mites help beetles win intraspecific contests for this scarce resource: mites raise beetle body temperature, which enhances beetle competitive prowess. However, mites confer this benefit only upon smaller beetles, which are otherwise condemned by their size to lose contests for carrion. Larger beetles need no assistance to win a carcass and then lose reproductive success when breeding alongside mites. Thus, the extent of mutualism is dependent on an individual's inability to compete successfully and singlehandedly with conspecifics. Mutualisms degrade into antagonism when interactions with a partner species start to yield a net fitness loss, rather than a net fitness gain. This study suggests that interactions with conspecifics determine where this tipping point lies.
Dansyl-Labelled Ag@SiO2 Core-Shell Nanostructures—Synthesis, Characterization, and Metal-Enhanced Fluorescence

The present work describes synthesis, characterization, and use of a new dansyl-labelled Ag@SiO2 nanocomposite as an element of a new plasmonic platform to enhance the fluorescence intensity. Keeping in mind that typical surface plasmon resonance (SPR) characteristics of silver nanoparticles coincide well enough with the absorption of dansyl molecules, we used them to build the core of the nanocomposite. Moreover, we utilized 10 nm amino-functionalized silica shell as a separator between silver nanoparticles and the dansyl dye to prevent the dye-to-metal energy transfer. The dansyl group was incorporated into Ag@SiO2 core-shell nanostructures by the reaction of aminopropyltrimethoxysilane with dansyl chloride and we characterized the new dansyl-labelled Ag@SiO2 nanocomposite using transmission electron microscopy (TEM) and Fourier-transform infrared spectroscopy (FTIR). Additionally, water wettability measurements (WWM) were carried out to assess the hydrophobicity and hydrophilicity of the studied surface. We found that the nanocomposite deposited on a semitransparent silver mirror strongly increased the fluorescence intensity of dansyl dye (about 87-fold) compared with the control sample on the glass, proving that the system is a perfect candidate for a sensitive plasmonic platform.
Inclusion of Olecranon Osteotomy With the Posterior Approach for Fixation of Distal Humerus Fractures (OTA/AO 13) Does Not Increase Surgical Complications

Objectives: To determine if inclusion of an olecranon osteotomy to the posterior paratricipital approach for operative fixation of distal humerus fractures significantly affects surgical complication rates (OTA/AO 13). Design: Retrospective comparative cohort study. Setting: Level 1 trauma center. Patients/Participants: Three hundred four patients underwent open reduction internal fixation of a distal humerus fracture between 2007 and 2017. Of those, 134 met inclusion criteria (≥15 years, OTA/AO fracture type 13A, B, or C, and posterior surgical approach) for the study (n = 64 with olecranon osteotomy; n = 70 without olecranon osteotomy). Intervention: Open reduction internal fixation of distal humerus fractures performed using a posterior paratricipital approach with or without olecranon osteotomy. Main Outcome Measure: Ulnar neuropathy (UN), fracture site bony nonunion, and surgical site infection (SSI). Results: Thirty-one (33.3%) who underwent the paratricipital approach without olecranon osteotomy, and 15 patients (26.8%) who underwent olecranon osteotomy reported postoperative UN with no significant difference between approaches (P = 0.438). There was no significant difference in rates of SSI (P = 0.418) or fracture site nonunion (P = 0.263) when comparing the approaches. Subjects with Charlson comorbidity index ≥2 were more likely to not undergo an olecranon osteotomy (P = 0.01), whereas subjects with more complex fractures by OTA/AO classification were more likely to have an olecranon osteotomy approach (P = 0.001). Conclusions: Addition of an olecranon osteotomy with the paratricipital approach for fixation of distal humerus fractures does not result in higher rates of UN, fracture site nonunion, or SSI. Level of Evidence: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Rheological Properties of Cement Paste with Nano-Fe3O4 under Magnetic Field: Flow Curve and Nanoparticle Agglomeration

Understanding the influence of magnetic fields on the rheological behavior of flowing cement paste is of great importance to achieve active rheology control during concrete pumping. In this study, the rheological properties of cementitious paste with water-to-cement (w/c) ratio of 0.4 and nano-Fe3O4 content of 3% are first measured under magnetic field. Experimental results show that the shear stress of the cementitious paste under an external magnetic field of 0.5 T is lower than that obtained without magnetic field. After the rheological test, obvious nanoparticle agglomeration and bleeding are observed on the interface between the cementitious paste and the upper rotating plate, and results indicate that this behavior is induced by the high magnetic field strength and high-rate shearing. Subsequently, the hypothesis about the underlying mechanisms of nanoparticles migration in cementitious paste is illustrated. The distribution of the nanoparticles in the cementitious paste between parallel plates is examined by the magnetic properties of the powder as determined by a vibrating sample magnetometer. It is revealed that the magnetization of cementitious powders at different sections and layers provides a solid verification of the hypothesis.
Starting and stopping movement by the primate brain

We review the current knowledge about the part that motor cortex plays in the preparation and generation of movement, and we discuss the idea that corticospinal neurons, and particularly those with cortico-motoneuronal connections, act as ‘command’ neurons for skilled reach-to-grasp movements in the primate. We also review the increasing evidence that it is active during processes such as action observation and motor imagery. This leads to a discussion about how movement is inhibited and stopped, and the role in these for disfacilitation of the corticospinal output. We highlight the importance of the non-human primate as a model for the human motor system. Finally, we discuss the insights that recent research into the monkey motor system has provided for translational approaches to neurological diseases such as stroke, spinal injury and motor neuron disease.