Miracle-dz/UniFAR-FTUs huggingface dataset:
Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications

Peroxisomes, which are ubiquitous organelles in all eukaryotes, are highly dynamic organelles that are essential for development and stress responses. Plant peroxisomes are involved in major metabolic pathways, such as fatty acid β-oxidation, photorespiration, ureide and polyamine metabolism, in the biosynthesis of jasmonic, indolacetic, and salicylic acid hormones, as well as in signaling molecules such as reactive oxygen and nitrogen species (ROS/RNS). Peroxisomes are involved in the perception of environmental changes, which is a complex process involving the regulation of gene expression and protein functionality by protein post-translational modifications (PTMs). Although there has been a growing interest in individual PTMs in peroxisomes over the last ten years, their role and cross-talk in the whole peroxisomal proteome remain unclear. This review provides up-to-date information on the function and crosstalk of the main peroxisomal PTMs. Analysis of whole peroxisomal proteomes shows that a very large number of peroxisomal proteins are targeted by multiple PTMs, which affect redox balance, photorespiration, the glyoxylate cycle, and lipid metabolism. This multilevel PTM regulation could boost the plasticity of peroxisomes and their capacity to regulate metabolism in response to environmental changes.
Population, reproduction and foraging of pigeon guillemots at Naked Island, Alaska, before and after the Exxon Valdez oil spill. Bird study number 9. Exxon Valdez oil spill state/federal natural resource damage assessment final report

Following the 1989 Exxon Valdez oil spill in Prince William Sound (PWS), Alaska, we studied pigeon guillemots (Cepphus columba) breeding just 30 km from the grounding site. The post-spill population was 43% less than the pre-spill population, but we could not attribute the entire decline to the spill because a decline in the PWS guillemot population may have predated the spill. However, relative declines in the population were greater along oiled shorelines, suggesting that the spill was responsible for some of the decline. The most likely explanation for the few effects observed is that oil was present on the surface waters of the study area for a relatively short period before the guillemots returned to begin their annual reproductive activities.
Spatial heterogeneity in subglacial drainage driven by till erosion

The distribution and drainage of meltwater at the base of glaciers sensitively affects fast ice flow. Previous studies suggest that thin meltwater films between the overlying ice and a hard-rock bed channelize into efficient drainage elements by melting the overlying ice. However, these studies do not account for the presence of soft deformable sediment observed underneath many West Antarctic ice streams, and the inextricable coupling that sediment exhibits with meltwater drainage. Our work presents an alternate mechanism for initiating drainage elements such as canals where meltwater films grow by eroding the sediment beneath. We conduct a linearized stability analysis on a meltwater film flowing over an erodible bed. We solve the Orr–Sommerfeld equation for the film flow, and we compute bed evolution with the Exner equation. We identify a regime where the coupled dynamics of hydrology and sediment transport drives a morphological instability that generates spatial heterogeneity at the bed. We show that this film instability operates at much faster time scales than the classical thermal instability proposed by Walder. We discuss the physics of the instability using the framework of ripple formation on erodible beds.
Identiﬁcation and Expression Analysis of EPSPS and BAR Families in Cotton

: Weeds seriously affect the yield and quality of crops. Because manual weeding is time-consuming and laborious, the use of herbicides becomes an effective way to solve the harm caused by weeds in ﬁelds. Both 5-enolpyruvyl shikimate-3-phosphate synthetase ( EPSPS ) and acetyltransferase genes (bialaphos resistance, BAR ) are widely used to improve crop resistance to herbicides. However, cotton, as the most important natural ﬁber crop, is not tolerant to herbicides in China, and the EPSPS and BAR family genes have not yet been characterized in cotton. Therefore, we explore the genes of these two families to provide candidate genes for the study of herbicide resistance mechanisms. In this study, 8, 8, 4, and 5 EPSPS genes and 6, 6, 5, and 5 BAR genes were identiﬁed in allotetraploid Gossypium hirsutum and Gossypium barbadense , diploid Gossypium arboreum and Gossypium raimondii , respectively. Members of the EPSPS and BAR families were classiﬁed into three subgroups based on the distribution of phylogenetic trees, conserved motifs, and gene structures. In addition, the promoter sequences of EPSPS and BAR family members included growth and development, stress, and hormone-related cis -elements. Based on the expression analysis, the family members showed tissue-speciﬁc expression and differed signiﬁcantly in response to abiotic stresses. Finally, qRT-PCR analysis revealed that the expression levels of GhEPSPS3 , GhEPSPS4, and GhBAR1 were signiﬁcantly upregulated after exogenous spraying of herbicides. Overall, we characterized the EPSPS and BAR gene families of cotton at the genome-wide level, which will provide a basis for further studying the functions of EPSPS and BAR genes during growth and development and herbicide stress
Identiﬁcation and Characterization of a Novel Microalgal Strain from the Antofagasta Coast Tetraselmis marina AC16-MESO (Chlorophyta) for Biotechnological Applications

: The wide rocky coastline of the Antofagasta hosts an intertidal ecosystem in which the species that inhabit it are routinely exposed to a wide range of physical and chemical conditions and have therefore evolved to tolerate extremes. In the search for new species of potential biotechnological interest with adaptations to a wide range of environmental conditions, the isolation and characterization of microalgae from these ecosystems is of great interest. Here, a new microalgal strain, Tetraselmis marina AC16-MESO, is described, which was isolated from a bioﬁlm collected on the intertidal rocks of the Antofagasta coast (23 ◦ 36 (cid:48) 57.2 (cid:48)(cid:48) S, 70 ◦ 23 (cid:48) 33.8 (cid:48)(cid:48) W). In addition to the morphological characterization, 18S and ITS sequence as well as ITS-2 secondary structure analysis revealed an identity of 99.76% and 100% with the species Tetraselmis marina , respectively. The analyses of the culture characteristics and biochemical content showed similarities with other strains that are frequently used in aquaculture, such as the species Tetraselmis suecica . In addition, it is tolerant of a wide range of salinities, thus allowing its culture in water of varying quality. On the other hand, added to these characteristics, the results of the improvement of the lipid content in stressful situations of salinity observed in this study, together with other antecedents such as the potential in bioremediation already published for this strain by the same research group, present a clear example of its biotechnological plasticity. It is noteworthy that this strain, due to its characteristics, allows easy collection of its biomass by decantation and, therefore, a more cost-efﬁcient harvesting than for other microalgal strains. Therefore, this new strain of Tetraselmis marina , ﬁrst report of this species in Chile, and its morphologically, molecularly and biochemically description, presents promising characteristics for its use in biotechnology and as feed for aquaculture.
Genome-Wide Identiﬁcation and Characterization of WRKY Transcription Factors in Betula platyphylla Suk. and Their Responses to Abiotic Stresses

: The WRKY transcription factor (TF) family is one the largest plant-speciﬁc transcription factor families. It has been proven to play signiﬁcant roles in multiple plant biological processes, especially stress response. Although many WRKY TFs have been identiﬁed in various plant species, WRKYs in white birch ( Betula platyphylla Suk.) remain to be studied. Here, we identiﬁed a total of 68 BpWRKYs, which could be classiﬁed into four main groups. The basic physiochemical properties of these TFs were analyzed using bioinformatics tools, including molecular weight, isoelectric point, chromosome location, and predicted subcellular localization. Most BpWRKYs were predicted to be located in the nucleus. Synteny analysis found 17 syntenic gene pairs among BpWRKY s and 52 syntenic gene pairs between BpWRKY s and AtWRKY s. The cis -acting elements in the promoters of BpWRKY s could be enriched in multiple plant biological processes, including stress response, hormone response, growth and development, and binding sites. Tissue-speciﬁc expression analysis using qRT-PCR showed that most BpWRKY s exhibited highest expression levels in the root. After ABA, salt (NaCl), or cold treatment, different BpWRKY s showed different expression patterns at different treatment times. Furthermore, the results of the Y2H assay proved the interaction between BpWRKY17 and a cold-responsive TF, BpCBF7. By transient expression assay, BpWRKY17 and BpWRKY67 were localized in the nucleus, consistent with the previous prediction. Our study hopes to shed light for research on WRKY TFs and plant stress response.
Effects of pocket money on weight status among junior high school students: A longitudinal study in China

Overweight and obesity among adolescents has become a common public health problem, and both obesity rates and the amount of pocket money among adolescents in China are rising. We investigated to what extent the increase in pocket money could lead to weight gain of junior high school students and how this association may vary by school environment in China. Researchers utilized 3 waves of data from the China Education Panel Survey, a national longitudinal study, to investigate the likelihood of overweight and obesity. The Generalized Estimation Equation was employed to analyze the data. Three Generalized Estimation Equation models were constructed to explore the relationship between pocket money and overweight and obesity in 2 distinct food environments surrounding schools. A total of 8903 individuals (4604 boys and 4299 girls) from the China Education Panel Survey were analyzed. After adjusting for confounding factors, it was found that girls who received 20 to 49 yuan and ≥ 50 yuan per week had a higher risk of overweight and obesity compared to those who received 0 to 9 yuan per week (OR = 1.34, 95% CI: 1.07–1.69, OR = 1.53, 95% CI: 1.22–1.92). However, no significant association was observed between pocket money and overweight and obesity when food around the school was not easily accessible. The prevalence of overweight among Chinese teenagers has steadily increased from Wave1 to Wave3. Moreover, junior high school girls who receive more pocket money are at a greater risk of developing obesity and overweight issues.
Postsecondary biology students’ ways of participating in the critique and discussion of primary scientific literature

Science advances through the interplay of idea construction and idea critique. Our goal was to describe varied forms of productive disciplinary engagement that emerged during primary literature discussions. Such descriptions are necessary for biology educators and researchers to design for and recognize diverse repertoires of participation in the critique and discussion of primary scientific literature. We identified three cases (a lower-division ecology course, an upper-division organismal course, and a journal club embedded in a summer research program) that were each designed with weekly primary literature discussions. We analyzed 12 discussions (four from each case) to describe what postsecondary students attend to when they critique and what forms of participation emerged from students reading and discussing primary scientific literature. Students participated in critique in all three cases and patterns in the substance and framing of critiques reflected the level of the context (lower- or upper-division). Students also shaped how they participated in ways that were relevant to the science classroom communities in each case. Our findings suggest that structuring primary literature discussions in ways that both elevate and connect students’ agency and personal relevance is important for fostering varied forms of productive disciplinary engagement within a science classroom community.
Effects of duration of follow-up and lag in data collection on the performance of adaptive clinical trials.

Different combined outcome-data lags (follow-up durations plus data-collection lags) may affect the performance of adaptive clinical trial designs. We assessed the influence of different outcome-data lags (0-105 days) on the performance of various multi-stage, adaptive trial designs (2/4 arms, with/without a common control, fixed/response-adaptive randomisation) with undesirable binary outcomes according to different inclusion rates (3.33/6.67/10 patients/day) under scenarios with no, small, and large differences. Simulations were conducted under a Bayesian framework, with constant stopping thresholds for superiority/inferiority calibrated to keep type-1 error rates at approximately 5%. We assessed multiple performance metrics, including mean sample sizes, event counts/probabilities, probabilities of conclusiveness, root mean squared errors (RMSEs) of the estimated effect in the selected arms, and RMSEs between the analyses at the time of stopping and the final analyses including data from all randomised patients. Performance metrics generally deteriorated when the proportions of randomised patients with available data were smaller due to longer outcome-data lags or faster inclusion, that is, mean sample sizes, event counts/probabilities, and RMSEs were larger, while the probabilities of conclusiveness were lower. Performance metric impairments with outcome-data lags ≤45 days were relatively smaller compared to those occurring with ≥60 days of lag. For most metrics, the effects of different outcome-data lags and lower proportions of randomised patients with available data were larger than those of different design choices, for example, the use of fixed versus response-adaptive randomisation. Increased outcome-data lag substantially affected the performance of adaptive trial designs. Trialists should consider the effects of outcome-data lags when planning adaptive trials.
Optimisation of a Method for the Differentiation of Human Umbilical Cord-derived Mesenchymal Stem Cells Toward Renal Epithelial-like Cells

Human umbilical cord-derived mesenchymal stem cells (hucMSCs) can differentiate into multiple cell lineages, but few methods have been developed to generate kidney lineage cells. Due to their human origin, pluripotent nature and immunomodulatory properties, these stem cells are attractive candidates for clinical applications such as the repair or regeneration of damaged organs. This study evaluated the renal differentiation potential of hucMSCs, when exposed for 10 days to optimised concentrations of retinoic acid, activin-A and bone morphogenetic protein-7 (BMP-7) in various combinations, with and without the priming of the cells with a Wnt signalling pathway activator (CHIR99021). The hucMSCs were isolated and characterised according to surface marker expression (CD73, CD90, CD44, CD146 and CD8) and tri-lineage differentiation potential. The expression of key marker genes (OSR1, TBXT, HOXA13, SIX2, PAX2, KRT18 and ZO1) was examined by qRT-PCR. Specific marker protein expression (E-cadherin, cytokeratin-8 and cytokeratin-19) was analysed by immunocytochemistry. CHIR99021-primed cells treated with the retinoic acid, activin-A and BMP-7 cocktail showed epithelial cell-like differentiation — i.e. distinct phenotypic changes, as well as upregulated gene and protein expression, were observed that were consistent with an epithelial cell phenotype. Thus, our results showed that hucMSCs can efficiently differentiate into renal epithelial-like cells. This work may help in the development of focused therapeutic strategies, in which lineage-defined human stem cells can be used for renal regeneration.
Development of an Aerogel-Based Wet Electrode for Functional Electrical Stimulation

Functional electrical stimulation (FES) has been a useful therapeutic tool in rehabilitation, particularly for people with paralysis. To deliver stimulation in its most basic setup, a stimulator and at least a pair of electrodes are needed. The electrodes are an essential part of the system since they allow the transduction of the stimulator signals into the body. Their performance can influence the experience of both patient and therapist in terms of movement generation, comfort, and ease of use. For non-invasive surface stimulation, current electrode options have several limitations involving their interfacing with the skin, practical inconveniences, and short-term functionality. Standard hydrogel electrodes tend to lose their adhesion with the skin quickly, while dry or textile electrodes require constant wetting to be comfortable. In this paper, we present the fabrication, characterization, and FES testing of a new aerogel-based wet electrode for surface stimulation applications for long-term and reusable FES applications. We investigated its functionality by stimulating the biceps brachii of twelve healthy individuals and collected elbow joint torque and comfort ratings for three different intensity levels (low, moderate, and high) of FES. Comparing to standard hydrogel electrodes, no statistically significant difference was found for any intensity of stimulation in either torque or comfort. Overall, the new aerogel-based electrode has an appropriate impedance, is flexible and soft, is conformable to the skin, has a high water absorption and retention, and can be used for FES purposes.
Application of parallax for the measurement of visibility distances in the open-road environment

This paper describes a parallax technique, which was developed to assist research into the assessment of visibility and legibility of traffic signs while drivers are in the open road environment. Older drivers have a high traffic accident rate and difficulties with sign recognition have been cited as a problem. However, those studies which have investigated the sign visibility problems of older drivers have been conducted under laboratory conditions, which do not adequately reflect the dynamic complexity of the normal driving environment. Yet these are the conditions with which the elderly report the most difficulty. The technique utilised two commercially available JVC GR-DVl digital video cameras affixed to the research vehicle. Under dynamic conditions, subjects indicated when they first recognised a given sign by activating an image identification system. This system identifies pairs of stereoscopic images which are later downloaded, and parallax values of road furniture measured. The visibility distances of signs from the moving vehicle were then determined. The method was tested in the open road over a series of predetermined reference distances and a high level of agreement was obtained between distances measured by this technique and the reference distances. The method has been used successfully for the assessment of visibility distances and this paper presents data from subjects tested under daytime and nighttime conditions. The results demonstrate that this technique based on photogrammetric principles can accurately, reliably and economically measure visibility distances of road furniture under varying driving conditions for a range of drivers.
RvE1 Promotes Axin2+ Cell Regeneration and Reduces Bacterial Invasion

Vital pulp therapy and root canal therapy (RCT) are the dominant treatment for irreversible pulpitis. While the success rate of these procedures is favorable, they have some limitations. For instance, RCT leads to removing significant dentin in the coronal third of the tooth that increases root-fracture risk, which forces tooth removal. The ideal therapeutic goal is dental pulp regeneration, which is not achievable with RCT. Specialized proresolving mediators (SPMs) are well known for inflammatory resolution. The resolution of inflammation and tissue restoration or regeneration is a dynamic and continuous process. SPMs not only have potent immune-modulating functions but also effectively promote tissue homeostasis and regeneration. Resolvins have been shown to promote dental pulp regeneration. The purpose of this study was to explore further the cellular target of Resolvin E1 (RvE1) therapy in dental pulp regeneration and the impact of RvE1 in infected pulps. We investigated the actions of RvE1 on experimentally exposed pulps with or without microbial infection in an Axin2 Cre-Dox ;Ai14 genetically defined mouse model. Our results showed RvE1 promoted Axin2-tdTomato+ cell expansion and odontoblastic differentiation after direct pulp capping in the mouse, which we used to mimic reversible pulpitis cases in the clinic. In cultured mouse dental pulp stem cells (mDPSCs), RvE1 facilitated Axin2-tdTomato+ cell proliferation and odontoblastic differentiation and also rescued impaired functions after lipopolysaccharide stimulation. In infected pulps exposed to the oral environment for 24 h, RvE1 suppressed inflammatory infiltration, reduced bacterial invasion in root canals, and prevented the development of apical periodontitis, while its proregenerative impact was limited. Collectively, topical treatment with RvE1 facilitated dental pulp regenerative properties by promoting Axin2-expressing cell proliferation and differentiation. It also modulated the resolution of inflammation, reduced infection severity, and prevented apical periodontitis, presenting RvE1 as a novel therapeutic for treating endodontic diseases.
How to check a simulation study

Abstract Simulation studies are powerful tools in epidemiology and biostatistics, but they can be hard to conduct successfully. Sometimes unexpected results are obtained. We offer advice on how to check a simulation study when this occurs, and how to design and conduct the study to give results that are easier to check. Simulation studies should be designed to include some settings in which answers are already known. They should be coded in stages, with data-generating mechanisms checked before simulated data are analysed. Results should be explored carefully, with scatterplots of standard error estimates against point estimates surprisingly powerful tools. Failed estimation and outlying estimates should be identified and dealt with by changing data-generating mechanisms or coding realistic hybrid analysis procedures. Finally, we give a series of ideas that have been useful to us in the past for checking unexpected results. Following our advice may help to prevent errors and to improve the quality of published simulation studies.