Miracle-dz/UniFAR-FTUs huggingface dataset:
Interspecific variation in the size‐dependent resprouting ability of temperate woody species and its adaptive significance

Resprouting of woody species after above‐ground damage may help plants to persist longer at a given site and quickly reoccupy disturbed sites, thereby strongly influencing forest dynamics. Resprouting has been discussed from two adaptation perspectives: recovery from damage by catastrophic disturbance and survival in frequently disturbed shaded understorey. However, few studies have comprehensively dealt with both adaptation types to understand resprouting strategies. To understand the adaptive significance of resprouting, we assessed the size dependence of resprouting ability after stem clipping for 24 deciduous broad‐leaved species, including shrubs, sub‐canopy and canopy trees, in a cool‐temperate forest in Japan. The community assembly includes species adapted to past catastrophic disturbances (e.g. fire, logging) and to stable forest with intermittent treefall (currently the dominant disturbance). We correlated resprouting ability with life‐history strategies based on demographic parameters and plant functional traits, such as leaf mass per area (LMA), leaf toughness and wood density. All the studied species could resprout in juveniles, and resprouting ability increased as stump size increased. Most sub‐canopy and canopy trees lost their ability to resprout after attaining a particular stump size, whereas shrub species retained the ability to resprout throughout their lifetimes. The relative growth rate, LMA and foliar nitrogen did not greatly influence the resprouting ability of a species. In contrast, species with smaller maximum size, lower leaf toughness and lower wood density had better juvenile resprouting ability. This better resprouting ability may have evolved because these characteristics make them more vulnerable to shaded understorey. However, species with larger maximum size and lower leaf toughness retained their ability to resprout to a larger size. Synthesis. A better resprouting ability is related to the ability to survive frequent disturbances, in juveniles, which are characteristics of both forest understorey and frequent fire or drought. To retain resprouting ability until grown seems to be an adaptation to survive infrequent large disturbances. Light‐demanding species, which generally have better resprouting ability than shade‐tolerants both in juveniles and adults, are adapted to disturbances of various scale and frequency; however, shade‐tolerants could survive well in the understorey due to a combination of stronger physical defences and resprouting ability.
Development of Willow Tree Yield-Mapping Technology

With today’s environmental challenges, developing sustainable energy sources is crucial. From this perspective, woody biomass has been, and continues to be, a significant research interest. The goal of this research was to develop new technology for mapping willow tree yield grown in a short-rotation forestry (SRF) system. The system gathered the physical characteristics of willow trees on-the-go, while the trees were being harvested. Features assessed include the number of trees harvested and their diameter. To complete this task, a machine-vision system featuring an RGB-D stereovision camera was built. The system tagged these data with the corresponding geographical coordinates using a Global Navigation Satellite System (GNSS) receiver. The proposed yield-mapping system showed promising detection results considering the complex background and variable light conditions encountered in the outdoors. Of the 40 randomly selected and manually observed trees in a row, 36 were successfully detected, yielding a 90% detection rate. The correctly detected tree rate of all trees within the scenes was actually 71.8% since the system tended to be sensitive to branches, thus, falsely detecting them as trees. Manual validation of the diameter estimation function showed a poor coefficient of determination and a root mean square error (RMSE) of 10.7 mm.
Capturing Patient‐Reported Outcomes During the COVID‐19 Pandemic: Development of the COVID‐19 Global Rheumatology Alliance Patient Experience Survey

The coronavirus disease 2019 (COVID-19) Global Rheumatology Alliance (C19-GRA) was formed in March 2020 as a grassroots organization to coordinate the response of the international rheumatology community to the pandemic [1]. The C19-GRA launched an international, secure, de-identified physician registry of patients with rheumatic diseases infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to provide insights into the management and treatment of COVID-19 in this population.
Specificity in the biosynthesis of the universal tRNA nucleoside N6-threonylcarbamoyl adenosine (t6A)—TsaD is the gatekeeper

N6-threonylcarbamoyl adenosine (t6A) is a nucleoside modification found in all kingdoms of life at position 37 of tRNAs decoding ANN codons, which functions in part to restrict translation initiation to AUG and suppress frameshifting at tandem ANN codons. In Bacteria the proteins TsaB, TsaC (or C2), TsaD, and TsaE, comprise the biosynthetic apparatus responsible for t6A formation. TsaC(C2) and TsaD harbor the relevant active sites, with TsaC(C2) catalyzing the formation of the intermediate threonylcarbamoyladenosine monophosphate (TC-AMP) from ATP, threonine, and CO2, and TsaD catalyzing the transfer of the threonylcarbamoyl moiety from TC-AMP to A37 of substrate tRNAs. Several related modified nucleosides, including hydroxynorvalylcarbamoyl adenosine (hn6A), have been identified in select organisms, but nothing is known about their biosynthesis. To better understand the mechanism and structural constraints on t6A formation, and to determine if related modified nucleosides are formed via parallel biosynthetic pathways or the t6A pathway, we carried out biochemical and biophysical investigations of the t6A systems from E. coli and T. maritima to address these questions. Using kinetic assays of TsaC(C2), tRNA modification assays, and NMR, our data demonstrate that TsaC(C2) exhibit relaxed substrate specificity, producing a variety of TC-AMP analogs that can differ in both the identity of the amino acid and nucleotide component, whereas TsaD displays more stringent specificity, but efficiently produces hn6A in E. coli and T. maritima tRNA. Thus, in organisms that contain modifications such as hn6A in their tRNA, we conclude that their origin is due to formation via the t6A pathway.
Collagen microarchitecture mechanically controls myofibroblast differentiation

Significance Pathologic fibrosis is associated with altered collagen microarchitecture, but the functional impact of these changes on myofibroblast differentiation remains poorly understood. We experimentally and computationally analyzed the effect of collagen microstructure on matrix mechanics and determined its functional consequences on adipose-derived stem cells (ASCs), a cell type contributing to obesity- and cancer-associated fibrosis. Our findings highlight that collagen networks with thicker fibers and larger pores exhibit higher shear moduli than their similarly concentrated counterparts with thinner fibers and smaller pores. These differences promoted ASC mechanosignaling and consequential differentiation into α-smooth muscle actin-positive, contractile, and proangiogenic myofibroblasts. Insights from this work will advance the design of biomaterials for tissue engineering applications as well as antifibrotic therapies. Altered microarchitecture of collagen type I is a hallmark of wound healing and cancer that is commonly attributed to myofibroblasts. However, it remains unknown which effect collagen microarchitecture has on myofibroblast differentiation. Here, we combined experimental and computational approaches to investigate the hypothesis that the microarchitecture of fibrillar collagen networks mechanically regulates myofibroblast differentiation of adipose stromal cells (ASCs) independent of bulk stiffness. Collagen gels with controlled fiber thickness and pore size were microfabricated by adjusting the gelation temperature while keeping their concentration constant. Rheological characterization and simulation data indicated that networks with thicker fibers and larger pores exhibited increased strain-stiffening relative to networks with thinner fibers and smaller pores. Accordingly, ASCs cultured in scaffolds with thicker fibers were more contractile, expressed myofibroblast markers, and deposited more extended fibronectin fibers. Consistent with elevated myofibroblast differentiation, ASCs in scaffolds with thicker fibers exhibited a more proangiogenic phenotype that promoted endothelial sprouting in a contractility-dependent manner. Our findings suggest that changes of collagen microarchitecture regulate myofibroblast differentiation and fibrosis independent of collagen quantity and bulk stiffness by locally modulating cellular mechanosignaling. These findings have implications for regenerative medicine and anticancer treatments.
Designing 3D-MoS2 Sponge as Excellent Cocatalysts in Advanced Oxidation Processes for Pollutant Control.

3D-MoS2 can adsorb organic molecules and provide multidimensional electron transport pathways, implying a signiﬁcant potential application for environment remediation. Here, we study the degradation of aromatic organics in AOPs by a 3D-MoS2 sponge loaded with MoS2 nanospheres and graphene oxide (GO). Exposed Mo4+ active sites on 3D-MoS2 can significantly improve the concentration and stability of Fe2+ in AOPs, and keep the Fe3+/Fe2+ in a stable dynamic cycle, thus effectively promoting the activation of H2O2/PMS. The degradation rate of organic pollutants in the 3D-MoS2 system is ~50 times higher than that in the case without cocatalyst. Even after 140 L pilot-scale experiment, it still maintains high efficiency and stable AOPs activity. After 16 days of continuous reaction, the 3D-MoS2 can achieve the degradation rate of 120 mg/L antibiotic wastewater up to 97.87%. The operating cost of treating a ton of wastewater is only 0.33 $, suggesting it has huge industrial applications.
Dietary Approaches to Stop Hypertension, Mediterranean, and Alternative Healthy Eating indices are associated with bone health among Puerto Rican adults from the Boston Puerto Rican Osteoporosis Study.

BACKGROUND Conflicting results on associations between dietary quality and bone have been noted across populations, and this has been understudied in Puerto Ricans, a population at higher risk of osteoporosis than previously appreciated. OBJECTIVE To compare cross-sectional associations between 3 dietary quality indices [Dietary Approaches to Stop Hypertension (DASH), Alternative Health Eating Index (AHEI-2010), and Mediterranean Diet Score (MeDS)] with bone outcomes. METHOD Participants (n = 865-896) from the Boston Puerto Rican Osteoporosis Study (BPROS) with complete bone and dietary data were included. Indices were calculated from validated food frequency data. Bone mineral density (BMD) was measured using DXA. Associations between dietary indices (z-scores) and their individual components with BMD and osteoporosis were tested with ANCOVA and logistic regression, respectively, at the lumbar spine and femoral neck, stratified by male, premenopausal women, and postmenopausal women. RESULTS Participants were 59.9 y ± 7.6 y and mostly female (71%). Among postmenopausal women not taking estrogen, DASH (score: 11-38) was associated with higher trochanter (0.026 ± 0.006 g/cm2, P <0.001), femoral neck (0.022 ± 0.006 g/cm2, P <0.001), total hip (0.029 ± 0.006 g/cm2, P <0.001), and lumbar spine BMD (0.025 ± 0.007 g/cm2, P = 0.001). AHEI (score: 25-86) was also associated with spine and all hip sites (P <0.02), whereas MeDS (0-9) was associated only with total hip (P = 0.01) and trochanter BMD (P = 0.007) in postmenopausal women. All indices were associated with a lower likelihood of osteoporosis (OR from 0.54 to 0.75). None of the results were significant for men or premenopausal women. CONCLUSIONS Although all appeared protective, DASH was more positively associated with BMD than AHEI or MeDS in postmenopausal women not taking estrogen. Methodological differences across scores suggest that a bone-specific index that builds on existing indices and that can be used to address dietary differences across cultural and ethnic minority populations should be considered.
Electrospun Nano-Fibers for Biomedical and Tissue Engineering Applications: A Comprehensive Review

Pharmaceutical nano-fibers have attracted widespread attention from researchers for reasons such as adaptability of the electro-spinning process and ease of production. As a flexible method for fabricating nano-fibers, electro-spinning is extensively used. An electro-spinning unit is composed of a pump or syringe, a high voltage current supplier, a metal plate collector and a spinneret. Optimization of the attained nano-fibers is undertaken through manipulation of the variables of the process and formulation, including concentration, viscosity, molecular mass, and physical phenomenon, as well as the environmental parameters including temperature and humidity. The nano-fibers achieved by electro-spinning can be utilized for drug loading. The mixing of two or more medicines can be performed via electro-spinning. Facilitation or inhibition of the burst release of a drug can be achieved by the use of the electro-spinning approach. This potential is anticipated to facilitate progression in applications of drug release modification and tissue engineering (TE). The present review aims to focus on electro-spinning, optimization parameters, pharmacological applications, biological characteristics, and in vivo analyses of the electro-spun nano-fibers. Furthermore, current developments and upcoming investigation directions are outlined for the advancement of electro-spun nano-fibers for TE. Moreover, the possible applications, complications and future developments of these nano-fibers are summarized in detail.
Comparing Phylogenetic Approaches to Reconstructing Cell Lineage From Microsatellites With Missing Data

Due to the imperfect fidelity of DNA replication, somatic cells acquire DNA mutations at each division which record their lineage history. Microsatellites, tandem repeats of DNA nucleotide motifs, mutate more frequently than other genomic regions and by observing microsatellite lengths in single cells and implementing suitable inference procedures, the cell lineage tree of an organism can be reconstructed. Due to recent advances in single cell Next Generation Sequencing (NGS) and the phylogenetic methods used to infer lineage trees, this work investigates which computational approaches best exploit the lineage information found in single cell NGS data. We simulated trees representing cell division with mutating microsatellites, and tested a range of available phylogenetic algorithms to reconstruct cell lineage. We found that distance-based approaches are fast and accurate with fully observed data. However, Maximum Parsimony and the computationally intensive probabilistic methods are more robust to missing data and therefore better suited to reconstructing cell lineage from NGS datasets. We also investigated how robust reconstruction algorithms are to different tree topologies and mutation generation models. Our results show that the flexibility of Maximum Parsimony and the probabilistic approaches mean they can be adapted to allow good reconstruction across a range of biologically relevant scenarios.
Parasitism and host reproductive effort

Adaptive changes in reproductive effort (RE) of parasitized hosts may account for both inverse and positive relationships between host reproductive output and incidence or degree of parasitism. This hypothesis can be made more general (adaptive changes in patterns of allocation to reproductive functions), but has been largely ignored in the fields of behavioral and evolutionary ecology. In fact, definitive examples of such adaptive responses are lacking. Yet theory on life-history trade-offs predicts that hosts may minimize the impact of parasites by altering their own RE. Such alterations may occur with or without induction of defenses against parasites
Spatial and Temporal Patterns of Rust Infection on Jewelweed (Impatiens capensis)

Disease epidemiology has rarely been examined in natural plant‐pathogen systems exhibiting obligate alteration of host species. We quantified rust infection in populations of jewelweed; its effect on host mating system, potential biotic and abiotic correlates of infection; and spatial patterns within populations. Jewelweed (Impatiens capensis) is a woodland annual that can become infected with the heteroecious rust, Puccinia recondita, whose alternate hosts are often grasses. It produces dimorphic self‐pollinated cleistogamous (CL) flowers and open‐pollinated chasmogamous (CH) flowers. Infected plants may have fewer resources, so we predicted a decrease in CH flowering relative to that of uninfected plants. Infection occurred early in the growing season and disappeared by midsummer, although plants continued to grow and flower until the frost. We found no clustering of infection within populations. Infection prevalence did not vary among sites in 2005, but one site had more disease in 2004 than in 2005. Rust infection showed negative host density dependence, which is unusual for most pathogens but not unexpected for heterocyclic rusts. Infection decreased host fitness but increased proportional allocation to CH flowering, potentially increasing the production of resistant offspring by susceptible plants. These results indicate that disease varies over time and with host density and can affect host fitness and mating system.
Analysis of genes associated with prognosis of lung adenocarcinoma based on GEO and TCGA databases

Abstract Backgrounds: Lung adenocarcinoma (LUAD) is one of the most common malignancies, and is a serious threat to human health. The aim of the present study was to assess potential biomarkers for the prognosis of LUAD through the analysis of gene expression microarrays. Methods: The gene expression data for GSE118370 was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between normal lung and LUAD samples were screened using the R language. The DAVID database was used to analyze the functions and pathways of DEGs. The STRING database was used to the map protein–protein interaction (PPI) networks, and these were visualized with the Cytoscape software. Finally, the prognostic analysis of the hub gene in the PPI network was performed using the Kaplan–Meier tool. Results: A total of 406 downregulated and 203 upregulated DEGs were identified. The GO analysis results revealed that downregulated DEGs were significantly enriched in angiogenesis, calcium ion binding and cell adhesion. The upregulated DEGs were significantly enriched in the extracellular matrix disassembly, collagen catabolic process, chemokine-mediated signaling pathway and endopeptidase inhibitor activity. The KEGG pathway analysis revealed that downregulated DEGs were enriched in neuroactive ligand-receptor interaction, hematopoietic cell lineage and vascular smooth muscle contraction, while upregulated DEGs were enriched in phototransduction. In addition, the top 10 hub genes and the most closely interacting modules of the top 3 proteins in the PPI network were screened. Finally, the independent prognostic value of each hub gene in LUAD patients was analyzed through the Kaplan–Meier plotter. Seven hub genes (ADCY4, S1PR1, FPR2, PPBP, NMU, PF4, and GCG) were closely correlated to overall survival time. Conclusion: The discovery of these candidate genes and pathways reveals the etiology and molecular mechanisms of LUAD, providing ideas and guidance for the development of new therapeutic approaches to LUAD.
Electrical Resistivity Measurement with Spherical-Tipped Cylindrical Electrode Embedded on Two Layers

Complex geological processes form multiple layers and change pore water chemistry, saturation level, and temperature. Eventually, the strata hinder interpreting electrical resistivity data. There are no studies that theoretically explore the effects of electrode geometries and multiple layered systems on laboratory electrical resistivity measurements. This study formulates a theoretical electrical resistance between half spherical-tipped cylindrical electrodes embedded on two horizontal layers. The electrical resistivity of each layer is considered separately in the general electrical potential equation with different equipotential surface areas. The finite element analysis is conducted to validate the theoretical equation. Further interpretation provides insights into the distribution of electrical current flow under electrical resistivity mismatch for discussion.
Simultaneous characterisation of multiple Psoraleae Fructus bioactive compounds in rat plasma by ultra-high-performance liquid chromatography coupled with triple quadrupole mass Spectrometry for application in sex-related differences in pharmacokinetics.

A method for the simultaneous quantification of thirteen bioactive compounds (psoralen, isopsoralen, isobavachin, bakuchalcone, neobabaisoflavone, bavachin, corylin, psoralidin, isobavachalcone, bavachinin, corylifol A, bavachalcone and bakuchiol) by ultra-high-performance liquid chromatography coupled with triple quadrupole mass Spectrometry has been developed and validated in rat plasma. Osthol was used as an internal standard and plasma samples were pretreated with one-step liquid-liquid extraction. These analytes were separated using a gradient mobile phase system of water and acetonitrile at a flow rate of 0.2 mL/min on a reverse-phase C18 column and analyzed in the selected multiple reactions monitoring mode. All calibration curves were linear (r>0.9952) over the tested ranges. The intra- and inter-day accuracy and precisions of these analytes at three different concentration levels were within the acceptable limits of <15% at all concentrations. The mean recoveries of these analytes at three concentrations were more than 60.2% and the matrix effects were in the range of 85%-115%. Stability studies proved that the analytes were stable under the tested conditions. The developed method was applied to evaluating the pharmacokinetic study of thirteen bioactive compounds after oral administration of Psoraleae Fructus in rat of different genders. Some active compounds in Psoraleae Fructus had sex-related pharmacokinetics. This article is protected by copyright. All rights reserved.
Twenty-eight years of experience measuring autonomy using the Dempster Practice Behavior Scale.

BACKGROUND Autonomy in practice is an important attribute of all professions and a cornerstone of advanced nursing practice. The Dempster Practice Behavior Scale was conceptualized, constructed, and psychometrically tested to make available a generalizable, empirically sound, and useful tool capable of measuring previously unrecognized dimensions of autonomy in practice. Nurse practitioner (NP) practice continues to evolve as new models of care emerge, requiring more autonomy in the NP role. PURPOSE The purpose was to describe the development and psychometric testing of the Dempster Practice Behavior Scale (DPBS), review the extant research on its use in research on nursing and other professions, and determine where future research is needed on the concept of autonomy in professional practice with a focus on advanced practice registered nurses (APRNs). METHODS Research articles, theses, dissertations using the DPBS as an instrument to measure practice autonomy were reviewed. RESULTS Twenty-one unique publications were examined for reports of psychometric properties in various populations. For the APRN population (total N = 1,669 in 10 studies), psychometrics for the DPBS support the reliability of the instrument for research. The remaining 11 studies included 2,285 participants who were not APRNs. IMPLICATIONS FOR PRACTICE Questions remain about the relationships between autonomy and external factors such as regulatory environment, practice setting, models of care, years of experience, and practice mix.