Miracle-dz/UniFAR-FTUs huggingface dataset:
Building a bridge between adaptive capacity and adaptive potential to understand responses to environmental change

Adaptive capacity is a topic at the forefront of environmental change research with roots in both social, ecological, and evolutionary science. It is closely related to the evolutionary biology concept of adaptive potential. In this systematic literature review, we: (1) summarize the history of these topics and related fields; (2) assess relationship(s) between the concepts among disciplines and the use of the terms in climate change research, and evaluate methodologies, metrics, taxa biases, and the geographic scale of studies; and (3) provide a synthetic conceptual framework to clarify concepts. Bibliometric analyses revealed the terms have been used most frequently in conservation and evolutionary biology journals, respectively. There has been a greater growth in studies of adaptive potential than adaptive capacity since 2001, but a greater geographical extent of adaptive capacity studies. Few studies include both, and use is often superficial. Our synthesis considers adaptive potential as one process contributing to adaptive capacity of complex systems, notes “sociological” adaptive capacity definitions include actions aimed at desired outcome (i.e., policies) as a system driver whereas “biological” definitions exclude such drivers, and suggests models of adaptive capacity require integration of evolutionary and social–ecological system components.
Class II phosphatidylinositol 3-kinase isoforms in vesicular trafficking

Phosphatidylinositol 3-kinases (PI3Ks) are critical regulators of many cellular processes including cell survival, proliferation, migration, cytoskeletal reorganization, and intracellular vesicular trafficking. They are a family of lipid kinases that phosphorylate membrane phosphoinositide lipids at the 3′ position of their inositol rings, and in mammals they are divided into three classes. The role of the class III PI3K Vps34 is well-established, but recent evidence suggests the physiological significance of class II PI3K isoforms in vesicular trafficking. This review focuses on the recently discovered functions of the distinct PI3K-C2α and PI3K-C2β class II PI3K isoforms in clathrin-mediated endocytosis and consequent endosomal signaling, and discusses recently reported data on class II PI3K isoforms in different physiological contexts in comparison with class I and III isoforms.
Development and Prospective Validation of a Novel Risk Score for Predicting the Risk of Lower Extremity Deep Vein Thrombosis Among Trauma Patients

Background: Trauma patients have an increased risk of deep vein thrombosis (DVT). Early identification of patients with a high risk of DVT after trauma is crucial for thromboembolism prophylaxis. We aimed to develop and prospectively validate a novel risk score based on a nomogram to predict lower extremity DVT among trauma patients.Methods: Clinical data were collected from 281 trauma patients who were admitted to our trauma center within 24 h of admission from September 2016 to January 2019 to develop a novel DVT risk score. The DVT risk estimates were then calculated prospectively based on the score in a new study cohort from February 2019 to July 2020. The technique of least absolute shrinkage and selection operator (LASSO) was used to select variables for the early prediction of DVT in trauma patients. The DVT risk assessment score (DRAS) was constructed by incorporating related features based on the LASSO analysis and nomogram prediction model. Further, the trauma patients were divided into various risk groups according to the DRAS. The incidence of lower extremity DVT was compared between groups and the discrimination of the DRAS was assessed using the area under the curve (AUC). Results: Based on the LASSO method, eight variables (age, injury severity score, body mass index, D-dimer level, fibrin degradation products, prothrombin time, prealbumin level, and hemoglobin level) were included in the DRAS. A total of 166 trauma patients were enrolled in this prospective study. Increased risk of DVT after trauma was related to higher DRAS. The area under the receiver operating characteristic (ROC) curve for the DRAS was 0.890(0.840–0.939) in the validation cohort. Moreover, the discriminatory capacity of the DRAS was superior to that of each variable independently and the Modified Wells score (P<0.05). Conclusions: We developed and prospectively validated the DRAS to predict the risk of lower extremity DVT among trauma patients, which may facilitate early identification of high-risk patients.
The diffusion of electrolytes in a cation-exchange resin membrane I. Theoretical

An equation for the flux of electrolyte through a water-swollen cation-exchange resin membrane separating two solutions of the same electrolyte at different concentrations is derived on the basis of several assumptions regarding the physical nature of a swollen resinous exchanger. The complete flux equation contains three terms, one determined by the concentration difference across the membrane, another determined by the variation of the activity coefficient of the electrolyte with concentration in the membrane and a third concerned with the rate of osmotic or hydrostatic flow through the membrane. If ions in the resin are transported entirely in an internal aqueous phase, the mobilities required for the flux equation can be related to mobilities in aqueous solution and to the volume fraction of resin in the swollen membrane. The treatment is readily extended to anion exchangers.
In vitro study of Hesperetin and Hesperidin as inhibitors of zika and chikungunya virus proteases

The potential outcome of flavivirus and alphavirus co-infections is worrisome due to the development of severe diseases. Hundreds of millions of people worldwide live under the risk of infections caused by viruses like chikungunya virus (CHIKV, genus Alphavirus), dengue virus (DENV, genus Flavivirus), and zika virus (ZIKV, genus Flavivirus). So far, neither any drug exists against the infection by a single virus, nor against co-infection. The results described in our study demonstrate the inhibitory potential of two flavonoids derived from citrus plants: Hesperetin (HST) against NS2B/NS3pro of ZIKV and nsP2pro of CHIKV and, Hesperidin (HSD) against nsP2pro of CHIKV. The flavonoids are noncompetitive inhibitors and the determined IC50 values are in low µM range for HST against ZIKV NS2B/NS3pro (12.6 ± 1.3 µM) and against CHIKV nsP2pro (2.5 ± 0.4 µM). The IC50 for HSD against CHIKV nsP2pro was 7.1 ± 1.1 µM. The calculated ligand efficiencies for HST were > 0.3, which reflect its potential to be used as a lead compound. Docking and molecular dynamics simulations display the effect of HST and HSD on the protease 3D models of CHIKV and ZIKV. Conformational changes after ligand binding and their effect on the substrate-binding pocket of the proteases were investigated. Additionally, MTT assays demonstrated a very low cytotoxicity of both the molecules. Based on our results, we assume that HST comprise a chemical structure that serves as a starting point molecule to develop a potent inhibitor to combat CHIKV and ZIKV co-infections by inhibiting the virus proteases.
Combined protective effects of icariin and selenomethionine on novel chronic tubulointerstitial nephropathy models in vivo and in vitro

Abstract Chronic tubulointerstitial nephropathy (CTIN) is one of the most common kidney diseases. However, treatment for CTIN has multiple limits. Adjuvant therapy through nutritional regulation has become a hot research topic at present. Icariin (ICA), an extraction of Chinese herbal medicine epimedium, has many pharmacological functions including anti-inflammation and tonifying kidney. Selenomethionine (SeMet) possesses the effects of antioxidant and lightening nephrotoxicity. However, little is known about the combined nephroprotection of them. This study was investigated to evaluate the joint effects of ICA and SeMet on CTIN and explore the mechanism. Based on a novel CTIN model developed in our previous study, mice were randomly divided into five groups (a: control; b: model; c: model + ICA; d: model + SeMet; e: model + ICA + SeMet). Renal tubule epithelial cells were treated with cyclosporine A and ochratoxin A without/with ICA or/and SeMet. The results showed that ICA or/and SeMet ameliorated CTIN by inhibiting the uptrends of blood urine nitrogen, serum creatinine, urine protein, urine gravity, histopathological damage degree and collagen I deposition. ICA or/and SeMet also increased cell proliferation and decreased apoptosis and the expression of transforming growth factor-beta 1 and α-smooth muscle actin. Emphatically, ICA and SeMet joint had better nephroprotection than alone in most indexes including fibrosis. Furthermore, ICA and SeMet joint decreased the activation of toll-like receptor 4 (TLR4)/NFκB pathway induced by CTIN. TLR4 overexpression counteracted the joint protection of ICA and SeMet. Therefore, ICA and SeMet in combination could protect against CTIN through blocking TLR4/NFκB pathway. The study will provide novel insights to explore an adjuvant therapeutic orientation.
Glial insulin regulates cooperative or antagonistic Golden goal/Flamingo interactions during photoreceptor axon guidance

Transmembrane protein Golden goal (Gogo) interacts with atypical cadherin Flamingo (Fmi) to direct R8 photoreceptor axons in the Drosophila visual system. However, the precise mechanisms underlying Gogo regulation during columnar- and layer-specific R8 axon targeting are unknown. Our studies demonstrated that the insulin secreted from surface and cortex glia switches the phosphorylation status of Gogo, thereby regulating its two distinct functions. Non-phosphorylated Gogo mediates the initial recognition of the glial protrusion in the center of the medulla column, whereas phosphorylated Gogo suppresses radial filopodia extension by counteracting Flamingo to maintain a one axon-to-one column ratio. Later, Gogo expression ceases during the midpupal stage, thus allowing R8 filopodia to extend vertically into the M3 layer. These results demonstrate that the long- and short-range signaling between the glia and R8 axon growth cones regulates growth cone dynamics in a stepwise manner, and thus shapes the entire organization of the visual system.
Diagnostic accuracy of ultra-low-dose chest computed tomography in an emergency department

Background This study examined whether ultra-low-dose chest computed tomography (ULD-CT) could improve detection of acute chest conditions. Purpose To determine (i) whether diagnostic accuracy of ULD-CT is superior to supine chest X-ray (sCXR) for acute chest conditions and (ii) the feasibility of ULD-CT in an emergency department. Material and Methods From 1 February to 31 July 2019, 91 non-traumatic patients from the Emergency Department were prospectively enrolled in the study if they received an sCXR. An ULD-CT and a non-contrast chest CT (NCCT) scan were then performed. Three radiologists assessed the sCXR and ULD-CT examinations for cardiogenic pulmonary edema, pneumonia, pneumothorax, and pleural effusion. Resources and effort were compared for sCXR and ULD-CT to evaluate feasibility. Diagnostic accuracy was calculated for sCXR and ULD-CT using NCCT as the reference standard. Results The mean effective dose of ULD-CT was 0.05±0.01 mSv. For pleural effusion and cardiogenic pulmonary edema, no difference in diagnostic accuracy between ULD-CT and sCXR was observed. For pneumonia and pneumothorax, sensitivities were 100% (95% confidence interval [CI] 69–100) and 50% (95% CI 7–93) for ULD-CT and 60% (95% CI 26–88) and 0% (95% CI 0–0) for sCXR, respectively. Median examination time was 10 min for ULD-CT vs. 5 min for sCXR (P<0.001). For ULD-CT 1–2 more staff members were needed compared to sCXR (P<0.001). ULD-CT was rated more challenging to perform than sCXR (P<0.001). Conclusion ULD-CT seems equal or better in detecting acute chest conditions compared to sCXR. However, ULD-CT examinations demand more effort and resources.
Fabrication of hybrid scaffolds obtained from combinations of PCL with gelatin or collagen via electrospinning for skeletal muscle tissue engineering

Abstract The creation of skeletal muscle tissue in vitro is a major topic of interest today in the field of biomedical research, due to the lack of treatments for muscle loss due to traumatic accidents or disease. For this reason, the intrinsic properties of nanofibrillar structures to promote cell adhesion, proliferation, and cell alignment presents an attractive tool for regenerative medicine to recreate organized tissues such as muscle. Electrospinning is one of the processing techniques often used for the fabrication of these nanofibrous structures and the combination of synthetic and natural polymers is often required to achieve optimal mechanical and physiochemical properties. Here, polycaprolactone (PCL) is selected as a synthetic polymer used for the fabrication of scaffolds, and the effect of protein addition on the final scaffolds' properties is studied. Collagen and gelatin were the proteins selected and two different concentrations were analyzed (2 and 4 wt/vol%). Different PCL/protein systems were prepared, and a structural, mechanical and functional characterization was performed. The influence of fiber alignment on the properties of the final scaffolds was assessed through morphological, mechanical and biological evaluations. A bioreactor was used to promote cell proliferation and differentiation within the scaffolds. The results revealed that protein addition produced a decrease in the fiber size of the membranes, an increase in their hydrophilicity, and a softening of their mechanical properties. The biological study showed the ability of the selected systems to harbor cells, allow their growth and, potentially, develop musculoskeletal tissues.
Adsorption of estrone on nanofiltration and reverse osmosis membranes in water and wastewater treatment

Adsorption of the trace contaminant estrone, a natural hormone and commonly abundant in surface waters and in treated as well as untreated wastewaters, to eight commercial nanofiltration and reverse osmosis membranes was investigated under well defined conditions. Experiments were conducted in stainless steel stirred cells by spiking trace levels (100 ng.L-1) of estrone into five different matrices, namely MilliQ water, a bicarbonate solution, synthetic natural waters containing natural organics, and secondary effluent. Results show that estrone is adsorbed to the membranes to varying degrees with extent of adsorption influenced by the feedwater composition with different mechanisms of association controlling adsorption to different membrane types. Increase in membrane resistance is typically observed to result in decrease in extent of estrone adsorption. Keywords Adsorption; endocrine disrupter; estrone; hormone; nanofiltration; natural organic matter; reverse osmosis; wastewater treatment; water treatment
Differential responses to folic acid in an established keloid fibroblast cell line are mediated by JAK1/2 and STAT3

Keloids are a type of disordered scar formation which not only show heterogeneity between individuals and within the scar itself, but also share common features of hyperproliferation, abnormal extra-cellular matrix deposition and degradation, as well as altered expression of the molecular markers of wound healing. Numerous reports have established that cells from keloid scars display Warburg metabolism—a form of JAK2/STAT3-induced metabolic adaptation typical of rapidly dividing cells in which glycolysis becomes the predominant source of ATP over oxidative phosphorylation (OxPhos). Using the JAK1/2 inhibitor ruxolitinib, along with cells from patients with STAT3 loss of function (STA3 LOF; autosomal dominant hyper IgE syndrome) we examined the role of JAK/STAT signaling in the hyperproliferation and metabolic dysregulation seen in keloid fibroblasts. Although ruxolitinib inhibited hyperactivity in the scratch assay in keloid fibroblasts, it paradoxically exacerbated the hyper-glycolytic state, possibly by further limiting OxPhos via alterations in mitochondrial phosphorylated STAT3 (pSTAT3Ser727). In healthy volunteer fibroblasts, folic acid exposure recapitulated the exaggerated closure and hyper-glycolytic state of keloid fibroblasts through JAK1/2- and STAT3-dependent pathways. Although additional studies are needed before extrapolating from a representative cell line to keloids writ large, our results provide novel insights into the metabolic consequences of STAT3 dysfunction, suggest a possible role for folate metabolism in the pathogenesis of keloid scars, and offer in vitro pre-clinical data supporting considerations of clinical trials for ruxolitinib in keloid disorder.
Luminescent quantum-dot-sized conjugated polymer nanoparticles—nanoparticle formation in a miniemulsion system

The synthesis of semiconducting polymer nanospheres (SPNs) by miniemulsion methods has been reported previously,1,2 however the resulting materials have typically been significantly larger than quantum dots, the nanomaterial of choice for cell imaging. In the current work, we aimed to obtain quantum-dot-sized poly(ethylene-glycol) (PEG) functionalised SPNs by optimising the miniemulsion method reported previously.1,3 We report that PEG functionalised SPNs with a narrow distribution of quantum dot sizes were successfully synthesised, with mean diameters ranging between 2 and 5 nm. PEG-dithiol was also used in one variant of the syntheses, allowing the purified sample to be examined by mass spectrometry (using sulfur as a reporter), confirming the inclusion of a significant number of PEG molecules in the nanoparticles. Also, the presence of PEG was found to significantly affect the yield of the reaction, suggesting it played a role in nanoparticle formation. The nanoparticles were characterized by TEM, absorption and emission spectroscopy, and were found to be stable in solution for months.
Hydrogen Evolution on Supported Incomplete Cubane-type (Mo3S4) 4+ Electrocatalysts

Electrocatalytic properties of biomimetic supported incomplete cubane-type [Mo3S4]4+ clusters are investigated. The activity toward the hydrogen evolution reaction (HER) is evaluated on both a high surface area gas diffusion electrode in a membrane electrode assembly and on highly orientated pyrolytic graphite (HOPG) supports. Sub-monolayers of the clusters were imaged by means of scanning tunnelling microscopy (STM) prior to electrochemical characterization. This enabled the quantification of the activity on a per cluster basis for the HER and the comparison of the activity with other HER catalysts. We find that the HER activity of the [Mo3S4]4+ is comparable with that of the edge sites of MoS2. The supported [Mo3S4]4+ molecules were also characterized by X-ray photoelectron spectroscopy (XPS), and the observed deterioration in electrocatalytic activity with time was assigned to slow [Mo3S4]4+ cathodic desorption from the catalyst support.
Kangite, (Sc,Ti,Al,Zr,Mg,Ca,⃞)2O3, a new ultra-refractory scandia mineral from the Allende meteorite: Synchrotron micro-Laue diffraction and electron backscatter diffraction

Abstract Kangite (IMA 2011-092), (Sc,Ti,Al,Zr,Mg,Ca,⃞)2O3, is a new scandia mineral, occurring as micrometer-sized crystals with REE-rich perovskite and spinel in a davisite-dominant ultra-refractory inclusion from the Allende CV3 carbonaceous chondrite. The phase was characterized by SEM, EBSD, synchrotron micro-Laue diffraction, micro-Raman, and EPMA. The mean chemical composition of the type kangite is (wt%) TiO2 36.6, Sc2O3 26.4, ZrO2 11.3, Al2O3 7.0, Y2O3 5.4, CaO 3.9, MgO 3.14, Dy2O3 1.8, SiO2 1.7, V2O3 1.31, Er2O3 0.92, FeO 0.8, Gd2O3 0.60, Ho2O3 0.40, Tb2O3 0.18, Cr2O3 0.09, ThO2 0.04, O -0.3, sum 101.28, which leads to an empirical formula calculated on the basis of 3 O atoms of [(Sc0.54Al0.16Y0.07V0.03Gd0.01Dy0.01Er0.01)3+∑0.83(Ti0.66Zr0.13)4+∑0.79(Mg0.11Ca0.06 Fe0.02)2+∑0.19 ⃞0.19]∑2.00O3. Synchrotron micro-Laue diffraction (i.e., an energy scan by a high-flux X-ray monochromatic beam) on one type domain at submicrometer resolution revealed that kangite has a cation-deficient Ia3 bixbyite-type cubic structure. The cell parameters are a = 9.842(1) Å, V = 953.3(1) Å3, Z = 16, which leads to a calculated density of 3.879 g/cm3. Kangite is a new ultra-refractory mineral, likely originating through low-temperature oxidation of a Sc-,Ti3+-enriched high-temperature condensate oxide dating to the birth of the Solar System.
Synthesis of a β‐Ketophosphonate Bioisostere of UDP‐N‐acetylglucosamine

A concise route to a new β-ketophosphonate analog of glycosyl nucleotides is described. Such a diphosphate bioisostere is a stable mimic of enzyme substrates involved in peptidoglycan biosynthesis and will be the starting point for the development of new potential antibiotics. The synthesis is carried out by condensing a lithiomethylenephosphonate derivative on a methyl N-acetylglucosaminylacetate followed by esterification with a uridine derivative. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Understanding the binding affinities between SFRP1 CRD , SFRP1 Netrin , Wnt 5B and frizzled receptors 2, 3 and 7 using MD simulations

Abstract cWnt-signalling plays a crucial role in stem cell maintenance and tissue homeostasis. Secreted frizzled-related proteins(SFRP), Wnt inhibitors consist of the N-terminal cysteine rich domain(CRD) and the C-terminal netrin(NTR) domain. SFRP1 binds to the Wnt ligands and frizzled receptors(FZ) either through its SFRP1CRD or through its SFRP1Netrin domains; however, very little is known on these binding affinities. Here, we attempted to understand the interactions and binding affinities of SFRP1-Wnt5B, SFRP1-FZ(2, 3 & 7) and Wnt5B-FZ(2, 3 & 7) that are mainly expressed in murine hair follicle stem cells. SFRP1CRD, SFRP1Netrin, Wnt5B and FZ(2, 3 & 7) structures were built using homology modelling, followed by their molecular dynamics simulations. SFRP1CRD showed lower fluctuation when in complex with FZ2, FZ3 and FZ7 and Wnt5B as compared to SFRP1Netrin using RMSF and RMSD. However, free energy showed SFRP1Netrin was energetically more stable than SFRP1CRD. SFRP1Netrin formed more number of interactions with FZ as compared to SFRP1CRD. Importantly, SFRP1Netrin favoured binding to the FZ receptors(FZ3 > FZ7 > FZ2) as compared to Wnt5B ligand. Conversely, the SFRP1CRD showed more affinity towards the Wnt5B ligand as compared to FZ receptors. Wnt5B showed the best binding affinity with FZ3 followed by SFRP1CRD and SFRP1Netrin. Therefore, SFRP1Netrin can bind to the FZ3 with higher binding affinity and may inhibit non-canonical Wnt-signalling pathway. Our study provides the comprehensive information on the binding affinities among the Wnt5B, SFRP1CRD/Netrin and FZ(2, 3 & 7). Thus, this information might also help in designing novel strategies to inhibit aberrant Wnt-signalling. Communicated by Ramaswamy H. Sarma
Aptamer and rolling circle amplification-involved sandwich assay for platelet-derived growth factor-BB with absorbance analysis

This paper described an aptamer-based absorbance assay combining rolling circle amplification (RCA) for platelet-derived growth factor-BB (PDGF-BB). PDGF-BB was specifically captured by an antibody on a microplate, and then bound with an anti-PDGF-BB aptamer connected with a primer sequence, forming a sandwich complex. The primer sequence was extended by RCA reaction to generate a long single-stranded DNA with repeated copies. The amplified DNA product was hybridized with many biotinylated short DNA probes, and then labeled with streptavidin–horseradish peroxidase conjugate (SA–HRP). The HRP catalyzed the conversion of a substrate to a colored product, which was measured by simple absorbance analysis to achieve the detection of PDGF-BB. By involving RCA and HRP catalysis amplification, sensitive detection of PDGF-BB with a good selectivity was obtained; the detection limit reached 3.1 pM.