bluuebunny/crossref_metadata_2025 huggingface dataset:
RAB5A expression is a predictive biomarker for trastuzumab emtansine in breast cancer
Authors: Engebraaten Olav , Yau Christina , Berg Kristian , Borgen Elin , Garred Øystein , Berstad Maria E. B. , Fremstedal Ane S. V. , DeMichele Angela , Veer Laura van ’t , Esserman Laura , Weyergang Anette
Published: November 2021

HER2 is a predictive biomarker for HER2-targeted therapeutics. For antibody–drug conjugates (ADCs; e.g., trastuzumab emtansine (T-DM1)), HER2 is utilized as a transport gate for cytotoxic agents into the cell. ADC biomarkers may therefore be more complex, also reflecting the intracellular drug transport. Here we report on a positive correlation between the early endosome marker RAB5A and T-DM1 sensitivity in five HER2-positive cell lines. Correlation between RAB5A expression and T-DM1 sensitivity is confirmed in breast cancer patients treated with trastuzumab emtansine/pertuzumab in the I-SPY2 trial (NCT01042379), but not in the trastuzumab/paclitaxel control arm. The clinical correlation is further verified in patients from the KAMILLA trial (NCT01702571). In conclusion, our results suggest RAB5A as a predictive biomarker for T-DM1 response and outline proteins involved in endocytic trafficking as predictive biomarkers for ADCs.
Neoadjuvant T-DM1/pertuzumab and paclitaxel/trastuzumab/pertuzumab for HER2+ breast cancer in the adaptively randomized I-SPY2 trial
Authors: Clark Amy S. , Yau Christina , Wolf Denise M. , Petricoin Emanuel F. , van ‘t Veer Laura J. , Yee Douglas , Moulder Stacy L. , Wallace Anne M. , Chien A. Jo , Isaacs Claudine , Boughey Judy C. , Albain Kathy S. , Kemmer Kathleen , Haley Barbara B. , Han Hyo S. , Forero-Torres Andres , Elias Anthony , Lang Julie E. , Ellis Erin D. , Yung Rachel , Tripathy Debu , Nanda Rita , Wulfkuhle Julia D. , Brown-Swigart Lamorna , Gallagher Rosa I. , Helsten Teresa , Roesch Erin , Ewing Cheryl A. , Alvarado Michael , Crane Erin P. , Buxton Meredith , Clennell Julia L. , Paoloni Melissa , Asare Smita M. , Wilson Amy , Hirst Gillian L. , Singhrao Ruby , Steeg Katherine , Asare Adam , Matthews Jeffrey B. , Berry Scott , Sanil Ashish , Melisko Michelle , Perlmutter Jane , Rugo Hope S. , Schwab Richard B. , Symmans W. Fraser , Hylton Nola M. , Berry Donald A. , Esserman Laura J. , DeMichele Angela M.
Published: November 2021

HER2-targeted therapy dramatically improves outcomes in early breast cancer. Here we report the results of two HER2-targeted combinations in the neoadjuvant I-SPY2 phase 2 adaptive platform trial for early breast cancer at high risk of recurrence: ado-trastuzumab emtansine plus pertuzumab (T-DM1/P) and paclitaxel, trastuzumab and pertuzumab (THP). Eligible women have >2.5 cm clinical stage II/III HER2+breast cancer, adaptively randomized to T-DM1/P, THP, or a common control arm of paclitaxel/trastuzumab (TH), followed by doxorubicin/cyclophosphamide, then surgery. Both T-DM1/P and THP arms ‘graduate’ in all subtypes: predicted pCR rates are 63%, 72% and 33% for T-DM1/P (n = 52), THP (n = 45) and TH (n = 31) respectively. Toxicity burden is similar between arms. Degree of HER2 pathway signaling and phosphorylation in pretreatment biopsy specimens are associated with response to both T-DM1/P and THP and can further identify highly responsive HER2+tumors to HER2-directed therapy. This may help identify patients who can safely de-escalate cytotoxic chemotherapy without compromising excellent outcome.
Stability and molecular pathways to the formation of spin defects in silicon carbide
Authors: Lee Elizabeth M. Y. , Yu Alvin , de Pablo Juan J. , Galli Giulia
Published: November 2021

Spin defects in wide-bandgap semiconductors provide a promising platform to create qubits for quantum technologies. Their synthesis, however, presents considerable challenges, and the mechanisms responsible for their generation or annihilation are poorly understood. Here, we elucidate spin defect formation processes in a binary crystal for a key qubit candidate—the divacancy complex (VV) in silicon carbide (SiC). Using atomistic models, enhanced sampling simulations, and density functional theory calculations, we find that VV formation is a thermally activated process that competes with the conversion of silicon (VSi) to carbon monovacancies (VC), and that VV reorientation can occur without dissociation. We also find that increasing the concentration of VSi relative to VC favors the formation of divacancies. Moreover, we identify pathways to create spin defects consisting of antisite-double vacancy complexes and determine their electronic properties. The detailed view of the mechanisms that underpin the formation and dynamics of spin defects presented here may facilitate the realization of qubits in an industrially relevant material.
NRG1/ErbB signalling controls the dialogue between macrophages and neural crest-derived cells during zebrafish fin regeneration
Authors: Laplace-Builhé Béryl , Barthelaix Audrey , Assou Said , Bohaud Candice , Pratlong Marine , Severac Dany , Tejedor Gautier , Luz-Crawford Patricia , Nguyen-Chi Mai , Mathieu Marc , Jorgensen Christian , Djouad Farida
Published: November 2021

Fish species, such as zebrafish (Danio rerio), can regenerate their appendages after amputation through the formation of a heterogeneous cellular structure named blastema. Here, by combining live imaging of triple transgenic zebrafish embryos and single-cell RNA sequencing we established a detailed cell atlas of the regenerating caudal fin in zebrafish larvae. We confirmed the presence of macrophage subsets that govern zebrafish fin regeneration, and identified afoxd3-positive cell population within the regenerating fin. Genetic depletion of thesefoxd3-positive neural crest-derived cells (NCdC) showed that they are involved in blastema formation and caudal fin regeneration. Finally, chemical inhibition and transcriptomic analysis demonstrated that thesefoxd3-positive cells regulate macrophage recruitment and polarization through the NRG1/ErbB pathway. Here, we show the diversity of the cells required for blastema formation, identify a discretefoxd3-positive NCdC population, and reveal the critical function of the NRG1/ErbB pathway in controlling the dialogue between macrophages and NCdC.
Estimating disease prevalence in large datasets using genetic risk scores
Authors: Evans Benjamin D. , Słowiński Piotr , Hattersley Andrew T. , Jones Samuel E. , Sharp Seth , Kimmitt Robert A. , Weedon Michael N. , Oram Richard A. , Tsaneva-Atanasova Krasimira , Thomas Nicholas J.
Published: November 2021

Clinical classification is essential for estimating disease prevalence but is difficult, often requiring complex investigations. The widespread availability of population level genetic data makes novel genetic stratification techniques a highly attractive alternative. We propose a generalizable mathematical framework for determining disease prevalence within a cohort using genetic risk scores. We compare and evaluate methods based on the means of genetic risk scores’ distributions; the Earth Mover’s Distance between distributions; a linear combination of kernel density estimates of distributions; and an Excess method. We demonstrate the performance of genetic stratification to produce robust prevalence estimates. Specifically, we show that robust estimates of prevalence are still possible even with rarer diseases, smaller cohort sizes and less discriminative genetic risk scores, highlighting the general utility of these approaches. Genetic stratification techniques offer exciting new research tools, enabling unbiased insights into disease prevalence and clinical characteristics unhampered by clinical classification criteria.
A Fe3N/carbon composite electrocatalyst for effective polysulfides regulation in room-temperature Na-S batteries
Authors: Qi Yuruo , Li Qing-Jie , Wu Yuanke , Bao Shu-juan , Li Changming , Chen Yuming , Wang Guoxiu , Xu Maowen
Published: November 2021

The practical application of room-temperature Na-S batteries is hindered by the low sulfur utilization, inadequate rate capability and poor cycling performance. To circumvent these issues, here, we propose an electrocatalyst composite material comprising of N-doped nanocarbon and Fe3N. The multilayered porous network of the carbon accommodates large amounts of sulfur, decreases the detrimental effect of volume expansion, and stabilizes the electrodes structure during cycling. Experimental and theoretical results testify the Fe3N affinity to sodium polysulfides via Na-N and Fe-S bonds, leading to strong adsorption and fast dissociation of sodium polysulfides. With a sulfur content of 85 wt.%, the positive electrode tested at room-temperature in non-aqueous Na metal coin cell configuration delivers a reversible capacity of about 1165 mA h g−1 at 167.5 mA g−1, satisfactory rate capability and stable capacity of about 696 mA h g−1 for 2800 cycles at 8375 mA g−1.
Association between serum retinol and overall and cause-specific mortality in a 30-year prospective cohort study
Authors: Huang Jiaqi , Weinstein Stephanie J. , Yu Kai , Männistö Satu , Albanes Demetrius
Published: November 2021

How retinol as a clinical indicator of vitamin A status is related to long-term mortality is unknown. Here we report the results of a prospective analysis examining associations between serum retinol and risk of overall and cause-specific mortality. During a 30-year cohort follow-up, 23,797 deaths were identified among 29,104 men. Participants with higher serum retinol experienced significantly lower overall, CVD, heart disease, and respiratory disease mortality compared to men with the lowest retinol concentrations, reflecting 17–32% lower mortality risk (Ptrend < 0.0001). The retinol-overall mortality association is similar across subgroups of smoking intensity, alcohol consumption, body mass index, trial supplementation, serum alpha-tocopherol and beta-carotene concentrations, and follow-up time. Mediation analysis indicated that <3% of the effects of smoking duration and diabetes mellitus on mortality were mediated through retinol concentration. These findings indicate higher serum retinol is associated with lower overall mortality, including death from cardiovascular, heart, and respiratory diseases.
A sandcastle worm-inspired strategy to functionalize wet hydrogels
Authors: Zhang Donghui , Liu Jingjing , Chen Qi , Jiang Weinan , Wang Yibing , Xie Jiayang , Ma Kaiqian , Shi Chao , Zhang Haodong , Chen Minzhang , Wan Jianglin , Ma Pengcheng , Zou Jingcheng , Zhang Wenjing , Zhou Feng , Liu Runhui
Published: November 2021

Hydrogels have been extensively used in many fields. Current synthesis of functional hydrogels requires incorporation of functional molecules either before or during gelation via the pre-organized reactive site along the polymer chains within hydrogels, which is tedious for polymer synthesis and not flexible for different types of hydrogels. Inspired by sandcastle worm, we develop a simple one-step strategy to functionalize wet hydrogels using molecules bearing an adhesive dibutylamine-DOPA-lysine-DOPA tripeptide. This tripeptide can be easily modified with various functional groups to initiate diverse types of polymerizations and provide functional polymers with a terminal adhesive tripeptide. Such functional molecules enable direct modification of wet hydrogels to acquire biological functions such as antimicrobial, cell adhesion and wound repair. The strategy has a tunable functionalization degree and a stable attachment of functional molecules, which provides a tool for direct and convenient modification of wet hydrogels to provide them with diverse functions and applications.
Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit
Authors: Boone Morgane , Ramasamy Pathmanaban , Zuallaert Jasper , Bouwmeester Robbin , Van Moer Berre , Maddelein Davy , Turan Demet , Hulstaert Niels , Eeckhaut Hannah , Vandermarliere Elien , Martens Lennart , Degroeve Sven , De Neve Wesley , Vranken Wim , Callewaert Nico
Published: November 2021

While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50–100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.
A sensory memory to preserve visual representations across eye movements
Authors: Akbarian Amir , Clark Kelsey , Noudoost Behrad , Nategh Neda
Published: November 2021

Saccadic eye movements (saccades) disrupt the continuous flow of visual information, yet our perception of the visual world remains uninterrupted. Here we assess the representation of the visual scene across saccades from single-trial spike trains of extrastriate visual areas, using a combined electrophysiology and statistical modeling approach. Using a model-based decoder we generate a high temporal resolution readout of visual information, and identify the specific changes in neurons’ spatiotemporal sensitivity that underly an integrated perisaccadic representation of visual space. Our results show that by maintaining a memory of the visual scene, extrastriate neurons produce an uninterrupted representation of the visual world. Extrastriate neurons exhibit a late response enhancement close to the time of saccade onset, which preserves the latest pre-saccadic information until the post-saccadic flow of retinal information resumes. These results show how our brain exploits available information to maintain a representation of the scene while visual inputs are disrupted.
Structure and activation mechanism of the hexameric plasma membrane H+-ATPase
Authors: Zhao Peng , Zhao Chaoran , Chen Dandan , Yun Caihong , Li Huilin , Bai Lin
Published: November 2021

The S. cerevisiae plasma membrane H+-ATPase, Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H+-ATPases, Pma1 assembles and functions as a hexamer, a property unique to this subfamily among the larger family of P-type ATPases. It has been unclear how Pma1 organizes the yeast membrane into MCP microdomains, or why it is that Pma1 needs to assemble into a hexamer to establish the membrane electrochemical proton gradient. Here we report a high-resolution cryo-EM study of native Pma1 hexamers embedded in endogenous lipids. Remarkably, we found that the Pma1 hexamer encircles a liquid-crystalline membrane domain composed of 57 ordered lipid molecules. The Pma1-encircled lipid patch structure likely serves as the building block of the MCP. At pH 7.4, the carboxyl-terminal regulatory α-helix binds to the phosphorylation domains of two neighboring Pma1 subunits, locking the hexamer in the autoinhibited state. The regulatory helix becomes disordered at lower pH, leading to activation of the Pma1 hexamer. The activation process is accompanied by a 6.7 Å downward shift and a 40° rotation of transmembrane helices 1 and 2 that line the proton translocation path. The conformational changes have enabled us to propose a detailed mechanism for ATP-hydrolysis-driven proton pumping across the plasma membrane. Our structures will facilitate the development of antifungal drugs that target this essential protein.
MMAB promotes negative feedback control of cholesterol homeostasis
Authors: Goedeke Leigh , Canfrán-Duque Alberto , Rotllan Noemi , Chaube Balkrishna , Thompson Bonne M. , Lee Richard G. , Cline Gary W. , McDonald Jeffrey G. , Shulman Gerald I. , Lasunción Miguel A. , Suárez Yajaira , Fernández-Hernando Carlos
Published: November 2021

Intricate regulatory networks govern the net balance of cholesterol biosynthesis, uptake and efflux; however, the mechanisms surrounding cholesterol homeostasis remain incompletely understood. Here, we develop an integrative genomic strategy to detect regulators of LDLR activity and identify 250 genes whose knockdown affects LDL-cholesterol uptake and whose expression is modulated by intracellular cholesterol levels in human hepatic cells. From these hits, we focus on MMAB, an enzyme which catalyzes the conversion of vitamin B12 to adenosylcobalamin, and whose expression has previously been linked with altered levels of circulating cholesterol in humans. We demonstrate that hepatic levels of MMAB are modulated by dietary and cellular cholesterol levels through SREBP2, the master transcriptional regulator of cholesterol homeostasis. Knockdown of MMAB decreases intracellular cholesterol levels and augments SREBP2-mediated gene expression and LDL-cholesterol uptake in human and mouse hepatic cell lines. Reductions in total sterol content were attributed to increased intracellular levels of propionic and methylmalonic acid and subsequent inhibition of HMGCR activity and cholesterol biosynthesis. Moreover, mice treated with antisense inhibitors of MMAB display a significant reduction in hepatic HMGCR activity, hepatic sterol content and increased expression of SREBP2-mediated genes. Collectively, these findings reveal an unexpected role for the adenosylcobalamin pathway in regulating LDLR expression and identify MMAB as an additional control point by which cholesterol biosynthesis is regulated by its end product.
Mass of Abrikosov vortex in high-temperature superconductor YBa$$_2$$Cu$$_3$$O$$_{7-\delta }$$
Authors: Tesař Roman , Šindler Michal , Kadlec Christelle , Lipavský Pavel , Skrbek Ladislav , Koláček Jan
Published: November 2021

For more than four decades, mass of Abrikosov vortices defied experimental observations. We demonstrate a method of its detection in high-temperature superconductors. Similarly to electrons, fluxons circulate in the direction given by the magnetic field, causing circular dichroism. We report the magneto-transmittance of a nearly optimally doped thin YBa$$_2$$

2

Cu$$_3$$

3

O$$_{7-\delta }$$

7
-
δ

film, measured using circularly polarized submillimeter waves. The circular dichroism emerges in the superconducting state and increases with dropping temperature. Our results confirm the dominant role of quasiparticle states in the vortex core and yield the diagonal fluxon mass of $$2.2 \times 10^8$$

2.2
×

10
8

electron masses per centimeter at 45 K and zero-frequency limit, and even larger off-diagonal mass of $$4.9 \times 10^8 m_e$$

4.9
×

10
8

m
e

/cm.
Tissue, age, sex, and disease patterns of matrisome expression in GTEx transcriptome data
Authors: Nieuwenhuis Tim O. , Rosenberg Avi Z. , McCall Matthew N. , Halushka Marc K.
Published: November 2021

The extracellular matrix (ECM) has historically been explored through proteomic methods. Whether or not global transcriptomics can yield meaningful information on the human matrisome is unknown. Gene expression data from 17,382 samples across 52 tissues, were obtained from the Genotype-Tissue Expression (GTEx) project. Additional datasets were obtained from The Cancer Genome Atlas (TCGA) program and the Gene Expression Omnibus for comparisons. Gene expression levels generally matched proteome-derived matrisome expression patterns. Further, matrisome gene expression properly clustered tissue types, with some matrisome genes including SERPIN family members having tissue-restricted expression patterns. Deeper analyses revealed 382 gene transcripts varied by age and 315 varied by sex in at least one tissue, with expression correlating with digitally imaged histologic tissue features. A comparison of TCGA tumor, TCGA adjacent normal and GTEx normal tissues demonstrated robustness of the GTEx samples as a generalized matrix control, while also determining a common primary tumor matrisome. Additionally, GTEx tissues served as a useful non-diseased control in a separate study of idiopathic pulmonary fibrosis (IPF) matrix changes, while identifying 22 matrix genes upregulated in IPF. Altogether, these findings indicate that the transcriptome, in general, and GTEx in particular, has value in understanding the state of organ ECM.
A machine learning framework for rapid forecasting and history matching in unconventional reservoirs
Authors: Srinivasan Shriram , O’Malley Daniel , Mudunuru Maruti K. , Sweeney Matthew R. , Hyman Jeffrey D. , Karra Satish , Frash Luke , Carey J. William , Gross Michael R. , Guthrie George D. , Carr Timothy , Li Liwei , Viswanathan Hari S.
Published: November 2021

We present a novel workflow for forecasting production in unconventional reservoirs using reduced-order models and machine-learning. Our physics-informed machine-learning workflow addresses the challenges to real-time reservoir management in unconventionals, namely the lack of data (i.e., the time-frame for which the wells have been producing), and the significant computational expense of high-fidelity modeling. We do this by applying the machine-learning paradigm of transfer learning, where we combine fast, but less accurate reduced-order models with slow, but accurate high-fidelity models. We use the Patzek model (Proc Natl Acad Sci 11:19731–19736, https://doi.org/10.1073/pnas.1313380110, 2013) as the reduced-order model to generate synthetic production data and supplement this data with synthetic production data obtained from high-fidelity discrete fracture network simulations of the site of interest. Our results demonstrate that training with low-fidelity models is not sufficient for accurate forecasting, but transfer learning is able to augment the knowledge and perform well once trained with the small set of results from the high-fidelity model. Such a physics-informed machine-learning (PIML) workflow, grounded in physics, is a viable candidate for real-time history matching and production forecasting in a fractured shale gas reservoir.
Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
Authors: Fanidis Dionysios , Moulos Panagiotis , Aidinis Vassilis
Published: November 2021

Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been limited efforts to comparatively analyse/mine the numerous related publicly available datasets, to fully exploit their potential on the validation/creation of novel research hypotheses. In this context and towards that goal, we present Fibromine, an integrated database and exploration environment comprising of consistently re-analysed, manually curated transcriptomic and proteomic pulmonary fibrosis datasets covering a wide range of experimental designs in both patients and animal models. Fibromine can be accessed via an R Shiny application (http://www.fibromine.com/Fibromine) which offers dynamic data exploration and real-time integration functionalities. Moreover, we introduce a novel benchmarking system based on transcriptomic datasets underlying characteristics, resulting to dataset accreditation aiming to aid the user on dataset selection. Cell specificity of gene expression can be visualised and/or explored in several scRNA-seq datasets, in an effort to link legacy data with this cutting-edge methodology and paving the way to their integration. Several use case examples are presented, that, importantly, can be reproduced on-the-fly by a non-specialist user, the primary target and potential user of this endeavour.
Identification of the antibacterial mechanism of cryptotanshinone on methicillin-resistant Staphylococcus aureus using bioinformatics analysis
Authors: Zhong Jiwei , Wang Haidan , Zhuang Yun , Shen Qun
Published: November 2021

Cryptotanshinone (CT) is an extract from the traditional Chinese medicineSalvia miltiorrhiza, which inhibits the growth of methicillin-resistantStaphylococcus aureus(MRSA) in vitro. This study aims to determine the antibacterial mechanisms of CT by integrating bioinformatics analysis and microbiology assay. The microarray data of GSE13203 was retrieved from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) ofS. aureusstrains that were treated with CT treatment. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to identify the potential target of CT. Data mining on the microarray dataset indicated that pyruvate kinase (PK) might be involved in the antimicrobial activities of CT. The minimum inhibition concentrations (MICs) of CT or vancomycin against the MRSA strain ATCC43300 and seven other clinical strains were determined using the broth dilution method. The effects of CT on the activity of PK were further measured. In vitro tests verified that CT inhibited the growth of an MRSA reference strain and seven other clinical strains. CT hampered the activity of the PK of ATCC43300 and five clinical MRSA strains. CT might hinder bacterial energy metabolism by inhibiting the activity of PK.
Blue light promotes vascular reconnection, while red light boosts the physiological response and quality of grafted watermelon seedlings
Authors: Bantis Filippos , Panteris Emmanuel , Dangitsis Christodoulos , Carrera Esther , Koukounaras Athanasios
Published: November 2021

The wound inflicted during grafting of watermelon seedlings requires rapid and sufficient vascular development which is affected by light quality. Our objective was to investigate the effect of light spectra emitted by light-emitting diodes (LEDs) during healing of grafted watermelon (Citrullus lanatus) seedlings on their vascular development, physiological and phytohormonal profile, and root architecture. Three LEDs emitting red (R), blue (B), and RB with 12% blue (12B) were tested in a healing chamber. During the first three days, the photosynthetic apparatus portrayed by PIABS, φP0, ψE0, and ΔVIP was less damaged and faster repaired in B-treated seedlings. B and 12B promoted vascular reconnection and root development (length, surface area and volume). This was the result of signaling cascade between phytohormones such as indole-3-acetic acid and others. After vascular reconnection the seedlings switched lights for 3 more days and the picture was reversed. Seedlings treated with B for the first 3 days and R for days 4 to 6 had better photosynthetic characteristics, root system development, morphological, shoot and root biomass, and quality (i.e. Dickson’s quality index) characteristics. We concluded that blue light is important during the first 3 days of healing, while the presence of red is necessary after vascular reconnection.
The global burden of decubitus ulcers from 1990 to 2019
Authors: Zhang Xianghong , Zhu Na , Li Zhihong , Xie Xiangtao , Liu Tang , Ouyang Guoqing
Published: November 2021

There are no studies assessing the epidemiology and burden of decubitus ulcers at global, regional, and national levels. We aim to report this issue from 1990 to 2019 by extracting data from the Global Burden of Disease Study (GBD) 2019 and stratifying it by age, gender, and socio-demographic index (SDI). Globally, the number of prevalent cases of decubitus ulcers in 2019 is 0.85 (95% UI 0.78 to 0.94) million. The age-standardized rates of prevalence, incidence, and years lived with disability (YLDs) in 2019 are 11.3 (95% UI 10.2 to 12.5), 41.8 (37.8 to 46.2), and 1.7 (1.2 to 2.2) per 100,000 population, and compared with 1990, it has decreased by 10.6% (95% UI 8.7% to 12.3%), 10.2% (8.2 to 11.9%), and 10.4% (8.1 to 12.5%), respectively. In addition, the global prevalence rate of decubitus ulcers increases with age, peaking at the > 95 age group among men and women. At the regional and national levels, we observe a positive correlation between age-standardized YLDs and SDI. Malaysia, Saudi Arabia, and Thailand experienced the most significant increases in age-standardized prevalence rates at the national level. Finally, we concluded that the age-standardized prevalence, incidence, and YLDs rates of decubitus ulcer declined from 1990 to 2019, with significant regional differences. In order to monitor the dynamic changes of decubitus ulcers burden, it is recommended to improve the quality of decubitus ulcer health data in all regions and countries.
New chalcone derivatives as potential antimicrobial and antioxidant agent
Authors: Okolo Emelda N. , Ugwu David I. , Ezema Benjamin E. , Ndefo Joseph C. , Eze Florence U. , Ezema Chidimma G. , Ezugwu James A. , Ujam Oguejiofo T.
Published: November 2021

Seven chalcone derivatives were synthesized by the Claisen-Schmidt condensation. The structures of the compounds were confirmed by spectral data (Ultraviolet/visible, infrared, nuclear magnetic resonance and mass spectroscopy). The compounds were tested for their in silico and in vitro antimicrobial and antioxidant activities. The molecular docking assessments showed that all the compounds exhibited good binding affinity with the target microorganism proteins but, compounds 6e and 6g showed better binding affinity compared with the standards. The antimicrobial test revealed that all the compounds screened were active against Staphylococcus aureus and Bacillus subtilis and had minimum inhibitory concentrations (MIC) between 0.4 and 0.6 mg/mL. Compounds 6a, 6c and 6d had moderate activities on Salmonella typhi. Compounds 6b and 6c had moderate activity on Escherichia coli. Compound 6c had moderate activity on Aspergillus niger while compounds 6a and 6e had poor activity. All the compounds except compound 6e had no inhibition against Pseudomonas aeruginosa. The in-vitro antioxidant activity was assessed using ethylenediaminetetraacetate (EDTA) as the standard. Compounds 6c, 6e and 6g gave excellent inhibitory activity better than the standard. Compound 6a gave good activity at 500 μg/mL and 1000 μg/mL concentrations but, below the standard at 250 μg/mL and no inhibition at 125 μg/mL. Compound 6d had good inhibition at 500 μg/mL and 1000 μg/mL but, no inhibition at 125 μg/mL and 250 μg/mL. Compound 6b was found to be inactive in all the concentrations. Absorption, distribution, metabolism and excretion properties of the compounds were assessed using SwissADME. The results of lead likeness showed that compound 6e is a lead-like molecule.
A general solvent system for the analysis of lignosulfonates by 31P NMR
Authors: Wurzer Gerhild K. , Bacher Markus , Hettegger Hubert , Sumerskii Ivan , Musl Oliver , Fackler Karin , Bischof Robert H. , Potthast Antje , Rosenau Thomas
Published: November 2021

The new solvent system [emim]Cl/DMF/pyridine enables the quantitative determination of hydroxy groups of previously insoluble lignosulfonates by means of 31P-NMR.
Highly sensitive microRNA detection by a duplex-specific nuclease amplification triggered three-dimensional DNA machine
Authors: Chen Chaohui , He Rongxiang , Liu Xiaoyun , Zhang Zhengtao , Chen Long
Published: November 2021

A dual signal amplification method has been developed for direct miRNA detection by combining the duplex-specific nuclease (DSN)-assisted recycling amplification and the nicking enzyme (NEase)-powered three dimensional (3D) DNA walker.
A triple-pore tessellated square array by a metal-hexagonal ligand with reinforced tetra-connectors
Authors: Li Suqing , Zhao He , Chen Mingzhao , Wang Jun , Zhong Wanying , Jiang Zhilong , Liu Die , Liu Hui , Wang Pingshan
Published: November 2021

This manuscript describes an unexplored triple-pore tessellated square array with three different kinds of pores. The discrete array can be assembled into multichannel tubular nanostructures through molecular packing.
Reversible electrowetting transitions on superhydrophobic surfaces
Authors: Vanzo D. , Luzar A. , Bratko D.
Published: November 2021

The transition from the Cassie to the Wenzel state of an electrowetted surface strongly depends on the polarity of the electric field.
Unveiling the role of 2D monolayer Mn-doped MoS2material: toward an efficient electrocatalyst for H2evolution reaction
Authors: Ekka Joy , Upadhyay Shrish Nath , Keil Frerich J. , Pakhira Srimanta
Published: November 2021

Two-dimensional (2D) monolayer Mn-doped MoS2transition metal dichalcogenide has shown excellent electrocatalytic activities for effective hydrogen evolution reaction due to the Mn-doping in the pristine MoS2.
Mechanistic insights into CoOx–Ag/CeO2 catalysts for the aerobic oxidation of 5-hydroxymethylfurfural to 2,5-furandicarboxylic acid
Authors: Fu Mengchen , Yang Weiyao , Yang Chenyu , Zhang Yiwen , Shen Chun
Published: November 2021

CoOx–Ag/CeO2 catalysts achieve satisfactory FDCA yield from HMF, and a fundamental understanding about the reaction mechanism is provided.
Mechanistic investigation of a visible light mediated dehalogenation/cyclisation reaction using iron(iii), iridium(iii) and ruthenium(ii) photosensitizers
Authors: Aydogan Akin , Bangle Rachel E. , De Kreijger Simon , Dickenson John C. , Singleton Michael L. , Cauët Emilie , Cadranel Alejandro , Meyer Gerald J. , Elias Benjamin , Sampaio Renato N. , Troian-Gautier Ludovic
Published: November 2021

The identification of reaction mechanisms unique to the iron, ruthenium, and iridium PS represents progress towards the long-sought goal of utilizing earth-abundant, first-row transition metals for emerging energy and environmental applications.
Emerging investigator series: the red sky: investigating the hurricane Ophelia Saharan dust and biomass burning aerosol event
Authors: Wyche Kevin P. , Ricketts Hugo , Brolly Mathew , Smallbone Kirsty L.
Published: November 2021

On 16th October 2017 ex-hurricane Ophelia passed over the UK, bringing with it a unique mixture of particulates which caused the sky to turn a dramatic red colour.
O2 reduction by iron porphyrins with electron withdrawing groups: to scale or not to scale
Authors: Amanullah Sk , Saha Paramita , Dey Abhishek
Published: November 2021

Iron porphyrins are synthesized by systematically introducing electron withdrawing groups (EWGs) on pyrroles to evaluate the relationship between rate (k) and overpotential (η).
Protective effect of sterols extracted from Lotus plumule on ethanol-induced injury in GES-1 cells in vitro
Authors: Zhang Ying , Liang Jiao , Jiang Hao , Qian Min , Zhao Wenhong , Bai Weidong
Published: November 2021

Sterols isolated from Lotus plumule played a positive role against ethanol-induced damage in GES-1 cells, which suggested the potential application of Lotus plumule sterols as bioactive ingredient for healthy foods.
Visible-light-induced intermolecular aminoselenation of alkenes
Authors: Liu Gong-Qing , Zhou Chen-Fan , Zhang Yun-Qian , Yi Wei , Wang Peng-Fei , Liu Ji , Ling Yong
Published: November 2021

A visible-light-induced intermolecular aminoselenation of alkenes is disclosed, wherein 1,2-bis(selenide) is involved as the key intermediate.
Metal-free visible-light-promoted C(sp3)–H functionalization of aliphatic cyclic ethers using trace O2
Authors: Niu Ben , Blackburn Bryan G. , Sachidanandan Krishnakumar , Cooke Maria Victoria , Laulhé Sébastien
Published: November 2021

Presented is a light-promoted C–C bond forming reaction yielding sulfone and phosphate derivatives at room temperature in the absence of metals or photoredox catalyst.
On-chip miRNA extraction platforms: recent technological advances and implications for next generation point-of-care nucleic acid tests
Authors: Petrou Loukia , Ladame Sylvain
Published: November 2021

Circulating microRNAs (or miRNAs) can be extracted from bodily fluids using off-chip or on-chip sample processing platforms that hold the key to the next generation of diagnostic and predictive nucleic acid tests.
An ionic hydrogel with stimuli-responsive, self-healable and injectable characteristics for the targeted and sustained delivery of doxorubicin in the treatment of breast cancer
Authors: Kuddushi Muzammil , Pandey Deepak K. , Singh Dheeraj K. , Mata Jitendra , Malek Naved
Published: November 2021

Targeted and sustained release of doxorubicin was achieved through a self-healable and injectable ionic hydrogel.
Insights into the modular design of kinase inhibitors and application to Abl and Axl
Authors: Phadke Sameer , Lopez-Barcons Lluis , Vandecan Nathalie , Wu Zhifen , Johnson Taylor K. , Lachacz Eric J. , Merajver Sofia D. , Soellner Matthew B.
Published: November 2021

Selectivity analysis and biological testing of a matched set of kinase inhibitors led to the identification of potent, selective inhibitors of Abl (wild-type and T315I) and Axl kinases.
Energetic metal–organic frameworks achieved from furazan and triazole ligands: synthesis, crystal structure, thermal stability and energetic performance
Authors: Gong Lishan , Chen Guo , Liu Yue , Wang Tingwei , Zhang Jianguo , Yi Xiaoyi , He Piao
Published: November 2021

Energetic metal–organic frameworks (EMOFs) have witnessed increasing development and been proved as promising candidates for new high energy density materials (HEDMs).
Molecular structure recognition by blob detection
Authors: Lu Qing
Published: November 2021

Molecular structure recognition is fundamental in computational chemistry.
Dry electrochemical polishing of copper alloy in a medium containing ion-exchange resin
Authors: Min Rui , Wang Lishi , Cheng Yihang , Hu Xinbin
Published: November 2021

At each collision between resin particles and material surface, a micro electrolytic cell is formed at the contact point and an anode reaction occurs. Metal ions from the reaction enter the resin and are carried away at the end of the collision.
Bioorthogonal regulation of DNA circuits for smart intracellular microRNA imaging
Authors: Chen Yingying , Gong Xue , Gao Yuhui , Shang Yu , Shang Jinhua , Yu Shanshan , Li Ruomeng , He Shizhen , Liu Xiaoqing , Wang Fuan
Published: November 2021

An on-site bioorthogonal regulated DNA circuit was developed by introducing an endogenous DNA repairing enzyme-mediated sequential activation strategy to achieve cancer cell-selective microRNA imaging with high anti-interference ability.
Boosting the photocatalytic H2 evolution activity of a CdS/N-doped ZnIn2S4 direct Z-scheme heterostructure using a band alignment regulation strategy
Authors: Cai Xiaoyan , Su Miao , Zeng Zhongtian , Weng Haifeng , Cai Zhiguo , Zhang Junying , Mao Liang
Published: November 2021

CdS/N-doped ZnIn2S4 Z-scheme heterostructured photocatalyst is developed for H2 evolution basing on a band alignment regulation strategy, where the enlarged Fermi level difference facilitates a stronger built-in electric field for charge separation.
Investigating oxygen reduction pathways on pristine SOFC cathode surfaces by in situ PLD impedance spectroscopy
Authors: Siebenhofer Matthäus , Riedl Christoph , Schmid Alexander , Limbeck Andreas , Opitz Alexander Karl , Fleig Jürgen , Kubicek Markus
Published: November 2021

Temperature and p(O2) dependences of the oxygen exchange kinetics of SOFC cathode materials were correlated with point defect concentrations. Defect chemical contributions were identified as a major part of effectively measured activation energies.
Controlling thermoelectric transport via native defects in the diamond-like semiconductors Cu2HgGeTe4 and Hg2GeTe4
Authors: Qu Jiaxing , Porter Claire E. , Gomes Lídia C. , Adamczyk Jesse M. , Toriyama Michael Y. , Ortiz Brenden R. , Toberer Eric S. , Ertekin Elif
Published: November 2021

Defect analysis and phase boundary mapping of Cu2HgGeTe4 and Hg2GeTe4 reveal reciprocal doping potential despite their similar crystal structures. Measurements validate predictions of Cu2HgGeTe4 as highly degenerate and Hg2GeTe4 as an intrinsic semiconductor.
Carbazol-phenyl-phenothiazine-based sensitizers for dye-sensitized solar cells
Authors: Jiao Yunfei , Liu Shuaishuai , Shen Zhongjin , Mao Le , Ding Yongjie , Ren Dan , Eickemeyer Felix Thomas , Pfeifer Lukas , Cao Dapeng , Xu Wenjuan , Song Juan , Mi Baoxiu , Gao Zhiqiang , Zakeeruddin Shaik M. , Huang Wei , Grätzel Michael
Published: November 2021

Heteroaromatic units are commonly used as π-spacers for sensitizers and show significant roles in tuning molecular properties and DSSCs performances.
Atypical phase-change alloy Ga2Te3: atomic structure, incipient nanotectonic nuclei, and multilevel writing
Authors: Tverjanovich Andrey , Khomenko Maxim , Benmore Chris J. , Bereznev Sergei , Sokolov Anton , Fontanari Daniele , Kiselev Aleksei , Lotin Andrey , Bychkov Eugene
Published: November 2021

Emerging brain-inspired computing needs phase-change materials of the next generation with lower energy consumption and wider temperature range. Gallium tellurides appear to be promising candidates enable to achieve the necessary requirements.
Methylamine gas healing of perovskite films: a short review and perspective
Authors: Hao Lianzheng , Zhao Qiangqiang , Wang Xiao , Pang Shuping , Cui Guanglei
Published: November 2021

We summarize the internal chemical mechanism, crystallization kinetics and future prospects of the MA0 healing process.
DC‐link low‐frequency current and voltage ripple analysis in multiphase voltage source inverters with unbalanced load
Authors: Vujacic Marija , Dordevic Obrad , Mandrioli Riccardo , Grandi Gabriele
Published: November 2021

Inverter's performance and operating mode may be negatively affected by inverter input (dc‐link) current and voltage ripple. It is a common experience that even theoretically balanced loads with perfectly balanced supply voltages, such as multiphase ac motors supplied by pulse‐width modulation (PWM) inverters, in practice show a certain degree of current unbalance, in the range of a few percent, which introduces a low‐frequency instantaneous power oscillation. This reflects in current and voltage low‐frequency ripple on the dc‐link inverter side (i.e. at the double‐fundamental frequency). A possible method to analyse this matter is through the symmetric sequence components. In particular, based on the first negative current sequence component and by considering the equivalent dc‐link impedance calculated at the dominant double‐fundamental frequency, the amplitude of the corresponding dc‐link voltage ripple component is calculated in this work for a general multiphase load. Finally, the design of the dc‐link capacitor in multiphase inverters is proposed considering requirements referred to the double‐fundamental dc voltage ripple. The feasibility of the proposed developments has been verified for three‐, five‐ and seven‐phase inverters by both numerical simulations and comprehensive experimental tests, always showing a good matching.
Virtual Power Plant (VPP) scheduling with uncertain multiple Locational Marginal Prices
Authors: Khandelwal Meenakshi , Mathuria Parul , Bhakar Rohit
Published: November 2021

Aggregation of heterogeneous distributed energy resources (DERs) and prosumers for profit maximisation by virtue of the market interface has evolved into virtual power plants (VPPs). The VPP operator optimises its aggregated resources to maximise profit by participating in the wholesale electricity market. VPP resources may be geographically dispersed and connected to a transmission grid at various nodes having different locational marginal prices (LMPs). These LMPs vary throughout the day and exhibit mutual correlation. Considering this, the current study presents a profit maximisation framework for VPP operators working under multiple LMPs, with their correlated uncertainties. This work also provides VPP resource scheduling for profit maximisation, considering optimal trading at various LMP nodes for a constrained internal network. This decision is devised using Markowitz's mean‐variance (M‐V) criterion under expedient correlation between volatile LMPs. A numerical case study on the proposed model with the PJM market demonstrates that LMP correlation alters the role of the VPP operator. This affects its trading and scheduling decisions as a buyer/seller at various time intervals to improve its profit–risk trade‐off and consequently the market interfacing of the VPP operator. The proposed model is relevant in practical market conditions for day‐ahead/medium‐term VPP planning while managing market uncertainty.
Using genetic programming on GPS trajectories for travel mode detection
Authors: Namdarpour Farnoosh , Mesbah Mahmoud , Gandomi Amir H. , Assemi Behrang
Published: November 2021

The widespread and increased use of smartphones, equipped with the global positioning system (GPS), has facilitated the automation of travel data collection. Most studies on travel mode detection that used GPS data have employed hand‐crafted features that may not have the capabilities to detect all complex travel behaviours since their performance is highly dependent on the skills of domain experts and may limit the performance of classifiers. In this study, a genetic programming (GP) approach is proposed to select and construct features for GPS trajectories. GP increased the macro‐average of the F1‐score from 77.3 to 80.0 in feature construction when applied to the GeoLife dataset. It could transform the decision tree into a competitive classifier with support vector machines (SVMs) and neural networks that are both able to extract high‐level features. Simplicity, interpretability, and a relatively lower risk of overfitting allow the proposed model to be readily used for passive travel data collection even on smartphones with limited computational capacities. The model is validated by a second dataset from Australia and New Zealand, which indicated that a decision tree with the GP constructed features as its input has a considerably higher transferability than SVMs and neural networks.
Equity‐oriented vehicle routing optimization for catering distribution services with timeliness requirements
Authors: Wang Shuai , Yang Liya , Yao Yu , Zhang Qin , Shang Pan
Published: November 2021

The rapid development in the catering services and urban logistics industries has significantly promoted the prosperity of business‐to‐consumer (B2C) e‐commerce urban logistics distribution, which is gaining increasing interest from food producers, distribution platforms, and consumers. Unlike traditional logistics supply chains, catering distribution services have strong timeliness and consideration of delivery delay. Traditional distribution platforms usually group commodities by their origins or destinations and then transport each group with one logistics vehicle. However, for a logistics distribution area with limited commodities, the vehicle capacity cannot be fully utilized if one vehicle can only transport commodities with the same origin or destination. Therefore, a mixed‐load strategy is proposed in which commodities with different origins or destinations in a distribution area could be transported by the same vehicle to improve vehicle capacity utilization. A mixed‐load strategy would further cause delivery sequencing problems, leading to different delivery delays for customers. This study proposed an equity‐oriented vehicle routing problem for food distribution services with timeliness requirements considering a mixed‐loading strategy and vehicle capacity constraints. For the above problem, a multi‐commodity flow optimization model was constructed for the equity‐oriented vehicle routing problem and a mixed‐load strategy based on a time‐discretized space‐time‐state network representation. An augmented Lagrangian relaxation approach was utilized to reformulate the original model and thus effectively solve the proposed model. Furthermore, the augmented Lagrangian model was decomposed and linearized into a series of shortest path searching subproblems and iteratively solved by a dynamic programming algorithm using an alternating direction method of multipliers (ADMM)‐based solution framework. Finally, the proposed model and solution approaches were tested on numerous networks.