bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual‐Inhibition of Human N‐Myristoyltransferase Subtypes Halts Common Cold Pathogenesis: Atomistic Perspectives from the Case of IMP‐1088**
Authors: Agoni Clement , Salifu Elliasu Y. , Enslin Gill , Kwofie Samuel K. , Soliman Mahmoud E. 
Published: December 2021

AbstractThe pharmacological inhibition of human N‐myristoyltransferase (HsNMT) has emerged as an efficient strategy to completely prevent the replication process of rhinoviruses, a potential treatment for the common cold. This was corroborated by the recent discovery of compound IMP‐1088, a novel inhibitor that demonstrated a dual‐inhibitory activity against the two HsNMT subtypes 1 and 2 without inducing cytotoxicity. However, the molecular and structural basis for the dual‐inhibitory potential of IMP‐1088 has not been investigated. As such, we employ molecular modelling techniques to resolve the structural mechanisms that account for the dual‐inhibitory prowess of IMP‐1088. Sequence and nanosecond‐based analyses identified Tyr296, Phe190, Tyr420, Leu453, Gln496, Val181, Leu474, Glu182, and Asn246 as residues common within the binding pockets of both HsNMT1 and HsNMT2 subtypes whose consistent interactions with IMP‐1088 underpin the basis for its dual inhibitory potency. Nano‐second‐based assessment of interaction dynamics revealed that Tyr296 consistently elicited high‐affinity π‐π stacked interaction with IMP‐1088, thus further highlighting its cruciality corroborating previous report. An exploration of resulting structural changes upon IMP‐1088 binding further revealed a characteristic impeding of residue fluctuations, structural compactness, and a consequential burial of crucial hydrophobic residues, features required for HsNMT1/2 functionality. Findings present essential structural perspectives that augment previous experimental efforts and could also advance drug development for treating respiratory tract infections, especially those mediated by rhinoviruses.
Anti‐Inflammatory and Antimicrobial Activities of Fermented Ocimum sanctum Linn. Extracts against Skin and Scalp Microorganisms
Authors: Chaiyana Wantida , Punyoyai Chanun , Sriyab Suwannee , Prommaban Adchara , Sirilun Sasithorn , Maitip Jakkrawut , Chantawannakul Panuwan , Neimkhum Waranya , Anuchapreeda Songyot 
Published: December 2021

AbstractThis study aimed to revealed anti‐inflammatory and antimicrobial activities of fermented Ocimum sanctum Linn. (FE). The fermentation process with Lactobacillus plantarum was compared with the solvent extraction methods. Antimicrobial activity against the growth of Staphylococcus aureus, Staphylococcus epidermidis, Propionibacterium acnes, Candida albicans, and Malassezia furfur was investigated via broth dilution method. High performance thin layer chromatography was used to determine eugenol content. The anti‐inflammation was investigated by means of nuclear factor kappa B (NF‐κB) expression inhibition by Western blot analysis. FE yielded the highest amount (11.93 % w/w), the highest eugenol content (39.3±12.6 % w/w), and the highest antimicrobial activities comparing to the extracts obtained from the solvent extractions. The fungal inhibition against M. furfur 656 was equivalent to that of ketoconazole. Furthermore, the bacterial inhibition on S. aureus and S. epidermidis was compared to that of Penicillin G at minimum inhibitory concentration (MIC) of 0.125 mg/mL and 0.25 mg/mL, respectively. Interestingly, FE had lower MIC and minimum bactericidal concentration against P. acnes than Penicillin G and also possessed comparable anti‐inflammatory activity to indomethacin with the NF‐κB suppression of 42.7±4.6 %. Therefore, FE are potentially natural anti‐inflammation and antimicrobial agents for topical applications in the pharmaceutical and cosmetic industries.
The Two‐Steps Reaction Fluorescent Probe for the Selective Detection of Cysteine and Its Applications**
Authors: Liu Xueliang , Wei Haiyuan , Yan Mengdi , Hai Guangfan , Li Qin , Yan Ruifang , Zhao Shan , Zhao Xiaoxia , Sun Xiaoqing , Zhang Tao 
Published: December 2021

AbstractWe reported the specific fluorescent probe (MC‐BOD‐XDS) with two‐steps reaction based on monosulfanyl‐coumarin‐BODIPY for selective detection of cysteine, high activity sulfanyl‐coumarin as the multiple reaction group instead of a group internal standard fluorophore. The reaction mechanism of MC‐BOD‐XDS for detecting cysteine was different from the reported probes about the nucleophilic aromatic substitution reaction (SNAr) of chlorinated BODIPY. The fluorescent color of MC‐BOD‐XDS changed from yellow to red, and then to orange. The linear calibration diagram showed that it can potentially be used for quantitatively detection of Cys. Its potential applications were demonstrated by employing it for detection of Cys in artificial urine and in fluorescent imaging in HeLa cells.
Malignant transformation of mature cystic teratoma into undifferentiated carcinoma: A case report
Authors: Aryal Vinayak , Maharjan Rubina , Singh Moushami , Marhatta Adwait , Bajracharya Anu , Dhakal Hari Prasad 
Published: December 2021

AbstractMalignant transformation of mature cystic teratoma (MCTO) is a rare entity. Even rarer is the transformation of MCTO into undifferentiated carcinoma. We report a case of an 80‐year‐old woman with undifferentiated carcinoma and squamous cell carcinoma component originating from mature cystic teratoma of the ovary.
Transition‐Metal‐Mediated Glycosylation with Thioglycosides
Authors: Escopy Samira , Demchenko Alexei V. 
Published: December 2021

AbstractThioglycosides are among the most common glycosyl donors that find broad application in the synthesis of glycans and glycoconjugates. However, the requirement for toxic and/or large access of activators needed for common glycosylations with thioglycosides remains a notable drawback. Due to the increased awareness of the chemical waste impact on the environment, synthetic studies have been driven by the goal of finding non‐toxic reagents. The main focus of this review is to highlight recent methods for thioglycoside activation that rely on transition metal catalysis.
Comparative Study of Nitro‐ and Azide‐Functionalized ZnII‐Based Coordination Polymers (CPs) as Fluorescent Turn‐On Probes for Rapid and Selective Detection of H2S in Living Cells
Authors: Saha Subhajit , Roy Pritam Kumar , Maity Kartik , Mandal Mahitosh , Biradha Kumar 
Published: December 2021

AbstractSelective detection of H2S in the cellular systems using fluorescent CPs/MOFs is of great scientific interest due to their outstanding aqueous stability, biocompatibility and real‐time detection ability. Fabrication of such materials using complete biologically essential elements and applying them as an efficient biosensor is still quite challenging. In this context, two newly synthesized CPs containing biologically essential metal ion (Zn) and nitro/azido functional groups into the framework to sense extracellular and intracellular H2S by reducing into respective amines are presented. The CP‐1 containing the azide group acted as an efficient fluorescent turn‐on probe with the lowest detection limit (7.2 μM) and shortest response time (30 s) among the Zn‐based probes reported till date. Moreover, CP‐1 exhibited green luminescence in live cells after imaging a very low concentration of H2S, whereas the nitro analogue CP‐2 could not detect the target analyte due to its framework disruption.
Tunable Surface Electric Field of Electrocatalysts via Constructing Schottky Heterojunctions for Selective Conversion of Trash Ions to Treasures
Authors: Zhang Shi‐Nan , Gao Peng , Sun Lu‐Han , Chen Jie‐Sheng , Li Xin‐Hao 
Published: December 2021

AbstractSurface electric field of catalyst is widely recognized as one of the key points to boost catalytic activity. However, there is still a lack of convenient ways to tune the surface electric field to selectively boost the catalytic conversions of different types of reactants in specific catalytic reactions. Here, we introduce a conceptually new method to tune the surface electric field of electrode materials by adjusting the number and density of heterojunctions inside. Both theoretical and experimental results prove that the well‐designed surface electric field of an electrocatalyst plays a key role in facilitating pre‐adsorption and/or activation of reactants for selective conversion of trash ions to useful products in hydrogen and oxygen evolution reactions as well as NOx− reduction reactions.
Interstitial Hydrides in Nanoclusters can Reduce M(I) (M=Cu, Ag, Au) to M(0) and Form Stable Superatoms
Authors: van Zyl Werner E. , Liu C. W. 
Published: December 2021

AbstractHigh‐nuclearity clusters resemble the closest model between the determination of atomically precise chemical species and the bulk metallic version thereof, and both impacts on a variety of applications, including catalysis, optics, sensors, and new energy sources. Our interest lies with the nanoclusters of the Group 11 (Cu, Ag, Au) metals stabilized by dichalcogenido and hydrido ligands. Herein, we describe superatoms formed by the clusters and their relationship with precursor hydrido clusters. Specifically, our concept seeks to demonstrate a possible correlation that exist between hydrido clusters (and nanoalloys) and the formation of superatoms, with the loss of hydrides and typically with release of H2 gas. These reactions appear to be internal self‐redox reactions and require no additional reducing agent, but does seem to require a similar core structure. Knowledge of such processes could provide insight into how clusters grow and an understanding in bridging the atomically precise cluster – metal nanoparticle mechanism.
Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications
Authors: Aroulanda Christie , Lesot Philippe 
Published: December 2021

AbstractThe study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order‐dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I > 1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide‐based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in‐solution conformational distribution of flexibles solutes using NMR in polypeptide‐based aligned solvents is also proposed.
BUSCO: Assessing Genomic Data Quality and Beyond
Authors: Manni Mosè , Berkeley Matthew R. , Seppey Mathieu , Zdobnov Evgeny M. 
Published: December 2021

AbstractEvaluation of the quality of genomic “data products” such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single‐copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome‐assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto‐lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO “plugin” workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.[Correction added on May 16, 2022, after first online publication: CSAL funding statement has been added.]Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manuallyBasic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCOBasic Protocol 3: Assessing multiple inputsAlternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto‐lineage workflow and SnakemakeSupport Protocol 1: BUSCO setupSupport Protocol 2: Visualizing BUSCO resultsSupport Protocol 3: Building phylogenomic trees
A reduction in the vascular smooth muscle cell focal adhesion component syndecan‐4 is associated with abdominal aortic aneurysm formation
Authors: Hu Jiaxin , Li Yuyu , Wei Zhonghai , Chen Haiting , Sun Xuan , Zhou Qing , Zhang Qi , Yin Yong , Guo Meng , Chen Jianzhou , Zhai Guangyao , Xu Biao , Xie Jun 
Published: December 2021

AbstractBackgroundAbdominal aortic aneurysm (AAA) is a serious vascular disease for which there is no effective drug treatment. The incidence of AAA increases significantly as a subject ages, and the molecular mechanism of AAA formation remains elusive. In the present study, we investigated the role of syndecan‐4 (SDC4), an important component of focal adhesions, in AAA formation and its association with phenotypic changes in vascular smooth muscle cells (VSMCs).Methods and resultsThe protein expression levels of SDC4 were significantly decreased in human AAA tissue and those of an AAA mouse model. Moreover, SDC4 knockout (KO) in mice accelerated the formation and rupture of AAAs induced by angiotensin II (Ang II) and calcium chloride (CaCl2)Mechanistically, the decrease in SDC4 led to the transformation of cultured VSMCs from a contractile to a secretory phenotype. The RhoA‐F/G‐actin‐myocardin‐related transcription factor‐A (MRTF‐A) signalling pathway was shown to be involved in SDC4‐dependent VSMC alteration. Sphingosine‐1‐phosphate (S1P), a G‐protein‐coupled receptor, attenuated the AAA formation in SDC4‐KO and wild‐type (WT) mice in response to Ang II and CaCl2 stimulation.ConclusionWe herein demonstrated that silencing SDC4 was associated with increased AAA formation and phenotypic changes in VSMCs via the RhoA‐F/G‐actin‐MRTF‐A pathway. These findings indicated that a reduction in SDC4 expression was an important pathological alteration and potential therapeutic target for AAA formation.
METTL1‐m7G‐EGFR/EFEMP1 axis promotes the bladder cancer development
Authors: Ying Xiaoling , Liu Bixia , Yuan Zusen , Huang Yapeng , Chen Cong , Jiang Xu , Zhang Haiqing , Qi Defeng , Yang Shulan , Lin Shuibin , Luo Junhang , Ji Weidong 
Published: December 2021

AbstractBackgroundThe posttranscriptional modifications of transfer RNA (tRNA) are critical for all aspects of the tRNA function and have been implicated in the tumourigenesis and progression of many human cancers. By contrast, the biological functions of methyltransferase‐like 1 (METTL1)‐regulated m7G tRNA modification in bladder cancer (BC) remain obscure.ResultsIn this research, we show that METTL1 was highly expressed in BC, and its level was correlated with poor patient prognosis. Silencing METTL1 suppresses the proliferation, migration and invasion of BC cells in vitro and in vivo. Multi‐omics analysis reveals that METTL1‐mediated m7G tRNA modification altered expression of certain target genes, including EGFR/EFEMP1. Mechanistically, METTL1 regulates the translation of EGFR/EFEMP1 via modifying certain tRNAs. Furthermore, forced expression of EGFR/EFEMP1 partially rescues the effect of METTL1 deletion on BC cells.ConclusionsOur findings demonstrate the oncogenic role of METTL1 and the pathological significance of the METTL1‐m7G‐EGFR/EFEMP1 axis in the BC development, thus providing potential therapeutic targets for the BC treatment.
Biobank Participants’ Attitudes toward Requiring Understanding for Biobank Consent
Authors: Kasperbauer T.J. , Halverson Colin , Garcia Abigail , Schmidt Karen K. , Schwartz Peter H. 
Published: December 2021

ABSTRACTBiobank participants often do not understand the information they are provided during the informed consent process. Ethicists and other stakeholders have disagreed, however, on the appropriate response to these failures in understanding. This paper describes an attempt to address this issue by conducting knowledge tests with 22 recent biobank enrollees, followed by in‐depth, semistructured interviews about the goal of understanding in biobank consent. The interviews revealed that while biobank enrollees thought the information on the knowledge test was important, they did not think that performance on the test should affect whether individuals are permitted to enroll in a biobank. Three main themes emerged from the interviews: helping others by contributing to research is more important than understanding consent forms, less understanding is required because biobank‐based research is low risk, and only a small amount of information in the consent form is really essential. These perspectives should be considered in discussing the ethics and governance of biobank consent processes.
Standard metabolic rate does not associate with age‐at‐maturity genotype in juvenile Atlantic salmon
Authors: Åsheim Eirik R. , Prokkola Jenni M. , Morozov Sergey , Aykanat Tutku , Primmer Craig R. 
Published: December 2021

AbstractAtlantic salmon (Salmo salar) is a species with diverse life‐history strategies, to which the timing of maturation contributes considerably. Recently, the genome region including the gene vgll3 has gained attention as a locus with a large effect on Atlantic salmon maturation timing, and recent studies on the vgll3 locus in salmon have indicated that its effect might be mediated through body condition and accumulation of adipose tissue. However, the cellular and physiological pathways leading from vgll3 genotype to phenotype are still unknown. Standard metabolic rate is a potentially important trait for resource acquisition and assimilation and we hypothesized that this trait, being a proxy for the maintenance energy expenditure of an individual, could be an important link in the pathway from vgll3 genotype to maturation timing phenotype. As a first step to studying links between vgll3 and the metabolic phenotype of Atlantic salmon, we measured the standard metabolic rate of 150 first‐year Atlantic salmon juveniles of both sexes, originating from 14 different families with either late‐maturing or early‐maturing vgll3 genotypes. No significant difference in mass‐adjusted standard metabolic rate was detected between individuals with different vgll3 genotypes, indicating that juvenile salmon of different vgll3 genotypes have similar maintenance energy requirements in the experimental conditions used and that the effects of vgll3 on body condition and maturation are not strongly related to maintenance energy expenditure in either sex at this life stage.
A review of spatial capture–recapture: Ecological insights, limitations, and prospects
Authors: Tourani Mahdieh 
Published: December 2021

AbstractFirst described by Efford (2004), spatial capture–recapture (SCR) has become a popular tool in ecology. Like traditional capture–recapture, SCR methods account for imperfect detection when estimating ecological parameters. In addition, SCR methods use the information inherent in the spatial configuration of individual detections, thereby allowing spatially explicit estimation of population parameters, such as abundance, survival, and recruitment. Paired with advances in noninvasive survey methods, SCR has been applied to a wide range of species across different habitats, allowing for population‐ and landscape‐level inferences with direct consequences for conservation and management. I conduct a literature review of SCR studies published since the first description of the method and provide an overview of their scope in terms of the ecological questions answered with this tool, taxonomic groups targeted, geography, spatio‐temporal extent of analyses, and data collection methods. In addition, I review approaches for analytical implementation and provide an overview of parameters targeted by SCR studies and conclude with current limitations and future directions in SCR methods.