bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes
Authors: Kagra Deepika , Jangra Raman , Sharma Purshotam 
Published: November 2021

AbstractA nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X‐ray structures of RNA : protein complexes were analyzed for hydrogen bonds between amino‐acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino‐acid residue, as well as the rN and amino‐acid atoms participating in the hydrogen bonding. 80 possible hydrogen‐bonding combinations (4 (rNs)×20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously‐selected DNA:protein complexes reveals that the absence of 2′‐OH group in DNA mainly accounts for the differences in DNA:protein and RNA : protein hydrogen bonding. Search for intrinsically‐stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well‐defined RNA : protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid‐protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA : protein recognition.
Assays to Study Enzymatic and Non‐Enzymatic Protein Lysine Acetylation In Vitro
Authors: Graf Leonie G. , Vogt Robert , Blasl Anna‐Theresa , Qin Chuan , Schulze Sabrina , Zühlke Daniela , Sievers Susanne , Lammers Michael 
Published: November 2021

AbstractProteins can be lysine‐acetylated both enzymatically, by lysine acetyltransferases (KATs), and non‐enzymatically, by acetyl‐CoA and/or acetyl‐phosphate. Such modification can be reversed by lysine deacetylases classified as NAD+‐dependent sirtuins or by classical Zn2+‐dependent deacetylases (KDACs). The regulation of protein lysine acetylation events by KATs and sirtuins/KDACs, or by non‐enzymatic processes, is often assessed only indirectly by mass spectrometry or by mutational studies in cells. Mutational approaches to study lysine acetylation are limited, as these often poorly mimic lysine acetylation. Here, we describe protocols to assess the direct regulation of protein lysine acetylation by both sirtuins/KDACs and KATs, as well as non‐enzymatically. We first describe a protocol for the production of site‐specific lysine‐acetylated proteins using a synthetic biological approach, the genetic code expansion concept (GCEC). These natively folded, lysine‐acetylated proteins can then be used as direct substrates for sirtuins and KDACs. This approach addresses various limitations encountered with other methods. First, results from sirtuin/KDAC‐catalyzed deacetylation assays obtained using acetylated peptides as substrates can vary considerably compared to experiments using natively folded substrate proteins. In addition, producing lysine‐acetylated proteins for deacetylation assays by using recombinantly expressed KATs is difficult, as these often do not yield proteins that are homogeneously and quantitatively lysine acetylated. Moreover, KATs are often huge multi‐domain proteins, which are difficult to recombinantly express and purify in soluble form. We also describe protocols to study the direct regulation of protein lysine acetylation, both enzymatically, by sirtuins/KDACs and KATs, and non‐enzymatically, by acetyl‐CoA and/or acetyl‐phosphate. The latter protocol also includes a section that explains how specific lysine acetylation sites can be detected by liquid chromatography coupled to tandem mass spectrometry (LC‐MS/MS). The protocols described here can be useful for providing a more detailed understanding of the enzymatic and non‐enzymatic regulation of lysine acetylation sites, an important aspect to judge their physiological significance. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Preparation of N‐(ε)‐lysine‐acetylated proteins using the genetic code expansion concept (GCEC)Basic Protocol 2: In vitro sirtuin (SIRT)‐catalyzed deacetylation of lysine‐acetylated proteins prepared by the GCECBasic Protocol 3: In vitro KDAC/HDAC‐catalyzed deacetylation of lysine‐acetylated proteinsBasic Protocol 4: In vitro lysine acetylation of recombinantly expressed proteins by lysine acetyltransferases (KATs)Basic Protocol 5: In vitro non‐enzymatic lysine acetylation of proteins by acetyl‐CoA and/or acetyl‐phosphate
Preparation of Sulfur‐doped Carbon for Supercapacitor Applications: A Review
Authors: Shaheen Shah Syed , Abu Nayem S. M. , Sultana Nasrin , Saleh Ahammad A. J. , Abdul Aziz Md. 
Published: November 2021

AbstractElectrochemical capacitors, also known as supercapacitors (SCs), have lately played an important role in energy storage and conversion systems due to their specific characteristics such as high strength, durability, and environmental friendliness. A wide range of materials is used as electrodes for SC applications because the electrochemical efficiency is primarily determined by the electrode materials used. Carbonaceous materials with unique surface, chemical, electrochemical, and electronic characteristics have become attractive for energy storage research, but they cannot meet the rising need for high specific energy and specific power. Besides, heteroatom‐doped carbon materials have shown pseudocapacitance characteristics and improved specific energy, specific power, and conductivity. This makes them more adaptable in SC application. Among different heteroatom doping of carbon, S‐doped carbon has gained considerable attention in SC applications due to its unpaired electrons and easily polarizable nature. S‐doped carbon materials‐based SCs have demonstrated enhanced surface wettability, improved conductivity, and induced pseudocapacitance effect, thereby delivering improved specific energy and specific power. Many reports on S‐doped carbon for SC applications have been published, but there is no specific Review on the preparation of S‐doped carbon for SC applications. This Review focuses on recent developments in the field of SC electrodes made from S‐doped carbon materials. Herein, the preparation methods and applications of S‐doped carbon for SCs were summarized following a brief discussion of different electrochemical characterization techniques of SCs. Finally, the challenges of S‐doped carbon materials and their potential prospects were discussed to give crucial insights into the favorable factors for future innovations of SC electrodes. This Review aims to provide insight for further research on the preparation of S‐doped carbon for electrochemical energy storage applications.
Reliable identification and quantification of neural cells in microscopic images of neurospheres
Authors: Förster Nils , Butke Joshua , Keßel Hagen Eike , Bendt Farina , Pahl Melanie , Li Lu , Fan Xiaohui , Leung Ping‐chung , Klose Jördis , Masjosthusmann Stefan , Fritsche Ellen , Mosig Axel 
Published: November 2021

AbstractNeurosphere cultures consisting of primary human neural stem/progenitor cells (hNPC) are used for studying the effects of substances on early neurodevelopmental processes in vitro. Differentiating hNPCs migrate and differentiate into radial glia, neurons, astrocytes, and oligodendrocytes upon plating on a suitable extracellular matrix and thus model processes of early neural development. In order to characterize alterations in hNPC development, it is thus an essential task to reliably identify the cell type of each migrated cell in the migration area of a neurosphere. To this end, we introduce and validate a deep learning approach for identifying and quantifying cell types in microscopic images of differentiated hNPC. As we demonstrate, our approach performs with high accuracy and is robust against typical potential confounders. We demonstrate that our deep learning approach reproduces the dose responses of well‐established developmental neurotoxic compounds and controls, indicating its potential in medium or high throughput in vitro screening studies. Hence, our approach can be used for studying compound effects on neural differentiation processes in an automated and unbiased process.
Oxygen‐Doped PAH Electrochromes: Difurano, Dipyrano, and Furano‐Pyrano Containing Naphthalene‐Cored Molecules
Authors: Fletcher‐Charles Jack , Ferreira Rúben R. , Abraham Michael , Romito Deborah , Oppel Markus , González Leticia , Bonifazi Davide 
Published: November 2021

AbstractIn this work, we report the synthesis of O‐doped naphthalene‐based electrochromes. Exploiting the CuO‐mediated Pummerer oxidative cycloetherification reaction, a series of 1,4‐ and 1,5‐disubstituted naphthalene‐cored dipyrano, difurano, and furano‐pyrano polycyclic aromatic hydrocarbons (PAHs) have been prepared. Steady‐state UV‐Vis absorption and emission investigations showed that the spectroscopic profile strongly depends on the O‐doping topology, with the dipyrano and the difurano derivatives demonstrating the most red‐shifted and blue‐shifted electronic transition, respectively. Computational investigations revealed that the cycloetherification reaction raises the HOMO energy level (while the LUMO remains largely unaffected), with the dipyrano derivatives displaying the highest values. Spectroelectrochemical measurements showed that, depending on the O‐topology and the type of O‐ring, different electrochromic responses could be obtained with colour transitions featuring high contrasts involving yellow, pink, orange or blue colours.
Increasing prevalence of chronic non‐cancer pain in Denmark from 2000 to 2017: A population‐based survey
Authors: Ekholm Ola , Diasso Pernille Døssing Kwateng , Davidsen Michael , Kurita Geana Paula , Sjøgren Per 
Published: November 2021

AbstractBackgroundThis investigation comprised information from the Danish population to analyse the development of chronic non‐cancer pain (CNCP) prevalence according to sex, age, physical job demand and educational level.MethodsData derives from the Danish Health and Morbidity Surveys based on random samples of adults living in Denmark. The analysed samples were composed by 10,457 in 2000 (response rate: 62.7%), 5686 in 2005 (52.1%), 15,165 in 2010 (60.1%), 14,265 in 2013 (57.1%) and 14,022 in 2017 (56.1%). CNCP was defined as pain lasting 6 months or more. Individuals with a self‐reported history of cancer were excluded. Calibration weighting was applied to reduce the impact of potential non‐response bias. The Relative and the Absolute Concentration Index were calculated to measure educational inequalities.ResultsCNCP prevalence has increased 8.3 percentage points during 2000–2017 (19.5%–27.8%) and is highest among women (22.1% to 30.8%). Higher CNCP prevalence among men aged 45–64 years exceeded the men aged >65 years in 2017 (31.9% and 29.8%, respectively). There was a continuous increase in CNCP prevalence in individuals with sedentary work or low physical demand at job from 2000 to 2017; among those with moderate or high physical demand at job the prevalence increased sharply from 2000 to 2010 after which the prevalence remained stable. Higher CNCP prevalence persisted among individuals with lower level of education regardless of gender and the inequalities remained stable over time.ConclusionThe Danish prevalence of chronic pain has increased in the last two decades and higher numbers are observed in some sociodemographic groups.SignificanceThis study provides an overview of the development of chronic non‐cancer pain in a country and analyses the trends with socioeconomic inequalities. The continuous increasing prevalence may have huge social and economic implications. This study reveals an urgent need for measures to attenuate the increasing prevalence, which should be a priority for public health policy.
Dual Electrode Detection in LC‐EC Analysis of Sanger‐tagged Amino Acids: Electrochemical Reduction of Aromatic Nitro Groups
Authors: Balasingam Miththira , Becker John D. , Guerrero‐Almaraz Paulina , Sun Haoran , Koppang Miles D. 
Published: November 2021

AbstractAnalysis of amino acids is crucial to protein structure elucidation. Amino acids, amenable to separation by liquid chromatography (LC), can be detected by sensitive detectors used in liquid chromatograph including absorbance, fluorescence or electrochemical detector when derivatized. Derivatization of amino acids using suitable reagents enhances the separation and detection of amino acids using liquid chromatography. Sanger's reagent (1‐fluoro‐2,4‐dinitrobenzene, DNFB) makes amino acids suitable for absorbance detection. However, little has been done in terms of liquid chromatography with electrochemical detection (LC‐EC) of the DNFB derivatized amino acids. Furthermore, sensor development based on electrochemistry of nitroaromatics has increased dramatically for explosive detection. Since nitroaromatics are electrochemically active, it is essential to determine the reduction pathway. Cyclic voltammetry (CV), rotating disk electrode (RDE) and rotating ring disk electrode (RRDE) experiments have been performed on nitrobenzene (NB) and N‐methyl‐2,4‐dinitroaniline (NMDNA). The results showed that the nitro group was reduced to hydroxylamine in aqueous solutions by addition of four electrons and four protons per nitro group and the hydroxylamine can be reversibly oxidized into a nitroso by removal of two electrons and two protons. Electrochemical detection of the nitro groups is appropriate for dual electrode detection of DNFB labeled amino acids in which reduction can occur on an upstream electrode and corresponding oxidation of the reduction product occurs on the downstream electrode.
Thermoplastic Electrode (TPE)‐based Enzymatic Glucose Sensor Using Polycaprolactone‐graphite Composites
Authors: Clark Kaylee M. , Henry Charles S. 
Published: November 2021

AbstractCarbon composite electrodes are frequently used for enzymatic electrodes but suffer from poor electrocatalytic activity and/or are single use. Our group has recently developed thermoplastic electrodes (TPEs) that use a thermopolymer binder. The electrodes can be easily molded without extensive use of organic solvents enabling catalysts and enzymes to be added directly to the electrode material. The TPE material is bulk‐modified with cobalt phthalocyanine and glucose oxidase, resulting in a robust sensor that is stable for over 100 minutes. These sensors can be molded into intricate shapes and sanded for surface renewal, allowing the sensors to be continuously reused.
Power responses of a building subjected to pulse‐like ground motions
Authors: Lin Jui‐Liang 
Published: November 2021

AbstractCompared with non‐pulse‐like ground motions, pulse‐like ground motions are usually near‐fault motions with forward directivity or fling‐step effect. These pulse‐like ground motions are characterized by prominent velocity pulses. The impact force caused by such velocity pulses is generally more destructive than the inertia force induced by ground accelerations. The impact force infuses substantial energy into structures within a rather short period. The power responses of buildings are thus crucial for understanding the risk potential posed by pulse‐like ground motions. This study innovatively defines the power responses of a building as the product of story shear and inter‐story velocity. It investigates the power responses of a vertically irregular three‐story building subjected to two ensembles of pulse‐like and non‐pulse‐like ground motion records. The results show that power demand is a competent measure that reflects the effect of pulse‐like ground motions on building structures.
Economic feasibility of electric vehicles: A case study
Authors: Cheok Quentin , Husaini Nurul Hafizan , Nauman Malik Muhammad 
Published: November 2021

AbstractPersonal transportation is prevalent in Brunei Darussalam because of the lack of adequate public transportation. However, Brunei is not immune to the effects of climate change and as such, has launched a national policy to mitigate the impacts. As electric vehicles presently are very rare to Brunei, this article seeks to determine the total cost of ownership of internationally popular electric vehicles (EVs) and internal combustion engine vehicles (ICEVs) to put things in perspective for the Brunei market. The methodology investigated how the total cost of ownership (TCO) is affected by depreciation, interest repayment, maintenance and repair, fuel costs, taxation, and insurance premiums. We have determined that without any subsidies, predictably TCOs of EVs are higher than popular ICEVs; however, they are comparable to TCOs of European premium brands. The Tesla Model 3 has a TCO of USD 760 per month whereas a Mercedes Benz C200 has a TCO USD800 per month. The authors have suggested that a 30% subsidy on the showroom price of EVs be introduced and to improve charging infrastructure as this would be vital to governmental policy planning as Brunei seeks to increase the ownership of electric vehicles to 60% by 2035.
Transoral robotic surgery (TORS) using the da Vinci Xi: prospective analysis of feasibility, safety, and outcomes
Authors: Meulemans Jeroen , Vanermen Margaux , Goeleven Ann , Clement Paul , Nuyts Sandra , Laenen Annouschka , Delaere Pierre , Vander Poorten Vincent 
Published: November 2021

AbstractBackgroundThe da Vinci Xi system is not Food and Drug Administration approved for transoral robotic surgery (TORS), resulting in limited data.MethodsThis prospective study evaluates the feasibility, safety, and outcomes of Xi‐TORS in an oncological setting.ResultsSixty‐one patients with head and neck cancer were consecutively included for Xi‐TORS. Adequate exposure and macroscopically complete resection were achieved in 59 patients (success rate = 96.7%). Intraoperative difficulties and complications were encountered in 47.5% and 20.3% of patients, respectively. Postoperative hemorrhage occurred in 11.9%; no treatment‐related deaths were encountered. Two‐year overall survival and disease‐specific survival were 90.5% and 95.6%, respectively. No long‐term (>1 month) tracheotomies were necessary, and only two patients remained tube‐feeding dependent. The functional baseline level was regained at 12 months for the MD Anderson Dysphagia Inventory and at 24 months for the Swallowing quality‐of‐life questionnaire. QLQ‐H&N35‐assessed QOL returned to baseline 6 months postoperatively.ConclusionsXi‐TORS is safe, feasible, and with high oncological and functional effectiveness.
The thymic microenvironment gradually modulates the phenotype of thymus‐homing peripheral conventional dendritic cells
Authors: Herppich Susanne , Beckstette Michael , Huehn Jochen 
Published: November 2021

AbstractBackground & AimsThymic conventional dendritic cells (t‑DCs) are crucial for the development of T cells. A substantial fraction of t‑DCs originates extrathymically and migrates to the thymus. Here, these cells contribute to key processes of central tolerance like the clonal deletion of self‑reactive thymocytes and the generation of regulatory T (Treg) cells. So far, it is only incompletely understood which impact the thymic microenvironment has on thymus‑homing conventional DCs (cDCs), which phenotypic changes occur after the entry of peripheral cDCs into the thymus and which functional properties these modulated cells acquire.Materials & MethodsIn the present study, we mimicked the thymus‑homing of peripheral cDCs by introducing ex vivo isolated splenic cDCs (sp‑DCs) into reaggregated thymic organ cultures (RTOCs).ResultsAlready after two days of culture, the transcriptomic profile of sp‑DCs was modulated and had acquired certain key signatures of t‑DCs. The regulated genes included immunomodulatory cytokines and chemokines as well as costimulatory molecules. After four days of culture, sp‑DCs appeared to have at least partially acquired the peculiar Treg cell‐inducing capacity characteristic of t‑DCs.Discussion & ConclusionTaken together, our findings indicate that peripheral cDCs possess a high degree of plasticity enabling them to quickly adapt to the thymus‐specific microenvironment. We further provide indirect evidence that thymus‐specific properties such as the efficient induction of Treg cells under homeostatic conditions can be partially transferred to thymus‑homing peripheral cDC subsets.
Cyanobacteria derived compounds: Emerging drugs for cancer management
Authors: Shahid Aqsa , Khurshid Mohsin , Aslam Bilal , Muzammil Saima , Mehwish Hafiza Mahreen , Rajoka Muhammad Shahid Riaz , Hayat Hafiz Fakhar , Sarfraz Muhammad Hassan , Razzaq Muhammad Khuram , Nisar Muhammad Atif , Waseem Muhammad 
Published: November 2021

AbstractThe wide diversity of cyanobacterial species and their role in a variety of biological activities have been reported in the previous few years. Cyanobacteria, especially from marine sources, constitutes a major source of biologically active metabolites that have gained great attention especially due to their anticancer potential. Numerous chemically diverse metabolites from various cyanobacterial species have been recognized to inhibit the growth and progression of tumor cells through the induction of apoptosis in many different types of cancers. These metabolites activate the apoptosis in the cancer cells by different molecular mechanisms, however, the dysregulation of the mitochondrial pathway, death receptors signaling pathways, and the activation of several caspases are the crucial mechanisms that got considerable interest. The array of metabolites and the range of mechanisms involved may also help to overcome the resistance acquired by the different tumor types against the ongoing therapeutic agents. Therefore, the primary or secondary metabolites from the cyanobacteria as well as their synthetic derivates could be used to develop novel anticancer drugs alone or in combination with other chemotherapeutic agents. In this study, we have discussed the role of cyanobacterial metabolites in the induction of cytotoxicity and the potential to inhibit the growth of cancer cells through the induction of apoptosis, cell signaling alteration, oxidative damage, and mitochondrial dysfunctions. Moreover, the various metabolites produced by cyanobacteria have been summarized with their anticancer mechanisms. Furthermore, the ongoing trials and future developments for the therapeutic implications of these compounds in cancer therapy have been discussed.
Research on corrosion assessment model for buried steel pipelines under dynamic DC stray current based on machine learning
Authors: Ma Shuaijie , Du Yanxia , Che Kun , Qin Huimin , Su Yanjing 
Published: November 2021

AbstractCoupon tests on the pipeline subjected to metro dynamic DC interference were conducted. The pipe‐to‐soil from 78 sites including off‐potentials (Eoff), on‐potentials (Eon), and corrosion rate data were obtained, and then the dynamic fluctuation parameters of pipe‐to‐soil potentials were analyzed statistically. Further, the Pearson correlation between dynamic statistical parameters of pipe‐to‐soil potentials and corrosion rates was analyzed and showed that the statistical parameter of “roff ⩾ −0.85 V” and “mean[Eoff,cmax]” have a greater correlation with corrosion rate than others. Based on the statistical parameters of Eoff and the machine learning method, the optimal feature subset of the corrosion rate model was selected; meanwhile, it is proved that the negative shift of Eoff plays an important role in the prediction of corrosion rate. Finally, the corrosion rate model for buried steel pipeline under dynamic DC interference was established by random forest (rfr) method on 66 training data, then generalization performance of the model was verified on 12 test data. The results show that mean absolute error and R2 are 0.0358 mm/a and 0.56, respectively, on test data.