bluuebunny/crossref_metadata_2025 huggingface dataset:
hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution
Authors: Jackson Chris , McLay Todd , Schmidt‐Lebuhn Alexander N.
Published: July 2023

Premise

The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate inference of evolutionary relationships. Algorithmic approaches using gene tree topologies for the inference of ortholog groups are computationally efficient and broadly applicable to non‐model organisms, especially in the absence of a known species tree.

Methods and Results

We containerized and expanded the functionality of both HybPiper and a pipeline for the inference of ortholog groups, providing novel options for the treatment of target capture sequence data, and allowing seamless use of the outputs of the former as inputs for the latter. The Singularity container presented here includes all dependencies, and the corresponding pipelines (hybpiper‐nf and paragone‐nf, respectively) are implemented via two Nextflow scripts for easier deployment and to vastly reduce the number of commands required for their use.

Conclusions

The hybpiper‐nf and paragone‐nf pipelines are easily installed and provide a user‐friendly experience and robust results to the phylogenetic community. They are used by the Australian Angiosperm Tree of Life project. The pipelines are available at https://github.com/chrisjackson-pellicle/hybpiper-nf and https://github.com/chrisjackson-pellicle/paragone-nf.
Regulating Zinc Deposition via Zincophilic 2D‐Cu2Te as the Current Collector to Suppress Dendrite Formation toward High Performance Aqueous Zinc‐Ion Batteries
Authors: Tsai Ming‐Hsuan , Lin Tuan‐Yue , Su Tian‐Shun , Chen Guan‐Min , Liu Yu‐chen , Chen Yu‐Ze
Published: July 2023

Invited for this month's cover is the group of Nano Horizons Lab hosted by Prof. Yu‐Ze Chen. The cover picture shows the lateral deposition of Zn guided by zincophilic Cu2Te flakes, resulting in the suppression of dendrite growth. Read the full text of the Research Article at 10.1002/batt.202300107.
Detection and identification of imperatorin metabolites in rat, dog, monkey, and human liver microsomes by ultra‐high‐performance liquid chromatography combined with high‐resolution mass spectrometry and Compound Discoverer software
Authors: He Fan , Zeng Fenglian , Situ Xiaohong , He Runmin , Zheng Wei , Chen Yongzhuang , Ou Dinghong , Chen Yilu
Published: July 2023

Imperatorin, a furanocoumarin that widely exists in many umbelliferous herbs, has been demonstrated to have a variety of pharmacological effects, including anti‐inflammatory, antiosteoporosis, and antitumor activities. The purpose of this study was to investigate the metabolism of imperatorin using liver microsomes. The metabolites were generated by individually incubating imperatorin with rat, dog, monkey, and human liver microsomes. To trap the reactive metabolites during microsomal metabolism, glutathione (GSH) was included in the incubation. A LC technique coupled with benchtop orbitrap MS with full mass/data‐dependent tandem mass spectrometry acquisition mode was used to detect and identify the generated metabolites. The possible structures of the metabolites were characterized according to their accurate masses and fragment ions. Under the current conditions, a total of 10 metabolites, including four GSH adducts, were identified. The results indicated that imperatorin underwent extensive metabolic reactions including hydroxylation, oxidation, glucuronidation, and GSH conjugation. This study provides essential data on the metabolism of imperatorin, which will be helpful for us to understand the safety and efficacy of this bioactive compound.
Non‐sustainable buying behavior: How the fear of missing out drives purchase intentions in the fast fashion industry
Authors: Bläse Richard , Filser Matthias , Kraus Sascha , Puumalainen Kaisu , Moog Petra
Published: July 2023

Movements like “Fridays for Future” have heightened attention to the need for sustainability, particularly among Generations X, Y, and Z. However, the consumption of fast fashion and so‐called ultra‐fashion products—an ecologically harmful business model—continues to gain momentum, especially among young consumers, not least due to fear of missing out (FOMO). FOMO is well‐known among marketing professionals as a strong trigger for frequently recurring buying behavior. Over the past 5 years, scholars have become increasingly interested in how FOMO triggers buying behavior and have begun to incorporate FOMO in their cognitive models. However, the influence of FOMO on individual fashion purchases and the relationship between brand credibility and sustainable fashion production is not yet well understood. Utilizing cross‐sectional data from three distinct samples in Switzerland and the United States, our study, which included over 650 participants, reveals that brand credibility and FOMO exert direct influences on consumers' purchase intentions for fast fashion products. We identify that FOMO has a negative moderating effect on the relationship between brand credibility and fast fashion purchase intentions. Suggesting that consumers with strong FOMO are less interested in brand credibility when making a purchase decision than those without FOMO. Additionally, we demonstrate that our findings apply to both fast and slow fashion, the latter encompassing sustainably produced fashion. Ultimately, we provide novel empirical evidence of FOMO's influence on buying behavior and shed light on the complex interplay between brand credibility, sustainability, and consumer behavior in the fashion industry.
Early cryptococcosis infection in a liver transplant patient: A case report
Authors: Sadeghi Boogar Shahrokh , Sivandzadeh Gholam Reza , Sehatpour Faezeh , Dadashpour Nazanin , Goodarzian MReza , Parvar Seyedeh Yasamin
Published: July 2023

Key Clinical Message

In order to early diagnose and prevent the infection dissemination in both suspected solid organ donors and recipients after transplantation, pretransplantation screening tests for rare etiologies like Cryptococcus neoformans should be necessitated, as they can affect many vital organs, especially the brain, liver, and lungs.

Cryptococcosis is a systemic fungal infection mainly affecting immunocompromised patients. The infection is occasionally seen in 16–21 months after organ transplantation, while early involvement is uncommon within <30 days posttransplantation. In the present study, we reported an unusual case of cryptococcosis infection 21 days after transplantation, limited to the transplanted liver in a 60‐year‐old male. Treatment with an antifungal agent showed prompt improvement in his clinical condition.
Hydrodynamics in a Bubble Column – Part 1: Two‐Phase Flow
Authors: Sommer Anna-Elisabeth , Draw Mazen , Wang Lantian , Schmidtpeter Jan , Hessenkemper Hendrik , Gatter Josefine , Nam Haein , Eckert Kerstin , Rzehak Roland
Published: July 2023

Multiphase computational fluid dynamics (CFD) simulation is a useful tool to study the hydrodynamics in a bubble column if appropriate closure models are known. Systematic assessment of different models is an ongoing venture that benefits from improved validation data. The present study accumulates a database on two‐phase flow experiments in a bubble column. This is achieved by using a combination of particle image velocimetry and shadowgraphy to measure the liquid velocity field and gas dispersion properties simultaneously. This methodology is applied for different needle diameters and gas flow rates. The experimental data are compared with CFD simulations which show good predictions. A systematic investigation of the three‐phase flow in the bubble column will appear as a sequel.
Methods to Characterise Enzyme Kinetics with Biological and Medicinal Substrates: The Case of Alkaline Phosphatase
Authors: Harroun Scott G. , Vallée‐Bélisle Alexis
Published: July 2023

Alkaline phosphatase (AP) enzymes are of broad interest in fields ranging from biochemistry and medicine to biotechnology and nanotechnology. Characterising the catalytic activity of AP is typically realised by either employing non‐natural signal‐generating substrates that are detectable by absorbance and fluorescence spectroscopy or by quantifying the release of inorganic phosphate by the classic malachite green assay. The latter method is often required for studying “spectroscopically silent” biomolecular substrates, but it does not enable continuous monitoring of kinetics in real‐time. In recent years, newer techniques for studying AP function have been developed to circumvent this limitation, including fluorescent and colourimetric substrate‐specific assays based on supramolecular chemistry, organic probes and nanomaterials, as well as other assays based on isothermal titration calorimetry, direct detection with infrared spectroscopy and mass spectrometry, and monitoring conformational change by fluorescent nanoantennas. Here, we review these strategies and comment on their strengths and weaknesses in the context of AP.
Versa DB: Assisting 13C NMR and MS/MS Joint Data Annotation Through On‐Demand Databases
Authors: Cordonnier Julien , Remy Simon , Renault Jean‐Hugues , Nuzillard Jean‐Marc
Published: July 2023

Compound identification in complex mixtures by NMR and MS is best achieved through experimental databases (DB) mining. Experimental DB frequently show limitations regarding their completeness, availability or data quality, thus making predicted database of increasing common use. Querying large databases may lead to select unlikely structure candidates. Two approaches to dereplication are thus possible: filtering of a large DB before search or scoring of the results after a large scale search. The present work relies on the former approach. As far as we know, nmrshiftdb2 is the only open‐source 13NMR chemical shift predictor that can be freely operated in batch mode. CFM‐ID 4.0 is one of the best‐performing open‐source tools for ESI‐MS/MS spectra prediction. LOTUS is a freely usable and comprehensive collection of secondary metabolites. Integrating the open source database and software LOTUS, CFM‐ID, and nmrshiftdb2 in a dereplication workflow requires presently programming skills, owing to the diversity of data encoding and processing procedures. A graphical user interface that integrates seamlessly chemical structure collection, spectral data prediction and database building still does not exist, as far as we know. The present work proposes a stand–alone software tool that assists the identification of mixture components in a simple way.
Camera traps reveal that terrestrial predators are pervasive at riverscape cold‐water thermal refuges
Authors: Sullivan Christopher J. , Rittenhouse Chadwick D. , Vokoun Jason C.
Published: July 2023

Perceived predation risks by terrestrial predators are major ecological forces in aquatic systems, particularly for aggregating fish. Riverscape thermal refuges are discrete, localized cold‐water patches where fish temporarily aggregate to buffer against heat events. Predation pressures by terrestrial predators at thermal refuges may decrease the thermoregulatory benefits of refuge use, but quantifying such effects can be challenging and controversial when sampling can impose additional stress on fish. We passively monitored terrestrial predator visitation patterns and predation at four thermal refuges in the Housatonic River, Connecticut, USA, between May 18th and September 29th, 2022, with camera traps, a common wildlife monitoring method. Specifically, we (1) assessed diel visitation patterns by different categories of terrestrial predators at thermal refuges and determined if patterns varied among predator categories or with prevailing environmental conditions, and (2) estimated the probability of predation by hour of the day combined across all predator categories, quantifying general predation pressures at refuges. We detected at least one terrestrial predator at a thermal refuge each day, and mean hourly visitation rates (count/h) were highly variable across predator categories and sampling dates. The most supported generalized additive mixed model indicated that terrestrial predator visitation rates (count/h/day) varied with mean daily river discharge and water temperature differential, and relationships differed across categories of terrestrial predators. We observed 22 separate predation attempts on thermoregulating salmonids and predicted that the probability of predation by any terrestrial predator increased from 0.002 to 0.017 throughout a 24 h day (p = .004). Camera traps provided novel evidence that terrestrial predators are pervasive at riverine thermal refuges, which is relevant for refuge conservation and management globally. We recommend the implementation of a coordinated monitoring network across riverine thermal refuges using camera traps, further enriching our ecological understanding of cumulative predator effects in refuges across complex riverscapes.
Temperature dependence ofESDeffects on 28 nmFD‐SOI MOSFETs
Authors: Xiao Yiping , Liu Chaoming , Zhang Yanqing , Qi Chunhua , Ma Guoliang , Wang Tianqi , Huo Mingxue
Published: July 2023

The failure mechanisms caused by electrostatic discharge (ESD) effects at ambient temperatures ranging from −75 to 125°C are investigated by Silvaco TCAD simulator. The devices are NMOS transistors fabricated with 28 nm fully depleted silicon‐on‐insulator (FDSOI) technology. Results indicate that with an increase in temperature, the first breakdown voltage of the device decreased by 27.32%, while the holding voltage decreased by approximately 8.49%. The total current density, lattice temperature, potential, and so forth were extracted for a detailed insight into the failure process. These findings provide valuable references for the design and development of ESD protection devices applied at different temperature ranges.
Impact of endorsement policy on the performance of blockchain‐based VANET
Authors: Gaba Priyanka , Raw Ram Shringar
Published: July 2023

With the revolution in technology, VANET has emerged as a new generation of technology and used globally for intelligent traffic management systems. VANET uses a PKI‐based protocol to maintain privacy and security. Still, some crucial issues remain unresolved, like blind belief in communicated messages, lack of vehicle's interest in participation, revealing the sender vehicle's identity, and maintaining integrity. The solution to these issues will prevent vehicles from propagating fake messages while concurrently protecting the confidentiality of each involved vehicle against tracking attacks. Blockchain, a peer‐to‐peer, immutable, distributed ledger‐based technology, can be adapted as a robust solution to overcome critical challenges and make VANET more secure and reliable. This paper proposes a novel blockchain‐based VANET architecture, blockchain‐based vehicular ad‐hoc network (B‐VANET), implemented on the Hyperledger Fabric platform. B‐VANET aims to secure the network by validating road events before actually updating it on the network. For validation, the trust factor of each vehicle and their past involvement in the network is maintained. Trust factor value decides the trustworthiness of a vehicle. Based on this trust factor, a dynamic endorsement policy is designed. Endorsement policy, part of the smart contract, plays a vibrant role in Hyperledger Fabric. It decides how many and which particular peers can endorse the transaction to make it valid and add it to the ledger. Multiple possible approaches to endorsement policies are identified for B‐VANET and are analyzed using the Hyperledger Caliper tool. These approaches are evaluated for data integrity, confidentiality, and real‐time system issues. An appropriate approach for the B‐VANET system is recognized, giving the best throughput and latency in all possible scenarios. It is analyzed that compared to the worst approach, the best approach achieves an almost 15% increase in throughput and reduces latency by nearly half. We also compared the performance of B‐VANET and other approaches to show that our proposed system better meets VANET's security needs.
A coupled SPH‐EBG numerical model for deformations of MCF7 cancer cell in a microchannel flow
Authors: Lee Jia Min , Chan Wai Lee
Published: July 2023

Properties of a cell can determine its deformations, which can aggravate cancer metastasis. In laboratory, microfluidic technology has been adopted to study cell deformations. However, quantifying the effects of cell deformations has remained difficult. To this end, this paper presents a two‐dimensional particle‐based model that can capture flow‐induced cell deformations in a microchannel. The numerical model is validated with an experimental dataset for MCF7 cell. The simulations show that cell deformations are dominantly attributed to flow acceleration. Stress analyses, conducted by inputting the simulated cell deformations as boundary conditions, show that the maximum normal stresses correspond well to high deformations. Shear stress is in general proportional to the cell's distance from a wall. The simulations also suggest a deformed cell shape that apparently may reduce the average normal stresses. This study highlights the potential of the numerical model to relate the measurable cell deformations to the more elusive cell properties.
Ionizing radiation promotes, whereas calorie restriction suppresses, NASH and hepatocellular carcinoma in mice
Authors: Shang Yi , Morioka Takamitsu , Daino Kazuhiro , Nakayama Takafumi , Nishimura Mayumi , Kakinuma Shizuko
Published: July 2023

The pathological conditions of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis (NASH) are the major risk factors for hepatocellular carcinoma (HCC). Exposure to DNA‐damaging agents such as ionizing radiation is another risk factor for HCC; calorie restriction (CR), however, effectively delays the onset of radiation‐induced HCC. We investigated whether NASH is relevant to radiation‐induced HCC and the cancer‐preventing effect of CR. Eight‐day‐old male B6C3F1 mice were irradiated with 3.8 Gy of X‐rays and then fed a standard diet or 30% CR diet from 49 days of age until necropsy, which was performed from 56 to 600 days with ~100‐day intervals to assess both pathological changes and gene expression levels. We found that early‐life exposure to radiation accelerated lipid accumulation and NASH‐like histopathological changes in the liver, accompanied by accelerated development of HCC. CR ameliorated the changes in lipid metabolism in the liver and reversed the NASH‐like pathology, which effectively delayed HCC development. Gene‐expression profiling revealed the radiation‐related activation and CR‐related suppression of the peroxisome proliferator‐activated receptor gamma/Cd36 pathway of transmembrane fatty‐acid translocation before development of the NASH‐like state. Thus, early‐life exposure to radiation affects lipid metabolism and induces a steatoinflammatory microenvironment that favors HCC development. Therefore, targeting this pathway by CR (or measures that mimic CR) may be a promising strategy for preventing HCC caused by either radiation or other DNA‐damaging agents.
Muscone attenuates susceptibility to ventricular arrhythmia by inhibiting NLRP3 inflammasome activation in rats after myocardial infarction
Authors: Yang Shuang , Bi Yingying , Wei Yanzhao , Li Wei , Liu Jiangwen , Mao Tuohua , Tang Yanhong
Published: July 2023

Fibrosis and abnormal expression of connexin 43 (Cx43) in the ventricle play vital roles in ventricular arrhythmias (VAs) after myocardial infarction (MI). Muscone, an active monomer of heart‐protecting musk pill, has various biological activities, but its effect on susceptibility to VAs in rats with MI has not been determined. In the present study, we investigated the effects of muscone on ventricular inflammation, fibrosis, Cx43 expression, and the occurrence of VAs after MI. An MI model was established by ligating the proximal left anterior descending coronary artery. Then, the MI model rats were administered muscone (2 mg/kg/day) or vehicle (saline)via intragastric injection for 14 days. Cardiac function was evaluated by echocardiography, and an in vivo electrophysiological study was performed on Day 14. Cardiac inflammation, fibrosis, and Cx43 expression were determined by histochemical analysis and western blot analysis. Our results indicated that muscone treatment significantly improved cardiac function and inhibited ventricular inflammation, fibrosis, and nucleotide‐binding oligomerization domain, leucine‐rich repeat, and pyrin domain containing 3 (NLRP3) inflammasome activation. Electrocardiogrphy and electrophysiology studies showed that muscone shortened the QRS interval, QT interval, QTc interval, and action potential duration; prolonged the effective refractory period; and reduced susceptibility to VAs in rats after MI. Furthermore, Cx43 expression in the BZ was increased by muscone treatment, and this change was coupled by inhibition of the NLRP3/IL‐1β/p38 MAPK pathway. Taken together, our results demonstrated that muscone reduces susceptibility to VA, mainly by decreasing ventricular inflammation and fibrosis, and attenuates abnormal Cx43 expression by inhibiting NLRP3 inflammasome activation after myocardial infarction in rats.
The New S7B/E14 Q&A Document Provides Additional Opportunities to Replace the Thorough QT Study
Authors: Darpo Borje , Leishman Derek J.
Published: July 2023

Since 2015, concentration–QTc (C–QTc) analysis has been used to exclude the possibility that a drug has a concerning effect on the QTc interval. This has enabled the replacement of the designated thorough QT (TQT) study with serial electrocardiograms (ECGs) in routine clinical pharmacology studies, such as the first‐in‐human (FIH) study. The E14 revision has led to an increased proportion of FIH studies with the added objective of QT evaluation, with the intention of replacing the TQT study. With the more recent revision of the S7B/E14 Q&A document in February 2022, nonclinical assays/studies can be brought into the process of regulatory decisions at the time of marketing application. If the hERG (human ether‐a‐go‐go‐related gene) and the non‐rodent in vivo study are conducted according to the described best practices and are negative, the previous requirement that a QTc effect of >10 milliseconds must be excluded in healthy subjects at plasma concentrations 2‐fold above what can be seen in patients can be reduced to covering the concentrations seen in patients. For drugs that cannot be safely given in high doses to healthy subjects, ECG evaluation is often performed at the therapeutic dose in patients. If a QTc effect of >10 milliseconds can be excluded, an argument can be made that the drug should be considered as having a low likelihood of proarrhythmic effects due to delayedrepolarization, if supported by negative best practices hERG and in vivo studies. In this article, we describe what clinicians involved in early clinical development need to understand in terms of the hERG and in vivo studies to determine whether these meet best practices and therefore can be used in an integrated clinical/nonclinical QT/QTc risk assessment.
Early family socioeconomic status and later leadership role occupancy: A multisource lifespan study
Authors: Barling Julian , Granger Steve , Weatherhead Julie G. , Turner Nick , Pupco Shani
Published: July 2023

We investigate the indirect effects of socioeconomic status, both at birth and at age 5, on the likelihood of holding a formal leadership position 26 years later via two sequential mechanisms: children's self‐control at age 10 and adolescents' psychological well‐being at age 16. We test this model using multisource data from the British Cohort Study, an ongoing research project studying individuals born in England, Scotland, and Wales in the week of April 5–11, 1970. The data were collected at five different time points, from birth through early adulthood. Results show that the cumulative effects of early socioeconomic status predict children's self‐control at age 10, and self‐control in turn predicts a higher likelihood of leadership role occupancy at age 26 via psychological well‐being at age 16. The findings of the current study illustrate how a range of individual and family factors measured across the lifespan predict leadership role occupancy, with implications for better understanding how socioeconomic adversity and privilege enhance individuals' likelihood of becoming leaders early in their careers.
Unravelling social barriers in ecological restoration decision‐making: A network analysis approach
Authors: Mañas‐Navarro José Javier , Aledo Antonio , Ortiz Guadalupe , Cortina‐Segarra Jordi
Published: July 2023

Ecological restoration (ER hereafter) is situated within a complex socio‐political landscape, characterized by competing interests that can hinder effective decision‐making and implementation of ER initiatives. Despite its importance, these social factors influencing ER decision‐making processes have not been comprehensively examined or interconnected in a systemic manner. This research aims to identify and systematically analyse the social barriers that obstruct ER decision‐making processes in the case of the Valencian Autonomous Region, Spain. Employing a qualitative methodological approach, this study utilized causal maps and network analysis to create a systemic representation of social barriers impacting ER, as identified by the key actors involved in the decision‐making process. The findings establish a relational model of social barriers that influence ER decision‐making. Central nodes of the process, as revealed by this network analysis, include the lack of private sector interest in ER initiatives, the excessive electoral motivation of political decisions and the inefficient civil service structure. This research contributes to a better understanding of the socio‐political dimensions of ER and provides valuable insights for overcoming barriers in the decision‐making process.
Differentiation characteristics of karst vegetation resilience and its response to climate and ecological restoration projects
Authors: Tiantian Chen , Qiang Wang , Yuxi Wang , Li Peng
Published: July 2023

In light of the recent pressure from global warming, extreme drought events, and deleterious human activity, the strength and long‐term change trends of vegetation in karst regions—in terms of their resistance to external disturbances—have not been studied systematically. Therefore, herein, we quantified the vegetation resilience and its nonlinear change trends in south China karst under different environmental gradients by measuring the lag‐1 autocorrelation to time‐series Normalized Difference Vegetation Index (1990–2018), clarifying the driving forces of vegetation resilience changes. It was shown that the vegetation resilience change in south China karst was not monotonous. In the first stage (pre‐2002), precipitation and warming promoted the increase of regional vegetation resilience (slope = −0.045, p < 0.0001). In the second stage (during 2002–2010), the increasing trend of vegetation resilience was not obvious and vegetation resilience was difficult to keep up with vegetation productivity, indicating the time‐lagged effect of ecological restoration projects to vegetation resilience. In the third stage (post‐2010), due to the continuous advancement of ecological restoration projects, vegetation resilience increased significantly and had the largest amplitude (slope = −0.128, p < 0.0001). Simultaneously, under different environmental gradients, vegetation resilience showed significant differentiation characteristics. In comparison to non‐karst regions, increases in the vegetation resilience were more obvious in karst regions especially in the post‐2010. With increases in the soil depth, the vegetation resilience exhibited an increasing trend, indicating its dependence on soil. At slopes >25°, the vegetation resilience increased most obviously and the resilience of meadows was the largest, which can be the preferred vegetation type for ecological restoration projects. This research provides another perspective to understand karst vegetation ecosystem and the results will facilitate the protection of karst ecosystems.
Isolation and functional analysis of phage‐displayed antibody fragments targeting the staphylococcal superantigen‐like proteins
Authors: Alanko Ida , Sandberg Rebecca , Brockmann Eeva‐Christine , de Haas Carla J. C. , van Strijp Jos A. G. , Lamminmäki Urpo , Salo‐Ahen Outi M. H.
Published: July 2023

Staphylococcus aureus produces numerous virulence factors that manipulate the immune system, helping the bacteria avoid phagocytosis. In this study, we are investigating three immune evasion molecules called the staphylococcal superantigen‐like proteins 1, 5, and 10 (SSL1, SSL5, and SSL10). All three SSLs inhibit vital host immune processes and contribute to S. aureus immune evasion. This study aimed to identify single‐chain variable fragment (scFvs) antibodies from synthetic antibody phage libraries, which can recognize either of the three SSLs and could block the interaction between the SSLs and their respective human targets. The antibodies were isolated after three rounds of panning against SSL1, SSL5, and SSL10, and their ability to bind to the SSLs was studied using a time‐resolved fluorescence‐based immunoassay. We successfully obtained altogether 44 unique clones displaying binding activity to either SSL1, SSL5, or SSL10. The capability of the SSL‐recognizing scFvs to inhibit the SSLs' function was tested in an MMP9 enzymatic activity assay, a P‐selectin glycoprotein ligand 1 competitive binding assay, and an IgG1‐mediated phagocytosis assay. We could show that one scFv was able to inhibit SSL1 and maintain MMP9 activity in a concentration‐dependent manner. Finally, the structure of this inhibiting scFv was modeled and used to create putative scFv‐SSL1‐complex models by protein–protein docking. The complex models were subjected to a 100‐ns molecular dynamics simulation to assess the possible binding mode of the antibody.
Association of m1A modification gene polymorphisms with glioma risk in Chinese children
Authors: Liao Fan , Hua Rui‐Xi , Jia Xingyu , Liao Yuxiang , Yuan Li , Ruan Jichen , Li Tianfeng , Zhuo Zhenjian , He Jing
Published: July 2023

Glioma is a highly heterogeneous malignancy with a high mortality rate and poor prognosis. m1A methylation modifications are associated with gliomagenesis. However, whether single nucleotide polymorphisms (SNPs) of m1A modification genes are associated with glioma risk is unclear. We successfully genotyped 20 SNPs of m1A‐modified genes TRMT10C, TRMT61B, TRMT6, TRM61, ALKBH1, YTHDC1, YTHDF1, and YTHDF2 in 314 pediatric glioma patients and 380 cancer‐free controls using TaqMan probes. Associations of polymorphisms with glioma risk were assessed by the odds ratios and 95% confidence intervals generated by logistic regression models. Stratified analysis was performed by age, gender, tumor subtype, and clinical stage. The results showed that TRMT10C rs2303476, TRMT10C rs4257518, TRM61 rs2296484, and YTHDF2 rs3738067 polymorphisms were significantly associated with an increased risk of glioma, TRMT61B rs4563180, YTHDC1 rs2293595, and YTHDC1 rs3813832 polymorphisms were significantly associated with a reduced risk of glioma. In addition, analysis of the expression quantitative trait loci‐showed that the TRM61 rs2296484 T allele significantly increased TRM61 messenger RNA (mRNA) expression, the YTHDF2 rs3738067 G allele significantly increased YTHDF2 mRNA expression, and the TRMT61B rs4563180 C allele significantly decreased TRMT61B mRNA expression. Overall, we identified several promising candidates for m1A modification gene polymorphisms as biomarkers of glioma risk.
Adaptive scatter kernel deconvolution modeling for cone‐beam CT scatter correction via deep reinforcement learning
Authors: Piao Zun , Deng Wenxin , Huang Shuang , Lin Guoqin , Qin Peishan , Li Xu , Wu Wangjiang , Qi Mengke , Zhou Linghong , Li Bin , Ma Jianhui , Xu Yuan
Published: July 2023

Background

Scattering photons can seriously contaminate cone‐beam CT (CBCT) image quality with severe artifacts and substantial degradation of CT value accuracy, which is a major concern limiting the widespread application of CBCT in the medical field. The scatter kernel deconvolution (SKD) method commonly used in clinic requires a Monte Carlo (MC) simulation to determine numerous quality‐related kernel parameters, and it cannot realize intelligent scatter kernel parameter optimization, causing limited accuracy of scatter estimation.

Purpose

Aiming at improving the scatter estimation accuracy of the SKD algorithm, an intelligent scatter correction framework integrating the SKD with deep reinforcement learning (DRL) scheme is proposed.

Methods

Our method firstly builds a scatter kernel model to iteratively convolve with raw projections, and then the deep Q‐network of the DRL scheme is introduced to intelligently interact with the scatter kernel to achieve a projection adaptive parameter optimization. The potential of the proposed framework is demonstrated on CBCT head and pelvis simulation data and experimental CBCT measurement data. Furthermore, we have implemented the U‐net based scatter estimation approach for comparison.

Results

The simulation study demonstrates that the mean absolute percentage error (MAPE) of the proposed method is less than 9.72% and the peak signal‐to‐noise ratio (PSNR) is higher than 23.90 dB, while for the conventional SKD algorithm, the minimum MAPE is 17.92% and the maximum PSNR is 19.32 dB. In the measurement study, we adopt a hardware‐based beam stop array algorithm to obtain the scatter‐free projections as a comparison baseline, and our method can achieve superior performance with MAPE < 17.79% and PSNR > 16.34 dB.

Conclusions

In this paper, we propose an intelligent scatter correction framework that integrates the physical scatter kernel model with DRL algorithm, which has the potential to improve the accuracy of the clinical scatter correction method to obtain better CBCT imaging quality.
The roadmap to net‐zero emission: Do geopolitical risk and energy transition matter?
Authors: Acheampong Alex O. , Opoku Eric Evans Osei , Aluko Olufemi Adewale
Published: July 2023

Global crises have heightened policy uncertainties and efforts to address global climate change. Limited evidence exists in the literature on geopolitical risk's direct and indirect roles in addressing global emissions. In this study, we examine whether geopolitical risk could impede or facilitate efforts to attain a net‐zero emissions target through energy transition using panel data for 42 countries from 1990 to 2020. Various econometric techniques were applied in this study to present robust findings and reliable conclusions. Estimates from the Driscoll‐Kraay, Lewbel two‐stage least squares and method of moment regression techniques consistently showed that countries' geopolitical risk directly increases emissions (total greenhouse gas, carbon, methane, and nitrous oxide). At the same time, energy transition, measured with renewable energy consumption, mitigates these emissions. In addition, evidence from the partial linear functional‐coefficient model technique indicates that renewable energy consumption consistently mitigates emissions when geopolitical is minimal (at a minimum and mean level). However, the role of renewable energy consumption in reducing emissions becomes weaker when geopolitical risk is heightened—thus, when geopolitical risk reaches its maximum level. We recommend that efforts to sustain renewable energy transition and maintain geopolitical stability are vital for achieving net‐zero emissions and climate change mitigation.
Surface modifications of TiO2 nanostructured materials induced by 120 MeV Ag ions
Authors: Tripathy Bipin Bihari , Rath Haripriya , Mishra Naresh Chandra , Das Jayashree , Mishra Dilip Kumar
Published: July 2023

The effect of swift heavy ion irradiation on structural, optical, and microstructural properties of TiO2 has been studied. Pellets prepared from TiO2 nanoparticles have been irradiated by 120 MeV Ag ions at different fluences ranging from 5 × 1011 to 1 × 1013 ions cm−2. X‐ray diffraction (XRD), Raman, UV–visible, and photoluminescence (PL) studies indicated anatase phase both in as‐prepared and irradiated pellets. XRD study revealed the crystallite size of the particles as ~16 nm, which is close to the upper limit of the particle size where anatase phase is most stable. Our study thus established the importance of the initial microstructure on the irradiation response of the nanoparticles. Though irradiation did not affect the crystal structure and the polycrystalline nature of the anatase TiO2, it suppressed the crystalline volume fraction. Poisson fitting of the suppression of XRD peak area with irradiation fluence revealed radius of the track of each 120 MeV Ag ion in TiO2 nanoparticles as ~2.1 nm. Irradiation, in addition to creating disorder, darkened the surface of the pellets because of the creation of oxygen vacancies in the TiO6 octahedra. Reorganization of these defects led to suppression of the band gap of TiO2 nanoparticles from 3.19 eV of the pristine sample to 3 eV for samples irradiated beyond a critical fluences 3 × 1012 ions cm−2. The size of the nanoparticles and their agglomeration remained unaffected by irradiation as indicated by field emission scanning electron micrographs.
A global phylogeny of grammitid ferns (Polypodiaceae) and its systematic implications
Authors: Zhou Xin‐Mao , Yang Jian‐Jun , Liang Zhen‐Long , Pollawatn Rossarin , Knapp Ralf , Parris Barbara , Sundue Michael , Ranker Tom A. , Zhou Lin , Lu Ngan Thi , Luong Thien Tam , Wan Xia , He Zhao‐Rong , Zhao Jing , Zhang Liang , Zhang Li‐Bing
Published: July 2023

Grammitidoideae are the largest subfamily in Polypodiaceae and contain about 911 species. Progress has been made in understanding the overall phylogeny and generic boundaries in the light of recent molecular works. However, the majority of species, especially Asian species, and some critical type species of genera remain unsampled. In this study, a dataset of six plastid markers of 1003 (112 new) accessions representing ca. 412 species of Grammitidoideae including the type species of Ctenopterella, Grammitis, Moranopteris, Radiogrammitis, and Themelium, was assembled to infer a phylogeny. Our major results include: (1) the type species of Grammitis is successfully sequenced using a next‐generation sequencing technique and is resolved in Grammitis s.str. as expected; (2) Ctenopterella is found to be polyphyletic and a new clade consisting of C. khaoluangensis is resolved as sister to Tomophyllum; (3) the type species of Ctenopterella is resolved in a clade sister to the C. lasiostipes clade; (4) Oreogrammitis is found to be polyphyletic and three clades outside of the core Oreogrammitis are identified containing O. subevenosa and allies, O. orientalis, and O. beddomeana (+ O. cf. beddomeana); (5) Prosaptia is found to be paraphyletic with P. nutans being sister to a clade containing the rest of Prosaptia and Archigrammitis; (6) the intergeneric and major relationships within the Asia‐Pacific clade are well resolved and strongly supported except for a few branches; (7) extensive cryptic speciation is detected in the Asia‐Pacific clade; and (8) based on the polyphyly of Ctenopterella we describe three new genera, Boonkerdia, Oxygrammitis, and Rouhania, for species formerly in Ctenopterella; because the type species of Grammitis belongs to Grammitis s.str., we describe five new genera, Aenigmatogrammitis, Grammitastrum (stat. nov.), Howeogrammitis, Nanogrammitis, and Thalassogrammitis for species formerly in Grammitis s.l. A key to the 35 Old‐World genera is given, a taxonomic treatment is presented, and the morphology of all new genera is shown with either a color plate and/or a line drawing.
Development of a wind turbine model and simulation platform using an acausal approach: Multiphysics modeling, validation, and control
Authors: Odeh Mohammad , Mohsin Kazi , Ngo Tri , Zalkind Daniel , Jonkman Jason , Wright Alan , Robertson Amy , Das Tuhin
Published: July 2023

This article presents the development of the Control‐oriented, Reconfigurable, and Acausal Floating Turbine Simulator (CRAFTS). CRAFTS has a modular, hierarchical model architecture that enables rapid and accurate simulation of wind turbines. The architecture facilitates the incorporation of model variants, and its system reconfiguration features help simulate multiple design variants. CRAFTS also supports the integration of models developed on a causality‐free platform (e.g., Modelica®) with existing causal models. This article focuses on the validation of a land‐based wind turbine models against OpenFAST, an industry‐standard platform, for several test cases. Closed‐loop scenarios are also tested using the standard ROSCO controller and compared against OpenFAST. In addition, a nonlinear controller developed in our prior work is also evaluated. The test cases demonstrate the user‐friendly and computationally efficient capabilities of CRAFTS to facilitate control co‐design, assist in incorporating multiphysics models, be adaptable to design variants, and allow for rapid simulations to validate models and evaluate controllers.
Towards Advanced Applications
Authors: Witczak Marcin , Seybold Lothar , Bulach Eric , Maucher Niko
Published: July 2023

The chapter aims at providing a list of selected potential applications of KIS.ME. They stems from the authors’ scientific deliberations and can be perceived as prospective proofs-of-concept, possible to be deployed in various industries. The chapter starts with modelling users and their interactions, which include various important components, e.g., experience and performance. The resulting models make it possible to schedule the work of human operators in a reasonable and predictable way. In particular, two cases are considered, i.e., assembly and transportation tasks. In the former, it is shown how to use these models for integrating user operators in a semi-automated assembly system. In the latter, the concept of human-operated multiple transporters is introduced. Additionally, as most indoor transporters use various kinds of accumulators, it is profitable to take into account their health. Thus, it is shown how to include such information in the scheduling procedure. As a result, the overall accumulator health of a transporter fleet can be balanced. Subsequently, an advanced training exercise is presented, which pertains to work scheduling of three workers operating a conveyor belt. Finally, the chapter is concluded with a concise summary.
The character table of the finite Chevalley group $$F_4(q)$$ for q a power of 2
Authors: Geck Meinolf
Published: July 2023

Let q be a prime power and $$F_4(q)$$

F
4

(
q
)

be the Chevalley group of type $$F_4$$

F
4

over a finite field with q elements. Marcelo and Shinoda (Tokyo J Math 18:303–340, 1995) determined the values of the unipotent characters of $$F_4(q)$$

F
4

(
q
)

on all unipotent elements, extending earlier work by Kawanaka and Lusztig to small characteristics. Assuming that q is a power of 2, we explain how to construct the complete character table of $$F_4(q)$$

F
4

(
q
)

.
Electrophysiological signatures of temporal context in the bisection task
Authors: Baykan Cemre , Zhu Xiuna , Zinchenko Artyom , Müller Hermann J. , Shi Zhuanghua
Published: July 2023

Despite having relatively accurate timing, subjective time can be influenced by various contexts, such as stimulus spacing and sample frequency. Several electroencephalographic (EEG) components have been associated with timing, including the contingent negative variation (CNV), offset P2, and late positive component of timing (LPCt). However, the specific role of these components in the contextual modulation of perceived time remains unclear. In this study, we conducted two temporal bisection experiments to investigate this issue. Participants had to judge whether a test duration was close to a short or long standard. Unbeknownst to them, we manipulated the stimulus spacing (Experiment 1) and sample frequency (Experiment 2) to create short and long contexts while maintaining consistent test ranges and standards across different sessions. The results revealed that the bisection threshold shifted towards the ensemble mean, and both CNV and LPCt were sensitive to context modulation. In the short context, the CNV exhibited an increased climbing rate compared to the long context, whereas the LPCt displayed reduced amplitude and latency. These findings suggest that the CNV represents an expectancy wave preceding a temporal decision process, while the LPCt reflects the decision-making process itself, with both components influenced by the temporal context.
The Solvability of Consensus in Iterated Models Extended with Safe-Consensus
Authors: Conde Rodolfo , Rajsbaum Sergio
Published: July 2023

The safe-consensus task was introduced by Afek, Gafni and Lieber (DISC’ 09) as a weakening of the classic consensus. When there is concurrency, the consensus output can be arbitrary, not even the input of any process. They showed that safe-consensus is equivalent to consensus, in a wait-free system. We study the solvability of consensus in three shared memory iterated models extended with the power of safe-consensus black boxes. In the first iterated model, for thei-th iteration, the processes write to memory, then they snapshot it and finally they invoke safe-consensus boxes. We prove that in this model, consensus cannot be implemented. In a second iterated model, processes first invoke safe-consensus, then they write to memory and finally they snapshot it. We show that this model is equivalent to the previous model and thus consensus cannot be implemented. In the last iterated model, processes write to the memory, invoke safe-consensus boxes and finally they snapshot the memory. We show that in this model, any wait-free implementation of consensus requires$$\Omega (n^{2})$$Ω(n2)safe-consensus black-boxes and this bound is tight.