bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radical Addition Reactions: Hierarchical Ab Initio Benchmark and DFT Performance Study
Authors: Hordijk Yuman , Dalla Tiezza Marco , Rodrigues Silva Daniela , Hamlin Trevor A. 
Published: September 2024

AbstractWe performed a hierarchical ab initio benchmark study of the gas‐phase radical addition reactions of X⋅+C2H2 and X⋅+C2H4 (X⋅ = CH3⋅, NH2⋅, OH⋅, SH⋅). The hierarchical series of ab initio methods (HF, MP2, CCSD, CCSD(T)) were paired with a hierarchal series of Dunning basis sets with and without diffuse functions ((aug)–cc–pVDZ, (aug)–cc–pVTZ, (aug)–cc–pVQZ). The HF ground‐state wavefunctions were transformed into quasi‐restricted orbital (QRO) reference wavefunctions to address spin contamination. Following extrapolation to the CBS limit, the energies from our highest‐ QRO–CCSD(T)/CBS+ level converged within 0.0–3.4 kcal mol−1 and 0.0–1.0 kcal mol−1 concerning the ab initio method and basis set, respectively. Our QRO–CCSD(T)/CBS+ reference data was used to evaluate the performance of 98 density functional theory (DFT) approximations. The MAE of the best functionals for reaction barriers and energies were: OLYP (1.9 kcal mol−1), BMK (1.0 kcal mol−1), M06–2X (0.9 kcal mol−1), MN12–SX (0.8 kcal mol−1) and CAM−B3LYP (0.8 kcal mol−1). These functionals also accurately reproduce key geometrical parameters of the stationary points within an average 2 % deviation from the reference QRO–CCSD(T)/cc–pVTZ level.
Establishing Primary and Stable Cell Lines from Frozen Wing Biopsies for Cellular, Physiological, and Genetic Studies in Bats
Authors: Deng Fengyan , Morales‐Sosa Pedro , Bernal‐Rivera Andrea , Wang Yan , Tsuchiya Dai , Javier Jose Emmanuel , Rohner Nicolas , Zhao Chongbei , Camacho Jasmin 
Published: September 2024

AbstractBats stand out among mammalian species for their exceptional traits, including the capacity to navigate through flight and echolocation, conserve energy through torpor/hibernation, harbor a multitude of viruses, exhibit resistance to disease, survive harsh environmental conditions, and demonstrate exceptional longevity compared to other mammals of similar size. In vivo studies of bats are challenging for several reasons, such as difficulty in locating and capturing them in their natural environments, limited accessibility, low sample size, environmental variation, long lifespans, slow reproductive rates, zoonotic disease risks, species protection, and ethical concerns. Thus, establishing alternative laboratory models is crucial for investigating the diverse physiological adaptations observed in bats. Obtaining quality cells from tissues is a critical first step for successful primary cell derivation. However, it is often impractical to collect fresh tissue and process the samples immediately for cell culture due to the resources required for isolating and expanding cells. As a result, frozen tissue is typically the starting resource for bat primary cell derivation, but cells in frozen tissue are usually damaged and have low integrity and viability. Isolating primary cells from frozen tissues thus poses a significant challenge. Herein, we present a successfully developed protocol for isolating primary dermal fibroblasts from frozen bat wing biopsies. This protocol marks a significant milestone, as this is the first protocol specifically focused on fibroblast isolation from bat frozen tissue. We also describe methods for primary cell characterization, genetic manipulation of primary cells through lentivirus transduction, and the development of stable cell lines. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Bat wing biopsy collection and preservationSupport Protocol 1: Blood collection from bat venipunctureBasic Protocol 2: Isolation of primary fibroblasts from adult bat frozen wing biopsySupport Protocol 2: Primary fibroblast culture and subcultureSupport Protocol 3: Determination of growth curve and doubling timeSupport Protocol 4: Cell banking and thawing of primary fibroblastsBasic Protocol 3: Lentiviral transduction of bat primary fibroblastsBasic Protocol 4: Bat stable fibroblast cell line developmentSupport Protocol 5: Bat fibroblast validation by immunofluorescence stainingBasic Protocol 5: Chromosome counting
Genetic Manipulation of Neisseria gonorrhoeae and Commensal Neisseria Species
Authors: Dillard Joseph P. , Chan Jia Mun 
Published: September 2024

AbstractThe sexually transmitted pathogen, Neisseria gonorrhoeae, undergoes natural transformation at high frequency. This property has led to the rapid dissemination of antibiotic resistance markers and the panmictic structure of the gonococcal population. However, high‐frequency transformation also makes N. gonorrhoeae one of the easiest bacterial species to manipulate genetically in the laboratory. Techniques have been developed that result in transformation frequencies >50%, allowing the identification of mutants by screening and without selection. Constructs have been created to take advantage of this high‐frequency transformation, facilitating genetic mutation, complementation, and heterologous gene expression. Similar methods have been developed for N. meningitidis and nonpathogenic Neisseria including N. mucosa and N. musculi. Techniques are described for genetic manipulation of N. gonorrhoeae and commensal Neisseria species, as well as for growth of these fastidious organisms. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Spot transformation of Neisseria gonorrhoeae on agar platesBasic Protocol 2: Spot transformation of commensal Neisseria on agar platesBasic Protocol 3: Transformation of Neisseria gonorrhoeae in liquid cultureBasic Protocol 4: Electroporation of Neisseria gonorrhoeaeBasic Protocol 5: Creation of unmarked mutations using a positive and negative selection cassetteBasic Protocol 6: In vitro mutagenesis of Neisseria gonorrhoeae chromosomal DNA using EZ‐Tn5Basic Protocol 7: Chemical mutagenesisBasic Protocol 8: Complementation on the Neisseria gonorrhoeae chromosomeAlternate Protocol 1: Complementation with replicating plasmidsAlternate Protocol 2: Complementation on the Neisseria musculi or Neisseria mucosa chromosomeBasic Protocol 9: Preparation of chromosomal DNA from Neisseria gonorrhoeae grown on solid mediumAlternate Protocol 3: Preparation of chromosomal DNA from Neisseria gonorrhoeae grown in brothSupport Protocol: Preparing PCR templates from Neisseria gonorrhoeae colonies
Periodic Acid Schiff Staining to Detect Mott Cells, Aberrant Plasma Cells Containing Immunoglobulin Inclusions Called Russell Bodies
Authors: Mahmoudi Aliabadi Pedram , Al‐Qaisi Khlowd , Reddy Vishnu , Radbruch Andreas , Kobayashi Makio , Kubagawa Hiromi 
Published: September 2024

AbstractHematoxylin and eosin staining is widely used for routine histopathological analysis under light microscopic examination to determine alterations of tissue architecture and cellular components in animal studies. Aside from hematoxylin/eosin staining, periodic acid Schiff (PAS) staining is used to detect polysaccharides and carbohydrate‐rich macromolecules, and is essential in immunological fields for evaluation of glomerular lesions of kidneys in autoimmune animals. Since erythrocytes are not stained by PAS, this stain is also helpful for identifying changes in immune cells in the red pulp of the spleen, which is filled with erythrocytes. This article describes a protocol to detect Mott cells, bizarre plasma cells containing immunoglobulin inclusion bodies (Russell bodies) in the cytoplasm. The protocol can be used for formalin‐fixed, paraffin‐embedded tissue sections, frozen tissue sections, tissue‐touch preparations, blood films, and cytocentrifuged cell smears. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Detection of Mott cells by PAS staining in formalin‐fixed, paraffin‐embedded tissue sectionsBasic Protocol 2: Detection of Mott cells by PAS staining in frozen tissue sections, touch preparations, blood films, and cytocentrifuged cell smears
Anode Glow Discharge Electrolysis Synthesis of Flower‐Like α‐MnO2 Nanospheres: Structure, Formation Mechanism, and Supercapacitor Performance
Authors: Yu Jie , Liu Manye , Wang Bo , Liang Chenxu , Wang Xuyi , Wang Kai , Lu Quanfang 
Published: September 2024

AbstractA novel green synthesis strategy–anode glow discharge electrolysis (AGDE) was employed for one‐step preparation of α‐MnO2 in 2 g L−1 KMnO4 solution, in which Pt needle and carbon rod were regarded as anode and cathode, respectively. The optimal preparation condition is 400 V for 60 min and the power consumption is below 45 W. The XRD, Raman spectra, XPS and EPR proved that α‐MnO2 with structural defects (oxygen vacancies) is obtained. SEM and TEM revealed that α‐MnO2 shows a flower‐like nanospheres with a diameter of 165 nm, which is assembled by many nanosheets. A possible formation mechanism is that the MnO2 is generated via the reduction of MnO4− by H⋅ and eaq− in plasma‐liquid interface. Electrochemical test found that MnO2 nanospheres exhibit a specific capacitance of 365 F g−1 at 1 A g−1, and capacity retention of 79.8 % after 10,000 cycles at 5 A g−1. The assembled asymmetric supercapacitor shows the maximum energy density of 23.1 Wh kg−1 at power density of 1.89 kW kg−1. In brief, AGDE is a simple, facile and green technique for the synthesis of α‐MnO2 without adding extra chemicals, and prepared α‐MnO2 can be considered as an excellent candidate of electrode materials for supercapacitor.
Recent Progress on Cross‐Linkable Fullerene‐Based Electron Transport Materials for Perovskite Solar Cells
Authors: Zhou Guorong , Luo Xin , Wang Zhen , Ding Changzeng , Guo Yuxiao , Ma Changqi , Xu Bo 
Published: September 2024

AbstractFullerene‐based derivatives are frequently used as electron transport materials (ETMs) and interface buffers for perovskite solar cells (PSCs) due to their excellent properties, including high electron affinity and mobility, low recombination energy, tunable energy levels, and solution processability. However, significant challenges arise because fullerene derivatives tend to aggregate and dimerize, which reduces exciton dissociation and charge transport capacity. Additionally, their chemical compatibility with perovskite absorbers facilitates halide diffusion and degradation of PSCs. This overlap causes delamination and dissolution during device fabrication, hindering the performance enhancement of fullerene‐based PSCs. To address these issues, researchers have developed cross‐linkable fullerene materials. These materials have been shown to not only significantly improve the power conversion efficiency (PCE) of PSCs but also effectively enhance the device stability. In this review, we summarized recent research progress on cross‐linkable fullerene derivatives as ETMs for PSCs. We systematically analyze the impact of these cross‐linked ETMs on device performance and long‐term stability, focusing on their molecular structures and working mechanisms. Finally, we discuss the future challenges that need to be overcome to advance the application of cross‐linkable fullerene materials in PSCs.
Do modern climatic niches distinguish extinct and extant plant genera in New Zealand?
Authors: Schlenker Nora , Lee William G. , Reichgelt Tammo , Ohlemüller Ralf 
Published: September 2024

AbstractPast climate changes have had large impacts on modern ecological patterns. Understanding if legacies are distinguishable in the climatic niches of extant and locally extinct taxa can provide insight into the importance of climate in extinction events. To better understand mid‐ to late‐Cenozoic New Zealand plant extinctions, which are often attributed to Cenozoic climate cooling, we identify 13 con‐familial extinct and extant New Zealand genus pairs, which have modern distributions in Australia. Using climatic niches derived from current geographic distributions in Australia, we compared (i) total niche breadth, (ii) niche overlap, and (iii) individual climate parameters, to investigate potential climate drivers of intrafamilial extinction and persistence patterns in New Zealand. A majority of New Zealand extinct genera (9 out of 13 pairs) do not indicate climate niche legacies consistent with susceptibility to extinction from changing climates, while the remaining four extinct/extant pairs show slight climatic niche legacies. Three extinct genera have warmer niches than their extant counterpart, which is consistent with extinction reflecting intolerance of cooling Cenozoic climates. The other genus pair with a climatic niche legacy has an extinct genus that is distinguished by a niche with smaller precipitation seasonality than its extant counterpart, suggesting that climate metrics other than temperature may also be important extinction drivers in some taxa. Our results show that the mechanisms of Cenozoic extinctions of New Zealand genera are likely more complex than taxa reaching environmental tolerances due to cooling climates. Comparisons of current climatic niches between extant and extinct sister taxa can provide useful insights into large‐scale, long‐term climatic legacies but more analyses, including trait and phylogeographic patterns, would lead to additional insights into alternative pathways of extinction.
Street‐side trees control pavement wetness in a moist‐temperate region with cold winters
Authors: Matlack Glenn R. , Khoury Issam , Naik Bhaven 
Published: September 2024

AbstractUrban tree canopies intercept rain and snowfall, potentially extending the service life of asphalt pavement below them. However, the process of pavement wetting has not been quantified and controlling factors are poorly understood. In this study, we document four forms of pavement moisture and experimentally test the role of trees in regulating wetness. Study plots were established on asphalt pavement under and adjacent to broad‐leaved street trees in a residential neighbourhood typical of cities in the Northeastern Unites States. Pavement wetting by rainfall, drying after experimental wetting, and accumulation and persistence of snow and ice were recorded. Pavement wetness under a tree canopy lagged 25 to 35 minutes behind pavement under an open sky, a delay that would prevent or reduce wetting in 28% of rain events in the study region. Pavement drying was 70% slower under a canopy than in open plots. Partially covered plots showed intermediate wetting and drying behaviour consistent with direct‐beam solar exposure. Significantly less snow was observed under the leafless canopy than under the open sky, and snow melted faster under the canopy. Ice cover and persistence were unrelated to canopy openness but strongly influenced by traffic and drainage. Pavement microclimate did not differ significantly with tree size or canopy porosity. We conclude that street trees control pavement moisture within ranges that potentially affect pavement structure and longevity. Tree‐scale arrangement appears to be more important than fine‐scale canopy structure.
Silver(I)‐Catalyzed Syntheses of Triarylmethanes (TRAMs)
Authors: Bouteille Quentin , Davies Clotilde , Labourdette Guillaume , Bibal Brigitte 
Published: September 2024

AbstractThe synthesis of triarylmethanes was evaluated in the presence of various Brønsted and Lewis acids under the same stoichiometric conditions. An efficient silver(I)‐catalyzed synthesis of triarylmethanes is reported. The reaction offers low catalyst loadings and quasi‐stoichiometric conditions (1–1.2 equiv. of electrophile) to access to symmetrical and unsymmetrical TRAMs in moderate to excellent yields (35 examples). Broad substrate scope was observed, including compatibility with ester and cyano groups.
Mercury Detection in Novel Foods by a Smart Pocket Sensor
Authors: Vitale Ilaria Antonia , Selvolini Giulia , Failli Sara , Truzzi Cristina , Marrazza Giovanna 
Published: September 2024

AbstractMercury is one of the most well‐known toxic contaminants of natural and anthropogenic origin in aquatic ecosystems that can bioaccumulate in vegetal and animal organisms. In this work, we propose a smart detection system for Hg(II) ions by square wave anodic stripping voltammetry at nanocomposite graphite screen‐printed electrodes, as an analytical tool to be applied in food quality control. The nanocomposite surfaces were obtained by the modification of screen‐printed graphite electrodes with poly(l‐aspartic acid) and gold nanoparticles and were characterized by means of electrochemical techniques. An exhaustive study of the experimental conditions involved both in the electropolymerization and in the voltammetric stripping measurements was addressed to develop a reliable method capable of measuring Hg(II) concentration in the low μg/L range, both in conventional and drop configurations. The sensor was integrated in a smart setup, comprising a Sensit Smart pocket instrument connected to a smartphone, thus proving its applicability for in situ analysis due to its cost‐effectiveness. The analytical significance of the developed sensor was assessed by detecting Hg(II) in novel food samples.
Seismic risk prioritization of masonry building stocks using machine learning
Authors: Coskun Onur , Aktepe Rafet , Aldemir Alper , Yilmaz Ali Erhan , Durmaz Murat , Erkal Burcu Guldur , Tunali Engin 
Published: September 2024

AbstractThe seismic risk mitigation plans are vital since vulnerable structures are prone to partial or total collapse under the effect of future major earthquake events. Therefore, vulnerable structures in large building stocks should be determined using robust and accurate methods to prevent loss of lives and property. In the current state‐of‐the‐art, the risk states (i.e., whether risky or not) of structures completely depend on the experience of the reconnaissance team of engineers, which could not result in standardized decisions. In this study, machine learning has been integrated into the decision‐making algorithm to classify more precise and reliable seismic risk states of masonry buildings, categorizing them into up to four risk categories. For this purpose, a large database, including 12 features and detailed seismic risk analysis results of 4356 masonry buildings, is formed. Firstly, the input variables are preprocessed using feature engineering methods. Then, several machine learning algorithms are utilized to produce a network to estimate the risk state of masonry buildings in association with the risk states obtained from the detailed analysis results. As a result of the analysis of these algorithms, the correct prediction percentages for the testing database of the proposed method for two, three, and four risk states classification are predicted as approximately 87.5%, 86.6%, and 79.0%, respectively. This new approach makes it possible to produce risk color maps of large building stocks and reduce the number of buildings that require immediate action.
Unveiling the microbial metabolites in ruminant milk for medicinal purposes
Authors: Jia Qingan , Yang Tongling , Chang Fan , Zhang Qinglin , Liang Junrong , Liao Xia , Shi Huaiping 
Published: September 2024

AbstractMilk, as a dietary supplement, is crucial for maintaining health and potentially preventing disease throughout life. Both traditional Chinese medicine and modern nutritional science have revealed that milk from different mammals can benefit humans, exhibiting distinct medicinal functions. It can be inferred that milk contains not only multiple nutrients but also an abundance of bioactive components that have health benefits for milk consumers. However, limited studies have focused on the differences in bioactive metabolites in milk derived from various ruminants and their distinct medical functions. Here, we present a comprehensive review of the diversity of microbial metabolites and their associated health benefits, which are primarily shaped by the rumen‐mammary gland axis. Our findings reveal the pivotal role played by microbial metabolites in facilitating the microbiome's influence on human physiology. Finally, we conclude that ruminant milk may offer a path to harness these metabolites’ therapeutic benefits. To increase these metabolites in milk, there is need to design dietary supplements for dairy ruminants, which could enhance milk's medicinal value and aroma, revolutionizing ruminant husbandry.
DNAJB6 is expressed in neurons and oligodendrocytes of the human brain
Authors: Hentze Jónvá , Folke Jonas , Aznar Susana , Nyeng Pia , Brudek Tomasz , Hansen Christian 
Published: September 2024

AbstractDNAJB6 is a suppressor of α‐synuclein aggregation in vivo and in vitro. DNAJB6 is strongly expressed in the brain, and its overall protein expression is altered in neurodegenerative conditions such as Parkinson's Disease (PD) and Multiple System Atrophy (MSA). These two diseases are characterized by accumulation of aggregated α‐synuclein in neurons and oligodendrocytes, respectively. To further explore this, we employed post‐mortem normal human brain material to investigate the regional and cell type specific protein expression of DNAJB6. We found that the DNAJB6 protein is ubiquitously expressed across various regions of the brain. Notably, we demonstrate for the first time that DNAJB6 is present in nearly half (41%–53%) of the oligodendrocyte population and in the majority (68%–80%) of neurons. However, DNAJB6 was only sparsely present in other cell types such as astrocytes and microglia. Given that α‐synuclein aggregation in oligodendrocytes is a hallmark of MSA, we investigated DNAJB6 presence in MSA brains compared to control brains. We found no significant difference in the percentage of oligodendrocytes where DNAJB6 was present in MSA brains relative to control brains. In conclusion, our results reveal an expression of the DNAJB6 protein across various regions of the human brain, and that DNAJB6 is almost exclusively present in neurons and oligodendrocytes. Since prior studies have shown that PD and MSA brains have altered levels of DNAJB6 relative to control brains, DNAJB6 may be an interesting target for drug development.
Generalized models for estimating cerebral lateralisation of young children using functional transcranial Doppler ultrasound
Authors: Quin‐Conroy Josephine E. , Thompson Paul A. , Bayliss Donna M. , Badcock Nicholas A. 
Published: September 2024

AbstractThompson et al., 2023 (Generalized models for quantifying laterality using functional transcranial Doppler ultrasound. Human Brain Mapping, 44(1), 35–48) introduced generalised model‐based analysis methods for determining cerebral lateralisation from functional transcranial Doppler ultrasound (fTCD) data which substantially decreased the uncertainty of individual lateralisation estimates across several large adult samples. We aimed to assess the suitability of these methods for increasing precision in lateralisation estimates for child fTCD data. We applied these methods to adult fTCD data to establish the validity of two child‐friendly language and visuospatial tasks. We also applied the methods to fTCD data from 4‐ to 7‐year‐old children. For both samples, the laterality estimates from the complex generalised additive model (GAM) approach correlated strongly with the traditional methods while also decreasing individual standard errors compared to the popular period‐of‐interest averaging method. We recommend future research using fTCD with young children consider using GAMs to reduce the noise in their LI estimates.