bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unlocking Biomolecular Activity through Pd‐Catalyzed Azides Reduction†
Authors: Fu Fang , Xiong Wei , Xu Xinyan , Liu Yongjie , Li Ming , Qi Qianqian , Liu Xingyu , Zhang Yuanyuan , Tian Tian , Zhou Xiang 
Published: May 2024

Comprehensive SummaryPd‐mediated bioorthogonal cleavage reactions have been extensively utilized in the activation of prodrug molecules, precise regulation of protein function, and cellular engineering. However, the availability of cleavable "caging" groups is quite limited, and their application in nucleic acid modification has seldom been reported. Herein, we introduce a method based on Pd‐catalyzed reduction amination of azides as a decaging strategy to activate the activity of biomolecules. We designed modifications on the bioactive sites with azides or their derivatives to mask the related biological function, followed by the release of biological activity through Pd‐catalyzed NaBH4 reduction amination reaction. This study has demonstrated that the strategy can effectively be used to activate bioactive molecules such as fluorescent probes, prodrugs, and to regulate the biological function of RNA, including reverse transcription extension, binding to ligands, and cleavage activity of the CRISPR‐Cas system. All results confirm that this strategy provides an efficient and controllable "OFF to ON" biological switch, capable of achieving significant regulatory effects substoichiometrically, and is expected to be extended to other biological applications.
Efficient Chemical Synthesis and Folding of Mirror‐Image Tropomyosin Receptor Kinase A Using the Strategy of Removable Glycosylation Modification†
Authors: Wang Tongyue , Shi Weiwei , Chu Guo‐Chao , Li Yi‐Ming 
Published: May 2024

Comprehensive SummaryThe strategy of removable glycosylation modification was used to overcome the low‐efficiency problem encountered in the chemical synthesis of the mirror‐image D‐version of the immunoglobulin (Ig)‐like domain of tropomyosin receptor kinase A (DlgCTrkA), a protein molecule needed for mirror‐image screening of D‐peptide ligands targeting this cell membrane receptor. It was found that O‐linked‐β‐N‐acetyl‐D‐glucosamine (O‐GlcNAc) modification at DSer312, or DSer320 can significantly improve the efficiency of DlgCTrkA synthesis and folding, while O‐GlcNAc modification at DSer330 showed barely any improvement. This study provides a new example demonstrating the power of the removable glycosylation modification strategy in the chemical synthesis and folding of difficult‐to‐obtain proteins. It also presents evidence that removable glycosylation modification at different sites would significantly affect the efficiency of protein folding promoted by this strategy.
Extractive Mass Transfer of Zr(IV) into a Hydrophobic Ionic Liquid Medium Containing Diglycolamide Extractant: Solvent Extraction and Spectroscopic Analysis
Authors: Rout Alok , Ramanathan Nagarajan 
Published: May 2024

AbstractSolvent extraction of Zr(IV) in ionic liquid (IL) medium is less known and Zr(IV) – IL chemistry indeed needs exploration to realize the coordination approach of Zr(IV) in IL phase. In view of this, in the present work, a strongly hydrophobic imidazolium based IL: 1‐methyl‐3‐octylimidazolium bis(trifluoromethylsulfonyl)imide ([C8mim][NTf2]) as the medium containing a diglycolamide (DGA) extractant: N,N,N’,N’‐tetra‐n‐octyldiglycolamide (TODGA) was opted to understand the extraction behavior of Zr(IV) from nitric acid medium. Different experimental parameters such as the concentration of initial nitric acid, initial feed metal concentration, equilibration time and ligand concentration were tuned to unravel the extraction efficiency of the proposed IL phase towards Zr(IV). The extraction scenario was completely dependent on the hydrophobicity of IL diluent and increasing extraction trend with an increase in feed acidity along with the coordination of two TODGA molecules ensured Zr(IV) ‐ complex formation in a neutral solvation mechanistic pathway. The extraction trend of Zr(IV) was compared with molecular diluent (n‐dodecane (n‐DD)) containing TODGA and a phase modifier: N,N‐dihexyloctanamide (DHOA). The coordination aspect of Zr(IV) with ligand in IL phase was ascertained spectroscopically to validate Zr(IV) loading in IL phase. Thermodynamics of Zr(IV) extraction revealed the nature of the extraction process and the complex formation.
Validation of Single‐Nucleotide Mosaic Variants Through Droplet Digital PCR
Authors: Grochowski Christopher M. , Gibbs Richard A. , Doddapaneni Harsha 
Published: May 2024

AbstractThe detection, validation, and subsequent interpretation of potentially mosaic single‐nucleotide variants (SNV) within next‐generation sequencing data remains a challenge in both research and clinical laboratory settings. The ability to identify mosaic variants in high genome coverage sequencing data at levels of ≤1% underscores the necessity for developing guidelines and best practices to verify these variants orthogonally. Droplet digital PCR (ddPCR) has proven to be a powerful and precise method that allows for the determination of low‐level variant fractions within a given sample. Herein we describe two precise ddPCR methods using either a fluorescent TaqMan hydrolysis probe approach or an EvaGreen fluorescent dye protocol. The TaqMan approach relies on two different fluorescent probes (FAM and HEX/VIC), each designed to amplify selectively only in the presence of a single nucleotide change denoting the variant or reference position. The fractional abundance is then calculated to determine the relative quantities of both alleles in the final sample. The EvaGreen protocol relies on two independent reactions with oligonucleotide primers designed with the single nucleotide change denoting the variant at the penultimate position of the primer. The relative amplification efficiency of both primer sets (reference and variant) can be compared to determine the mosaic level of a given variant. As the cost of high‐coverage sequencing continues to decrease, the identification of potentially mosaic variants will also increase. The approaches outlined will allow clinicians and researchers a more precise determination of the true mosaic level of a given variant allowing them to better assess not only its potential pathogenicity but also its possible recurrence risk when offering genetic counseling to families. © 2024 Wiley Periodicals LLC.Basic Protocol: Droplet digital PCR (ddPCR) with TaqMan hydrolysis probesAlternate Protocol: EvaGreen oligonucleotide‐specific ddPCR
Cytokine/Antibody Fusion Protein Design and Evaluation
Authors: Fabilane Charina S. , Stephenson A. Carson , Leonard Elissa K. , VanDyke Derek , Spangler Jamie B. 
Published: May 2024

AbstractCytokines constitute a class of secreted proteins that activate transmembrane receptors to coordinate a vast array of physiological processes, particularly those related to immune activity. Due to their vital role in immune regulation, cytokines have garnered great interest as potential therapeutic agents. Unfortunately, the clinical success of cytokine drugs has been limited by their multifunctional activities, which hinder therapeutic performance and lead to harmful toxicities. In addition, the strikingly short circulation half‐life of cytokines further hampers their efficacy as drugs. To overcome the translational challenges associated with natural cytokines, significant efforts have focused on engineering cytokines to target their activities and improve their pharmacological properties. One such strategy is the design of fusion proteins that tether a cytokine to an anti‐cytokine antibody that selectively biases its functions and extends its serum half‐life. These cytokine/antibody fusion proteins (termed immunocytokines) assemble intramolecularly to bias cytokine signaling behavior through multi‐layered structural and molecular effects. Here, we present a detailed workflow for the design, production, and functional validation of intramolecularly assembled immunocytokines. In‐depth procedures are presented for gene manipulation, mammalian cell‐based expression and purification, binding analysis via bio‐layer interferometry, and interrogation of cytokine signaling activity on human primary cells. In contrast with immunocytokines in which the tethered cytokine and antibody do not bind one another, intramolecularly assembled immunocytokines require special considerations with respect to their production to avoid oligomerization and/or aggregation. The protocol herein was developed based on experience with immunocytokines that incorporate interleukin‐2 (IL‐2); however, this modular approach can be extended to any cytokine of interest for a broad range of biomedical applications. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Design and generation of immunocytokine genesBasic Protocol 2: Immunocytokine expression and purificationBasic Protocol 3: Validation of immunocytokine assembly and binding by bio‐layer interferometryBasic Protocol 4: Analysis of immunocytokine signaling on human primary cells
Alkaline Modified Mesoporous Silica Supported Ruthenium Catalyst for Improved α‐Amino Acid Synthesis
Authors: Gao Mingxia , Ma Jiping , Fan Xiaomeng , Shi Song , Xu Jie 
Published: May 2024

AbstractAmino acids are a class of compounds with wide‐ranging applications. The synthesis of amino acids from biomass‐derived α‐keto acids and ammonia is a sustainable way but the unstable primary imine intermediates (R−C=NH) easily form oligomers. Herein, targeting this problem, alkaline modified mesoporous silica was employed as a support for ruthenium (Ru/M‐MCM‐41), which could be used as a bifunctional catalyst in the reductive amination of α‐keto acids to synthesize α‐amino acids. The incorporation of Sr improved the dispersion of Ru nanoparticles and enhanced metal‐support interactions via electron transfer from Sr to Ru, and the active Ru sites could efficiently hydrogenate primary imine intermediates to α‐amino acids, thus prohibiting the formation of oligomers. Moreover, the Sr‐dopant introduces base sites that could catalyze the hydrolysis of oligomers back to primary imine intermediates and finally hydrogenated to α‐amino acids. As a result, >99 % yield of glycine was achieved from glyoxylic acid over Ru/Sr‐MCM‐41, which is nearly three times that achieved over Ru/MCM‐41 (32.2 %).
Amplitude modulation and nonlinear dynamics of small amplitude ion‐acoustic waves in five component cometary plasmas
Authors: Kolay Debaditya , Dutta Debjit , Sahu Biswajit 
Published: May 2024

AbstractThe formation and propagation dynamics of the finite‐amplitude ion‐acoustic wave (IAW) structures (e.g., soliton, breather, rogue wave, etc.) is theoretically investigated in a plasma comprising of kappa distributed solar and cometary electrons of different temperatures, a hot drift ion component, and a pair of oppositely charged oxygen ion components. The modified‐KdV (mKdV) equation is derived in order to study the propagation dynamics of the ion‐acoustic solitary wave (IASW). It is then converted into the nonlinear Schrödinger equation (NLS) through appropriate algebraic manipulation in order to observe the amplitude modulation of the IAWs. Also, the appearance of envelope soliton and the possibility of breather structure formation have been studied from the NLS equation. The dependence of plasma parameters on the formation and propagation of IAW structures has been briefly discussed. The modified‐KdV equation is reduced in a dynamical system through the application of coordinate transformation. The existence of finite‐amplitude nonlinear and supernonlinear IAWs is demonstrated by phase plane analysis. Due to the fact that the results are primarily associated with cometary plasma, they possibly provide greater insight of the nonlinear characteristics of cometary plasma.
Population density and ranging behaviour of a generalist carnivore varies with human population
Authors: Alting Brendan F. , Pitcher Benjamin J. , Rees Matthew W. , Ferrer‐Paris José R. , Jordan Neil R. 
Published: May 2024

AbstractCanid species are highly adaptable, including to urban and peri‐urban areas, where they can come into close contact with people. Understanding the mechanisms of wild canid population persistence in these areas is key to managing any negative impacts. The resource dispersion hypothesis predicts that animal density increases and home range size decreases as resource concentration increases, and may help to explain how canids are distributed in environments with an urban‐natural gradient. In Australia, dingoes have adapted to human presence, sometimes living in close proximity to towns. Using a targeted camera trap survey and spatial capture‐recapture models, we estimated spatial variation in the population density and detection rates of dingoes on Worimi Country in the Great Lakes region of the NSW coast. We tested whether dingo home range and population densities varied across a gradient of human population density, in a mixed‐use landscape including, urban, peri‐urban, and National Park environs. We found human population density to be a strong driver of dingo density (ranging from 0.025 to 0.433 dingoes/km2 across the natural‐urban gradient), and to have a negative effect on dingo home range size. The spatial scale parameter changed depending on survey period, being smaller in the peak tourism period, when human population increases in the area, than in adjacent survey periods, potentially indicating reduced home range size when additional resources are available. Our study highlights the potential value of managing anthropogenic resource availability to manage carnivore densities and potential risk of human‐carnivore interactions.
Chronic wasting disease alters the movement behavior and habitat use of mule deer during clinical stages of infection
Authors: Barrile Gabriel M. , Cross Paul C. , Stewart Cheyenne , Malmberg Jennifer , Jakopak Rhiannon P. , Binfet Justin , Monteith Kevin L. , Werner Brandon , Jennings‐Gaines Jessica , Merkle Jerod A. 
Published: May 2024

AbstractIntegrating host movement and pathogen data is a central issue in wildlife disease ecology that will allow for a better understanding of disease transmission. We examined how adult female mule deer (Odocoileus hemionus) responded behaviorally to infection with chronic wasting disease (CWD). We compared movement and habitat use of CWD‐infected deer (n = 18) to those that succumbed to starvation (and were CWD‐negative by ELISA and IHC; n = 8) and others in which CWD was not detected (n = 111, including animals that survived the duration of the study) using GPS collar data from two distinct populations collared in central Wyoming, USA during 2018–2022. CWD and predation were the leading causes of mortality during our study (32/91 deaths attributed to CWD and 27/91 deaths attributed to predation). Deer infected with CWD moved slower and used lower elevation areas closer to rivers in the months preceding death compared with uninfected deer that did not succumb to starvation. Although CWD‐infected deer and those that died of starvation moved at similar speeds during the final months of life, CWD‐infected deer used areas closer to streams with less herbaceous biomass than starved deer. These behavioral differences may allow for the development of predictive models of disease status from movement data, which will be useful to supplement field and laboratory diagnostics or when mortalities cannot be quickly retrieved to assess cause‐specific mortality. Furthermore, identifying individuals who are sick before predation events could help to assess the extent to which disease mortality is compensatory with predation. Finally, infected animals began to slow down around 4 months prior to death from CWD. Our approach for detecting the timing of infection‐induced shifts in movement behavior may be useful in application to other disease systems to better understand the response of wildlife to infectious disease.
It's not easy being green: Comparing typical skin colouration among amphibians with colour abnormalities associated with chromatophore deficits
Authors: Gould John , McHenry Colin 
Published: May 2024

AbstractAmphibians can obtain their colour from a combination of several different pigment and light reflecting cell types called chromatophores, with defects in one or several of the cells leading to colour abnormalities. There is a need for better recording of colour abnormalities within wild amphibian populations, as this may provide baseline data that can be used to determine changes in environmental conditions and population dynamics, such as inbreeding. In this study, we provide records of several types of chromatophore deficiencies, including those involving iridophores, xanthophores and melanophores, among two Australian tree frog species; the green and golden bell frog, Litoria aurea, and the eastern dwarf tree frog, L. fallax. We explore these colour abnormalities in terms of the chromatophores that have likely been affected and associated with their expression, in combination with typical colour phenotypes, colour variations and colour changes for these species. We intend for our photographs to be used as a visual guide that addresses the need for more accessible information regarding the physical manifestation of different chromatophore defects among amphibians.
Spatial ecology and microhabitat selection of the nocturnal pitviper Viridovipera stejnegeri (Squamata: Viperidae) in relation to prey
Authors: Tan Song‐Wen , Wu Ya‐Yong , Wang Jia‐Jun , Lyu Bing , Yu Min , Zhang He , Guo Peng , Shi Lei 
Published: May 2024

AbstractHabitat is fundamental for facilitating various life activities in animals, for instance, snakes procure essential energy for survival and reproduction by selecting ambush microhabitats. While there has been extensive research on the selection of microhabitat for feeding in terrestrial and aquatic snakes, little is known about arboreal snakes. In the present study, we analyzed the ambush microhabitat preferences of Viridovipera stejnegeri, a widely distributed Asian pitviper in China, conducted association analysis between snake microhabitat and prey microhabitat and abundance to determine the ro5le of microhabitat selection in feeding. Employing random forest analysis and habitat selection functions, we further constructed a predictive framework for assessing the probability of ambush site selection by V. stejnegeri. Our results revealed that V. stejnegeri exhibited a distinct microhabitat preference for ambush prey. Among the 13 environmental factors assessed, V. stejnegeri showed pronounced preferences towards 12 of these factors, including climatic factors, geographical factors, and vegetation factors. Furthermore, although the preferences of V. stejnegeri overlapped substantially with those of its prey across multiple habitat factors, food abundance shows no significant association with various habitat factors of V. stejnegeri, and does not have significant predictive effect on habitat selection of V. stejnegeri. Therefore, we infer that V. stejnegeri does not preferentially select microhabitats with the highest food abundance, which does not support the hypothesis that “snakes select habitats based on the spatial distribution of prey abundance.” By analyzing the characteristics of vegetation, geography, and climate, we conclude that V. stejnegeri tends to choose microhabitats with better ambush conditions to increase attack success rate, thereby achieving the optimal feeding success rate at the microhabitat scale, which is in line with the predictions of optimal foraging theory. This study provides new insights into the predation ecology and habitat selection of snakes.
The influence of climate and management on transpiration of residential trees during a bark beetle infestation
Authors: Litvak Elizaveta , Pataki Diane E. 
Published: May 2024

AbstractTrees in residential environments are affected by a unique combination of environmental and anthropogenic factors, including occasional insect outbreaks that are increasing in frequency and severity due to climate change. We studied loblolly pine trees infested by bark beetles in a residential backyard in a southeastern US city. We investigated the responses of tree and stand‐level transpiration to environmental factors (solar radiation, atmospheric vapor pressure deficit, and soil moisture), severe weather events (strong winds and heavy storms), bark beetle infestation, and human actions (insecticide treatments and tree removals). We used constant heat dissipation probes to make continuous sap flux measurements (J0) in tree boles. Over 22 months of the study, J0 of trees with confirmed infestation decreased from ~90 to ~60 g cm−2 day−1 and J0 of the rest of the trees increased from ~60 to ~80 g cm−2 day−1. One infested tree died, as its J0 steadily declined from 110 g cm−2 day−1 to zero over the course of 2 months, followed by a loss of foliage and visible signs of severe infestation 6 months later. J0 was sensitive to variations in incoming solar radiation and atmospheric vapor pressure deficit. In most trees, J0 linearly responded to soil water content during drought periods. Yet despite complex dynamics of J0 variations, plot‐level transpiration at the end of the study was the same as at the beginning due to compensatory increases in tree transpiration rates. This study highlights the intrinsic interplay of environmental, biotic, and anthropogenic factors in residential environments where human actions may directly mediate ecosystem responses to climate.
Demonstration of application of redox flow battery for securing demand‐supply reserve power and improvement of grid resiliency
Authors: Omine Eitaro , Murakami Shinichi , Kusunose Nobuhiko , Kitano Riichi , Ooka Toshio , Shibata Toshikazu 
Published: May 2024

AbstractIn order to achieve net‐zero carbon emissions by introducing enormous amount of renewable energy, it is essential to secure the reserve power to improve the power quality of the grid. On the other hand, improvement of the grid resiliency is also needed in case of emergency such as outage of the grid. The energy storage system can be the solution for both of securing the reserve power and improving grid resiliency. The authors have conducted demonstration project to validate the applicability of Redox Flow (RF) battery for securing the reserve power and improving grid resiliency. The results of the demonstration validated that the RF battery makes it possible to be used as reserve power and earn revenue through energy and ancillary market transactions during normal operations, in addition to providing power to blackout areas or the areas that outages are assumed, as an independent power source, during an emergency such as natural disasters and planned outages.
Proposal of angle detection method for concentrated winding bearingless motors with less magnetic interference due to current
Authors: Miyoshi Masahito , Nakamura Yuichiro , Furutani Shinichi , Kajino Keita , Sugimoto Hiroya 
Published: May 2024

AbstractThis paper proposes a method for detecting the angle of a bearingless motor with less magnetic interference due to the current. Bearingless motors have suspension windings and motor windings that generate leakage flux. Owing to this electromagnetic phenomenon, the signal of the linear Hall‐effect sensor for angle detection is disturbed, and it has to be avoided to place Hall sensors near the winding conventionally. To solve this interference problem, this paper clarifies the ideal combinations between sensor positions and the number of poles and slots of concentrated winding bearingless motors.