bluuebunny/crossref_metadata_2025 huggingface dataset:
Local control of cellular proliferation underlies neuromast regeneration in zebrafish
Authors: Lavalle Natalia G. , Miranda-Rodríguez Jerónimo , Cura Costa Emanuel , Borges Augusto , Viader-Llargués Oriol , López-Schier Hernán , Chara Osvaldo
Published: October 2024

Biological systems are never at equilibrium but maintain stability despite perennial external disturbance. A prime example is organ regeneration, whereby despite intrinsically stochastic damage, organs are rebuilt via controlled cellular proliferation. Here, we use a mathematical approach to understand how a cell decides to re-enter and exit mitosis during organ repair. Using empirical data from regenerating neuromasts in larval zebrafish, we identify a minimal model based on ordinary differential equations (ODEs). Remarkably, the ODEs model reproduces the regeneration kinetics by assuming a cell-proliferation switch that depends on the type and the number of the neuromast cells. Additionally, a two-dimensional Cellular Potts Model (CPM) predicts that cell proliferation is a delayed response to injury. The CPM recapitulates the experimental results qualitatively and quantitatively, showing that cell proliferation is locally controlled by a switch, where each cell division stops when the type-dependent number of neighbouring cells exceeds a deterministic critical value. An intriguing corollary of our results is that a local negative feedback loop among identical cells may be a general property of organ-level proportional homeostasis.
Temperature-dependent and sex-specific phenotypic plasticity inHeliconius charithonia
Authors: Seixas Fernando , Guerrero Sammy , Xiong Tianzhu , Mallet James
Published: October 2024

External environmental cues can influence the development trajectory of organisms and lead to the formation of distinct phenotypes from the same genotype. Phenotypic plasticity is common in Lepidoptera, with temperature frequently playing a key role. The zebra-longwing (Heliconius charithonia) gets its name from its characteristic black wings with yellow stripes. In some populations, yellow scales are sometimes partially replaced by orange (‘rusty’) scales. The proportion of individuals with rusty scales varies geographically and individuals within the same population can vary drastically for this phenotype. Whether such variation is genetically encoded, or environment-dependent is not known. Here we test the influence of temperature in producing the rusty scales phenotype, as well as on the developmental rates, weight, and mortality in this species. Only female butterflies reared in warm controlled conditions develop rusty scales on the yellow parts of their wings. However, under more extreme (warmer) conditions, both males and females exhibit pronounced rusty scale phenotypes, indicating a sexually dimorphic response to temperature that affects both sexes. This temperature-sensitive trait can be triggered during both larval and pupal stages. Temperature also affects life-history traits, and we observed a trade-off between developmental rate and mortality. Individuals raised in warmer conditions develop more rapidly than those in cooler environments, but this accelerated growth is accompanied by higher mortality across all developmental stages.
AnimalMotionViz: an interactive software tool for tracking and visualizing animal motion patterns using computer vision
Authors: De Castro Angelo L. , Wang Jin , Bonney-King Jessica G. , Morota Gota , Miller-Cushon Emily K. , Yu Haipeng
Published: October 2024

Monitoring the movement patterns of dairy cattle can provide important insight into space utilization or space occupancy in a barn. Although several precision livestock technologies have been developed to record dairy cattle movements, there is a lack of open source tools to track and visualize cattle movement patterns. Therefore, we developed an open-source computer vision software tool, AnimalMotionViz, that allows users to track and visualize dairy cattle movement patterns using a motion heatmap. The software comes with an easy-to-use web-based graphical user interface built with the Python Dash package. It implements a set of background subtraction algorithms in the OpenCV package to track animal motion patterns in real time. The software processes each frame of the input video and identifies the background and foreground using these algorithms. Foreground objects are then subtracted from the background across all frames and cumulatively overlaid on an empty mask image created with the first frame of the input video to visualize the intensity or frequency of motion across different regions. The user can generate motion heatmaps in an image and video, and also track specific regional motion with a custom mask. The software also returns the top three peak intensity locations, the total percentage of regions used, and the within-quadrant percentage of regions used. In four 5 min sample videos, quadrants with peak intensity of space use, as identified using the software, aligned with quadrants where calves spent the greatest duration of time, according to continuous recording of behavior from video. The motion heatmaps generated by AnimalMotionViz can be used to understand space utilization or space occupation by animals, as well as to assess how space allocation affects dairy cow movement. We conclude that the newly developed AnimalMotionViz is a user-friendly and efficient tool to support research developments in precision livestock farming towards enhancing cattle management practices and improving pen designs.
Binding profiles for 961DrosophilaandC. eleganstranscription factors reveal tissue-specific regulatory relationships
Authors: Kudron Michelle , Gevirtzman Louis , Victorsen Alec , Lear Bridget C. , Gao Jiahao , Xu Jinrui , Samanta Swapna , Frink Emily , Tran-Pearson Adri , Huynh Chau , Vafeados Dionne , Hammonds Ann , Fisher William , Wall Martha , Wesseling Greg , Hernandez Vanessa , Lin Zhichun , Kasparian Mary , White Kevin , Allada Ravi , Gerstein Mark , Hillier LaDeana , Celniker Susan E. , Reinke Valerie , Waterston Robert H.
Published: October 2024

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.
First combined tuning on transverse kinematic imbalance data with and without pion production constraints
Authors: Li Weijun , Roda Marco , Tena-Vidal Júlia , Andreopoulos Costas , Lu Xianguo , Ashkenazi Adi , Barrow Joshua , Dytman Steven , Gallagher Hugh , Soto Alfonso Andres Garcia , Gardiner Steven , Goldenberg Matan , Hatcher Robert , Hen Or , Kakorin Igor D. , Kuzmin Konstantin S. , Meregalia Anselmo , Naumov Vadim A. , Papadopoulou Afroditi , Perdue Gabriel , Plows Komninos-John , Sportes Alon , Steinberg Noah , Syrotenko Vladyslav , Wolcott Jeremy , Yan Qiyu ,   GENIE Collaboration
Published: October 2024

We present the first combined tuning, using , of four transverse kinematic imbalance measurements of neutrino-hydrocarbon scattering, both with and without pion final states, from the T2K and MINERvA experiments. As a proof of concept, we have simultaneously tuned the initial state and final-state interaction models (SF-CFG and hA, respectively), producing a new effective model that more accurately describes the data.

Published by the American Physical Society
2024
Cold-Atom Particle Collider
Authors: Su Guo-Xian , Osborne Jesse J. , Halimeh Jad C.
Published: October 2024

A major objective of the strong ongoing drive to realize quantum simulators of gauge theories is achieving the capability to probe collider-relevant physics on them. In this regard, a highly pertinent and sought-after application is the controlled collisions of elementary and composite particles, as well as the scattering processes in their wake. Here, we propose particle-collision experiments in a cold-atom quantum simulator for a 1+1D (one spatial and one temporal dimension) U(1) lattice gauge theory with a tunable topological θ term, where we demonstrate an experimentally feasible protocol to impart momenta to elementary (anti)particles and their meson composites. We numerically benchmark the collisions of moving wave packets for both elementary and composite particles, uncovering a plethora of rich phenomena, such as oscillatory string dynamics in the wake of elementary (anti)particle collisions due to confinement. We also probe string inversion and entropy production processes across Coleman’s phase transition through far-from-equilibrium quenches. We further demonstrate how collisions of composite particles unveil their internal structure. Our work paves the way towards the experimental investigation of collision dynamics in state-of-the-art quantum simulators of gauge theories, and sets the stage for microscopic understanding of collider-relevant physics in these platforms.

Published by the American Physical Society
2024
Crystal structure, Hirshfeld surface analysis, and DFT and molecular docking studies of 6-cyanonaphthalen-2-yl 4-(benzyloxy)benzoate
Authors: Harish Kumar Mahadevaiah , Santhosh Kumar Shivakumar , Devarajegowda Hirehalli Chikkegowda , Srinivasa Hosapalya Thimmaiah , Palakshamurthy Bandrehalli Siddagangaiah
Published: October 2024

In the title compound, C25H17NO3, the torsion angle associated with the phenyl benzoate group is −173.7 (2)° and that for the benzyloxy group is −174.8 (2)° establishing an anti-type conformation. The dihedral angles between the ten-membered cyanonaphthalene ring and the aromatic ring of the phenyl benzoate and the benzyloxy fragments are 40.70 (10) and 87.51 (11)°, respectively, whereas the dihedral angle between the aromatic phenyl benzoate and the benzyloxy fragments is 72.30 (13)°. In the crystal, the molecules are linked by weak C—H...O interactions forming S(4) chains propagating parallel to [010]. The packing is consolidated by three C—H...π interactions and two π–π stacking interactions between the aromatic rings of naphthalene and phenyl benzoate with centroid-to-centroid distances of 3.9698 (15) and 3.8568 (15) Å, respectively. Intermolecular interactions were quantified using Hirshfeld surface analysis. The molecular structure was further optimized by density functional theory (DFT) at the B3LYP/6–311+ G(d,p) level, revealing that the energy gap between HOMO and LUMO is 3.17 eV. Molecular docking studies were carried out for the title compound as a ligand and SARS-Covid-2(PDB ID:7QF0) protein as a receptor giving a binding affinity of −9.5 kcal mol−1.
Do metaverse implementation announcements enhance firms’ stock market value in China? A signaling theory perspective
Authors: Wang Shichao , Shao Jinan , Zhang Yueyue , Shangguan Wuyue
Published: October 2024

Purpose

The metaverse has garnered increasing attention from researchers and practitioners, yet numerous firms remain hesitant to invest in it due to ongoing debates about its potential financial benefits. Therefore, it is crucial to analyze how the implementation of metaverse initiatives affects firms’ stock market value – an area that remains underexplored in the existing literature. Additionally, there is a significant lack of research on the contingency factors that shape the stock market reaction, leaving a noticeable gap in managerial guidance on the timing and benefits of investments in the metaverse. To narrow these gaps, we examine whether and when the implementation of metaverse initiatives enhances firms’ stock market value.

Design/methodology/approach

Based on 73 metaverse implementation announcements disclosed by Chinese listed firms during January 2021–August 2023, we employ an event study approach to test the hypotheses.

Findings

We find that metaverse implementation announcements elicit a positive stock market reaction. Moreover, the stock market reaction is stronger for technology-focused announcements and smaller firms, or when public attention to the metaverse is higher. Nevertheless, firms’ growth prospects do not significantly alter the stock market reaction.

Originality/value

This study extends the nascent literature on the metaverse by applying signaling theory to offer novel insights into the signaling effect of metaverse implementation announcements on stock market value and the boundary conditions under which the effectiveness of the signal varies. Besides, it provides managers with important implications regarding how to tailor the investment and information disclosure strategies of the metaverse to more effectively enhance firms’ stock market value.
Reshoring concepts: definitions and a structured bibliometric review
Authors: Siddiqui Muhammad Farooq , Khalid Warda , Arsalan Muhammad
Published: October 2024

Purpose

The aim of this paper is to clearly mark the clusters in the related literature using bibliometric analysis and draw useful implications for the academic research purposes especially in the stream of Supply Chain Management (SCM).

Design/methodology/approach

By employing rigorous selection criteria, sample articles were selected for synthesizing and conducting a bibliometric analysis. This paper tries to identify the significance of the concept of reshoring with the aspect of SCM, operations, logistics etc. Starting from sample selection, systematic selection criteria has been used to generate the database, using Scopus. The sample size was 184. Using VOSViewer, statistical and graphical representations were generated for clusters in the literature that will be useful for judging the trends of research under shoring concepts.

Findings

Findings show that unclear difference compared to other supply chain concepts obstructs further theory development within reshoring concepts. To address this challenge, the review categorizes themes and defines boundaries. Based on the analysis findings, this paper advocates for additional research in areas that are crucial but have received limited or no attention. Specifically, there is a need for action research on motivations, governance modes, and location selection concerning reshoring decisions.

Research limitations/implications

This review has a few limitations. The absence of publications in other language, than English, may result in a significant loss of knowledge. This research paper cited a few relevant publications in the form of conference papers, industry reports, books, and book chapters. Nonetheless, they were excluded from the organized bibliometric audit. To further advance the knowledge in this field, exploratory longitudinal case studies will bring to focus the changes on manufacturing strategies using the shoring and reshoring stages.

Practical implications

A current example of this is a French company named Stil (Terzian, 2020) which brought its glass thermometer production back to its home after the unexpected closure of its suppliers from China. Another Italian firm has restarted production of disposal bio-degradable face masks after 15 years to compete with low-cost alternatives from China (Greco, 2020). Reshoring concepts are now under consideration of organizations including Boeing, Bosch, Phillips and more.

Originality/value

To the best of our knowledge, this represents one of the earliest efforts to conceptualize and define reshoring concepts, aiming to distinguish them from one another appropriately. To accomplish this, the earlier demarcated clusters precede this section’s classification of reshoring concepts illustrated in Table 8. Based on the synthesis of definitions and thematic clusters above, we have concluded the literature review in this emerging field. It is intended to contribute to theory development and practitioner support in reshoring decisions by clarifying the dimensions.
Temporal host–symbiont dynamics in community contexts: Impacts of host fitness and vertical transmission efficiency on symbiosis prevalence
Authors: Gundel Pedro E. , Ueno Andrea C. , Casas Cecilia , Miller Tom E. X. , Pérez Luis I. , Cuyeu Romina , Omacini Marina
Published: October 2024

Symbiotic associations play a role in plant ecology and evolution, but the outcome of the interaction depends on the life‐history traits of the partners and the environmental context. Although symbiosis with vertically transmitted microorganisms should result in mutualism, it is not clear how the transmission process aligns with the outcome of the context‐dependent symbiosis.

For 3 years, we sampled individuals of an annual plant species that forms symbiosis with a vertically transmitted fungal endophyte, in paired stands of two contrasting vegetation communities (humid mesophytic meadows [HMM]: productive/low stress, and humid prairies [HP]: less productive/high stress). We estimated the prevalence of symbiosis at the population level, and the fitness of the plant, the symbiotic status and vertical transmission efficiency at the individual level.

Over 3 years, the prevalence of symbiosis was ≈100% in HMM and ≈75% in HP. Plant fitness was very low and high in years with precipitation below and above the yearly mean, respectively. The higher fitness of endophyte‐symbiotic plants was evident in the HMM and high precipitation years. Vertical transmission of endophytes was higher in HMM (≈96%) compared to HP (≈93%) and was not related to plant fitness. Despite transmission inefficiencies in HP, changes in prevalence within the growing season (from seeds to the final plant stand) suggest a fitness advantage for symbiotic plants.

Vertical transmission is expected to promote mutualism as it aligns partners' fitness. Although symbiotic plants showed higher fitness and the probability of transmission failures was higher among low‐fitness plants, the variation in transmission efficiency between plants and vegetation communities was not related to the fitness of the individual host. Our study provides evidence that context‐dependent vertical transmission efficiency and endophyte‐mediated fitness advantages interact complexly to determine the prevalence of symbiosis in populations that occur in contrasting vegetation communities.

Read the free Plain Language Summary for this article on the Journal blog.
Hierarchies inferred from different agonistic behaviours are not always comparable
Authors: Smit Nikolaos
Published: October 2024

Social hierarchies are widely used to predict life‐history patterns and priority of access to resources. Yet, behavioural ecology and social sciences lack a consistent relationship between specific behaviours and social rank across studies.

I used published data sets from 42 groups of 25 species representing several taxa to determine whether hierarchies inferred from different behaviours are similar or (in)consistently different at both individual and group levels.

Ranks inferred from yielding interactions in the absence of aggression ('ritualized') were often comparable to ranks inferred from decided aggression (unambiguous outcome) but not to ranks inferred from undecided aggression. Accordingly, hierarchies inferred from data sets including only decided interactions were steeper than those inferred from data sets including undecided aggression.

These results support the hypothesis that aggression can be context‐dependent and might reflect less stable or mutually recognized relationships than (ritualized) yielding interactions.

I discuss the consequences of choosing different behaviours to infer social hierarchies and the difficulty of making generalizations from one species or taxon to another. Finally, I recommend that the use of ritualized yielding and certainly the use of decided over undecided interactions to infer social hierarchies should be preferred, especially in comparative studies which go beyond taxon‐specific idiosyncrasies.
Predictors of outplanted marine bivalve survival in restoration: A review and synthesis
Authors: Overton Kathy , Dempster Tim , Swearer Stephen E. , Morris Rebecca L. , Barrett Luke T.
Published: October 2024

Global declines in marine shellfish have resulted in widespread efforts to restore populations. Previous research has predominantly focused on substrate‐limited rather than recruitment‐limited systems, yet given increased use of aquaculture‐produced stock to restore marine bivalves, there is a need to understand differences in the survival of hatchery‐produced and translocated wild stock. We conducted a systematic review and synthesis of studies that quantified the survival of outplanted marine bivalves.

The systematic review identified 893 unique stocking events across 111 studies for 29 species across 10 families. Most research has occurred in temperate regions (73%), across four bivalve families (Ostreidae 37%, Pectinidae 20%, Veneridae 16% and Mytilidae 11%). More stockings have outplanted hatchery‐produced (66%) than translocated stock (34%).

We conducted quantitative analyses for five species to determine how stock origin, size at outplant, outplant density, substrate co‐deployment, predator exclusion and time since outplant influences survival. Survival consistently decreased through time across all species. Substrate co‐deployment, stock origin and size at outplant did not influence survival, while predator exclusion and outplant density affected some species.

Synthesis and applications. Our analyses broadly demonstrate variability in the survival of outplanted bivalves through time, however predicted survival was poor after 2 years (<3%). Generally low survival highlights difficulties associated with conducting scalable restoration in recruitment‐limited systems. Based on our findings, using hatchery‐produced stock, mitigating predation and outplanting epifaunal bivalves at high densities may increase survival probabilities when outplanting stock for restoration. Further exploration is needed to understand whether use of aquaculture‐produced stock results in similar ecosystem structure, function, and service provisioning to natural and restored shellfish reefs in recruitment‐limited systems.
Differential responses to weather and land‐cover conditions explain spatial variation in winter abundance trends in a migratory bird of conservation concern
Authors: Schindler Alexander R. , Fox Anthony D. , Wikle Christopher K. , Ballard Bart M. , Walsh Alyn J. , Kelly Seán B. A. , Weegman Mitch D.
Published: October 2024

Effective conservation strategies for animal populations require knowledge of relationships between population dynamics and their environmental drivers. However, these processes often vary within animal populations, requiring site‐specific conservation planning. Given limited financial resources, identifying groups of sites with similar population dynamics can help practitioners efficiently implement conservation programs to larger areas. We evaluated spatial patterns and environmental drivers of wintering site trends in a migratory bird of conservation concern, the Greenland white‐fronted goose (Anser albifrons flavirostris).

We used latent class analysis to identify trend patterns in 35 years of abundance data among 59 geographically discrete Greenland white‐fronted goose wintering sites. We developed a state‐space abundance model in a Bayesian framework to quantify the effects of weather and land‐cover conditions experienced throughout spring migration, summer breeding, autumn migration and wintering periods on variation in wintering site abundance.

We identified two main patterns in Greenland white‐fronted goose abundance trends: northeastern wintering sites declined on average by 3% per year, while southwestern wintering sites declined on average by 14% per year. Differential responses to weather and habitat conditions likely explained variation among groups, as geese at southwestern wintering sites were more negatively affected by harsh weather conditions (e.g. low temperatures and high precipitation on breeding areas) and poor habitat conditions (i.e. low‐quality grasslands and croplands) on wintering areas.

Future conservation efforts to improve the suitability and nutritional quality of agricultural areas, especially cereal croplands in autumn and early winter and grasslands in late winter and early spring, could potentially improve local habitat conditions, especially in the southwestern wintering sites where abundance declines were steepest.

Synthesis and applications. We demonstrate the potential to delineate animal populations based on spatial patterns in population dynamics using long‐term abundance monitoring data, which are commonly the only available data for conservation practitioners. By grouping sites based on spatial patterns in local abundance trends, we can further test hypotheses about how these groups are differentially affected by changing environmental conditions. This information is important for informing efficient conservation planning over large areas when financial resources are limited.
The synergistic effect of α‐tocopherol and phloretin‐loaded nanoemulsions on improvement of the stability, antioxidant, and tyrosinase inhibitory potentiality
Authors: Wang Junguo , Wang Hongyue , Guo Keshuang , Zhang Xindi , Zhang Xiangrong
Published: October 2024

The purpose of this study was to prepare and evaluate the formulation of nanoemulsions (NEs) to encapsulate phloretin (PT) to improve its stability, antioxidant, and tyrosinase inhibitory competence. The aim of this study was to improve the stability, antioxidant, and tyrosinase inhibitory effects of PT via NEs. The formulations were prepared using low energy emulsification method for PT‐VE‐NEs, α‐tocopherol (Vitamin E) and medium chain triglycerides (MCT) were used as the oil phase, and Tween 60 was used as the emulsifier and PEG‐400 as the co‐emulsifier. The droplet size and zeta potential of oil‐in‐water NEs were evaluated using dynamic light scattering. The PT‐VE‐NEs were also characterized by transmission electron microscopy and Fourier transform infrared spectroscopy. The mean droplet diameter was 14.85 ± 0.14 nm, with a zeta potential of −2.47 ± 0.51 mV. Fourier transform infrared spectroscopy revealed the formation of molecular interactions in the NEs formulations. PT‐VE‐NEs size was maintained the same during the in vitro digestion study. The particle size of PT‐VE‐NE remained stable during in vitro digestion. The addition of VE significantly improved the antioxidant, tyrosinase inhibitory effects, as well as thelion and physical stability of PT‐VE‐NE. The results revealed that NEs is a promising strategy to improve the functionality and stability of PT and VE. PT‐VE‐NEs will be applied for the preservation of fruits.
Analytical insight into caffeine extraction from typica coffee leaves based on crystallinity enhancement, optical phonon vibration upshift, and morphological evolution
Authors: Latunra Andi Ilham , Heryanto Heryanto , Tahir Dahlang , Ardiansa Ardiansa
Published: October 2024

Caffeine extracted from callus cultures by in vitro technique induced from typica coffee (Coffea arabica L. var. typica) leaves was successfully carried out by a simple Soxhlet method. Analysis of X‐ray diffraction patterns showed an increase in crystallinity fraction from leaves (13.56%) to callus (14.46%) and then to caffeine (39.18%). Crystallite size also varied, with average sizes of 18 ± 6, 69 ± 51, and 32.5 ± 17 nm for leaves, callus, and caffeine, respectively. Fourier transmission infrared absorption data confirmed the presence of hydroxyl (OH) groups bound to carbon (C─COH), indicating caffeine content. The high stability of the C─COH is indicated by the broad optical phonon vibrations of the leaves: 247 cm−1 to caffeine: 963 cm−1. Quantitative analysis of dielectric function and electron loss function intensity peaks of each sample showed that leaves efficiently capture and store light energy while caffeine has less potency. Scanning electron microscopy analysis showed irregular shapes of leaves, oval round shapes for callus, and rectangular crystals for caffeine due to crystal orientation during transformation and had a strong correlation with crystallinity fraction. Finally, the structure‐based identification, chemistry, optical‐dielectric function, and micro‐surface properties have been fully studied, thus unmasking the phenomenon of slow transformation from leaves to caffeine form.

Practical Application

The result of this study can be applied to uncover new methodologies related to the classification, and biotechnological utilization of callus culture based on structural properties, optical‐dielectric function, and micro‐surface analysis. Methodologically, the resulting callus culture provides a sustainable and controllable supply of plant material for caffeine extraction, thereby reducing traditional methods involving field‐grown plants and avoiding the use of pesticides.
Quantifying the sweetness intensity and impact of aroma in honey from four floral sources
Authors: Mulheron Hannah , DuBois Aubrey , Mayhew Emily J.
Published: October 2024

Unlike many commercial sweeteners for which sweetness dose‐response curves have been constructed, honey's sweetness has yet to be quantified. Honey differs from most commercial sweeteners in that it has a robust aroma; this aroma may impact its perceived sweetness. This study quantified the sweetness intensity and the impact of aroma on the perceived sweetness of four different honey varieties (clover, wildflower, alfalfa, and orange) compared to sucrose. Each sweetener evaluated was diluted to six concentrations in water ranging from 12.5 g/L to 125 g/L. Panelists (n = 55) rated the sweetness intensities with and without aroma, in replicate, on the Global Sensory Intensity Scale. Additionally, the volatile organic compounds in the honey samples were profiled using gas chromatography‐mass spectrometry (GC/MS) analysis. Honey and sugar were equivalently sweet at a given concentration (g/L), with aroma present (p = 0.251). Additionally, honey and sugar were not equivalently sweet without aroma; aroma significantly increased sweetness intensities for all sweeteners (p = 0.042) and especially honeys. In a 100 g/L solution, the aromas in honey increased its sweetness by 23%–43%, depending on the floral source. Compounds with sweet aroma characteristics were identified at high concentrations in all honey samples using GC/MS analysis, including furfural, benzaldehyde, benzene acetaldehyde, and dimethyl sulfide. Additionally, (S)‐limonene and toluene were present in high quantities in the orange and alfalfa samples. This study can inform appropriate honey usage levels and identify major volatiles that may enhance sweetness.

Practical Application

Honey sweetness has not been determined quantitatively, despite the widespread use of honey among consumers and product formulators. Sweetness enhancement by honey aroma volatiles may support a reduction in added sugars while maintaining sweetness intensity.
Preparation and characterization of W/O/W purple potato anthocyanin nanoparticles: Antioxidant effects and gut microbiota improvement in rats
Authors: Zang Jianwei , Xiao Pinjian , Liu Zebo , Liu Yuanzhi , Zhang Qingfeng , Chen Jiguang , Yin Zhongping
Published: October 2024

Purple potato anthocyanins (PPAs) are recognized for their broad physiological activities, including significant antioxidant, antimicrobial, and gut microbiota‐regulating effects. However, their limited bioavailability in biological systems restricts the full realization of these potentials. In order to improve the bioavailability of PPA, this paper established and optimized the preparation process of W/O/W purple potato anthocyanin nanoparticles (PPA‐NPs). Based on the determination of the metabolites of PPA‐NPs, in vivo experiments were conducted in rats to investigate the absorption and metabolism, antioxidant activity, and the impact on the intestinal microbiota of PPA‐NPs. UPLC‐Q‐TOF‐MSMS analysis showed that the absorption of anthocyanins was increased by 220.36% in rats gavaged with PPA‐NPs compared to rats gavaged with PPA directly. Subsequent in vivo experiments revealed that PPA‐NPs significantly bolster primary antioxidant markers, evidenced by elevated glutathione and superoxide dismutase levels and reduced malondialdehyde content. Moreover, PPA‐NPs were found to positively alter the gut microbiome structure in aged rats, notably increasing the abundance of beneficial bacteria, such as Lactobacillus and Rothia, and improving microbial diversity. These findings suggest that W/O/W PPA‐NPs markedly improve the bioavailability of PPAs, showcasing promising antioxidant properties and potential health benefits for gut health in vivo. Overall, this research presents a novel approach for developing nanodelivery systems aimed at enhancing the bioavailability of water‐soluble substances.
Comparative study of volatile compounds of cold‐pressed oils extracted from three different oilseeds after gamma irradiation
Authors: Zhang Zhen‐Shan , Zhang Ya‐Zhe , Liu Xing‐Xin , Le Wu , Xiang Peng‐Fei
Published: October 2024

To investigate the effect of gamma irradiation on the volatile compounds of edible oils. Three types of oilseeds, including peanut, sesame, and flaxseed, were subjected to 8 kGy gamma irradiation, followed by cold pressing to extract their oils. The volatile compounds of the oils were isolated by simultaneous distillation extraction and analyzed by gas chromatography‐mass spectrometry. A total of 91 volatile compounds were identified, which can be grouped into eight categories: hydrocarbons, aldehydes, ketones, alcohols, acids, esters, furans, and benzene derivatives. Irradiation treatment resulted in a significant increase in the levels of hydrocarbons, aldehydes, and ketones in all oil samples (p < 0.05), with the greatest increase observed in hydrocarbons (4–14 times). In contrast, changes in alcohols, acids, esters, furans, and benzene derivatives were related to oilseed type. The increased hydrocarbons mainly originated from the degradation of palmitic, stearic, oleic, and linoleic acids. The irradiation resistance of the three oilseeds varied considerably, in the order: flaxseed > sesame > peanut. Based on the odor activity value, 11 key aroma compounds were selected, and (E)‐2‐decenal (tallow, oily, and orange), 1‐octanol (soapy and oily), and 1‐nonanol (floral and soapy) were only detected in the irradiated samples. Principal component analysis revealed that the oil samples of the three oilseeds could be well classified based on their key aroma compounds, and that the irradiation treatment had no remarkable effect on their intrinsic aroma.
Overview of oxidative stress and inflammation in diabetes
Authors: Weinberg Sibony Roni , Segev Omri , Dor Saar , Raz Itamar
Published: October 2024

The global prevalence of diabetes has increased significantly, leading to various complications and a negative impact on quality of life. Hyperglycemia hyperglycemic‐induced oxidative stress (OS) and inflammation are closely associated with the development and progression of type 2 diabetes mellitus (T2D) and its complications. This review explores the effect of T2D on target organ damage and potential treatments to minimize this damage. The paper examines the pathophysiology of T2D, focusing on low‐grade chronic inflammation and OS and on their impact on insulin resistance. The review discusses the role of inflammation and OS in the development of microvascular and macrovascular complications. The findings highlight the mechanisms by which inflammatory cytokines, stress kinases, and reactive oxygen species (ROS) interfere with insulin signaling pathways, leading to impaired glucose metabolism and organ dysfunction. Lifestyle interventions, including a balanced diet and exercise, can help reduce chronic inflammation and OS, thereby preventing and controlling T2D and its associated complications. Additionally, various antioxidants and anti‐inflammatory agents show potential in reducing OS and inflammation. Some anti‐diabetic drugs, like pioglitazone, metformin, and glucagon‐like peptide‐1 (GLP‐1) agonists, may also have anti‐inflammatory effects. Further research, including randomized controlled trials, is needed to evaluate the efficacy of these interventions.

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Genotyping Error Detection and Customised Filtration for SNP Datasets
Authors: Kan‐Lingwood Noa Yaffa , Sagi Liran , Mazie Shahar , Shahar Naama , Zecherle Bitton Lilith , Templeton Alan , Rubenstein Daniel , Bouskila Amos , Bar‐David Shirli
Published: October 2024

A major challenge in analysing single‐nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the ‘true’ genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four‐step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non‐invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.
Sediment Core DNA‐Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives
Authors: Blattner Lucas André , Lapellegerie Pierre , Courtney‐Mustaphi Colin , Heiri Oliver
Published: October 2024

Chironomidae, so‐called non‐biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21–35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate‐universal (FWH) and a newly designed Chironomidae‐specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage‐specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species‐level resolution datasets.
First‐line chemoimmunotherapy for patients with small‐cell lung cancer and interstitial lung abnormality: CIP risk and prognostic analysis
Authors: Li Yu , Jiang Yuxin , Pan Luyun , Yao Jun , Liang Shuo , Du Yanjun , Wang Dong , Liu Hongbing , Zhang Fang , Wang Qin , Lv Tangfeng , Zhan Ping
Published: October 2024

Background

Patients with non‐small‐cell lung cancer (NSCLC) receiving immunotherapy face a potential risk of developing checkpoint inhibitor‐related pneumonitis (CIP). However, there is no clear understanding of the specific link between interstitial lung abnormality (ILA) and CIP in patients with small‐cell lung cancer (SCLC). In addition, the prognosis of SCLC patients with ILA who receive chemoimmunotherapy is uncertain. Our study aimed to investigate the effect of ILA on the occurrence of CIP in SCLC patients receiving first‐line chemoimmunotherapy and to assess its relationship with prognosis.

Methods

We conducted a retrospective analysis of SCLC patients who received chemoimmunotherapy as a first‐line treatment between January 2018 and April 2024. The diagnosis of ILA was assessed by two experienced pulmonologists based on pretreatment chest computed tomography images. We investigated independent risk factors for CIP using logistic regression analysis and factors affecting PFS and OS using Cox regression analysis.

Results

A total of 128 patients with SCLC were included in the study. ILA was present in 41 patients (32.03%), and CIP occurred in 16 patients (12.50%). In multivariate logistic regression analysis, previous ILA (OR, 5.419; 95% CI, 1.574–18.652; p = 0.007) and thoracic radiation therapy (TRT) (OR, 5.259; 95% CI, 1.506–18.365; p = 0.009) were independent risk factors for CIP. ILA (HR, 2.083; 95% CI, 1.179–3.681; p = 0.012) and LDH (HR, 1.002; 95% CI, 1.001–1.002; p < 0.001) were statistically significant for increased mortality risk in multivariate Cox regression analysis.

Conclusions

In SCLC patients receiving first‐line chemoimmunotherapy, baseline ILA is a risk factor for CIP and is associated with poorer prognosis.
Forest and Biodiversity 2: A tree diversity experiment to understand the consequences of multiple dimensions of diversity and composition for long‐term ecosystem function and resilience
Authors: Cavender‐Bares Jeannine , Grossman Jake J. , Guzmán Q. J. Antonio , Hobbie Sarah E. , Kaproth Matthew A. , Kothari Shan , Lapadat Cathleen N. , Montgomery Rebecca A. , Park Maria
Published: October 2024

We introduce a new “ecosystem‐scale” experiment at the Cedar Creek Ecosystem Science Reserve in central Minnesota, USA to test long‐term ecosystem consequences of tree diversity and composition. The experiment—the largest of its kind in North America—was designed to provide guidance on forest restoration efforts that will advance carbon sequestration goals and contribute to biodiversity conservation and sustainability.

The new Forest and Biodiversity (FAB2) experiment uses native tree species in varying levels of species richness, phylogenetic diversity and functional diversity planted in 100 m2 and 400 m2 plots at 1 m spacing, appropriate for testing long‐term ecosystem consequences. FAB2 was designed and established in conjunction with a prior experiment (FAB1) in which the same set of 12 species was planted in 16 m2 plots at 0.5 m spacing. Both are adjacent to the BioDIV prairie‐grassland diversity experiment, enabling comparative investigations of diversity and ecosystem function relationships between experimental grasslands and forests at different planting densities and plot sizes.

Within the first 6 years, mortality in 400 m2 monoculture plots was higher than in 100 m2 plots. The highest mortality occurred in Tilia americana and Acer negundo monocultures, but mortality for both species decreased with increasing plot diversity. These results demonstrate the importance of forest diversity in reducing mortality in some species and point to potential mechanisms, including light and drought stress, that cause tree mortality in vulnerable monocultures. The experiment highlights challenges to maintaining monoculture and low‐diversity treatments in tree mixture experiments of large extent.

FAB2 provides a long‐term platform to test the mechanisms and processes that contribute to forest stability and ecosystem productivity in changing environments. Its ecosystem‐scale design, and accompanying R package, are designed to discern species and lineage effects and multiple dimensions of diversity to inform restoration of ecosystem functions and services from forests. It also provides a platform for improving remote sensing approaches, including Uncrewed Aerial Vehicles (UAVs) equipped with LiDAR, multispectral and hyperspectral sensors, to complement ground‐based monitoring. We aim for the experiment to contribute to international efforts to monitor and manage forests in the face of global change.