bluuebunny/crossref_metadata_2025 huggingface dataset:
Biogeographic context mediates multifaceted diversity-productivity relationships in island and mainland forests
Authors: Tolmos Maria Laura , Guerrero-Ramirez Nathaly R. , Ameztegui Aitor , Barajas Barbosa Martha Paola , Craven Dylan , Kreft Holger
Published: July 2023

Aim

Growing evidence suggests that impacts of biodiversity loss on ecosystem functioning and nature’s contributions to people are usually negative, yet the magnitude and direction of these impacts can be variable across naturally-assembled ecosystems. A potential driver of variation in diversity-productivity relationships is the biogeographical context, which may alter these relationshipsviaprocesses acting on the size and composition of the species pool like dispersal limitation, environmental filtering, speciation, and invasibility. However, the extent to which the relationships between biodiversity facets and forest productivity are shaped by the biogeographic context remains uncertain. Here, we examine the effects of taxonomic, phylogenetic, and functional tree diversity on aboveground productivity in climatically similar forests on islands and mainland.

Location

Continental and insular Spain.

Time period

1997-2018.

Major taxa studied

Trees.

Methods

Using plot data from a national forest inventory, we assessed the influence of taxonomic, phylogenetic, and functional diversity on aboveground productivity using linear models and structural equation models, while accounting for environmental conditions, non-native species, and the number of trees.

Results

We find that drier environmental conditions lead to a decrease in productivity and in the number of trees in both island and mainland forests. In island forests, non-native species increased productivity directly andviatheir effects on phylogenetic diversity.

Main conclusions

Our results suggest that multifaceted diversity, by capturing the diversity of evolutionary history, contributes to elucidating diversity-productivity relationships in island forests that could not be detected otherwise by taxonomic diversity alone. By filling empty niches in island forests, we find that non-native species are fundamentally altering ecosystem functioning on islands.
Zero-Shot Transfer of Protein Sequence Likelihood Models to Thermostability Prediction
Authors: Reeves Shawn , Kalyaanamoorthy Subha
Published: July 2023

Protein sequence likelihood models (PSLMs) are an emerging class of self-supervised deep learning algorithms which learn distributions over amino acid identities in structural and evolutionary contexts. Recently, PSLMs have demonstrated impressive performance in predicting the relative fitness of variant sequences without any task-specific training. In this work, we comprehensively analyze the capacity of six PSLMs to predict experimental measurements of thermostability for variants of hundreds of heterogeneous proteins. We assess performance of PSLMs relative to state-of-the-art supervised models, highlight relative strengths and weaknesses, and examine the complementarity between these models. We focus our analyses on stability engineering applications, assessing which methods and combinations of methods can most consistently identify and prioritize mutations for experimental validation. Our results indicate that structure-based PSLMs have competitive performance with the best existing supervised methods and can augment the predictions of supervised methods by integrating insights from their disparate training objectives.
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF
Authors: Adams Charlotte , Gabriel Wassim , Laukens Kris , Picciani Mario , Wilhelm Mathias , Bittremieux Wout , Boonen Kurt
Published: July 2023

Immunopeptidomics plays a crucial role in identifying targets for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. Low abundant peptides often occur in the field of immunopeptidomics, which is why the highly sensitive timsTOF instruments are increasingly gaining popularity. To improve PSM rescoring for immunopeptides measured using timsTOF instruments, we trained a deep learning-based fragment ion intensity prediction model. 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project were analyzed on a timsTOF-Pro to generate a ground-truth dataset, containing 93,227 MS/MS spectra of 74,847 unique peptides, that was used to fine-tune an existing Prosit model. By applying our fragment ion intensity prediction model, we demonstrate up to 3-fold improvement in the identification of immunopeptides. Furthermore, our approach increased detection of immunopeptides even from low input samples.
Estimation of contemporary effective population size in plant populations: limitations of genomic datasets
Authors: Gargiulo Roberta , Decroocq Véronique , González-Martínez Santiago C. , Paz-Vinas Ivan , Aury Jean-Marc , Lesur Kupin Isabelle , Plomion Christophe , Schmitt Sylvain , Scotti Ivan , Heuertz Myriam
Published: July 2023

Effective population size (Ne) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimateNehave been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium, in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A recently developed software based on linkage disequilibrium, GONE, looks particularly promising to estimate contemporary and recent-historicalNe(up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNPs genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimatingNeusing the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affectNeestimation using the linkage disequilibrium method, such as the occurrence of population structure. We show how accuracy and precision ofNeestimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data.
An mRNA-encoded, long-lasting Interleukin-2 restores CD8+T cell neoantigen immunity in MHC class I-deficient cancers
Authors: Beck Jan D. , Diken Mustafa , Suchan Martin , Streuber Michael , Diken Elif , Kolb Laura , Allnoch Lisa , Vascotto Fulvia , Peters Daniel , Beißert Tim , Türeci Özlem , Kreiter Sebastian , Vormehr Mathias , Sahin Ugur
Published: July 2023

MHC class I antigen presentation deficiency is considered to be the most prevalent cancer immune escape mechanism. Despite its increasing occurrence, the mechanistic implications, and potential strategies to address this challenge, remain poorly understood. Studying β2-microglobulin (B2M) deficient mouse tumor models, we found that MHC class I loss leads to a substantial immune desertification of the tumor microenvironment (TME) and broad therapeutic resistance to immune-, chemo- and radiotherapy. We show that treatment with long-lasting mRNA-encoded interleukin-2 (IL2) restores an immune cell infiltrated, IFNγ-promoted, highly proinflammatory TME signa-ture, and when combined with a tumor-targeting monoclonal antibody (mAb), can overcome ther-apeutic resistance. Surprisingly, we identified that effectiveness of this treatment is driven by ne-oantigen-specific IFNγ-releasing CD8+T cells that recognize neoantigens cross-presented by TME-resident activated macrophages that under IL2 treatment acquire augmented antigen presen-tation proficiency along with other M1-phenotype-associated features. Our findings highlight the unexpected importance of restoring neoantigen-specific immune responses in the treatment of cancers with MHC class I deficiencies.
Population genomics and epigenomics provide insights into the evolution of facultative asexuality in plants
Authors: Wang Yangzi , Duchen Pablo , Chávez Alexandra , Sree Sowjanya K. , Appenroth Klaus J. , Zhao Hai , Widmer Alex , Huber Meret , Xu Shuqing
Published: July 2023

Many organisms, particularly plants, are facultatively asexual. Because asexual reproduction is beneficial for the short term but costly for the long term, during the range expansion, natural selection should act on the genetic controls of asexuality in these facultatively asexual organisms. However, the genomic evidence of natural selection driving asexuality remains scarce, and the evolutionary consequences of facultatively asexuality on the genomic and epigenomic diversity remain controversial. Here, by analyzing population genomes and epigenomes ofSpirodela polyrhiza(L.) Schleid., a facultatively asexual plant that flowers rarely, we show that this plant has the lowest genomic diversity and DNA methylation levels among all studied multicellular eukaryotes. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revealed that multiple genes involved in flowering and embryogenesis were under positive selection, consistent with the hypothesis that natural selection drove the evolution of asexuality during the recent habitat expansions in this plant. Together, these results provide new insights into the evolution of plant reproductive systems and suggest that natural selection can drive the evolutionary changes of asexuality, which in turn alters the levels of genomic and epigenomic diversity.
Reference genome of the antLasius platythorax
Authors: Feldmeyer Barbara , Guiglielmoni Nadège , Kirangwa Joseph , Menzel Florian , Salces-Ortiz Judit , Fernández Rosa , Buena Atienza Elena , Ciofi Claudio , Diroma Maria Angela , Iannucci Alessio , Natali Chiara , Mc Cartney Ann M. , Riess Olaf , Casadei Nicolas , Waldvogel Ann-Marie
Published: July 2023

Ants are a highly diversified insect family of the order Hymenoptera, with many fascinating characteristics such as eusociality, chemical communication, farming, or social parasitism. Moreover, ants frequent a wide variety of habitats from dry deserts, grasslands, and savannas to cold temperate forests. The ability of ants to inhabit such diverse habitat ranges demonstrates their adaptability and ecological resilience. However, little is known about the genetic underpinnings of this vast array of traits and their adaptive potential. Here, we generated a high-quality genome assembly for the ant speciesLasius platythoraxusing long-read PacBio HiFi in combination with chromatin conformation capture (Hi-C) sequencing. We successfully assembled the genome into 15 chromosome-level scaffolds ranging from 7.9 to 19.2 Mb and encompassing 204.6 Mb out of 235.3 Mb (total assembly), and a BUSCO score of 86% (Hymenoptera_odb10). Comparative genomics between the two sister species will provide insights into the genomic basis of trait differentiation.
Mutational analysis reveals a novel role for hepatitis C virus NS5A domain I in cyclophilin-dependent genome replication
Authors: Chen Shucheng , Harris Mark
Published: July 2023

The hepatitis C virus (HCV) NS5A protein is comprised of three domains (D1-3). Previously, we observed that two alanine substitutions in D1 (V67A, P145A) abrogated replication of a genotype 2a (JFH-1 isolate) sub-genomic replicon (SGR) in Huh7 cells, but this phenotype was partially restored in Huh7.5 cells. To investigate the mechanism of this difference we extended this analysis to demonstrate that 5 additional residues, surface exposed and proximal to either V67 or P145, exhibited the same phenotype. In contrast, these mutants in a genotype 3a (DBN3a isolate) SGR retained their phenotype in each cell line.

The difference between Huh7 and Huh7.5 cells was reminiscent of the observation that cyclophilin (Cyp) inhibitors are more potent against HCV replication in the former and suggested a role for D1 in Cyp dependence. Consistent with this, all JFH-1 and DBN3a mutants exhibited increased sensitivity to cyclosporin A treatment compared to wildtype. Silencing of CypA in Huh7 cells inhibited replication of both JFH-1 and DBN3a. However, in Huh7.5 cells CypA silencing did not inhibit JFH-1 wildtype, but abrogated replication of all the JFH-1 mutants, and both DBN3a wildtype and all mutants. CypB silencing in Huh7 cells had no effect on DBN3a, but abrogated replication of JFH-1. CypB silencing in Huh7.5 cells had no effect on either SGR. These data demonstrate both a direct involvement of NS5A D1 in Cyp-dependent genome replication and functional differences between genotype 2 and 3 NS5A. Lastly, we confirmed that JFH-1 NS5A D1 interacted with CypAin vitro.
Coordinated inheritance of extrachromosomal DNA species in human cancer cells
Authors: Hung King L. , Jones Matthew G. , Wong Ivy Tsz-Lo , Lange Joshua T. , Luebeck Jens , Scanu Elisa , He Britney Jiayu , Brückner Lotte , Li Rui , González Rocío Chamorro , Schmargon Rachel , Dörr Jan R. , Belk Julia A. , Bafna Vineet , Werner Benjamin , Huang Weini , Henssen Anton G. , Mischel Paul S. , Chang Howard Y.
Published: July 2023

The chromosomal theory of inheritance has dominated human genetics, including cancer genetics. Genes on the same chromosome segregate together while genes on different chromosomes assort independently, providing a fundamental tenet of Mendelian inheritance. Extrachromosomal DNA (ecDNA) is a frequent event in cancer that drives oncogene amplification, dysregulated gene expression and intratumoral heterogeneity, including through random segregation during cell division. Distinct ecDNA sequences, herein termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells. However, how multiple ecDNA species within a tumor cell are assorted and maintained across somatic cell generations to drive cancer cell evolution is not known. Here we show that cooperative ecDNA species can be coordinately inherited through mitotic co-segregation. Imaging and single-cell analyses show that multiple ecDNAs encoding distinct oncogenes co-occur and are correlated in copy number in human cancer cells. EcDNA species are coordinately segregated asymmetrically during mitosis, resulting in daughter cells with simultaneous copy number gains in multiple ecDNA species prior to any selection. Computational modeling reveals the quantitative principles of ecDNA co-segregation and co-selection, predicting their observed distributions in cancer cells. Finally, we show that coordinated inheritance of ecDNAs enables co-amplification of specialized ecDNAs containing only enhancer elements and guides therapeutic strategies to jointly deplete cooperating ecDNA oncogenes. Coordinated inheritance of ecDNAs confers stability to oncogene cooperation and novel gene regulatory circuits, allowing winning combinations of epigenetic states to be transmitted across cell generations.
Stimulation-induced cytokine polyfunctionality as a dynamic concept
Authors: Portmann Kevin , Linder Aline , Eyer Klaus
Published: July 2023

Cytokine polyfunctionality is a well-established concept in immune cells, especially T cells, and their ability to concurrently produce multiple cytokines has been associated with better immunological disease control and subsequent effectiveness during infection and disease. To date, only little is known about the secretion dynamics of those cells, masked by the widespread deployment of mainly time-integrated endpoint measurement techniques that do not easily differentiate between concurrent and sequential secretion. Here, we employed a single-cell microfluidic platform capable of resolving secretion dynamics of individual PBMCs. To study the dynamics of poly-cytokine secretion, as well as the dynamics of concurrent and sequential polyfunctionality, we analyzed the response at different time points afterex vivoactivation. Firstly, we observed simultaneous secretion of cytokines over the measurement time for most stimulants in a subpopulation of cells only. Secondly, polyfunctionality generally decreased with prolonged stimulation times and revealed no correlation with the concentration of secreted cytokines in response to stimulation. However, we observed a general trend towards higher cytokine secretion in polyfunctional cells, with their secretion dynamics being distinctly different from mono-cytokine secreting cells. This study provided insights into the distinct secretion behavior of heterogenous cell populations after stimulation with well-described agents and such a system could provide better understanding for various immune dynamics in therapy and disease.
A novel ILK/STAT3 pathway controls plasticity in a neural stem cell model of glioblastoma
Authors: Loftus Alexander E. P. , Romano Marianna S. , Phuong Anh Nguyen , Muir Morwenna T. , Dawson John C. , Avalle Lidia , Douglas Adam T. , Mort Richard L. , Byron Adam , Carragher Neil O. , Pollard Steven M. , Brunton Valerie G. , Frame Margaret C.
Published: July 2023

Glioblastomas (GBM) are driven by malignant neural stem-like cells that display extensive heterogeneity and phenotypic plasticity, which drives tumour progression and therapeutic resistance. Here we show that the nodal extracellular matrix-cell adhesion protein integrin-linked kinase (ILK; a pseudokinase), is a key determinant of phenotypic plasticity and the mesenchymal-like, invasive cell state in mouse GBM stem cells. We found that a novel ILK-STAT3 signalling pathway is required for plasticity that enables the transition of GBM stem cells to an astrocyte-like state bothin vitroandin vivo. GBM cells genetically depleted of ILK become predominantly stabilised in a transcriptionally-defined progenitor-like state that is characterised by lack of response to differentiation cues and constitutive proliferation. Loss of ILK or interference with STAT3 impairs differentiation potential, reducing phenotypic plasticity of tumour cell populations; additionally, ILK loss causes a mesenchymal- to epithelial-like morphological transition and suppression of malignancy-associated features. Our work defines ILK as a central regulator of multiple GBM phenotypes including phenotypic plasticity and mesenchymal state.
“Sigo en lo Mismo”: the impact of papeles on the education of undocumented Latinx migrant and seasonal farmworkers
Authors: Gutiérrez Lorena
Published: July 2023

Purpose

The purpose of this paper is to explore the impact of documentation on the educational experiences, college readiness and aspirations of undocumented Latinx migrant and seasonal farmworkers.

Design/methodology/approach

This ethnographic study was conducted in a High School Equivalency Program at a large university in the Midwest. Data was collected during two semesters across a three-year span. Participants included six Mexican migrant and seasonal farmworkers who were preparing to earn their General Educational Development (GED) diploma. Using the grounded theory, data was collected and analyzed simultaneously where initial and focused coding took place, followed by cross-case analysis.

Findings

Analysis of student interviews, participant observations and in-depth fieldnotes that include the K-12 educational experiences, experiences during and after the High School Equivalency Program reveal that undocumented Latinx migrant and seasonal farmworkers aspire to earn a GED diploma to access a better future inclusive of college. However, the legal liminality, the uncertainty and ambiguity of being undocumented, impacts their educational journey prior to, during and beyond the High School Equivalency Program. Furthermore, undocumented Latinx migrant and seasonal farmworkers are unable to change their material conditions with a GED because of their documentation status.

Originality/value

Although researchers have studied the education experiences of Latinx migrant and seasonal farmworkers, analysis and consideration of documentation status is missing. This study contributes much needed findings about the impact of documentation status on the educational experiences, college readiness, and aspirations of Latinx migrant and seasonal farmworkers.
The role of saffron (Crocus sativusL) on testosterone and depression in andropause middle-aged and elderly men: a systematic review
Authors: Amini Shirin , Mohseni Houra , Abiri Behnaz , Jafarirad Sima
Published: July 2023

Purpose

Depression is one of the most overlooked psychiatric disorders among middle-aged and elderly men. Saffron (Crocus sativusL.) stigmas are a favorite and common spice that is used as an antidepressant, an anti-inflammatory and a sexual stimulant. This systematic review aimed to provide a comprehensive survey of the effects of saffron on depression in middle-aged and elderly men.

Design/methodology/approach

The authors searched Web of Science, PubMed, ProQuest, Cochrane, Science Direct, Scopus and Google Scholar databases to gather any relevant studies published from 1980 to September 2022. This review included studies that examined the relationship between depression and testosterone concentration (four studies) or saffron’s effects on testosterone and depression (six studies).

Findings

Observational research showed an association between testosterone and depression in middle-aged and elderly men. Furthermore, animal studies have found that saffron increased testosterone levels and decreased depression in males. There is evidence that testosterone may contribute to the mood. Besides its antioxidant and anti-inflammatory properties, this study proposed scientific mechanisms that saffron may also play a protective role against depression through its influence on testosterone, in middle-aged and elderly men. The general use of saffron at high doses or for prolonged periods may cause side effects; therefore, it is important to consult a health-care professional before the recommended dosage and duration of saffron supplementation, especially if a person has any underlying health conditions or is taking medications.

Originality/value

This study provides researchers with an additional perspective for conducting clinical trials on the use of saffron to enhance the mood of elderly men with testosterone deficiency.
Meta‐analysis and critical review of trophic discrimination factors (Δ13C and Δ15N): Importance of tissue, trophic level and diet source
Authors: Stephens Ryan B. , Shipley Oliver N. , Moll Remington J.
Published: July 2023

Robustly quantifying dietary resource use and trophic position using stable isotopes requires accurate trophic discrimination factors (TDF; Δ13C and Δ15N for carbon and nitrogen, respectively), defined as the isotopic difference between consumer and diet. Early TDF studies converged on values of around 1.0‰ for Δ13C and 3.4‰ for Δ15N but more recent work indicates that TDF values may be more nuanced, depending on taxa, tissues, trophic level and diets. Yet, the relative importance of these factors remains unclear.

Focusing on vertebrates (birds, fish, herptiles and mammals), we conducted a literature review of 279 studies that estimated TDF values and used a Bayesian framework to determine how tissue type, trophic level and diet source influence variation in Δ13C and Δ15N. Additionally, we reviewed 358 trophic ecology studies to determine if studies accounted for these factors during their TDF selection process.

For Δ13C, vertebrates showed consistent patterns among tissue types (likely influenced by amino acid composition) and between trophic levels and diet sources (likely a result of dietary protein content and metabolic routing). Comparatively, for Δ15N, vertebrates showed considerable variation among tissue types and trophic levels, likely due to differences in tissue synthesis and physiological capabilities. Overall, Δ13C ranged from −5.1‰ to 9.1‰ and Δ15N from −3.3‰ to 9.7‰, underscoring that 1.0‰ for Δ13C and 3.4‰ for Δ15N are not universally appropriate. Moreover, both Δ13C and Δ15N varied by more than 9‰ within a single species and tissue type, demonstrating that using TDF values from the same, or similar, species may not be appropriate if diet and trophic level are not considered.

Despite the importance of diet source on TDF values, most trophic ecology studies did not account for it. Further, most fish studies relied on literature review values that failed to account for tissue type, trophic level and diet source. To aid ecologists in diet and trophic assessments of vertebrates, we used our meta‐analysis to model taxon‐specific TDF estimates (mean ± SD) for each tissue type, trophic level and diet source combination. These more refined TDF values should improve ecological assessments that use stable isotopes.

Read the free Plain Language Summary for this article on the Journal blog.
Tumor budding and tumor‐infiltrating lymphocytes can predict prognosis in pT1b esophageal squamous cell carcinoma
Authors: Li Zhuo , Liu Linxiu , Wang Bingzhi , Ying Jianming , He Jie , Xue Liyan
Published: July 2023

Background

Tumor budding (TB) and tumor‐infiltrating lymphocyte (TIL) are significant predictive indicators of lymph node metastasis (LNM) and unfavorable prognosis in various tumors. Currently, there is no gold standard for TB and TIL evaluation in esophageal squamous cell carcinoma (ESCC). This study aimed to identify the standard of TB and TIL evaluations and build a predictive model for prognosis among patients with pT1b ESCC.

Methods

We retrospectively analyzed the prognostic values of TB and TIL in 150 pT1b ESCC cases. Hematoxylin and eosin (H&E) and immunohistochemistry (IHC) of anti‐pan cytokeratin (AE1/AE3) were used to analyze the threshold of TB, and intratumoral TIL and peritumoral TIL (pTIL) were evaluated using the receiver operating characteristic curves (ROC).

Results

We found that TB in a three‐tiered grading system (low‐TB: 0‐4; middle‐TB: 5–15; high‐TB: ≥16) displayed an excellent prognosis prediction for LNM and survival based on IHC staining using a 20× objective lens. Low pTIL level (≤20%) was a significant indicator of LNM and unfavorable prognosis (p < 0.05). Moreover, lower tumor location and lymphovascular invasion (LVI) were correlated with an unfavorable prognosis (p < 0.05). A nomogram developed based on TB, pTIL, LVI, and tumor location showed good discrimination, as shown by the area under the ROC and calibration curves.

Conclusion

We therefore recommend identifying TB using a 20× objective lens under IHC staining and TIL adjacent to the tumor. Additionally, a nomogram was built for facilitating individualized prediction of survival for patients with pT1b ESCC.
Natural killer cell‐mediated contact dermatitis‐like reaction induced by treatment with TLR3 ligand poly(I:C)
Authors: Majewska‐Szczepanik Monika , Kowalczyk Paulina , Askenase Philip W. , Szczepanik Marian
Published: July 2023

Introduction

Poly(I:C) is recognised by endosomal Toll‐like receptor 3 (TLR3) and activates cytotoxic CD8(+) lymphocytes and natural killer (NK) cells. It has been shown that the viral TLR3 agonist induces robust and long‐lasting T‐cell‐mediated responses. In addition, TLR3 modulates the contact hypersensitivity reaction.

Objective

This study aimed to determine whether poly(I:C) injection can induce NK‐mediated hapten reactivity in mice.

Methods

Mice were treated with poly(I:C), and their response to dinitrofluorobenzene hapten was measured by assessing ear swelling and serum interferon gamma (IFN‐γ) production. Adoptive cell transfer and cell sorting were used to investigate the mechanism of the reaction, and the phenotype of poly(I:C)‐activated liver NK cells was determined by flow cytometry analysis.

Results

The results showed that poly(I:C) administration increased ear swelling, serum IFN‐γ levels and the response to hapten in both immunocompetent and T‐ and B‐cell‐deficient mice. Only liver poly(I:C)‐activated DX5(+) NK cells were able to transfer reactivity to hapten into a naive recipient. Induction of liver NK cells after poly(I:C) administration was TLR3/TRIF‐ and IFN‐γ‐dependent, interleukin 12‐independent, and not modulated by MyD88.

Conclusion

This study provides new insights into how poly(I:C) stimulates NK‐mediated reactivity to hapten and suggests that liver NK cells may modulate the immune response to non‐pathogenic factors during viral infection.
Compound glycyrrhizin tablets combined with the 308 nm excimer laser in the treatment of vitiligo: A systematic review and meta‐analysis
Authors: Huang Fujun , Fu Qiang , Zhou Ziwenyan , Tang Lei , Zhao Mingdan , Huang Mengya , Zhou Xun
Published: July 2023

Background

Although the 308 nm excimer laser is commonly used to cure vitiligo, its clinical efficacy is limited. Experts have found that the efficacy of compound glycyrrhizin tablets combined with the 308 nm excimer laser in the treatment of vitiligo is significantly enhanced, but the specific research methods and clinical data must be clarified.

Objective

To determine the clinical efficacy of compound glycyrrhizin tablets combined with the 308 nm excimer laser in the treatment of vitiligo.

Methods

Until August 2022, studies were searched in PubMed, the Cochrane Library, the Chinese Biomedical Literature Database, the China National Knowledge Infrastructure, the Chinese Scientific Journal Database, and the Wan Fang Database. We also searched for clinical RCTs involving compound glycyrrhizin tablets combined with the 308 nm excimer laser for the treatment of vitiligo. The meta‐analysis was conducted in accordance with the Cochrane Handbook's recommendations. Two reviewers regulated the study selection, data extraction, and assessment of bias risk, and consulted a third reviewer as necessary. For the meta‐analysis, Review Manager 5.4 was utilized.

Results

Finally, 9 articles and 1052 patients were included. A systematic review compared the efficacy of compound glycyrrhizin tablets combined with the 308 nm excimer laser to that of the 308 nm excimer laser alone: OR = 3.33, p < 0.00001, 95% confidence interval [2.25, 4.92].

Conclusion

In the treatment of vitiligo, compound glycyrrhizin tablets combined with the 308 nm excimer laser are more effective than the 308 nm excimer laser alone, and there are no serious adverse reactions. It is a safe and efficient way of treatment.
Characterizing canopy complexity of natural and restored intertidal oyster reefs (Crassostrea virginica) with a novel laser‐scanning method
Authors: Cannon David J. , Kibler Kelly M. , Taye Jyotismita , Medeiros Stephen C.
Published: July 2023

The structural complexity of oyster reef canopy plays a major role in promoting biodiversity, balancing the sediment budget, and modulating hydrodynamics in estuarine systems. Although oyster canopy structure is both spatially and temporally heterogeneous, oyster canopies are generally characterized using simple first‐order quantities, like oyster density, which may lack the ability to sufficiently parameterize reef roughness. In this study, a novel laser‐scan approach was used to map the surface of intact reference and restored reefs (restoration age: 1–4 years) during low tide, when the oyster canopy was fully exposed. Measurements were used to estimate hydrodynamically relevant roughness characteristics over the entire reef surface (>140 m2; 0.50 m resolution), providing estimates of the canopy height (hc), standard deviation (), rugosity index (R), and fractal dimension (D). Average canopy heights ranged from 3.6 to 4.9 cm, with canopy height standard deviations between 1.4 and 2.0 cm. Mean rugosity indices and fractal dimensions were relatively low on the youngest (1 year) restored reef (R = 1.28;D = 2.67), with substantial increases observed for more mature reef canopies (4 years:R = 1.56;D = 2.71). Structural complexity was consistently greater on reef margins than in reef interiors. Increases in complexity were linked to restoration age, with older reefs exhibiting more complex oyster canopies. The highest fractal dimension was observed on the intact reference reef, highlighting the importance of sustained reef growth for maintaining higher‐order structural complexity. Results provide spatially explicit surface roughness characterizations for healthy, intertidal oyster reefs, with applications in both restoration science and natural and nature‐based feature design.
Transition from carbonatitic magmas to hydrothermal brines: Continuous dilution or fluid exsolution?
Authors: Yuan Xueyin , Zhong Richen , Xiong Xin , Gao Jing , Ma Yubo
Published: July 2023

Carbonatites are the most important primary sources for the rare earth elements (REEs). While fractional crystallization of carbonate minerals results in the enrichment of volatiles, alkalis, and REEs in the remaining melts, the transition from carbonatitic magmas to hydrothermal brines remains unclear. Here, we investigated the pressure-temperature-composition (P-T-X) properties of the Na2CO3-H2O system up to 700°C and 11.0 kbar using a hydrothermal diamond anvil cell and a Raman spectrometer. Our results show that Na2CO3becomes increasingly soluble under highP-Tconditions, leading to the disappearance of melt-fluid immiscibility and the continuous transition from Na2CO3melts to hydrothermal brines under deep crustal conditions. Given the abundance of Na2CO3in highly evolved carbonatitic systems, we suggest that the continuous melt-fluid transition in deep-seated carbonatites results in REEs being sufficiently concentrated in the brine-melts to form economic ore bodies, whereas in shallow systems, REEs preferentially partition into carbonatitic magmas over synmagmatic brines and disperse in carbonatite rocks that underwent limited fractionation.
Corporate Social Responsibility and Enterprise Performance: The Chain Mediating Effect Test Based on Corporate Reputation and Brand Value
Authors: Lu Xiaojian , Zhang Han , Zhang Minqiang , Chen Yanfen
Published: July 2023

Corporate social responsibility (hereinafter referred to as “CSR”) sometimes does not directly affect enterprise performance but through some mediator variable. Corporate reputation and brand value have chain-mediating effects in the influence mechanism of CSR on enterprise performance. Theoretically, this paper broadens the scope of study on CSR and enterprise performance, deeply explores the internal mechanism between them, and opens the “black box” in the process of transforming CSR into enterprise performance. Practically, it can encourage Chinese enterprises to actively undertake CSR, strengthen reputation management, enhance brand value, and finally promote the sustainable development of enterprises. A-share listed companies (listed companies in the Chinese A stock market) in Shanghai and Shenzhen stock exchanges from 2008 to 2020 in “China’s 500 Most Valuable Brands List” by World Brand Lab are studied in this paper. The results of the empirical study based on relevant data show a significant positive relationship between CSR and enterprise performance. It investigates the mediating chain effects of corporate reputation and brand value in the influence of CSR on enterprise performance. Listed companies must disclose the annual CSR report. CSR reports as an effective supplement to corporate financial information, which provides an important communication channel for the enterprise and stakeholders. Stakeholders can timely understand their rights and interests through the CSR information and have a more comprehensive and deeper understanding of enterprises. In turn, the enterprise can also win a good reputation, establish a good brand image, and get sustainable development.
Clustering of the causes of death in Northeast Iran: a mixed growth modeling
Authors: Talkhi Nasrin , Emamverdi Zohreh , Jamali Jamshid , Salari Maryam
Published: July 2023

Background

Processing and analyzing data related to the causes of mortality can help to clarify and monitor the health status, determine priorities, needs, deficiencies, and developments in the health sector in research and implementation areas. In some cases, the statistical population consists of invisible sub-communities, each with a pattern of different trends over time. In such cases, Latent Growth Mixture Models (LGMM) can be used. This article clusters the causes of individual deaths between 2015 and 2019 in Northeast Iran based on LGMM.

Method

This ecological longitudinal study examined all five-year mortality in Northeast Iran from 2015 to 2019. Causes of mortality were extracted from the national death registration system based on the ICD-10 classification. Individuals' causes of death were categorized based on LGMM, and similar patterns were placed in one category.

Results

Out of the total 146,100 deaths, ischemic heart disease (21,328), malignant neoplasms (17,613), cerebrovascular diseases (11,924), and hypertension (10,671) were the four leading causes of death. According to statistical indicators, the model with three classes was the best-fit model, which also had an appropriate interpretation. In the first class, which was also the largest class, the pattern of changes in mortality due to diseases was constant (n = 98, 87.50%). Second-class diseases had a slightly upward trend (n = 10, 8.92%), and third-class diseases had a completely upward trend (n = 4, 3.57%).

Conclusions

Identifying the rising trends of diseases leading to death using LGMM can be a suitable tool for the prevention and management of diseases by managers and health policy. Some chronic diseases are increasing up to 2019, which can serve as a warning for health policymakers in society.
Relationship between spiritual intelligence and lifestyle with life satisfaction among students of medical sciences
Authors: Senmar Mojtaba , Azimian Jalil , Noorian Sajad , Aliakbari Mohaddese , Chegini Najmeh
Published: July 2023

Background

Young people are the main resources of any country and entering university is considered a sensitive period in their lives. Satisfaction with life is one of the indicators of successful adaptation to life. Lifestyle and spiritual intelligence can complement and give meaning to this variable. The present study was conducted to investigate the relationship between spiritual intelligence and lifestyle with life satisfaction in students of Medical Sciences.

Methods

This descriptive-analytical study was conducted among the students of Qazvin University of Medical Sciences in 2017. One hundred thirty-nine students were included in this study. Data collection tools were the King's spiritual intelligence scale, Miller-Smith lifestyle assessment inventory, satisfaction with life scale (Diener), and demographic information checklist. To analyze the data, descriptive and analytical tests such as independent T-test and one-way analysis of variance and SPSS version 22 software were used. The significance level of all tests was considered less than or equal to 0.05.

Findings

In the present study, 108 were women and the rest were men. 49.6% of students were under twenty years old. The results of this research showed that there is a significant negative relationship between lifestyle and life satisfaction (r = -.33) and a significant positive relationship between spiritual intelligence and life satisfaction (r = .27) (p < 0.05). The mean scores of students in life satisfaction were 22.49 ± 5.92, lifestyle was 49.15 ± 8.35, and spiritual intelligence was 51.59 ± 11.43.

Conclusions

The findings of the present study showed the important role of spiritual intelligence and lifestyle in students' life satisfaction. These findings can be used by administrators and policymakers in formulating interventions and providing a suitable context to improve students' life satisfaction.
Default Risk and Option Returns
Authors: Vasquez Aurelio , Xiao Xiao
Published: July 2023

This paper studies the effects of default risk on expected equity option returns. In the cross-section, expected delta-hedged equity option returns have a negative relation with default risk measured by credit ratings or default probability. In the time series, credit rating downgrades (upgrades) lead to a decrease (increase) in the firm’s delta-hedged option return. Our results are consistent with a stylized capital structure model in which the negative relation between option returns and default risk is driven by firm leverage and asset volatility.

This paper was accepted by Lukas Schmid, finance.

Funding: A. Vasquez thanks the Asociación Mexicana de Cultura A.C. for financial support.

Supplemental Material: The online appendix and data are available at https://doi.org/10.1287/mnsc.2023.4796 .
Incidence and damage of the ambrosia beetle on cocoa plants in East Luwu District, South Sulawesi, Indonesia
Authors: NURIADI NURIADI , SJAM SYLVIA , GASSA AHDIN , DEWI VIEN SARTIKA
Published: July 2023

Abstract. Nuriadi, Sjam S, Gassa A, Dewi VS. 2023. Incidence and damage of the ambrosia beetle on cocoa plants in East Luwu District, South Sulawesi, Indonesia. Biodiversitas 24: 3592-3600. The attack of ambrosia beetle on cocoa plants (Theobroma cacao L.) in East Luwu District, South Sulawesi Province, was first reported in 2020 at the Wotu sub-district. However, there was no information on its intensity and the number of affected sub-districts. A survey and data collection were conducted from January to July 2021 by selecting a 1 hectare area from 7 out of the 11 affected sub-districts identified in the preliminary study. The parameters observed were attack intensity, the number of galleries in stems and branches, and the number of trapped ambrosia beetle. The results showed that the attack of the ambrosia beetle on cocoa plants in the 7 sub-districts ranged from moderate to severe intensity, causing damage to mature plants and seedlings. It was observed that the number of galleries was higher on stems than on branches. The intensity of attacks on cocoa plants aged 23-27 years is higher than the cocoa aged 8-15 years. Additionally, the obtained species of ambrosia beetle are Xylosandrus sp.1 (Coleoptera: Curculionidae), Xylosandrus sp.2 (Coleoptera: Curculionidae), Xyleborus sp. (Coleoptera: Scolytidae) and Hypothenemus sp. (Coleoptera: Scolytidae). The results are expected to provide important information about the invasion of the ambrosia beetle and the prevention steps of its spread on cocoa plantations in South Sulawesi.
‘My father’s village, my city’: Place-making in the cinema of NCR
Authors: Gangopadhyay Rudrani
Published: July 2023

This article reads the emerging cinema of the National Capital Region (NCR) of India as a primary archive that documents urban transformation in the rapidly developing area and examines the representation of space within the same. Using three films set in the region –Aurangzeb(Atul ),Titli(Kanu ) andGurgaon(Shanker ) – the article reads the effects of privatized city-making and the deeply unequal growth reflected within the diagetic place-making of the region and argues that theoretical frameworks like gentrification are not adequate to register the urban transformation in these postcolonial post-liberalization contexts, and that the films themselves serve as primary archives that offer a means to visibilize the unique nature of spatial change that also distort social ties in the region.
O que é que tem de especial?
Authors: Santos Carmo Cabral Lucas , Janz Woitowicz Karina
Published: July 2023

Este artigo tem como objetivo apresentar como os recursos do webjornalismo podem intensificar as características do jornalismo literário, de revista e das grandes reportagens. O objeto de análise compreende os especiais para internet da revista piauí nos anos de 2018 e 2019, em um recorte de quatro materiais que agregam conjuntos de reportagens. A investigação é feita com a proposta de aplicação de uma metodologia própria, na busca de realizar um cruzamento entre as características dos formatos trabalhados, tais como especificidades do on-line, apuração e estilo. Os aspectos encontrados estão longe de ser inovadores, mas permitem constatar que a internet funciona como dispositivo para intensificar fatores como a contextualização e o alto nível de detalhamento, presentes nos estudos sobre jornalismo literário.
Hybrid PDE-ABM models
Authors: Marzban Sadegh
Published: July 2023

This PhD thesis presents three new mathematical models aimed at advancing the current understanding of viral dynamics and cancer. The models are implemented in the HAL system and are applied to address current significant questions in the field. The first model, described in Chapter 3, is focused on the evolution of sensitive and resistant tumor cells and considers Darwinian selection, Lamarckian induction, and microvesicle transfer as mechanisms for resistance. The model is compared to an agent-based model and provides insight into the impact of microvesicles on the spread of cancer cells. Chapter 4 presents a hybrid partial differential equation - agent-based (PDE-ABM) model to describe the spatiotemporal viral dynamics in a cell population. The virus concentration is modeled as a continuous variable, while changes in the states of cells are represented by a stochastic agent-based model. The two subsystems are intertwined and the model is applied to predict SARS-CoV-2 and influenza infections. The results are compared to a classical ODE system of viral dynamics and demonstrate the importance of considering spatial patterns in predicting the spread of infections. In Chapter 6, the pharmacometric features of the novel antiviral drug Paxlovid for SARS-CoV-2 are explored using a hybrid multiscale mathematical approach. The results of the evaluation match clinical expectations and provide insight into the importance of early interventions and the sensitivity of the results to the diffusion coefficient of the virus. Overall, this PhD thesis makes a significant contribution to the current understanding of viral dynamics and cancer and demonstrates the potential of mathematical models to provide insight into these complex systems.
Blending parody: The case ofMy Corona
Authors: Hirsch Galia
Published: July 2023

This contribution is an attempt to integrate the notion of conceptual blending (Fauconnier and Turner 1998; Fauconnier and Turner 2002; and Fauconnier and Turner 2003) and Linda Hutcheon’s (1985) view of parody as a form of repetition maintaining a critical distance, through the analysis of a multimodal Internet meme. The case study chosen is a parodic music video of the Knack’s classic hitMy Sharona, showing the absurdity in everyday life during the times of the Covid-19 pandemic. The study is thus based on two conceptual paradigms: Blending Theory and Pragmatic Studies of Parody.
Corporalidad y conciencia de sí. Acercamiento a ‘La alemana’ de Gustavo Escanlar
Authors: Gutiérrez Ramírez Diana Carolina
Published: July 2023

El presente documento explora lo que ha venido a denominarse como ‘la nueva narrativa uruguaya’ y rastrea, a largos trazos, las identidades, las voces, los contextos e imaginarios que, haciendo acopio de la tradición literaria atribuida a Felisberto Hernández y Juan Carlos Onetti, propende a la recuperación de los tugurios como plataforma de sentido narrativa y, con ella, a una marcada propensión a perfilar personajes cuya vitalidad degradada construye una atmosfera limítrofe. En el compendio de novelas a las que se alude se instaura una sensibilidad atípica cuya ambición estética se manifiesta en la transgresión y el desdibujamiento de lo oficial y lo legítimo. Es así que de manera concreta importa el rostro transgresor como metáfora de los espacios marginales: el personaje como entramado identitario en el que se conjugan la cotidianidad, el deseo, la violencia, la corporalidad y lo amoral. Para tal comprensión del personaje se realiza un acercamiento al femenino protagónico de la novela La Alemana (2009) del escritor uruguayo Gustavo Escanlar (1962-2010).