bluuebunny/crossref_metadata_2025 huggingface dataset:
AptaDiff: de novo design and optimization of aptamers based on diffusion models
Authors: Wang Zhen , Liu Ziqi , Zhang Wei , Li Yanjun , Feng Yizhen , Lv Shaokang , Diao Han , Luo Zhaofeng , Yan Pengju , He Min , Li Xiaolin
Published: November 2023

Aptamers are single-stranded nucleic acid ligands, featuring high affinity and specificity to target molecules. Traditionally they are identified from large DNA/RNA libraries using in vitro methods, like Systematic Evolution of Ligands by Exponential Enrichment (SELEX). However, these libraries capture only a small fraction of theoretical sequence space, and various aptamer candidates are constrained by actual sequencing capabilities from the experiment. Addressing this, we proposed AptaDiff, the first in silico aptamer design and optimization method based on the diffusion model. Our Aptadiff can generate aptamers beyond the constraints of high-throughput sequencing data, leveraging motif-dependent latent embeddings from variational autoencoder, and can optimize aptamers by affinity-guided aptamer generation according to Bayesian optimization. Comparative evaluations revealed AptaDiff’s superiority over existing aptamer generation methods in terms of quality and fidelity across four high-throughput screening data targeting distinct proteins. Moreover, Surface Plasmon Resonance (SPR) experiments were conducted to validate the binding affinity of aptamers generated through Bayesian optimization for two target proteins. The results unveiled a significant boost of 87.9% and 60.2% in RU values, along with a 3.6-fold and 2.4-fold decrease in KD values for the respective target proteins. Notably, the optimized aptamers demonstrated superior binding affinity compared to top experimental candidates selected through SELEX, underscoring the promising outcomes of our AptaDiff in accelerating the discovery of superior aptamers.

Key Points

We proposed AptaDiff, the first in silico aptamer design method based on the diffusion model. Aptadiff can generate aptamers beyond the constraints of high-throughput sequencing data.

Aptadiff can optimize aptamers through affinity-guided generation via Bayesian optimization within a motif-dependent latent space, and the affinity of the optimized aptamers to the target protein is better than the best experimental candidate from traditional SELEX screening.

Aptadiff consistently outperforms the current state-of-the-art method in terms of quality and fidelity across high-throughput screening data targeting distinct proteins.
Prediction of Diabetes in Middle-Aged Adults: A Machine Learning Approach
Authors: Addo Gideon , Yeboah Bismark Amponsah , Obuobi Michael , Doh-Nani Raphael , Mohammed Seidu , Amakye David Kojo
Published: November 2023

Background

Diabetes is a serious and progressive medical condition demanding efficient diagnostic methods, especially since its associated symptoms overlap with the symptoms of other medical conditions. While various studies have explored early detection of diabetes across different age groups, there is a notable gap in specific attention to middle-aged adults. This study explicitly focused on this demographic, aiming to assess associations between symptoms and diabetes status, investigate the relevance and relative influence of certain symptomatic and demographic features in the prediction of diabetes, and identify the most efficient machine learning (ML) model for predicting diabetes.

Methods

Utilizing a dataset from a previous study conducted in the Sylhet Diabetes Hospital in Bangladesh, India, comprising 520 participants, including both diabetic and non-diabetic patients, we extracted and analyzed demographic and symptom-related information from 296 middle-aged adults aged from 40 to 60 years. Employing chi-square tests, we evaluated symptom-diabetes associations, while utilizing the Boruta algorithm to investigate symptom importance and influence. Seven ML models namely, K-Nearest Neighbor (KNN), Naïve Bayes (NB) classifier, Support Vector Machines with linear, polynomial, and radial basis function kernels, Random Forest (RF) classifier, and Logistic Regression were then assessed for optimal predictive performance.

Results

Out of the 296 participants of this study, 179 (60%) were diabetic. Significant associations were found between diabetes status in middle-aged adults and symptoms such as polyuria, polydipsia, weakness, sudden weight loss, partial paresis, polyphagia, and visual blurring, as confirmed by the p-values of their respective chi-square tests. All features studied, including demographics and symptoms, were confirmed as relevant for predicting diabetes in middle-aged adults. Notably, polyuria, polydipsia, gender, alopecia, irritability, and sudden weight loss were identified as the most influential features. Among the seven ML models, RF showed the highest sensitivity (98.59%), while KNN excelled in specificity (97.83%). RF demonstrated the best accuracy (96.58%) and area under the curve score (96.00%), making it the most efficient ML model for predicting diabetes among middle-aged adults.

Conclusion

The findings of this study emphasize the importance of using diabetes-related symptoms for early detection of diabetes within the middle-aged adult population. The RF model demonstrated robust diagnostic capabilities, emphasizing its potential in predicting diabetes in middle-aged adults. Further exploration of genetic, lifestyle, and environmental factors is warranted to enhance the understanding and diagnostic accuracy in this demographic.
Obesity Prevention Efforts in France, Italy, and Japan - A Scoping Review Protocol
Authors: Hammad Nour M. , Tobias DeirDre K.
Published: November 2023

Background

Population-level prevention efforts in the US have yet to correct the upward trends in increasing US obesity prevalence. Italy, France, and Japan are high-income countries that have employed approaches aimed at obesity prevention that may have contributed to their favorable obesity trends. It is plausible that these efforts could be culturally adapted with similar effectiveness to the US population. This paper outlines the protocol of a scoping review that will identify and characterize the range of obesity prevention efforts implemented in Italy, France, and Japan to inform potential strategies for obesity prevention in the US.

Methods and analysis

We will conduct a systematic search in PubMed, Embase, and Cochrane. We will assess articles that describe any national, regional, or local public health and/or clinical guideline, recommendation, intervention, campaign, policy or other population-level effort targeting obesity prevention in Italy, France, and Japan. Two independent reviewers will screen the articles, and a third independent reviewer will resolve conflicts that arise upon screening. Descriptive synthesis will be performed to describe the country-specific prevention strategies and summarize the available evidence for their effectiveness.

Discussion

The purpose of this paper is to describe the study protocol for a scoping review that will provide a comprehensive summary of available evidence for obesity prevention strategies that have been implemented in Italy, France, and Japan. These strategies will inform potential prevention efforts for consideration in the US.

Scoping review registration DOI

https://doi.org/10.17605/OSF.IO/M35YX.
GMAC: A simple measure to quantify upper limb use from wrist-worn accelerometers
Authors: Balasubramanian Sivakumar
Published: November 2023

Abstract

Various measures have been proposed to quantify upper-limb use through wrist-worn inertial measurement units. The two most popular traditional measures of upper-limb use – thresholded activity counts (TAC) and the gross movement (GM) score suffer from high sensitivity and specificity, respectively. We had previously proposed a hybrid version of these two measures – the GMAC – that showed better overall detection performance. However, the previously proposed GMAC used both accelerometer and gyroscope data and used the same parameter values from the TAC and GM measures. In this paper, we aim to answer two important questions to improve the usefulness of the GMAC measure: (a) can the GMAC measure be implemented using only the accelerometer data? (b) what are the optimal parameter values for the GMAC measure? We propose a modified version of the GMAC that works with only accelerometer data, and optimize this measure’s parameters. This optimized GMAC showed better detection performance than the previously proposed GMAC and surprisingly had comparable performance to that of the best-performing machine learning-based measure (random forest inter-subject model). Although intra-subject machine learning-based measures perform better than the optimized GMAC, the latter is simpler, well suited for real-time upper-limb use detection, and is the best option when a trained machine learning-based intra-subject model or labeled data is unavailable. The optimized GMAC measure can be a useful measure for either offline detection or for real-time detection and feedback of upper limb use.
SPECTRE: standardized global spatial data on terrestrial SPECies ThREats
Authors: Branco Vasco V. , Correia Luís , Cardoso Pedro
Published: November 2023

Motivation

SPECTRE is an open-source database containing standardised spatial data on global environmental and anthropogenic variables that are potential threats to terrestrial species and ecosystems. Its goal is to allow users to swiftly access spatial data on multiple threats at a resolution of 30 arc-seconds for all terrestrial areas. Following the standard set by Worldclim, this data allows full comparability and ease of use under common statistical frameworks for global change studies, species distribution modelling, threat assessments, quantification of ecosystem services and disturbance, among multiple other uses. A web user interface, a persistent online repository, and an accompanying R package with functions for downloading and manipulating data are provided.

Main types of variable contained

SPECTRE is a GIS product with 24 geoTiff raster layers (with plans to expand in the near future) with an approximate 1 km2resolution.
De novoclustering of long-read amplicons improves phylogenetic insight into microbiome data
Authors: Hui Yan , Nielsen Dennis Sandris , Krych Lukasz
Published: November 2023

Long-read amplicon profiling through read classification limits phylogenetic analysis of amplicons while community analysis of multicopy genes, relying on unique molecular identifier (UMI) corrections, often demands deep sequencing. To address this, we present a long amplicon consensus analysis (LACA) workflow employing multiplede novoclustering approaches based on sequence dissimilarity. LACA controls the average error rate of corrected sequences below 1% for the Oxford Nanopore Technologies (ONT) R9.4.1 and ONT R10.3 data, 0.2% for ONT R10.4.1, and 0.1% for high-accuracy ONT Duplex and Pacific Biosciences (PacBio) circular consensus sequencing (CCS) data in both simulated 16S rRNA and real 16-23S rRNA amplicon datasets. In high-accuracy PacBio CCS data, the clustering-based correction matched UMI correction, while outperforming 4×UMI correction in noisy ONT R10.3 and R9.4.1 data. Notably, LACA preserved phylogenetic fidelity in long operational taxonomic units and enhanced microbiome-wide phenotype characterization for synthetic mock communities and human vaginal samples.
Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea
Authors: Rubin-Blum Maxim , Makovsky Yizhaq , Rahav Eyal , Belkin Natalia , Antler Gilad , Sisma-Ventura Guy , Herut Barak
Published: November 2023

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22°C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 µg C L-1d-1ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a singleSulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (HalomonasandAlcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.
General remarks of the secondary promoter element regulating the genome replication of paramyxo- and filoviruses
Authors: Ashida Shoichi , Kojima Shohei , Okura Takashi , Kato Fumihiro , Urata Shuzo , Matsumoto Yusuke
Published: November 2023

Paramyxo- and filovirus genomes are equipped with bipartite promoters at their 3’ ends to initiate RNA synthesis. The two elements, the primary promoter element 1 (PE1) and the secondary promoter element 2 (PE2), are separated by a spacer region that must be precisely a multiple of six nucleotides, indicating these viruses are related to the “rule of six”. However, our knowledge of PE2 has been limited to a narrow spectrum of virus species. In this study, a comparative analysis of 1,647 paramyxoviral genomes from a public database revealed that the paramyxovirus PE2 can be clearly categorized into two distinct subcategories: one marked by C repeats at every six bases (exclusive to the subfamilyOrthoparamyxovirinae), and another characterized by CG repeats every six bases (observed in the subfamiliesAvulavirinaeandRubulavirinae). This unique pattern collectively mirrors the evolutionary lineage of these subfamilies. Furthermore, we showed that the PE2 of theRubulavirinae, with the exception of mumps virus, serves as part of the gene-coding region. This may be due to the fact that theRubulavirinaeis the only paramyxovirus that cannot propagate without RNA editing occurring. Zaire ebolavirus has eight sequential uracil (U) repeats every six bases within its genomic promoter. We showed that a minimum of four sequential U-containing hexamer repeats is imperative for genome replication. This discovery led to the identification of such quadruplet U-containing hexamer repeats within the genomic and antigenomic promoters of other viruses within the familyFiloviridae.

Significance

The genomic intricacies of paramyxo- and filoviruses are highlighted by the bipartite promoters—PE1 and PE2—at their 3’ termini. The spacer region between these elements follows the “rule of six”, crucial for genome replication. By a comprehensive analysis of paramyxoviral genome sequences, we identified distinct subcategories of PE2 based on C and CG repeats that were specific toOrthoparamyxovirinaeandAvulavirinae/Rubulavirinae, respectively, mirroring their evolutionary lineages. Notably, the PE2 ofRubulavirinaeis integrated in the gene-coding region, a unique trait potentially linked to its complete dependence on RNA editing for virus growth. This study also focused on the PE2 sequences in filovirus genomes. In filoviruses, four consecutive U-containing hexamer repeats appeared to be critical for their genome replication.
Loss of multi-level 3D genome organization during breast cancer progression
Authors: Rossini Roberto , Oshaghi Mohammadsaleh , Nekrasov Maxim , Bellanger Aurélie , Domaschenz Renae , Dijkwel Yasmin , Abdelhalim Mohamed , Collas Philippe , Tremethick David , Paulsen Jonas
Published: November 2023

Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in anin vitromodel of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) are overall maintained, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing theMYConcogene is inserted into a highly active subcompartment on chromosome 10. This insertion is accompanied by the formation ofde novoenhancer contacts and activation ofMYC, illustrating how structural genomic variants can alter the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the loss of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.
Geographic variation in the songs of two closely related song-learning species, Anna’s and Costa’s hummingbird (Calypte anna, C. costae)
Authors: Berger A. N. , Ye W. Y. , Padilla A. S. , Gumbi B. C. , Clark C. J. , Campbell P.
Published: November 2023

In species that learn their song, cultural transmission of song components can lead to the accumulation of variants that differ among populations, resulting in the formation of dialects. Three avian clades are thought to have independently evolved song learning – parrots, oscine passerines, and hummingbirds. Dialects have mainly been studied in passerines. We extend the study of dialects to the bee hummingbird clade, focusing on Anna’s and Costa’s hummingbirds (Calypte annaandC. costae). Both species are vocal learners. Anna’s produces complex, three phrase, multi-syllable songs and Costa’s produces simple, one phrase songs. We recorded 5-24 males per population (5 Costa’s and 6 Anna’s populations) across the species’ ranges in the Western United States and tested for evidence of geographic variation in song. We found minor population differences in frequency measures of Costa’s song, but song form was invariant across populations. Anna’s song was contrastingly variable with population differences in both syllable use and multiple spectral and temporal measures. The most strongly differentiated Anna’s population in our study, Seattle (Washington State), is the product of a recent northward range expansion facilitated by human activities that provide additional food sources for hummingbirds. The loss and modification of syllables in this population is suggestive of a founder effect on song. This study provides insight into song evolution in non-passerine vocal learners and contributes to understanding of how complex signals evolve.
Phytopathogenic cyclic glucohexadecaose from an inverting transglycosylase
Authors: Motouchi Sei , Komba Shiro , Nakai Hiroyuki , Nakajima Masahiro
Published: November 2023

Xanthomonasspecies contain numerous notoriously well-known plant pathogens. Among various pathogenic factors, the role of α-1,6-cyclized β-1,2-glucohexadecaose (CβG16α) produced byXanthomonas campestrispv.campestriswas shown previously to be vital for infecting model organismsArabidopsis thalianaandNicotiana benthamiana. However, enzymes responsible for biosynthesising CβG16α are essentially unknown, which limits the generation of agrichemicals that inhibit CβG16α synthesis. In this study, we discovered that OpgD fromX. campestrispv.campestrisconverts linear β-1,2-glucan to CβG16α. Structural and functional analyses revealed that OpgD fromX. campestrispv.campestrispossesses an anomer-inverting transglycosylation mechanism, which is unprecedented among carbohydrate-active enzymes. The discovery of this unprecedented glucan-generating mechanism reveals a new foundation for the enzymatic synthesis of carbohydrates. Furthermore, identifying CβG16α synthase highly conserved inXanthomonasprovides a broadly adaptable drug target for new-genre agrichemicals that overcome antimicrobial-resistant bacterial issues.
HECTOR: multimodal deep learning predicts recurrence risk in endometrial cancer
Authors: Fremond-Volinsky Sarah , Horeweg Nanda , Andani Sonali , Wolf Jurriaan Barkey , Lafarge Maxime W , de Kroon Cor , Ørtoft Gitte , Høgdall Estrid , Dijkstra Jouke , Jobsen Jan J , Lutgens Ludy CHW , Powell Melanie E , Mileshkin Linda R , Mackay Helen , Leary Alexandra , Katsaros Dionyssios , Nijman Hans W , de Boer Stephanie M , Nout Remi A , de Bruyn Marco , Church David , Smit Vincent THBM , Creutzberg Carien L , Koelzer Viktor H , Bosse Tjalling
Published: November 2023

Predicting distant recurrence of endometrial cancer (EC) is crucial for personalized adjuvant treatment. The current gold standard of combined pathological and molecular profiling is costly, hampering implementation. We developed HECTOR (Histopathology-basedEndometrialCancerTailoredOutcomeRisk), a multimodal deep learning prognostic model using hematoxylin-and-eosin-stained whole-slide-images and tumor stage as input, on 1,912 patients from seven EC cohorts including the PORTEC-1/-2/-3 randomized trials. HECTOR demonstrated C-indices in internal (n= 353) and external (n= 151) test sets of 0.788 and 0.816 respectively, outperforming the current gold-standard, and identified patients with markedly different outcomes (10-year distant recurrence-free probabilities of 97.0%, 77.7% and 58.1% for HECTOR low, intermediate and high risk groups). HECTOR also predicted adjuvant chemotherapy benefit better than current methods. Morphological and genomic feature extraction identified correlates of HECTOR risk groups, some with therapeutic potential. HECTOR improves on the current gold-standard and may help delivery of personalized treatment in EC.
A population genomics approach to unlock the genetic potential of lablab (Lablab purpureus), an underutilized tropical forage crop
Authors: Teshome A. , Habte E. , Cheema J. , Mekasha A. , Lire H. , Muktar M.S. , Quiroz-Chavez J. , Domoney C. , Jones C.S.
Published: November 2023

Background

In Sub-Saharan Africa (SSA) livestock production and productivity are severely restricted by the scarce supply of feedstuffs and forage crops, while those available are often of low nutritional quality resulting in poor animal productivity and leading to widespread malnutrition among the public, particularly women and children. Traditionally, several tropical forage crops have been used in the region both in the rangelands and as cut-and-carry cropping systems, but limited research attention has been paid to improve the quality of and access to these animal feeds. Lablab (Lablab purpureus(L.) is one of the conventionally grown multi-purpose underutilized crops that originated in Africa. It is an annual or short-lived perennial multi-purpose forage legume which has versatile uses (as a vegetable and dry seed), and as feed for animals, or as green manure. To develop new and highly productive lablab varieties, using genomics-assisted selection, the present study aimed to identify quantitative trait loci (QTL) associated with agronomically important traits in lablab and to assess the stability of these traits across two different agro-ecologies in Ethiopia.

Results

One hundred and forty-two cultivated and wild lablab accessions displayed significant agro-morphological variation in eight analysed traits, including plant height, total fresh weight, and total dry weight. Further, the agronomic performance of the accessions was significantly different across locations and years, highlighting the substantial genotype-by-environment interactions. The population genetic structure of the lablab accessions, based on half a million high quality single nucleotide polymorphisms (SNPs), revealed an independent domestication pattern for two-seeded and four-seeded lablab accessions. Furthermore, based on multi-environmental trial data, a genome-wide association study (GWAS) identified useful SNPs andk-mers for yield-related traits, such as plant height and total dry weight.

Conclusions

Genomic-assisted breeding is playing a key role in accelerating trait improvement in temperate forages, such as perennial ryegrass and alfalfa. Here we show that a similar approach could benefit underutilized crops such as lablab. The publicly available genomic tools and field evaluation data from this study will offer a valuable resource for plant breeders and researchers, to initiate genomic-assisted breeding in lablab which will fast-track genetic gain per unit time and ultimately contribute towards achieving food/nutritional security in the region.
Aging impairs skeletal muscle regeneration by promoting fibro/fatty degeneration and inhibiting inflammation resolution via fibro-adipogenic progenitors
Authors: Garcia-Carrizo Francisco , Gohlke Sabrina , Lenihan-Geels Georgia , Jank Anne-Marie , Leer Marina , Soultoukis George A. , Oveisi Masoome , Herpich Catrin , Garrido Claudia A. , Kotsaris Georgios , Pöhle-Kronawitter Sophie , Tsamo-Tetou Arnold , Graja Antonia , Ost Mario , Villacorta Laura , Knecht Raphael S. , Klaus Susanne , Schürmann Annette , Stricker Sigmar , Schmidt-Bleek Katharina , Cipitria Amaia , Duda Georg N. , Benes Vladimir , Müller-Werdan Ursula , Norman Kristina , Schulz Tim J.
Published: November 2023

Skeletal muscle regeneration depends on the function of fibro/adipogenic progenitors (FAPs). Here we show that aging impairs myogenic stem cells by disrupting the integration of extracellular matrix and immunomodulatory functions within the stem cell niche, thereby promoting fibro/fatty degeneration. We identify the FAP-secreted protein Periostin as a niche factor that is decreased in aged muscle and in circulation of aged humans with low-exercise lifestyle. Periostin controls FAP-expansion after injury and its depletion fate-regulates FAPs towards adipogenesis. This leads to delayed pro- to anti-inflammatory macrophage transition during regeneration. Transplantation of young FAPs with high Periostin secretion, but not Periostin-deficient FAPs, into aged muscle restores inflammation resolution and successful regeneration. Mechanistically, Periostin activates Focal adhesion kinase- and AKT-signaling in macrophages via integrins to promote an anti-inflammatory profile, which synchronizes matrix-derived mechanosensory signaling and immunomodulation. These results uncover a novel role of FAP-based regulation that orchestrates successful muscle regeneration and prevents fibro/fatty degeneration.
Genetically-clustered antifungal phytocytokines and receptor proteins function together to trigger plant immune signaling
Authors: Lintz Julie , Goto Yukihisa , Bender Kyle W. , Bchini Raphaël , Dubrulle Guillaume , Cawston Euan , Zipfel Cyril , Duplessis Sebastien , Petre Benjamin
Published: November 2023

Phytocytokines regulate plant immunity via cell-surface receptors.Populus trichocarpaRUST INDUCED SECRETED PEPTIDE 1 (PtRISP1) exhibits an elicitor activity in poplar, as well as a direct antimicrobial activity against rust fungi.PtRISP1gene directly clusters with a gene encoding a leucine-rich repeat receptor protein (LRR-RP), that we termed RISP- ASSOCIATED LRR-RP (PtRALR).

In this study, we used phylogenomics to characterize the RISP and RALR gene families, and functional assays to characterize RISP/RALR pairs.

BothRISPandRALRgene families specifically evolved in Salicaceae species (poplar and willow), and systematically cluster in the genomes. Two divergent RISPs, PtRISP1 andSalix purpureaRISP1 (SpRISP1), induced a reactive oxygen species (ROS) burst and mitogen- activated protein kinases (MAPKs) phosphorylation inNicotiana benthamianaleaves expressing the respective clustered RALR. PtRISP1 triggers a rapid stomatal closure in poplar, and both PtRISP1 and SpRISP1 directly inhibit rust pathogen growth.

Altogether, these results suggest that plants evolved phytocytokines with direct antimicrobial activities, and that the genes coding these phytocytokines co-evolved and physically cluster with their cognate receptors.
Investigating social communication in mice: a Two-intruders test approach
Authors: Morozova Maryana V. , Boldyreva Lidiya V. , Borisova Maria A. , Kozhevnikova Elena N.
Published: November 2023

Understanding the complex dynamics of social communication behaviors, such as exploration, communication, courtship, mating, and aggression in animal models is crucial to reveal key neural and hormonal mechanisms underlying these behaviors. The Two-intruders test is designed to investigate residents’ behavior toward a male and female intruders. During this test imitating natural conditions, several aspects of social interaction were investigated: exploration, courtship, mating, and aggressive behavior. As mating and aggression involve overlapping neural circuits, the behavioral setup testing both behaviors is best at reflecting their competitive nature. Our findings demonstrate that male mice exhibit strong preference to communicate with a female intruder, which correlates with baseline testosterone levels of test males. Relevant female preference in the Two-intruder test was also found in BALB/c males. Behavioral breakdown revealed the anogenital sniffing as a key behavioral feature that discriminates test male behavior toward intruders of different genders. At the same time, female preference was accompanied by neuronal activation in the ventromedial hypothalamus. We demonstrate that odor recognition underlies preference toward females in male residents, as experimental anosmia reduced communication with a female intruder. However, there was no correlation between female animal preference in the contact Two-intruder test and smell preference in the social odor preference test. We assume the Two-intruders test setup to be a useful tool to study the neurological basis of social communication in animal models. Combined with odor preference tests, this experimental paradigm can help to decipher neural circuits involved in social deficiency phenotypes in animal models of human diseases.

Significance Statement

The Two-intruders test proves to be a highly reproducible and robust approach to assess social communication in mice. We demonstrate that the results obtained in this experimental setting replicate in different mouse groups and strains. This test is indispensable in studies assessing the competitive nature of male- and female-driven behaviors and the underlying neural mechanisms. Resident’s social interactions in the described here set up reflects odor processing and circulating testosterone – the key physiological drivers of animal communication with conspecifics. While easy to perform, this test provides a broad spectrum of behavioral patterns to study in the models of complex neurological diseases. Largely overseen in the literature as compared to the resident-intruder setup, the Two-intruders test can provide superior performance when used to understand the neural mechanisms of mating, aggression and social communication.
Assessing language impoliteness of primary school teachers in Indonesia
Authors: Yusri Yusri , Mantasiah R. , Anwar Muhammad
Published: November 2023

Purpose

This study investigated the use of language impoliteness of primary school teachers in communicating with their students during the learning process.

Design/methodology/approach

The methodology of this study used a mixed-method approach by involving 100 primary school teachers in the fifth and sixth grades. The researcher used the language politeness/impoliteness scale developed by Mantasiah et al. (2019) to measure teachers' language impoliteness. This scale was developed based on Brown and Levinson's theory who divided politeness maxims into six consisting of tact maxim, generosity maxim, approbation maxim, appreciation maxim, agreement maxim and sympathy maxim. The levels of teachers' language impoliteness were divided into five categories (5 = always, 4 = often, 3 = sometimes, 2 = rarely, 1 = never).

Findings

The finding shows that 28% of teachers were in the sometimes category and 33% of teachers were in the rarely category. The results signify that some teachers tend to speak impolitely with the students during the learning process. They considered that it was acceptable as they did not know the negative effects caused by their impolite language. Moreover, teachers were more likely to violate sympathy, tact and agreement maxims than other maxims.

Practical implications

The finding of this study can be applied generally at all levels of education, ranging from primary education to higher education, as a base to develop a program to improve the soft skills of teachers especially the way teachers communicate with their students in the learning process. By understanding language politeness theory, the awareness of teachers in communicating in the learning process can be improved, which can affect positively to the quality of learning process.

Originality/value

Numerous studies conducted on communication skills of teachers focused on using communication sciences approach. This study tried to use another approach to portray the communication skills of teachers based on language politeness uttered using linguistics approach. Moreover, previous studies preferred to conduct language politeness and impoliteness of teachers in senior high schools and lecturers in university, and there is still lack of studies focusing on language politeness of primary school teachers.
Circular supply chain valorisation through sustainable value mapping in the post-consumer used clothing sector
Authors: Pal Rudrajeet , Sandberg Erik
Published: November 2023

Purpose

The purpose of this study is to explore the antecedents of uncaptured sustainable value and strategies to generate opportunities to capture it in the circular supply chain of post-consumer used clothing.

Design/methodology/approach

This study is based on an inductive analysis of 21 semi-structured interviews conducted with various stakeholders in the circular clothing supply chain (for-profit and not-for-profit) using the value mapping approach, as previously applied in the literature on sustainable business models.

Findings

Fifteen antecedents of uncaptured sustainable value, and thirteen value opportunity strategies were revealed that hinder or generate multi-dimensional value types. Economic value is impacted the most, while there is lack of explicit understanding of the impact of these antecedents and strategies on environmental and social value capture. From a multi-stakeholder perspective, the ecosystem is emerging as new for-profit actors are developing novel process technologies, while not-for-profit actors are consolidating their positions by offering new service options. There is also an emerging “coopetition” between the different stakeholders.

Research limitations/implications

More granularity in the different types of uncaptured value could be considered, and external supply chain stakeholders, such as the government, could be included, leading to more detailed value mapping.

Practical implications

This research provides practitioners with a value-mapping tool in circular clothing supply chains, thus providing a structured approach to explore, analyse and understand uncaptured value and value opportunities.

Originality/value

This extended value perspective draws upon the value-mapping approach from the sustainable business model literature and applies it in the context of the circular clothing supply chain. In doing so, this research illustrates circular clothing supply chains in a new way that facilitates an improved understanding of multi-dimensional and multi-stakeholder value for embedded actors.
Logistics outsourcing to provide supply chain agility in crisis time: an action research
Authors: Benatiya Andaloussi Manal
Published: November 2023

Purpose

The aim of this research is to underscore the pivotal role of warehouse management in the current turbulent global landscape exacerbated by the confluence of a health crisis and geopolitical instability in Europe. In today's interconnected global economy, the turbulence of the global supply chain causes a lack of its resilience among companies. Facing this critical crisis context, companies are refocusing on business processes and outsourcing support processes such as logistics. In this paper we have empirical and methodological objectives. Methodologically, we employ a qualitative research approach utilizing action research in a collaborative framework that involves academics and practitioners. The purpose of this methodology is to empirically investigate warehouse outsourcing as a solution for enhancing a company's performance and agility within the crisis context.

Design

The authors’ action research based on case study approach is conducted through an immersion within the ALCL French multinational company located in Morocco. The authors mobilize the theory of constraints, which allows us to set up a process of identification and optimization of managerial constraints (Goldratt, 1990). The approach allows to set up a retroactive loop to increase the performance of the constraint.

Findings

The study shows that ALCL has a storage over-dimension constraint due to the decrease of physical flows caused by the global crisis. The results of action research protocol show that the optimization of warehousing constraint is achieved by the total outsourcing of the process.

Originality

The study provides new insights into how action research can improve management practices within companies and explore concrete solutions to the logistical challenges faced by businesses.
Forgotten classics: Principles of Merchandising by Melvin T. Copeland (1924)
Authors: Shaw Eric H. , Liu Walter
Published: November 2023

Purpose

The purpose of this paper is to show that forgotten classics, such as Melvin T. Copeland’s (1924) Principles of Merchandising, can still teach lessons to students of the history of marketing thought.

Design/methodology/approach

The method involved using various key words on several internet search engines. The extensive internet search produced more than a dozen contemporaneous reviews and commentaries. Additionally, there was an intensive search through the histories of marketing thought literature. The extensive and intensive searches allowed a meta-analysis reexamining Copeland’s principles in light of future historical developments from the mid-1920s to the 21st century.

Findings

Historically, Copeland’s principles established the commodity school of marketing thought. (One of the three traditional approaches to understanding marketing taught to generations of students from the mid-1920s until the mid-1960s.) Although the traditional approaches/schools have long gone out of favor, Copeland’s classification of consumer and industrial (business) goods (products and services) have stood the test of time and are still in use 100 years later. Long overlooked, Copeland’s (1924) Principles of Merchandising also anticipated the marketing management/strategy as well as the consumer/buyer behavior schools of marketing thought, dominant in the discipline since the 1960s, for which he has seldom – if ever – been acknowledged.

Research limitations/implications

Historical research is limited because some relevant source material may no longer exist or may have been overlooked.

Originality/value

There have been no reviews of Copeland’s principles in almost a century, and no published meta-analysis of this forgotten classic exists. New discoveries reveal the value in studying marketing history and the history of marketing thought. For marketing as a social science to progress, it is invaluable to understand how ideas originated, were improved and integrated into larger conceptualizations, classification schema and theories over time.
SDG commentary: service ecosystems with the planet - weaving the environmental SDGs with human services
Authors: Teixeira Jorge Grenha , Gallan Andrew S. , Wilson Hugh N.
Published: November 2023

Purpose

Humanity and all life depend on the natural environment of Planet Earth, and that environment is in acute crisis across land, sea and air. One of a set of commentaries on how service can address the UN’s sustainable development goals (SDGs), the authors focus on environmental goals SDG 13 (climate action), SDG 14 (life below water) and SDG 15 (life on land). This paper aims to propose a conceptual framework that incorporates the natural environment into transformative services.

Design/methodology/approach

The authors trace the evolution of service thinking about the natural environment, from a stewardship perspective of the environment as a set of resources to be managed, through an acknowledgement of nonhuman organisms as actors that can participate in service exchange, towards an emergent concept of ecosystems as integrating human social actors and other biological actors who engage fully in value co-creation.

Findings

The authors derive a framework integrating human and other life forms as co-creating actors, drawing on shared natural resources to achieve mutualism, where each actor can have a net benefit from the relationship. Future research questions are posited that may help services research address SDGs 13–15.

Originality/value

The framework integrates ideas from environmental ecosystem literature to inform the nature of ecosystems. By integrating environmental actors and ecological insights into the understanding of service ecosystems, service scholars are well placed to make unique contributions to the global challenge of creating a sustainable future.
After the ‘Black Summer’ fires: Faunal responses to megafire depend on fire severity, proportional area burnt and vegetation type
Authors: Miritis Vivianna , Dickman Chris R. , Nimmo Dale G. , Doherty Tim S.
Published: November 2023

Climate change and human activities have disrupted historical fire regimes, leading to complex and far‐reaching impacts on global ecosystems. Despite extensive research in fire ecology, studies exploring vertebrate responses to megafires, and to nuanced fire characteristics, remain limited.

We collected camera trap data 3–27 months following Australia's 2019–20 ‘Black Summer’ megafires from 30 burnt sites and 10 unburnt sites. Our data included 14 animal species/groups, encompassing mammalian predators, small and medium‐sized mammals, large herbivores, and birds. We used generalised additive mixed models to assess the influence of time‐since‐the‐fires, burn status, fire severity, proportional area burnt, and vegetation type on species' activity.

Models that included fire variables were well‐supported for all species. The proportional cover of low‐moderate or high‐extreme severity fire had substantial support for five species, particularly herbivores, which generally showed a preference for burnt sites but at differing fire severities. The proportional area burnt, disregarding severity, was well supported for four species. At highly burned sites fox activity peaked shortly after the fires while small to medium‐sized mammal activity increased more gradually. Vegetation type strongly influenced the response of four species to fire; in particular, wet forest birds preferred unburnt areas.

Policy implications. We document variable short‐ to medium‐term responses of a range of species to fire which could help guide management interventions. We demonstrate that animal species' responses to fire are diverse and better captured using broader landscape scale fire variables. We found that species were strongly influenced by proportional area burnt, fire severity and vegetation type. Introduced foxes were attracted to recently burnt areas, so timely predator control may benefit vulnerable prey species. Wet forest species were sensitive to fires and could benefit from preservation and restoration of these habitats. Some species exploited low‐moderate severity burnt areas, while others preferred high‐severity burns. This suggests that species will face diverse challenges and opportunities in future extreme fire events. We emphasise the importance of using multi‐faceted approaches to account for the complex responses of co‐occurring species to fire events.
‘One child, two schools’: Teachers' perspectives on the dual enrolment of students with disabilities in private special and inclusive schools in the United Arab Emirates
Authors: Ali Mahra Saeed Haj , Opoku Maxwell Peprah
Published: November 2023

There are efforts being taken to provide students with disabilities access to education in a dual context, namely, some days at inclusive schools and others at special schools. However, there is limited information regarding how teachers are contending with such practices. This study explored teachers' perceptions of students with disabilities' education in the dual enrolment education system of the United Arab Emirates (UAE). Specifically, the social education model was conceptualised to understand teachers' perceptions, collaborative efforts, resources and challenges in terms of dual enrolment practices. The study's sample consisted of 10 teachers at private schools, consisting of five special education teachers and five general education teachers, recruited from Al Ain, the third largest city in the UAE. Despite the participants' positive responses concerning dual enrolment, the results showed the system's poor implementation for students with disabilities. This was the result of a lack of collaboration, communication and a shared plan to support the development of children with disabilities across schools. This study concludes by recommending a national framework to guide the implementation of a dual enrolment system in the UAE.
An assessment of South African small mammal barcode sequence libraries: Implications for future carnivore diet analyses by DNA
Authors: Siziba Vimbai I. , Willows‐Munro Sandi
Published: November 2023

DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome b (cyt b) and the hypervariable control region (D‐loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt b had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D‐loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species.