bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era
Authors: Huang Yu-Hao , Sun Yi-Fei , Li Hao , Li Hao-Sen , Pang Hong 
Published: February 2024

AbstractThe current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, traditional methods typically involve intricate and time-consuming procedures prior to core analyses. These procedures encompass assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive datasets. In this study, we present PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as reference for phylogenetic and evolutionary analyses. Through testing with both simulated and authentic datasets, PhyloAln demonstrates consistently robust performance in terms of alignment completeness and identity when compared to other reference-based tools. Additionally, we validate the tool’s adeptness in managing foreign and cross-contamination issues prevalent in sequencing data, which are often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments and reconstructing phylogenies from transcriptomes of ladybird beetles, plastid genes of peppers, and ultraconserved elements of turtles. These results underscore the versatility of our tool. Leveraging these advantages, PhyloAln stands poised to expedite phylogenetic and evolutionary analyses in the omic era. The tool is accessible athttps://github.com/huangyh45/PhyloAln.
Degradation of indole-3-acetic acid by plant-associated microbes
Authors: Wang Lanxiang , Liu Yue , Ni Haoran , Zuo Wenlong , Shi Haimei , Liao Weixin , Liu Hongbin , Bai Yang , Yue Hong , Huang Ancheng , Friedman Jonathan , Si Tong , Liu Yinggao , Chen Mo-Xian , Dai Lei 
Published: February 2024

ABSTRACTPlant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of microbes with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis andin vitroassays, we found that 21 out of 189 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their sole carbon and energy source.In planta, most of the IAA degrading strains mitigated Arabidopsis seedling root growth inhibition (RGI) triggered by exogenous IAA. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA-producers. In summary, our findings further the understanding of the functional diversity and roles of plant-associated microbes.
Differences in milk microbiota between healthy cows and cows with recurringKlebsiellamastitis
Authors: Yang Jingyue , Wu Naiwen , Xiong Yindi , Nobrega Diego B. , Barkema Herman W. , Liang Bingchun , Han Bo , Gao Jian 
Published: February 2024

AbstractKlebsiellaspp. infections continue to have a significant economic impact on the dairy industry, being an important cause of severe clinical mastitis, recurrent infections, and demonstrating poor response to antimicrobials. It is, therefore, essential to investigate the underlying causes ofKlebsiellaspp. infections. Here we used high-throughput DNA sequencing to characterize the milk microbiota of healthy dairy cows (HDC) and cows with history of recurrentKlebsiellamastitis (KLB). Our goal was to identify potential pathogenic genera associated with recurrentKlebsiellainfections in cows. The relative abundance ofFirmicutesandFaecalibacteriumwas greater in the KLB group than in the HDC group. In contrast,ProteobacteriaandLabrenziawere less abundant than in the HDC group. Although the species distributions differed between groups, diversity and abundance of communities were comparable. Notably, genera of increased occurrence in the KLB group were mostly intestinal-associated, which suggests that cows in the KLB group resided in a contaminated environment or had increased teat-end exposure to fecal bacteria. We did not detect major differences in microbiota among quarters, and also between fore-strip milk and milk collected after fore-stripping. Conversely, milk of heifers had increased alpha diversity in comparison to milk of multiparous cows.
A genome wide search for non-additive allele effects identifiesPSKH2as involved in the variability of Factor V activity
Authors: Gendre Blandine , Martinez-Perez Angel , Kleber Marcus E , van Hylckama Vlieg Astrid , Boland Anne , Olaso Robert , Germain Marine , Munsch Gaëlle , Moissl Angela Patricia , Suchon Pierre , Souto Juan Carlos , Soria José Manuel ,   CHARGE Hemostasis working group, Deleuze Jean-François , März Winfried , Rosendaal Frits R , Sabater-Lleal Maria , Morange Pierre-Emmanuel , Trégouët David-Alexandre 
Published: February 2024

AbstractBackgroundFactor V (FV) is a key molecular player in the coagulation cascade. FV plasma levels have been associated with several human diseases, including thrombosis, bleeding and diabetic complications. So far, two genes have been robustly found through genome wide association analyses to contribute in the inter-individual variability of plasma FV levels: structural F5 gene and PLXDC2.MethodsWe used the underestimated Brown-Forsythe methodology implemented in the Quicktest software to search for non-additive genetic effects that could contribute to the inter-individual variability of FV plasma activity. QUICKTEST was applied to 4 independent GWAS studies (LURIC, MARTHA, MEGA and RETROVE) totaling 4,505 participants of European ancestry with measured FV plasma levels. Results obtained in the 4 cohorts were meta-analyzed using a fixed-effect model. Additional analyses involved exploring haplotype and gene×gene interactions in downstream investigations.ResultsWe observed a genome-wide significant signal atPSKH2locus, on chr8q21.3 with lead variant rs75463553 with no evidence for heterogeneity across cohorts (p = 0.518). Although rs75463553 did not show association with mean FV levels (p = 0.49), it demonstrated a robust significant (p = 8.4 10-9) association with the variance of FV plasma levels. Further analyses confirmed the reported association ofPSKH2with neutrophil biology and revealed that rs75463553 likely interact with two loci,GRIN2AandPOM121L12, known for their involvement in smoking biology.ConclusionsThis comprehensive approach identifies the role ofPSKH2as a novel molecular player in the genetic regulation of FV, shedding light on the contribution of neutrophils to FV biology.
First evidence for the evolution of host manipulation by tumors during the long-term vertical transmission of tumor cells inHydra oligactis
Authors: Boutry Justine , Rieu Océane , Guimard Lena , Meliani Jordan , Nedelcu Aurora M. , Tissot Sophie , Stepanskyy Nikita , Ujvari Beata , Hamede Rodrigo , Dujon Antoine M. , Tökölyi Jácint , Thomas Frédéric 
Published: February 2024

AbstractWhile host phenotypic manipulation by parasites is a widespread phenomenon, whether tumors – which can be likened to parasite entities, can also manipulate their hosts is not known. Theory predicts that this should nevertheless be the case, especially when tumors (neoplasms) are transmissible. We explored this hypothesis in a cnidarianHydramodel system, in which spontaneous tumors can occur in the lab, and lineages in which such neoplastic cells are vertically transmitted (through host budding) have been maintained for over 15 years. Remarkably, the hydras with long-term transmissible tumors show an unexpected increase in the number of their tentacles, allowing for the possibility that these neoplastic cells can manipulate the host. By experimentally transplanting healthy as well as neoplastic tissues derived from both recent and long-term transmissible tumors, we found that only the long-term transmissible tumors were able to trigger the growth of additional tentacles. Also, supernumerary tentacles, by permitting higher foraging efficiency for the host, were associated with an increased budding rate, thereby favoring the vertical transmission of tumors. To our knowledge, this is the first evidence that, like true parasites, transmissible tumors can evolve strategies to manipulate the phenotype of their host.
Transferable deep generative modeling of intrinsically disordered protein conformations
Authors: Janson Giacomo , Feig Michael 
Published: February 2024

ABSTRACTIntrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. Molecular simulations are a valuable computational strategy for constructing structural ensembles of disordered proteins but are highly resource-intensive. Recently, machine learning approaches based on deep generative models that learn from simulation data have emerged as an efficient alternative for generating structural ensembles. However, such methods currently suffer from limited transferability when modeling sequences and conformations absent in the training data. Here, we develop a novel generative model that achieves high levels of transferability for intrinsically disordered protein ensembles. The approach, named idpSAM, is a latent diffusion model based on transformer neural networks. It combines an autoencoder to learn a representation of protein geometry and a diffusion model to sample novel conformations in the encoded space. IdpSAM was trained on a large dataset of simulations of disordered protein regions performed with the ABSINTH implicit solvent model. Thanks to the expressiveness of its neural networks and its training stability, idpSAM faithfully captures 3D structural ensembles of test sequences with no similarity in the training set. Our study also demonstrates the potential for generating full conformational ensembles from datasets with limited sampling and underscores the importance of training set size for generalization. We believe that idpSAM represents a significant progress in transferable protein ensemble modeling through machine learning.AUTHOR SUMMARYProteins are essential molecules in living organisms and some of them have highly dynamical structures, which makes understanding their biological roles challenging. Disordered proteins can be studied through a combination of computer simulations and experiments. Computer simulations are often resource-intensive. Recently, machine learning has been used to make this process more efficient. The strategy is to learn from previous simulations to model the heterogenous conformations of proteins. However, such methods still suffer from poor transferability, meaning that they tend to make incorrect predictions on proteins not seen in training data. In this study, we present idpSAM, a method based on generative artificial intelligence for modeling the structures of disordered proteins. The model was trained using a vast dataset and, thanks to its architecture and training procedure, it performs well on not just proteins in the training set but achieves high levels transferability to proteins unseen in training. This advancement is a step forward in modeling biologically relevant disordered proteins. It shows how the combination of generative modeling and large training sets and can aid us understand how dynamical proteins behave.
Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete,Musella, andMusaspecies) reveals amplification of flavonoid 3’,5’-hydroxylase
Authors: Cui Dongli , Xiong Gui , Ye Lyuhan , Gornall Richard , Wang Ziwei , Heslop-Harrison Pat , Liu Qing 
Published: February 2024

AbstractFlavonoids in Musaceae are involved in pigmentation and stress responses, including pathogen defense and UV protection, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this study, we identified 71 to 80 flavonoid biosynthetic genes in chromosome-scale genome sequence assemblies of Musaceae, including those ofEnsete glaucum,Musella lasiocarpa,Musa beccarii,M. acuminata,M. balbisiana, andM. schizocarpa,checking annotations with BLAST and determining the presence of conserved domains. The number of genes increased through segmental duplication and tandem duplication. Orthologues of both structural and regulatory genes in the flavonoid biosynthetic pathway are highly conserved across Musaceae. The flavonoid 3’,5’-hydroxylase geneF3’5’Hswas amplified in Musaceae and ginger compared with grasses (rice, Brachypodium,Avena longiglumis,and sorghum). One group of genes from this gene family amplified near the centromere of chromosome 2 in thex= 11 Musaceae species. Flavonoid biosynthetic genes displayed few consistent responses in the yellow and red bracts ofMusella lasiocarpawhen subjected to low temperatures. The expression levels ofMlDFR2/3increased whileMlLARwas reduced by half. These results establish the range of diversity in both sequence and copy number of flavonoid biosynthetic genes during evolution of Musaceae. The combination of allelic variants of genes, changes in their copy numbers, and variation in transcription factors with the modulation of expression under cold treatments and between bract-colours suggests the variation may be exploited in plant breeding programmes, particularly for improvement of stress-resistance in the banana crop.
Sources and pathways by which low-grade inflammation contributes to anaemia in rural African children from 6 months to 3 years of age: study protocol for observational studies IDeA 1 and IDeA 2
Authors: Ledger Elizabeth , Verhoef Hans , Jallow Amadou T , Cunningham Nicole , Prentice Andrew M. , Cerami Carla 
Published: February 2024

ABSTRACTBackgroundRecent work suggests that persistent inflammation, even at low levels, could be more important than low dietary iron intake in the aetiology of iron deficiency and iron deficiency anaemia (IDA) in young children living in poor environments.MethodsWe will conduct 2 parallel observational studies in well and unwell rural Gambian children to identify the origins of chronic low-grade inflammation and characterise its relationship to iron handling and iron deficiency anaemia. IDeA Study 1 will enrol 120 well children attending our regular paediatric well-child clinics at 6, 12 and 18 months of age. IDeA Study 2 will enrol 200 sick children suffering from upper-respiratory tract infection, lower respiratory tract infection, gastroenteritis or urinary tract infection and study them on Days 0, 3, 7 and 14 after initial presentation. At each visit, children will be assessed for signs of inflammation. Full blood count and iron-related biomarkers (serum ferritin, serum iron, unsaturated iron-binding capacity, soluble transferrin receptor, transferrin) will be measured before and after an oral dose of ferrous iron to assess status and acute iron absorption. Inflammatory markers (C-reactive protein andα1-acid glycoprotein), hepcidin, erythroferrone and erythropoietin will be measured to characterize the anaemia of inflammation in these children.ConclusionWe will assess the impact of acute and chronic low-grade inflammation on iron absorption and investigate the hypothesis that chronic inflammation, juxtaposed on a poor diet, causes a complex anaemia of inflammation which exacerbates iron deficiency by blocking both non-haem iron absorption and iron utilization by the bone marrow.
Coming to terms with a socially unsustainable fine dining business model
Authors: Mejia Cynthia , Wilson Katherine 
Published: February 2024

Purpose
The purpose of this study was to examine the global perceptions of social equity in the fine dining business model as a result of the surprise announcement for the 2024 planned closure of the Michelin three-star restaurant, Noma.

Design/methodology/approach
This study used critical discourse analysis to inductively analyze 91 source documents retrieved through a lexical database search. The analysis yielded five overarching themes and six subthemes.

Findings
Findings from this study serve as a benchmark in retrospect for capturing a rapidly accelerating global conversation from January to March 2023 around the long-term viability and social sustainability of the fine dining business model.

Research limitations/implications
Against the backdrop of labor challenges in the restaurant industry due to the Covid-19 pandemic and its aftermath, the announced closure of Noma precipitated criticism of the stage (unpaid intern) system and the intense pressures of attaining and maintaining Michelin star status.

Practical implications
Results from the discourse analysis suggest certification for fine dining restaurants, perhaps through the Michelin Guide, for demonstrating a commitment to social sustainability as a qualifier to achieve a Michelin star.

Social implications
Findings from this research reveal a palpable change in societal tolerance for a more socially sustainable fine dining restaurant business model that advances equitable solutions for its workers while assuring the economic sustainability of restaurants.

Originality/value
This study drew upon a foodscape lens to reveal a juxtaposition between well-executed environmentally sustainable initiatives in the fine dining business model and the threats to the social sustainability among its workers.
The impact of supply chain transparency on financing offerings to firms: the moderating role of supply chain concentration
Authors: Shi Rongrong , Yin Qiaoyi , Yuan Yang , Lai Fujun , Luo Xin (Robert) 
Published: February 2024

PurposeBased on signaling theory, this paper aims to explore the impact of supply chain transparency (SCT) on firms' bank loan (BL) and supply chain financing (SCF) in the context of voluntary disclosure of supplier and customer lists.Design/methodology/approachBased on panel data collected from Chinese-listed firms between 2012 and 2021, fixed-effect models and a series of robustness checks are used to test the predictions.FindingsFirst, improving SCT by disclosing major suppliers and customers promotes BL but inhibits SCF. Specifically, customer transparency (CT) is more influential in SCF than supplier transparency (ST). Second, supplier concentration (SC) weakens SCT’s positive impact on BL while reducing its negative impact on SCF. Third, customer concentration (CC) strengthens the positive impact of SCT on BL but intensifies its negative impact on SCF. Last, these findings are basically more pronounced in highly competitive industries.Originality/valueThis study contributes to the SCT literature by investigating the under-explored practice of supply chain list disclosure and revealing its dual impact on firms' access to financing offerings (i.e. BL and SCF) based on signaling theory. Additionally, it expands the understanding of the boundary conditions affecting the relationship between SCT and firm financing, focusing on supply chain concentration. Moreover, it advances signaling theory by exploring how financing providers interpret the SCT signal and enriches the understanding of BL and SCF antecedents from a supply chain perspective.
Ethics and aesthetics of adaptive heritage reuse in Europe: an introduction to what happens to territories when heritage is touched
Authors: Fava Federica 
Published: February 2024

PurposeThe paper introduces ethical and aesthetical implications emerging from participative forms of adaptive heritage reuse. Its aim is to depict the overall framework to contextualize the investigations explored in the Special Issue titled “Ethics and aesthetics of adaptive heritage reuse in Europe.” Therefore, the article confronts with potentialities and contradictions of “open” heritage processes, introducing key critical elements to recode heritage practices and planning in today’s conjuncture of global change.Design/methodology/approachThe paper drawn on a literature review, which combines different bodies of studies: heritage, urban studies, care studies and recent policy documents. A photographic essay, moreover, serves to “augment” the presented argumentations through a visual apparatus resulting from one of Gaia Ginevra Giorgi’s artwork, which develops in the intersection between performative art, participation and territorial reuse.FindingsThe author argues that for adaptive heritage reuse to be really sustainable, ethical and aesthetical heritage codes need to be reassessed and reoriented toward the present socio-ecological priorities, multiplicating the ways cultural heritage is conceived, valued and reused. The paper suggests proceeding along the creative paths of uncertainty, providing the first elements to develop political projects of abundance and enjoyment for current urban settlements.Practical implicationsThe presented argumentations can be used as a baseline by heritage managers and policymakers to experiment with participative processes of adaptive heritage reuse and to identify more environmentally and socially just trajectories of urban development.Originality/valueThe paper expands the concept of adaptive heritage reuse, considering the active participation of both human and non-human agents. Treating heritage in a laic way, namely free from absolute and preordered judgments of value, it deals with uncomfortable heritage materiality and contexts, illuminating the quality of unpleasant or odd forms of beauty.