bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated manual therapies: IASP taskforce viewpoint
Authors: Draper-Rodi Jerry , Newell Dave , Barbe Mary F. , Bialosky Joel 
Published: October 2024

Abstract

Introduction:
Manual therapy refers to a range of hands-on interventions used by various clinical professionals, such as osteopaths, osteopathic physicians, chiropractors, massage therapists, physiotherapists, and physical therapists, to treat patients experiencing pain.

Objectives:
To present existing evidence of mechanisms and clinical effectiveness of manual therapy in pain.

Methods:
This Clinical Update focuses on the 2023 International Association for the Study of Pain Global Year for Integrative Pain Care. Current models of manual therapy and examples of integrative manual therapy are discussed.

Results:
The evolution of concepts in recent years are presented and current gaps in knowledge to guide future research highlighted. Mechanisms of manual therapy are discussed, including specific and contextual effects. Findings from research on animal and humans in manual therapy are presented including on inflammatory markers, fibrosis, and behaviours. There is low to moderate levels of evidence that the effect sizes for manual therapy range from small to large for pain and function in tension headache, cervicogenic headache, fibromyalgia, low back pain, neck pain, knee pain, and hip pain.

Conclusion:
Manual therapies appear to be effective for a variety of conditions with minimal safety concerns. There are opportunities for manual therapies to integrate new evidence in its educational, clinical, and research models. Manual therapies are also well-suited to fostering a person-centred approach to care, requiring the clinician to relinquish some of their power to the person consulting. Integrated manual therapies have recently demonstrated a fascinating evolution illustrating their adaptability and capacity to address contemporary societal challenges.
Three-dimensional facial morphology in patients with craniofacial microsomia and microtia
Authors: Ronde Elsa M. , de Jong Guido A. , Nolte Jitske W. , Nienhuijs Marloes E.L. , Bulstrode Neil W. , Maal Thomas J.J. , Becking Alfred G. , Breugem Corstiaan C. ,   the 3DCFMM research consortium*
Published: October 2024

Introduction:
Craniofacial microsomia (CFM) is classified using the subjective Orbit, Mandible, Ear, Nerve and Soft tissue (OMENS) tool. Digital stereophotogrammetry (i.e. three-dimensional [3D] photography) can be used to capture facial shape objectively. This case-control study assessed the applicability of 3D photography in distinguishing between patients with CFM and individuals without craniofacial conditions, as well as classifying the severity of facial involvement.

Methods:
3D photographs of patients with CFM and/or microtia from the Amsterdam UMC, Radboudumc and the Great Ormond Street Hospital and of individuals without craniofacial conditions were assessed. Differences between patients and controls were explored through asymmetry index (ASI) and facial signature (FS) scores, as well as a principal components (PC) analysis of FS scores and logistic regression. Correlations between OMENS scores and ASI, FS and PC scores were evaluated.

Results:
A total of 179 patients and 210 controls were analyzed. ASI and FS scores differed significantly between patients and controls (p<0.001), and were correlated with several OMENS subscales. The logistic regression model distinguishing between patients and controls showed increasing asymmetry of the mandible and orbits with increasing Pruzansky-Kaban score. Patients with isolated microtia deviated from controls in the midface.

Conclusion:
Clinically significant differences in the facial morphology of patients with CFM and microtia were found compared to controls, suggesting that 3D photography can be used to assess the severity of facial involvement in a novel, objective and safe way in these patients.
Paracoccus spongiarum sp. nov., isolated from the marine sponge, Phakellia elegans
Authors: Kim Soo-Bin , Kim Kyung Hyun , Park Jin-Sook 
Published: October 2024

A facultative anaerobic Gram-negative bacterium, designated as strain 2205BS29-5T, was isolated from a marine sponge, Phakellia elegans, in Beomseom on Jeju Island, Republic of Korea, and taxonomically characterized. The cells were catalase and oxidase positive, non-motile, coccoid-rod shaped and capable of poly-β-hydroxybutyrate production. Growth was observed at 10–37 °C (optimum, 25 °C) and pH 5.0–8.0 (optimum, pH 7.0), and in the presence of 0–9% NaCl (w/v) (optimum, 3.0–4.0%). The major cellular fatty acids and respiratory quinone were identified as summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c) and Q-10, respectively. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, four phosphoglycolipids, two unidentified amino lipids and eight unidentified lipids. The DNA G+C content was 67.8%. Strain 2205BS29-5T was most closely represented by Paracoccus amoyensis 11-3T and P. caeni MJ17T with 97.8 and 97.5% 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA genes and whole-genome sequences showed that strain 2205BS29-5T was affiliated with the genus Paracoccus. Genomic analysis showed that strain 2205BS29-5T could synthesize vitamin B family (folate and cobalamin) and ectoine. The average nucleotide identity and digital DNA–DNA hybridization values between strain 2205BS29-5T and P. amoyensis 11-3T were 77.1% and 18.8%, respectively, and with P. caeni MJ17T were 78.4 and 21.2%, respectively. Based on phylogenetic, chemotaxonomic and genome relatedness analyses, strain 2205BS29-5T represents a novel species of the genus Paracoccus, for which the name Paracoccus spongiarum sp. nov. is proposed. The type strain is 2205BS29-5T (=LMG 33062T =KACC 23240T).
A comparative study of multidrug resistant bacteria (MDRB) isolated from various patients in different wards of a hospital during post Covid-19
Authors: Ojha Abhishek , Figueiredo Dwight , Khan Shabnum 
Published: October 2024

AbstractAntibacterial resistance is an alarming global concern and a public health challenge of the twenty-first century for which effective systems are required to track and treat ABR. We performed microbiological and antibiotic susceptibility testing on the samples to detect and characterize Multidrug-Resistant Bacteria (MDRB) isolated from patients segregating MDRB characteristics (types, prevalence and distribution of MDRB) based on time (i.e., during versus post covid-19) and location (i.e., different wards of a tertiary care hospital). We observed an increase of MDRB in 2022 as compared to 2021 and 2023. These MDRB had a Shannon and Simpson index values of 1.138 to 1.508 and 0.643 to 0.775, respectively and an observed evenness values of 0.780 to 1.042, which revealed the microbial diversity recovered from the patient samples. In keeping with previous MDR studies,Klebsiella,E.coli,Citrobacter,AcinetobacterandPseudomonaswere identified from the patient samples. Moreover, compared to previous reports, the percentage of MDR-bacteria, i.e.,Klebsiella(40 %),E.coli(28 %), andCitrobacter(19 %), populations were higher in this study. We observed that Gamma-proteobacteria were predominant across all the recovered samples, and thatAcinetobacterandKlebsiellaisolated from the samples were 100 % resistant to twenty and eleven antibiotics, respectively. Furthermore, the fatality rate was low compared with the available reports suggesting possibilities for effective recovery if given rapid and tailored treatment. Given the challenges faced by MDRB strains more surveillance and tracking is needed to ensure effective and specifically targeted treatment strategies.
The plastid-encoded RNA polymerase structures a logistic chain for light-induced photosynthesis
Authors: Gillet François-Xavier , Effantin Gregory , Freiherr von Scholley Gian Luca , Brugière Sabine , Turquand Maud , Pasha Noor , Fenel Daphna , Vallet Alicia , Couté Yohann , Cobessi David , Blanvillain Robert 
Published: October 2024

AbstractThe chloroplast is the semi-autonomous organelle of eukaryotes that performs photosynthesis. In higher plants, chloroplast biogenesis depends on a tight transcriptional coordination of both nuclear- and-plastid photosynthesis-associated genes. The plastid-encoded RNA-polymerase (PEP) is composed of a plastid-encoded catalytic core, similar to multi-subunit RNA polymerases, bound to fifteen nuclear-encoded PEP-associated proteins (PAPs). The binding of all the PAPs to the catalytic core is essential for plastid transcription of photosynthesis-associated genes. Our cryo-electron microscopy structure of the native 21-subunit PEP fromSinapis albareveals the distinctive patterning of PAP interactions, which evolved upon the ancestral cyanobacterial catalytic core acting as a scaffold. Using PAP8in plantaas bait for affinity purification and proximity labeling, we provide the protein landscapes surrounding the PEP and other PAP8-interacting complexes at the transition from skotomorphogenesis to photomorphogenesis. The data highlight multiple functional couplings in which plastid transcription is at the beginning of a spatial logistic chain, extending from transcription to the assembly of the photosynthetic apparatus into the thylakoids. In addition, dark-specific interactions between photoreceptors and PAP8 establish a physical link between an integrated light signaling and plastid functions.
LassoESM: A tailored language model for enhanced lasso peptide property prediction
Authors: Mi Xuenan , Barrett Susanna E. , Mitchell Douglas A. , Shukla Diwakar 
Published: October 2024

AbstractRibosomally synthesized and post-translationally modified peptides (RiPPs) comprise a structurally and functionally diverse group of natural products. Lasso peptides represent one of about 50 known molecular classes of RiPPs, which display a characteristic [1] rotaxane conformation formed by a lasso cyclase. This unique, threaded conformation endows lasso peptides with diverse biological activities and remarkable thermal and proteolytic stability. The prediction of lasso peptide properties, such as substrate compatibility with a particular lasso cyclase or desired biological activity, remains challenging due to limited experimental data and the intricate nature of the substrate fitness landscapes. Protein language models (PLMs) have demonstrated impressive performance in predicting protein structure and function. However, general-purpose PLMs perform poorly in lasso peptide-related predictive tasks. Therefore, there is a need to provide effective representations for lasso peptides to enable enhanced property prediction. In this study, we developed a lasso peptide-specific language model (LassoESM) by leveraging advances in pre-trained PLMs to aid the prediction of lasso peptide related properties and experimentally validate the model predictions. We demonstrate that LassoESM embeddings can accurately predict substrate compatibility for a lasso cyclase of interest when experimental data for model training was scarce. Using a deep learning framework incorporating cross-attention between lasso cyclase and substrate peptide embeddings, we identify non-cognate pairs of lasso cyclases and substrate peptides with predicted compatibility. We further show that LassoESM embeddings improve the prediction of RNA polymerase inhibitory activity, which represents a biological activity of several known lasso peptides. We anticipate that LassoESM and future iterations thereof will be instrumental for the rational design of lasso peptides with desired properties.
Dynamic Mechanism for Subtype Selectivity of Endocannabinoids
Authors: Dutta Soumajit , Zhao Lawrence , Shukla Diwakar 
Published: October 2024

AbstractEndocannabinoids are naturally occurring lipid-like molecules that bind to cannabinoid receptors (CB1and CB2) and regulate many of human bodily functions via the endocannabinoid system. There is a tremendous interest in developing selective drugs that target the CB receptors. However, the biophysical mechanisms responsible for the subtype selectivity for endocannbinoids have not been established. Recent experimental structures of CB receptors show that endocannbinoids potentially bind via membrane using the lipid access channel in the transmembrane region of the receptors. Furthermore, the N-terminus of the receptor could move in and out of the binding pocket thereby modulating both the pocket volume and its residue composition. On the basis of these observations, we propose two hypothesis to explain the selectivity of the endocannabinoid, anandamide for CB1receptor. First, the selectivity arises from distinct enthalpic ligand-protein interactions along the ligand binding pathway formed due to the movement of N-terminus and subsequent shifts in the binding pocket composition. Second, selectivity arises from the volumetric differences in the binding pocket allowing for differences in ligand conformational entropy. To quantitatively test these hypothesis, we perform extensive molecular dynamics simulations (∼0.9 milliseconds) along with Markov state modeling and deep learning-based VAMPnets to provide an interpretable characterization of the anandamide binding process to cannabinoid receptors and explain its selectivity for CB1. Our findings reveal that the distinct N-terminus positions along lipid access channels between TM1 and TM7 lead to different binding mechanisms and interactions between anandamide and the binding pocket residues. To validate the critical stabilizing interactions along the binding pathway, relative free energy calculations of anandamide analogs are used. Moreover, the larger CB2pocket volume increases the entropic effects of ligand binding by allowing higher ligand fluctuations but reduced stable interactions. Therefore, the opposing enthalpy and entropy effects between the receptors shape the endocannabinoid selectivity. Overall, the CB1selectivity of anandamide is explained by the dominant enthalpy contributions due to ligand-protein interactions in stable binding poses. This study shed lights on potential selectivity mechanisms for endocannabinoids that would aid in the discovery of CB selective drugs.
Characterizing the impacts of exotic species on the morphology of solitary threespine stickleback (Gasterosteus aculeatus) populations in southwestern British Columbia
Authors: Kienzle Hannah M. , Vamosi Steven M. 
Published: October 2024

AbstractExotic species are one of the greatest threats to native species, communities, and ecosystems. Introductions of multiple exotic species into an environment may have different effects on native populations compared to when exotic species are introduced individually. Threespine stickleback species pairs (Gasterosteus aculeatus) and neighbouring solitary populations in southwestern British Columbia, a textbook example of an adaptive radiation, are now under threat from multiple exotic species. We assessed whether variation in morphological characters and body shape among solitary threespine stickleback populations was associated with different combinations of introduced smallmouth bass (Micropterus dolomieu) and signal crayfish (Pacifastacus leniusculus). We also examined morphological changes over time spans of 18-43 years to determine whether contemporary characteristics have responded to the presence of exotic species. We found clear differences in stickleback traits and body shape among exotic species combinations. Stickleback coexisting with bass and crayfish were highly armoured, whereas bass-only lakes contained stickleback with reduced armour. Two stickleback populations that coexist with signal crayfish showed significant increases in size over time. These patterns suggest that smallmouth bass and signal crayfish may have significant and different impacts on stickleback morphology.
SpatialPPI 2.0: Enhancing Protein-Protein Interaction Prediction through Inter-Residue Analysis in Graph Attention Networks
Authors: Hu Wenxing , Ohue Masahito 
Published: October 2024

AbstractProtein-protein interactions (PPIs) are fundamental to cellular functions, and accurate prediction of these interactions is crucial to understanding biological mechanisms and facilitating drug discovery. SpatialPPI 2.0 is an advanced graph neural network-based model that predicts PPIs by utilizing interresidue contact maps derived from both structural and sequence data. By leveraging the comprehensive PINDER dataset, which includes interaction data from the RCSB PDB and the AlphaFold database, SpatialPPI 2.0 improves the specificity and robustness of the prediction of PPI. Unlike the original SpatialPPI, the updated version employs interaction interface prediction as an intermediate step, allowing for a more effective assessment of interactions between isolated proteins. The model utilizes Graph Attention Networks (GAT) and Graph Convolutional Networks (GCN) to capture both local and global structural features. SpatialPPI 2.0 outperforms several state-of-the-art PPI and interface predictors, demonstrating superior accuracy and reliability. Furthermore, the model shows robustness when using structures predicted by AlphaFold, indicating its potential to predict interactions for proteins without experimentally determined structures. SpatialPPI 2.0 offers a promising solution for the accurate prediction of PPIs, providing insight into protein function and supporting advances in drug discovery and synthetic biology. SpatialPPI 2.0 is available athttps://github.com/ohuelab/SpatialPPI2.0
PET microplastics increase the risk of insulin resistance and pancreatitis
Authors: Mierzejewski Karol , Kurzyńska Aleksandra , Golubska Monika , Gałęcka Ismena , Całka Jarosław , Bogacka Iwona 
Published: October 2024

AbstractMicroplastics and their effects on the body have recently been of great concern. Today it is clear that they are not indifferent to human health, but the full spectrum of their impact has not yet been fully described. Pancreatic diseases are becoming increasingly common worldwide, and their etiology is not well understood. Worryingly, these diseases have been increasingly diagnosed in children over the last 20 years, which was previously considered unusual. The aim of the study was therefore to determine the changes in the pancreas caused by PET microplastics in young organisms. For this purpose, the global metabolomic profile of the pancreas of piglets treated with a low (0.1 g/day) or high dose (1 g/day) of PET microplastics for 4 weeks was determined by UPLC-MS analysis. In addition, insulin levels and various biochemical parameters in the blood were analyzed. The study showed that PET microplastics affected the physiological processes in the pancreas at both low and high doses. We found that PET microplastics increased the tissue levels of important metabolites such as glucose, γ-aminobutyric acid, lysophosphatidylcholine or lysophosphatidylethanolamine. In addition, PET microplastics increased blood insulin concentrations and dose-dependently regulated lipase, cholesterol and calcium levels. These results suggest that PET microplastics increase the risk of insulin resistance and pancreatitis.
The Oscarella sponges genus: a hidden yet colorful diversity
Authors: Guiollot E. , Guillemain D. , Renard E. , Borchiellini C. , Schenkelaars Q. 
Published: October 2024

ABSTRACTThe identification and ranking of new taxa are crucial for advancing our understanding of biodiversity. However, assigning samples to new taxa requires a cautious and rigorous approach. Historically, taxonomy has heavily relied on morphological traits, which can be subjective and may not always correspond to underlying genetic divergence. This challenge is especially pronounced in organisms with limited diagnostic morphological traits. A prime example is the poriferans of the genusOscarella(Homoscleromorpha), where species delimitation often depends on insufficient morphological features and genetic data. In this study, we addressed these challenges by integrating a comprehensive genetic dataset, including both mitochondrial and nuclear markers, with systematic photographic documentation of 192 specimens collected in Western Mediterranean Sea (Marseille Bay, France). This method allowed us to provide a more robust assessment ofOscarelladiversity, leading to the identification of four species new to science. In addition, our phylogenetic multigene analyses enabled us to propose a meaningful evolutionary scenario for color polymorphism. Additionally, our data showed the critical limitation in current methodologies forOscarellastudies, such as the low resolution of the widely usedcytochrome c oxidase subunit I(cox1/COI) gene, the lack of genetic data for many species, and the insufficient information regarding their geographical distribution. These findings underscore the need for more rigorous genetic frameworks and comprehensive datasets to enhance species delimitation and taxonomy.
TheArabidopsisamino acid transporter UmamiT20 confersBotrytis cinereasusceptibility
Authors: Prior Matthew J. , Weidauer Diana , Liao Jui-Yu , Kuwata Keiko , Locci Federica , Deng Chen , Ye Hong Bo , Cai Qiang , Bezrutczyk Margot , Zhao Chengsong , Chen Li-Qing , Jonikas Martin C. , Pilot Guillaume , Jin Hailing , Parker Jane , Frommer Wolf B. , Kim Ji-Yun 
Published: October 2024

SummaryInduction of SWEET sugar transporters by bacterial pathogens via transcription activator-like (TAL) effectors is necessary for successful blight infection of rice, cassava and cotton, - likely providing sugars for bacterial propagation.Here, we show that infection ofArabidopsisby the necrotrophic fungusBotrytis cinereacauses increased accumulation of amino acid transporter UmamiT20 mRNA in leaves. UmamiT20 protein accumulates in leaf veins surrounding the lesions after infection. Consistent with a role during infection,umamiT20 knock-outmutants were less susceptible toB. cinerea.Functional assays demonstrate that UmamiT20 mediates amino acid transport of a wide range of amino acid substrates.Pathogen-induced UmamiT20 mRNA and protein accumulation support the hypothesis that transporter-mediated pathogen susceptibility is not unique to SWEETs in bacterial blight of rice but also for a necrotrophic fungus and implicate nutrients other than sucrose, i.e., amino acids, in nutrition or nutrient signaling related to immunity. We hypothesize that stacking of mutations in different types of susceptibility-related nutrient carriers to interfere with access to several nutrients may enable engineering robust pathogen resistance in a wide range of plant-pathogen systems.Lay AbstractPathogens infect plants to gain access to their nutrient resources, enabling the pathogens to cause disease and reproduce efficiently. Here we find that an amino acid transporter constitutes a susceptibility factor for the fungal pathogenB. cinerea.