bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is increased trunk flexion in standing up related to muscle weakness or pain avoidance in individuals with unilateral knee pain?; a simulation study
Authors: van der Kruk Eline , Geijtenbeek Thomas 
Published: December 2023

AbstractThe ‘Timed Up and Go’ test (TUG) is a widely used clinical tool for assessing gait and balance, relying primarily on timing as a measure. However, there are more observable biomechanical compensation strategies within TUG that are indicative of underlying neuromuscular issues and movement priorities. In individuals with unilateral knee osteoarthritis, an increased trunk flexion during TUG is a common phenomenon, often attributed to muscle weakness and/or pain avoidance. Unfortunately, it is difficult to differentiate between these underlying causes using experimental studies alone. This study aimed to distinguish between muscle weakness and pain avoidance as contributing factors, using predictive neuromuscular simulations of the sit-to-walk movement. Muscle weakness was simulated by reducing the maximum isometric force of the vasti muscles (ranging from 20% to 60%), while pain avoidance was integrated as a movement objective, ensuring that peak knee load did not exceed predefined thresholds (2-4 times body weight). The simulations demonstrate that a decrease in muscular capacity led to greater trunk flexion, while pain avoidance led to slower movement speeds and altered muscle recruitments, but not to greater trunk flexion. Our predictive simulations thus indicate that increased trunk flexion is more likely the result of lack of muscular reserve rather than pain avoidance. These findings align with reported differences in kinematics and muscle activations between moderate and severe knee osteoarthritis patients, emphasizing the impact of severe muscle weakness in those with advanced knee osteoarthritis. The simulations offer valuable insights into the mechanisms behind altered movement strategies, potentially guiding more targeted treatment.
Attitudes of chronic pain patients on long-term opioid therapy toward opioid tapering
Authors: Jabakhanji R. , Tokunaga F. , Rached G. , Vigotsky A.D. , Griffith J. , Schnitzer T.J. , Apkarian A. V. 
Published: December 2023

AbstractThe chronic pain and opioid addiction epidemics interact with each other, potentially exacerbating each respective condition. Despite having modest efficacy, millions of chronic pain patients in the USA continue to use opioids as their primary source of pain management. The Centers for Disease Control recommends opioid tapering to diminish the risk of opioid dependence in chronic pain patients. However, tapering, even with physician oversight, can introduce additional harm. Thus, many pain clinicians remain ambivalent about undertaking opioid tapering. Here, we surveyed attitudes on the topic from the viewpoint of chronic pain patients who have been consuming opioids over long durations. We queried 127 chronic pain patients (pain duration = 13.5 ± 9.6 years) on long-term opioids (10.3 ± 8.2 years), primarily consuming hydrocodone or oxycodone. Sixty-six percent of participants were “very” or “extremely” interested in participating in an opioid tapering study. Patients emphasized the importance of controlling their pain during opioid tapering, and over 50% were also worried about craving symptoms. Both the desire for tapering and the worry of pain control were more pronounced in participants with a higher magnitude of ongoing back pain. The study demonstrates that most chronic pain patients using opioids are interested in decreasing opioid consumption. Yet, they worry about losing control of their chronic pain. These results imply patient-physician strategies that may aid the engagement of both parties in opioid tapering.
Detailed microbiome analysis of sticker-stripped surface materials of acne lesions revealed acne-relatedCutibacterium acnessubtypes: a pilot study
Authors: Shimokawa Yutaka , Funatsu Osamu , Ohata Kazuma , Inoue Fukashi , Tachibana Kota , Dekio Itaru 
Published: December 2023

AbstractCutibacterium acnes (C. acnes)is known to play a central role in pathogenesis of acne vulgaris. It has been understood that multiple phylotypes ofC. acnesexist, with certain types being more prevalent in patient with acne vulgaris and others more common in healthy individuals. In this context, we conducted a preliminary study using self-collected samples via an adhesive sticker (MySkin® patch) to analyze the skin microbiome of Japanese women. The study aimed to determine the role ofC. acnesand its specific phylotypes in the development of acne vulgaris.Participants in this study were Japanese females aged between their 20s and 40s. Dermatologists evaluate the data from web-based questionnaires and smartphone image submissions to classify subjects into either Acne group (n = 219) or Non-acne group (n = 77). Quality assessment of DNA extracted from the sticker was conducted, followed by amplification of the16S rRNAregion using PCR. Subsequent microbial community analysis was performed using next-generation sequencing techniques. Genetic classification ofC. acneswas accomplished through single locus sequence typing.Results indicated a bacterial community composition on the facial skin surface predominantly consisting ofC. acnesclusters, with over half of these clusters constituted byC. acnes. Notably, the Acne group exhibited a significantly higher proportion ofC. acnesrelative to total bacterial presence compared to the Non-acne group. Analysis ofC. acnesphylotypes revealed a markedly lower presence of type III (subspecieselongatum) in the Acne group (vs. Non-acne group,p< 0.05). No significant differences were observed in the prevalence of Types IA1, IA2, II, and IB between the two groups. The predominantsequence types (ST) ofC. acnesidentified were IA2_2_F0 (23.9%), IA1_4_A0 (20.6%), and II_2_K0 (18.6%). Within the Acne group, an increase in IA2_1_F1 and a decrease in III_1_L0 were observed (vs. Non-acne group,p< 0.05).This study underscores the feasibility of using self-collected and mailed-in samples for qPCR and microbiome analysis, maintaining diagnostic quality comparable to in-person assessments. Furthermore, the variation in the expression ofC. acnesphylotypes across skin surfaces between acne-afflicted and healthy individuals could suggest that shifts in phylotype expression patterns may be indicative of skin susceptibilities to acne development.
Stage-sensitive potential of isolated rabbit ICM to differentiate into extraembryonic lineages
Authors: Filimonow Katarzyna , Chołoniewska Anna , Chołoniewski Jan , Madeja Zofia E. , Barłowska Katarzyna , Grabarek Joanna , Plusa Berenika , Piliszek Anna 
Published: December 2023

ABSTRACTIn the course of mammalian development initial state of totipotency must be lost to allow acquisition of specific cell fates. The first differentiation event results in the formation of trophectoderm (TE) and the inner cell mass (ICM). In the mouse embryo the cell fate of these two compartments is set quickly after formation of a blastocyst. However, recent reports suggest that plasticity of these two lineages might be extended in species other than the mouse. Here we investigated how the cellular plasticity of early mammalian embryos relates to developmental time scale and changes in gene expression using rabbit isolated ICMs. We studied the dynamics of rabbit blastocyst formation using time-lapse imaging and identified GATA3 as an early marker of rabbit TE and CDX2 as a marker of fully formed TE. We then analysed developmental potential of rabbit ICMs isolated by immunosurgery and subsequently culturedin vitro. ICMs originating from early- to mid-blastocyst stage embryos are able to re-form a blastocyst-like structure, with a functional TE, and an ICM containing both SOX2-positive epiblast cells and SOX17-positive primitive endoderm cells. We further observed that rabbit ICMs isolated from later blastocyst stages lose the ability for TE specification, instead forming a halo-like cavity with an outer layer of SOX17-positive cells. Our data indicate that in mammalian embryos the potential for TE differentiation gives way to formation of a different type of extraembryonic epithelial layer, suggesting potential common mechanism of pluripotency restriction between eutherian mammals.
On the expression of reproductive plasticity inDrosophila melanogasterfemales in spatial and socially varying environments!
Authors: Nwajei Oghenerho , Talagala Sanduni , Hampel Laura , Punj Bhavya , Li Nuek Yin , Long Tristan A.F. 
Published: December 2023

AbstractIndividuals often adjust their behaviour based on their perception and experiences with the social and/or physical environment. In this study, we examined the extent of reproductive plasticity expressed in mating rates, mating latencies, mating durations, and offspring production in female fruit flies,Drosophila melanogaster, that encountered different numbers of males in different sized chambers. We found that mating latency length decreased with more courting males and smaller environments and that matings durations were longer in larger chambers and in the presence of two males. These results illustrate the sensitivity of these behavioural phenotypes to changes in local environmental conditions.
TCRfp: a new fingerprint-based approach for TCR repertoire analysis
Authors: Mayol-Rullan Francesca , Bugnon Marine , Perez Marta A. S. , Zoete Vincent 
Published: December 2023

AbstractThe development of cancer immunotherapy has accelerated in recent years. Understanding the specificity of T cell receptors (TCR) for peptides presented by the major histocompatibility complex (pMHC) is a major step towards improving immunotherapy approaches, such as adoptive cell transfer and peptide vaccination. Despite recent computational advances, the unambiguous pairing of TCR with pMHC, from pools of thousands of candidates, remains out of reach. To tackle this challenge, we have developed a new tool that converts the 3D structure of TCR into individual one-dimensional structural fingerprints (TCRfp). We have modelled over 10’000 3D structures of paired TCR alpha and beta chains with known sequences and pMHC specificity and encoded them into 1D TCRfp. For future clinical needs, we have translated the TCR modelling process into a fast pipeline. Similarity measures between TCR FPs correlate with their ability to recognise similar or identical epitopes in the training set and in the external validation sets. TCRfp constitutes the first rapid approach for high-throughput TCR comparison and repertoire analysis based on molecular 3D structures, which is efficient enough to complement sequence-based approaches.
Cytokinins specify pluripotent stem cell identity in the mossPhyscomitrium patens
Authors: Hata Yuki , Ohtsuka Juri , Hiwatashi Yuji , Naramoto Satoshi , Kyozuka Junko 
Published: December 2023

AbstractThe shoot apical meristem (SAM) contains pluripotent stem cells that produce all the aerial parts of the plant. Stem cells undergo asymmetric cell divisions to self-renew and to produce differentiating cells. Our research focused on unraveling the mechanisms governing the specification of these two distinct cell fates following the stem cell division. For this purpose, we used the model organismPhyscomitrium patens, which features a singular pluripotent stem cell known as the gametophore apical cell. We show that the activity of cytokinins, critical stem cell regulators, is restricted to the gametophore apical cell due to the specific localization of PpLOG, the enzyme responsible of cytokinin activation. In turn, PpTAW, which promotes differentiating cell identity of the merophyte, is excluded from the gametophore apical cell by the action of cytokinins. We propose a cytokinin-based model for the establishment of asymmetry in the pluripotent stem cell division.One Sentence SummaryCytokinins are confined to the pluripotent stem cells and exclude the differentiation factor TAW1 to establish the SAM from a single stem cell.
PARP-1, EpCAM, and FRα as potential targets for intraoperative detection and delineation of endometriosis: a quantitative tissue expression analysis
Authors: Belmonte Beatrice , Di Lorenzo Giovanni , Mangogna Alessandro , Bortot Barbara , Bertolazzi Giorgio , Sammataro Selene , Merighi Simona , Martorana Anna , Zito Gabriella , Romano Federico , Giorgiutti Anna , Bottin Cristina , Zanconati Fabrizio , Romano Andrea , Ricci Giuseppe , Biffi Stefania 
Published: December 2023

AbstractEndometriosis is a gynecological disease characterized by the presence of endometrial tissue in abnormal locations, leading to severe symptoms, inflammation, pain, organ dysfunction, and infertility. Surgical removal of endometriosis lesions is crucial for improving pain and fertility outcomes, with the goal of complete lesion removal. Incomplete surgery often results in recurring symptoms and the need for additional interventions. This study aims to explore the biological significance of PARP-1, EpCAM, and FRα as potential targets for molecular imaging in endometriosis, assessing their suitability for targeted intraoperative imaging.Gene expression analysis was performed using the EndometDB. By immunohistochemistry, we investigated the presence and distribution of PARP-1, EpCAM, and FRα in endometriosis foci and adjacent tissue. We also applied an ad hoc platform for the analysis image to perform a quantitative immunolocalization analysis. Additionally, double immunofluorescence analysis was carried out for PARP-1 and EpCAM, as well as PARP-1 and FRα, to explore the expression of these combined markers within endometriosis foci and their potential simultaneous utilization in surgical treatment.The analysis of gene expression revealed that PARP-1, EpCAM, and FRα exhibit higher levels of expression in endometriotic lesions compared to the peritoneum, used for control tissue. Immunohistochemical analysis also highlighted a significant increase in expression of all three biomarkers in endometriosis foci compared to surrounding tissues, as well as the quantitative analysis of immunolocalization of the signal. Furthermore, the double immunofluorescence analysis consistently revealed nuclear expression of PARP-1 and membrane and cytoplasmatic expression of EpCAM and FRα, although relatively weaker.Overall, the three markers demonstrate significant potential for effective imaging of endometriosis. Particularly, the results emphasize the importance of PARP-1 expression as a possible indicator for distinguishing endometriotic lesions from adjacent tissue. PARP-1, as a potential biomarker for endometriosis, offers promising avenues for further investigation in terms of both pathophysiology and diagnostic-therapeutic approaches.
Distribution and Triazole Susceptibility of Aspergilli from Clinical, Soils and Veterinary Samples in Ogun State, Nigeria
Authors: Olugbenga O.M. , Easter T. , Shittu O.B. , Obuotor T.M. , Sam-Wobo S.O. , Ejilude O. , van Rhijn N. 
Published: December 2023

ABSTRACTResistance of Aspergilli to azole compounds have been on the rise globally with the majority of data coming from Europe and the Americas. However, little data from Africa is available comparing antifungal susceptibility of isolates from the environment and the clinic directly. Differences between fungal species present in the environment and their susceptibility will have a direct impact on human health and policies regarding fungal infections. Hence a One Health approach of the susceptibility of Aspergilli isolated from human, environment and veterinary samples from South western of Nigeria was carried out. Sputum, soil and animal litters/feeds samples were collected and processed using Potato Dextrose Agar (PDA) and Malt Extract Agar (MEA) supplemented with chloramphenicol to isolateAspergillusspecies. The majority of isolates recovered wereA. nigerandA. flavus, with littleA. fumigatusrecovered. Susceptibility testing to voriconazole was carried out using the microdilution method results interpreted according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. All isolates were found to be susceptible to itraconazole and voriconazole. These results show differences between species present in the environment and from patient samples compared to Europe and the Americas, highlighting a need for more fungal research focused on Africa.
Air monitoring by nanopore sequencing
Authors: Reska Tim , Pozdniakova Sofya , Borràs Sílvia , Schloter Michael , Cañas Lídia , Puente Albert Perlas , Rodó Xavier , Wang Yuanyuan , Winkler Barbro , Schnitzler Jörg-Peter , Urban Lara 
Published: December 2023

AbstractWhile the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome’s composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions throughde novometagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city’s boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.
Climate change impacts dryland multifunctionality: A cascade of precipitation variability to species replacement in multitrophic microbiota
Authors: Guo Xiaoyu , Li Hua , Wang Zuowen , Yang Haijian , Hu Chunxiang , Song Lirong , Wang Weibo 
Published: December 2023

AbstractIn the Anthropocene, the pervasive impacts of climate change on arid ecosystems are increasingly evident, resulting in significant alterations in both biodiversity and functionality. Although soil microbes are anticipated to be sensitive to changes in precipitation regimes, the mechanisms through which multifaceted precipitation changes impair the delivery of multiple functions by multitrophic microbiota in soils remain largely unexplored. In the drylands of Northwestern China, we examined the direct effects of historical precipitation regimes on the soil multifunctionality of biocrusts, a model system, and their indirect impacts mediated by microbial communities. Among abiotic predictors, precipitation variability, rather than mean annual precipitation, emerged as the primary driver of multifunctionality, leading to a convergence of less functionally beneficial species. By utilizing a biodiversity-ecosystem function relationship framework, our results underscore the crucial roles ofα- andβ-diversity of heterotrophic bacteria, fungi, and phototrophic cyanobacteria in maintaining soil functionality. However, the underlying mechanisms are distinct. We found that the local richness of heterotrophs and phylogenetic dissimilarity of photoautotrophs exert positive influences on multifunctionality, while species replacement, a component ofβ-diversity, primarily enhances the variance in soil multifunctionality. Importantly, the findings illuminate the cascading effect of precipitation variability on dryland ecosystems, amplified by microbial diversity, potentially triggering a silent collapse of vulnerable arid habitats. Our study highlights the importance of considering indirect climate impacts via soil microbiota, contributing to a deeper understanding of the real-world consequences of climate change on drylands, and offering valuable insights for the management of biodiversity theory-inspired ecosystem restoration.
Direct comparison of SARS-CoV-2 variant specific neutralizing antibodies in human and hamster sera
Authors: Rössler Annika , Netzl Antonia , Knabl Ludwig , Wilks Samuel H. , Mühlemann Barbara , Türeli Sina , Mykytyn Anna , von Laer Dorothee , Haagmans Bart L. , Smith Derek J. , Kimpel Janine 
Published: December 2023

AbstractAntigenic characterization of newly emerging SARS-CoV-2 variants is important to assess their immune escape and judge the need for future vaccine updates. As exposure histories for human sera become more and more complex, animal sera may provide an alternative for antigenic characterization of new variants. To bridge data obtained from animal sera with human sera, we here analyzed neutralizing antibody titers in human and hamster first infection sera in a highly controlled setting using the same live-virus neutralization assay performed in one laboratory. Using a Bayesian framework, we found that titer fold changes in hamster sera corresponded well to human sera and that hamster sera generally exhibited higher reactivity. Our results indicate that sera from infected hamsters are a good surrogate for the antigenic characterization of new variants.
Conformational Dynamics and metal-ion interactions in human small Ubiquitin-like modifier (SUMO2)
Authors: Kaur Anupreet , Singh Harpreet , Kumar Dinesh , Gahlay Gagandeep Kaur , Mithu Venus Singh 
Published: December 2023

AbstractSUMO (Small Ubiquitin-like Modifiers) proteins are involved in a crucial post-translational modification commonly termed as SUMOylation. Currently little is known about localisation and accumulation of SUMO2 conjugates in response to proteasome inhibitors. In this work, we have investigated a strong binding of Cu2+ions in the C-terminal region of SUMO2 resulting in its aggregation and seems to interefere in it’s non-covalent interaction with a V/I-X-V/I-V/I based SIM. In Ubiquitin-proteasome system, SUMO2 controls many targets in regulation of all aspects of metabolism. The conformational flexibility of SUMO2 could play a crucial role, therefore we have also characterized native-state flexibility of human SUMO2. We show that compared to SUMO1, several amino acids in SUMO2 around α1-helix region access energetically similar near-native conformations. This could play a fundamental role in its non-covalent interactions with SUMO interaction motifs (SIMs).
Temporal Dynamics of Faster Neo-Z Evolution in Butterflies
Authors: Höök Lars , Vila Roger , Wiklund Christer , Backström Niclas 
Published: December 2023

AbstractThe faster-Z/X hypothesis predicts that sex-linked genes should diverge faster than autosomal genes. However, studies across different lineages have shown mixed support for this effect. So far, most analyses have focused on old and well differentiated sex chromosomes, but less is known about divergence of more recently acquired neo-sex chromosomes. In Lepidoptera (moths and butterflies), Z-autosome fusions are frequent, but the evolutionary dynamics of neo-Z chromosomes have not been explored in detail. Here, we analysed the faster-Z effect inLeptidea sinapis, a butterfly with three Z chromosomes. We show that the neo-Z chromosomes have been acquired stepwise, resulting in strata of differentiation and masculinization. While all Z chromosomes showed evidence of the faster-Z effect, selection for genes on the youngest neo-Z chromosome (Z3) appears to have been hampered by a largely intact, homologous neo-W chromosome. However, the intermediately aged neo-Z chromosome (Z2), which lacks W gametologs, showed less evolutionary constraints, resulting in particularly fast evolution. Our results therefore support that neo-sex chromosomes can constitute temporary hot-spots of adaptation and divergence. The underlying dynamics are likely causally linked to shifts in selective constraints, evolution of gene expression, and degeneration of W-linked gametologs which gradually expose Z-linked genes to selection.