title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=138 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome link: https://peerj.com/articles/18602 last-modified: 2025-01-21 description: BackgroundThe initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns’ gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.MethodologyWe analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.ResultsB. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.DiscussionOur results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being. creator: Nicholas Pucci creator: Joanne Ujčič-Voortman creator: Arnoud P. Verhoeff creator: Daniel R. Mende uri: https://doi.org/10.7717/peerj.18602 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pucci et al. title: Three-dimensional analysis of facial morphology in nine-year-old children with different unilateral orofacial clefts compared to normative data link: https://peerj.com/articles/18739 last-modified: 2025-01-21 description: AimTo compare three-dimensional (3D) facial morphology of various unilateral cleft subphenotypes at 9-years of age to normative data using a general face template and automatic landmarking. The secondary objective is to compare facial morphology of 9-year-old children with unilateral fusion to differentiation defects.Methods3D facial stereophotogrammetric images of 9-year-old unilateral cleft patients were imported into 3DMedX® for processing. All images of patients with a right sided cleft were mirrored. A regionalized general facial template was used for standardization. This template was pre-aligned to each face using five automatically determined landmarks and fitted using MeshMonk. All cleft patients were compared to an age-and gender matched normative face using distance maps and inter-surface distances (mm). Average faces were created for five groups (unilateral cleft lip, alveolus, and/or palate (UCL/A/P), fusion and differentiation defects). The selected regions for the evaluation of facial morphology were: complete face, nose, upper lip, lower lip, chin, forehead, and cheeks.ResultsA total of 86 consecutive 3D-stereophotogrammetry images were acquired for examination. No statistically significant differences were observed among the UCL, UCLA, and UCLP groups for the complete face, cheeks, chin, forehead, lower lip, and nose. However, in the upper lip region a significant difference was observed between the UCLP and UCL groups (P = 0.004, CI [−2.93 to −0.48]). Further visual examination of the distance maps indicated that more severe clefts corresponded to increased retrusion in the midface and the tip of the nose, though these differences were not statistically significant across groups. For fusion vs differentiation defects, no statistically significant differences were observed, neither for the complete face nor for any of the individual regions.ConclusionThe findings demonstrate statistically significant differences in the upper lip region between children with UCL and those with UCLP, particularly with greater upper lip retrusion in the UCLP group. The use of color-coded distance maps revealed local variations and a trend of asymmetry in the nasal region, with increasing retrusion of the nose tip, upper lip, and cheeks correlating with the severity of the cleft. Although these trends were not statistically significant, they suggest a progressive facial retrusion pattern as cleft severity increases. For the secondary objective, no statistical differences were found between the facial morphology of children with fusion and differentiation defects, although a similar progression of maxillary retrusion was observed in the distance maps. creator: Marjolein Crins-de Koning creator: Robin Bruggink creator: Marloes Nienhuijs creator: Till Wagner creator: Ewald M. Bronkhorst creator: Edwin M. Ongkosuwito uri: https://doi.org/10.7717/peerj.18739 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Crins-de Koning et al. title: Attaching artificial Achilles and tibialis cranialis tendons to bone using suture anchors in a rabbit model: assessment of outcomes link: https://peerj.com/articles/18756 last-modified: 2025-01-21 description: ObjectiveThe purpose of this study was to investigate the timing and mode of failure of metallic screw-type suture anchors used to attach artificial tendons to bone in an in vivo New Zealand White rabbit model.Study DesignMetal suture anchors with braided composite sutures of varying sizes (United States Pharmacopeia (USP) size 1, 2, or 5) were used to secure artificial tendons replacing both the Achilles and tibialis cranialis tendons in 12 female New Zealand White rabbits. Artificial tendons were implanted either at the time of (immediate replacement, n = 8), or four/five weeks after (delayed replacement, n = 4) resection of the biological tendon. Hindlimb radiographs of the rabbits were obtained immediately after surgery and approximately every other week until the study endpoint (16 weeks post-surgery).ResultsAll suture anchors used for the tibialis cranialis artificial tendons remained secure and did not fail during the study. The suture anchor used to attach the Achilles artificial tendon to the calcaneus bone failed in nine of 12 rabbits. In all cases of suture anchor failure, the suture broke away from the knot, while the metallic screw remained securely embedded in the bone. Based on radiographic analysis, the mean estimated failure timepoint was 5.3 ± 2.3 weeks post-surgery, with a range of 2–10 weeks. Statistical analyses (Mann–Whitney U test and Fisher’s exact test) revealed no significant effect of tendon implantation timing or suture size on either the timing or frequency of suture anchor failure.ConclusionFor the suture anchors used to attach artificial tendons in this study, suture anchor failure was most likely due to suture wear or cutting against the eyelet of the anchor screw. Future studies are needed to test the effect of suture-eyelet interaction on suture strength under different loading conditions. creator: Obinna P. Fidelis creator: Caleb Stubbs creator: Katrina L. Easton creator: Caroline Billings creator: Alisha P. Pedersen creator: David E. Anderson creator: Dustin L. Crouch uri: https://doi.org/10.7717/peerj.18756 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fidelis et al. title: Morphometric analysis revealed two different Mediterranean horse mackerel (Trachurus mediterraneus) stocks in the Adriatic Sea link: https://peerj.com/articles/18765 last-modified: 2025-01-21 description: Phenotypical differentiation among individuals of Mediterranean horse mackerel Trachurus mediterraneus in the Adriatic Sea was investigated through the analysis of several morphometric characters. Overall, 426 individuals of Mediterranean horse mackerels were sampled from the northern, central and southern Adriatic Sea during the summers of 2012 and 2013. Forty-six morphometric characters were measured for each individual and then compared using multivariate techniques (linear discriminant analysis). Based on the morphometric characteristics, at least two different Mediterranean horse mackerel were identified: one comprising the northern and central Adriatic, and the other formed by individuals from the southern Adriatic basin. The northern and central areas showed stable populations, overlapping both in space and time. The southern area seemed to be more variable over the years, with a low degree of overlapping both in space and time. A possible hypothesis for this, to be further investigated, could be the flow of individuals from the Ionian and Aegean Seas populations through the Otranto Channel. The main differences between the two stocks were associated with the head characters of the fish. In particular, the northern and central Adriatic Sea individuals had shorter and thicker heads than the southern ones. This could be due to different feeding habits: the former mainly feed on small fishes, the latter mainly on euphausiids. A short mouth could reduce the power of suction of bigger preys, while a long mouth could increase the volume of water to be filtered to feed on small planktonic crustaceans. From this study, it becomes clear that the Mediterranean horse mackerel should not be managed as a single stock in the Adriatic Sea as it was evident that at least two morphologically different stocks are present in the basin. creator: Claudio Vasapollo uri: https://doi.org/10.7717/peerj.18765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vasapollo title: Geometrical determinants of cerebral artery fenestration for cerebral infarction link: https://peerj.com/articles/18774 last-modified: 2025-01-21 description: PurposeFew data are available on the causality of cerebral artery fenestration (CAF) triggering cerebral infarction (CI) and this study aims to identify representative morphological features that can indicate risks.MethodsA cohort comprising 89 patients diagnosed with CAF were enrolled from a total of 9,986 cranial MR angiographies. These patients were categorized into Infarction Group (n = 55) and Control Group (n = 34) according to infarction events. These two groups are divided into two subgroups depending on fenestration location (basilar artery or other cerebravascular location), respectively, i.e., BA Infarction Group (n = 37), BA Control Group (n = 23), Non_BA Infarction Group (n = 18), Non_BA Control Group (n = 11). This study firstly defined 12 indices to quantify the morphological characteristics of fenestration per se and its connecting arteries. The data were evaluated using either the independent sample t-test or the Mann–Whitney U test. Conducting univariate and multivariate logistic regression analyses to ascertain potential independent predictors of CI.ResultsThe initiation angle φ1 and confluence angle φ2 at the fenestration in the Infarction Group are both smaller compared to the Control Group, but only the Infarction Group and BA Infarction Group have significant difference (p < 0.05). The maximum left fenestration axis (fAL) and the left tortuosity index (TIL) were greater in the Infarction Group for CAFs than those in the Control Group (p < 0.05). In contrast, the maximum right fenestration axis (fAR) and the right tortuosity index (TIR) were smaller than those in Control Group (p < 0.05). The logistic regression analysis revealed that φ2 (AUC = 0.68, p = 0.02), fAL (AUC = 0.72, p < 0.01), and fAR (AUC = 0.70, p < 0.01) serve as independent risk factors influencing the occurrence of CI. The regression predictive model achieved an AUC of 0.83, enabling accurate classification of 77.5% of cases, indicating a robust predictive performance of the model.ConclusionMorphological results demonstrated a left-leaning type of fenestration with more narrow fenestration terminals indicating a higher risk of CI occurrence. Furthermore, the regression predictive model established in this study demonstrates a good predictive performance, enabling early prediction of CI occurrence in fenestrated patients and facilitating early diagnosis of CI. creator: Yuqian Mei creator: Xiaoqin Chen creator: Yao Zhang creator: Yanling Wang creator: Bo Wu creator: Mingcheng Hu creator: Quan Bao uri: https://doi.org/10.7717/peerj.18774 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mei et al. title: Development of metastasis and survival prediction model of luminal and non-luminal breast cancer with weakly supervised learning based on pathomics link: https://peerj.com/articles/18780 last-modified: 2025-01-21 description: ObjectiveBreast cancer stands as the most prevalent form of cancer among women globally. This heterogeneous disease exhibits varying clinical behaviors. The stratification of breast cancer patients into risk groups, determined by their metastasis and survival outcomes, is pivotal for tailoring personalized treatments and therapeutic interventions. The pathological sections of radical specimens encompass a diverse range of histological information pertinent to the metastasis and survival of patients. In this study, our objective is to develop a deep learning model utilizing pathological images to predict the metastasis and survival outcomes for breast cancer patients.MethodsThis study utilized pathological sections from 204 radical mastectomy specimens obtained between January 2013 and December 2014 at the Second Affiliated Hospital of the Medical College of Zhejiang University. The 204 pathological slices were scanned and transformed into whole slide imaging (WSI), with manual labeling of all tumor areas. The WSI was then partitioned into smaller tiles measuring 512 × 512 pixels. Three networks, namely Densely Connected Convolutional Network 121 (DenseNet121), Residual Network (ResNet50), and Inception_v3, were assessed. Subsequently, we combined patch-level predictions, probability histograms, and Term Frequency-Inverse Document Frequency (TF-IDF) features to create comprehensive participants representations. These features served as the foundational input for developing a machine learning algorithm for metastasis analysis and a Cox regression model for survival analysis.ResultOur results show that the Inception_v3 model shows a particularly robust patch recognition ability for estrogen receptor (ER) recognition. Our pathological model shows high accuracy in predicting tumor regions. The train area under the curve (AUC) of the Inception_v3 model based on supervised learning is 0.975, which is higher than the model established by weakly supervised learning. But the AUC of the metastasis prediction in training and testing sets is higher than value based on supervised learning. Furthermore, the C-index of the survival prediction model is 0.710 in the testing sets, which is also better than the value by supervised learning.ConclusionOur study demonstrates the significant potential of deep learning models in predicting breast cancer metastasis and prognosis, with the pathomic model showing high accuracy in identifying tumor areas and ER status. The integration of clinical features and pathomics signature into a nomogram further provides a valuable tool for clinicians to make individualized treatment decisions. creator: Hui Liu creator: Linlin Ying creator: Xing Song creator: Xueping Xiang creator: Shumei Wei uri: https://doi.org/10.7717/peerj.18780 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Melatonin attenuates MPP+-induced autophagy via heat shock protein in the Parkinson’s disease mouse model link: https://peerj.com/articles/18788 last-modified: 2025-01-21 description: BackgroundThis study investigates the protective properties of melatonin in an in vivo Parkinson’s disease (PD) model, focusing on the underlying mechanisms involving heat shock proteins (HSPs).MethodsTwelve adult male C57BL/6 mice were randomly divided into four groups (normal control, melatonin control, Parkinson’s model, and melatonin treatment; n = 3 per group) and housed in a single cage. 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was injected intraperitoneally in the Parkinson’s model and treatment groups to establish a subacute PD model, while controls received saline. Limb motor ability was assessed 1 h after the final injection using behavioral tests, including the open field test to evaluate central zone entries and average movement. Dopamine transporter (DAT) expression in the striatum was analyzed by immunohistochemistry, and Western blot was used to measure autophagy proteins and HSP70 levels.ResultsThe PD mouse model was successfully established through MPTP stimulation. Compared to the normal control group, the model group showed a significant reduction in the frequency of entering the central zone and average movement. The number of DAT-positive cells in the brain also decreased significantly. The expression levels of HSP70 and CDK5 were significantly lower, while the expression levels of LC3 II /LC3I and p62 increased significantly. In the MT treatment group, both the frequency of entering the central zone and the average movement were significantly higher compared to the model group. DAT-positive cells in the midbrain also increased significantly. The expression levels of HSP70 and CDK5 were significantly elevated, while the expression levels of LC3 II /LC3I and p62 protein were significantly decreased.ConclusionMelatonin exerts a protective effect against MPP+-induced damage to dopaminergic neurons, presumably by upregulating HSP70, which inhibits neuronal autophagy. creator: Yinli Guo creator: Chengbo Liu uri: https://doi.org/10.7717/peerj.18788 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo and Liu title: Controlled temperature contrasts of three native and one highly invasive annual plant species in California link: https://peerj.com/articles/18794 last-modified: 2025-01-21 description: Plant responses to changes in temperature can be a key factor in predicting the presence and managing invasive plant species while conserving resident native plant species in dryland ecosystems. Climate can influence germination, establishment, and seedling biomass of both native and invasive plant species. We tested the hypothesis that common and widely distributed native and an invasive plant species in dryland ecosystems in California respond differently to increasing temperatures. To test this, we examined the effects of temperature variation on germination, establishment, and per capita seedling biomass of three native and one invasive plant species (Bromus rubens) in independent 6 week growth trial experiments in a controlled greenhouse. Higher relative temperatures reduced the germination and establishment of the tested invasive species and two tested native species, however, per capita biomass was not significantly affected. Specifically, germination and establishment of the invasive species B. rubens and the native species Phacelia tanacetifolia was significantly reduced. This invasive species can often outcompete natives, but increasing temperature could potentially shift the balance between the germination and establishment of natives. A warming climate will likely have negative impacts on native annual plant species in California tested here because increasing temperatures can co-occur with drought. This study shows that our tested native annual plant species tested here have some resilience to relatively significant increases in temperature, and this can favor at least one native species relative to at least one highly noxious invasive plant species. creator: Mario Zuliani creator: Stephanie Haas-Desmarais creator: Laura Brussa creator: Jessica Cunsolo creator: Angela Zuliani creator: Christopher J. Lortie uri: https://doi.org/10.7717/peerj.18794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zuliani et al. title: Turkish validation of a resilience scale from older people’s perspectives: resilience scale for older adults link: https://peerj.com/articles/18837 last-modified: 2025-01-21 description: BackgroundAs the global population ages and life expectancy increases, older adults encounter challenges like chronic illnesses and losing loved ones; resilience is crucial for adapting to these difficulties. This study aims to culturally and linguistically adapt the psychological resilience scale designed for older adults to the Turkish context.MethodsThis methodological study included 566 individuals aged 65 and older. All participants completed the Resilience Scale for Older Adults, the Perceived Stress Scale, the Geriatric Depression Scale, and the Quality of Life in Older Adults Scale—Short Form. Construct validity was assessed through confirmatory and exploratory factor analyses, while convergent and discriminant validity were evaluated through the correlation of the scales. Reliability was determined using internal consistency and the split-half method.ResultsThe scale retains its original structure with 33 items and four sub-dimensions (Intrapersonal, Interpersonal, Spiritual, and Experiential). The content validity index of the scale is 0.98, with item loadings ranging from 0.406 to 0.947, according to exploratory factor analysis. Confirmatory factor analysis indicates good fit indices. Convergent validity is supported by a strong positive correlation (r = 0.657, p < 0.001) between the Resilience Scale for Older Adults and the Quality of Life in Older Adults Scale—Short Form. Reliability measures include a Cronbach’s alpha internal consistency coefficient of 0.93 and a Guttman split-half reliability coefficient of 0.723.ConclusionThe results show that the Turkish version of the Resilience Scale for Older Adults is a valid and reliable measurement tool. creator: Seher Palanbek Yavaş creator: Caner Baysan uri: https://doi.org/10.7717/peerj.18837 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Palanbek Yavaş and Baysan title: SSR marker-based genetic diversity and structure analyses of Camellia nitidissima var. phaeopubisperma from different populations link: https://peerj.com/articles/18845 last-modified: 2025-01-21 description: BackgroundCamellia nitidissima var. phaeopubisperma is a variety in the section Chrysantha of the genus Camellia of the family Theaceae which is native to Fangchenggang, Guangxi, China. To date, the genetic diversity and structure of this variety remains to be understood.MethodsIn the present study, eight simple sequence repeat (SSR) molecular markers previously screened were used to analyze the genetic diversity and structure of C. nitidissima var. phaeopubisperma natural populations from 14 growing areas in China, so as to determine the influence of environmental changes on genetic variations and provide the basis for introduction and selection of suitable growing sites of that variety.ResultsOur results show that, for the eight SSR loci, the observed numbers of alleles per locus (Na) and the effective numbers of alleles per locus (Ne) were nine and 3.206, respectively on average, and the Ne was lower than the Na for all loci; the observed heterozygosity (Ho) was lower than the expected heterozygosity (He). For all the eight loci, the fixation index (F) was greater than 0, and the intra-population inbreeding coefficient (Fis) for seven loci was positive. Three loci were moderately polymorphic (0.25 < polymorphism information content (PIC) <0.5), and five loci were highly polymorphic (PIC > 0.5); all eight loci had a moderate genetic differentiation level (0.05 < genetic differentiation coefficient (Fst) <0.25). As shown by the genetic diversity analysis, the He was bigger than the Ho for 10 populations, indicating the presence of a certain degree of intra-population inbreeding. The F had a negative value for four populations, suggesting that excessive random mating was present within each of them. Results of the analysis of molecular variance show that 19% of the total variation was attributed to among-individuals and 78% of the total variation originated from within-individuals. The adjusted Fst (F’st) was 0.073, indicative of a moderate level of genetic differentiation among the populations. The value of gene flow was greater than 1 (7.367), suggesting that genetic differentiation among populations was not caused by genetic drift. Results of the STRUCTURE analysis show that all the samples tested could be clustered into five ancestor groups. Results of the Unweighted Pair Group Method using Arithmetic Averages (UPGMA) clustering analyses show that the 84 plant samples could be divided into three clusters and natural populations from the 14 growing areas could be divided into two clusters. Clustering results of the populations were not affected by geographic distances, and gene flow occurred frequently among the populations, suggesting that the genetic variation among the natural populations of C. nitidissima var. phaeopubisperma from 14 growing areas was not influenced by environmental changes of these areas but mainly derived from the genetic variation present in pre-introduction populations. creator: Yang-Jiao Xie creator: Meng-Xue Su creator: Hui Gao creator: Guo-Yue Yan creator: Shuang-Shuang Li creator: Jin-Mei Chen creator: Yan-Yuan Bai creator: Jia-Gang Deng uri: https://doi.org/10.7717/peerj.18845 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al.