bluuebunny/crossref_metadata_2025_split huggingface dataset:
Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: Sex‐specificity and intergenerational stability
Authors: Venney Clare J. , Bouchard Raphaël , April Julien , Normandeau Eric , Lecomte Laurie , Côté Guillaume , Bernatchez Louis 
Published: February 2023

AbstractCaptive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery‐induced changes in DNA methylation is becoming abundant, though questions remain on the sex‐specificity of these effects, their persistence until spawning and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec, Canada. We identified two cohorts of hatchery‐reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex‐specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F0. There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex‐specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.
Feeding graded levels of dried Sea buckthorn (Hippophaes rhamnoides) berries to broiler chickens
Authors: Pirgozliev Vasil , Mansbridge Stephen C. , Whiting Izzy M. , Rose Stephen P. , Kljak Kristina , Johnson Amy E. , Drijfhout Falko , Orczewska‐Dudek Sylwia , Atanasov Atanas G. , Mihova Teodora 
Published: February 2023

AbstractThe aim of this study was to assess the effects of graded levels (0, 3, 6, 9 and 12 g/kg) of dry Sea buckthorn (SB) berries on growth performance, gastrointestinal tract (GIT) development, jejunal histomorphology, bird antioxidant status and caecal short‐chain fatty acid concentration when fed to female Ross 308 broiler chickens. In addition, expression of cytokine biomarker genes in the jejunum was evaluated. The five experimental diets were fed from 7 to 21 days age to 8 pens (two birds in each) following randomisation. Feeding SB did not influence bird growth performance (p > .05). There was a linear decrease in butyric, acetic and valeric acid concentrations in caecal digesta (p < .05) and a decrease (p < .05) in crypt depth. The expression of IFNG and CD40LG responded quadratically (p < .05), peaking at 6–9 g/kg dietary inclusion of SB, respectively. Other studied variables were not affected by dietary SB inclusion (p > .05). Feeding dry SB berries up to 12 g/kg of diet did not improve the zootechnical variables of healthy commercial‐strain broilers in this study.
The Tpl2‐MEK pathway plays a critical role in spheroid‐cultured endometriotic stromal cells
Authors: Minami Toshiyuki , Tsuzuki Yota , Tanaka Yukiko , Kitawaki Jo , Mori Taisuke 
Published: February 2023

AbstractProblemEndometriosis is a proliferative disease characterized by cytokine‐induced inflammation. The objective of this study was to assess cell growth and PGE2 production induced by TNF‐α in endometriotic stromal cells (ESCs) in spheroid cell culture and to identify the signaling pathway involved with a view to finding new therapeutic targets for endometriosis.Method of studyTissue samples were collected from patients with and without endometriosis. ESCs were isolated from ovarian endometrioma (OE). Gene expression was evaluated by real‐time PCR and DNA microarray analysis, the proliferative effect on ESCs by WST‐8 assay, and PGE2 production by ELISA. Protein phosphorylation was detected using western blotting.ResultsCOX‐2, aromatase and VEGFA mRNA expression and PGE2 production were significantly elevated in spheroid cell cultures compared to monolayer cell cultures. TNF‐α receptor (TNFR) 1 and TNFR2 mRNA was also significantly increased. TNF‐α promoted the proliferation and PGE2 production of ESCs in spheroid cell cultures significantly more than in monolayer cell cultures. TNF‐α increased the expression of several genes related to the pathophysiology of endometriosis in spheroid ESCs. DNA microarray analysis revealed that the Tpl2 gene, which codes for a MAPK upstream of MEK, was upregulated in OE and endometrium with endometriosis compared to normal endometrium. TNF‐α increased the phosphorylation and expression of Tpl2 and MEK, and Tpl2 and MEK inhibitors inhibited TNF‐α‐induced proliferation and PGE2 production in spheroid ESCs.ConclusionThe Tpl2‐MEK signaling pathway may play a critical role in the cell growth and PGE2 production induced by TNF‐α in spheroid ESCs.
Interaction alerts: A comparison of classifications and recommendations for clinical management between Janusmed and three other knowledge resources
Authors: Tukukino Carina , Eriksson Anna L. , Hamdan Walaa , Wallin Hybelius Frida , Wallerstedt Susanna M. 
Published: February 2023

AbstractClassifications of drug interaction alerts differ between knowledge resources, but agreement regarding recommendations for clinical management is less explored. Starting from the medication lists of 274 older patients with ≥2 drugs, all unique drug pairs that triggered a clinically significant interaction alert in Janusmed were included: 100 Category C (manageable by, e.g. dose adjustment) and nine Category D interactions (should be avoided). Out of 109 C/D alerts in Janusmed, 89 (82%), 75 (69%) and 45 (41%) drug pairs triggered an alert of similar clinical significance in Lexicomp, Micromedex® and Stockley's Drug Interactions/Checker (Stockley), respectively. Eight (7%), 20 (18%) and 10 (9%) drug pairs did not trigger any alert in these resources. For 81 (74%), 81 (74%) and 94 (86%) drug pairs, Lexicomp, Micromedex and Stockley provided at least one recommendation for clinical management similar to those provided by Janusmed. For 16 (15%), 9 (8%) and 21 (19%) drug pairs, these resources provided recommendation(s) entirely in agreement with Janusmed. Although many drug pairs elicit alerts of similar significance, and partly concordant recommendations, a non‐negligible proportion do not. The findings encourage medical/pharmaceutical reflection by prescribing clinicians and dispensing pharmacists; recommendations provided by knowledge resources vary considerably and cannot be considered definite.
Spatial genomic diversity associated with APOBEC mutagenesis in squamous cell carcinoma arising from ovarian teratoma
Authors: Tamura Ryo , Nakaoka Hirofumi , Yachida Nozomi , Ueda Haruka , Ishiguro Tatsuya , Motoyama Teiichi , Inoue Ituro , Enomoto Takayuki , Yoshihara Kosuke 
Published: February 2023

AbstractAlthough the gross and microscopic features of squamous cell carcinoma arising from ovarian mature cystic teratoma (MCT‐SCC) vary from case to case, the spatial spreading of genomic alterations within the tumor remains unclear. To clarify the spatial genomic diversity in MCT‐SCCs, we performed whole‐exome sequencing by collecting 16 samples from histologically different parts of two MCT‐SCCs. Both cases showed histological diversity within the tumors (case 1: nonkeratinizing and keratinizing SCC and case 2: nonkeratinizing SCC and anaplastic carcinoma) and had different somatic mutation profiles by histological findings. Mutation signature analysis revealed a significantly enriched apolipoprotein B mRNA editing enzyme catalytic subunit (APOBEC) signature at all sites. Intriguingly, the spread of genomic alterations within the tumor and the clonal evolution patterns from nonmalignant epithelium to cancer sites differed between cases. TP53 mutation and copy number alterations were widespread at all sites, including the nonmalignant epithelium, in case 1. Keratinizing and nonkeratinizing SCCs were differentiated by the occurrence of unique somatic mutations from a common ancestral clone. In contrast, the nonmalignant epithelium showed almost no somatic mutations in case 2. TP53 mutation and the copy number alteration similarities were observed only in nonkeratinizing SCC samples. Nonkeratinizing SCC and anaplastic carcinoma shared almost no somatic mutations, suggesting that each locally and independently arose in the MCT. We demonstrated that two MCT‐SCCs with different histologic findings were highly heterogeneous tumors with clearly different clones associated with APOBEC‐mediated mutagenesis, suggesting the importance of evaluating intratumor histological and genetic heterogeneity among multiple sites of MCT‐SCC.
Multifactorial glial responses and their contributions to Alzheimer's disease continuum
Authors: Hijioka Masanori , Manabe Tatsuya , Saito Takashi 
Published: February 2023

AbstractAlzheimer's disease (AD) is the most common neurocognitive disorder. Various factors are intricately intertwined before clinical symptoms appear, although both amyloid‐β peptide deposition and neurofibrillary tangle formation (i.e. pathological hallmarks of the AD brain) are established. Among such factors, glial responses have been increasingly recognized as important roles in the progression of these pathologies and viewed as one component of the AD continuum. However, the detailed molecular and cellular mechanisms of glial function underlying AD pathogenesis remain to be elucidated. Recent studies showed that peripheral immunity, gut microbiota or environmental factors influence brain pathophysiologies through communication with glial cells in the brain. This disease complexity makes understanding AD etiology difficult and hinders the development of effective therapeutic strategies to tackle this disease. Conversely, aged patients often suffer from multiple – not a single – diseases as multimorbidity, and AD pathogenesis might be related to pathologies caused by other diseases. Hence, investigating AD as a systemic disease has become critical for identifying therapeutic interventions. This review aimed to summarize current knowledge on AD research and share perspectives for understanding glial functions regarding AD pathophysiology.
Long‐term oncological outcomes for minimally invasive surgery versus open surgery for colon cancer—a population‐based nationwide study with a non‐inferiority design
Authors: Jadid Kaveh Dehlaghi , Cao Yang , Petersson Josefin , Sjövall Annika , Angenete Eva , Matthiessen Peter 
Published: February 2023

AbstractAimThe study aimed to compare 5‐year overall survival in a national cohort of patients undergoing curative abdominal resection for colon cancer by minimally invasive surgery (MIS) or by the open (OPEN) technique.MethodsAll patients diagnosed between 2010 and 2016 in Sweden with pathological Union International Contre le Cancer Stages I–III colon cancer localized in the caecum, ascending colon, hepatic flexure or sigmoid colon and those who underwent curative right sided hemicolectomy, sigmoid resection or high anterior resection by MIS or OPEN were included. Patients were identified in the Swedish Colorectal Cancer Registry from which all data were retrieved. The analyses were performed as intention‐to‐treat and the relationship between surgical technique (MIS or OPEN) and overall mortality within 5 years was analysed. For the primary research question a non‐inferiority hypothesis was assumed with a statistical power of 90%, a one‐side type I error of 2.5% and a non‐inferiority margin of 2%. For the secondary analyses, multilevel survival regression models with the patients matched by propensity scores were employed, adjusted for patient‐ and tumour‐related variables.ResultsA total of 11 605 pathological Union International Contre le Cancer Stages I–III patients were included with 3297 MIS (28.4%) and 8308 OPEN (71.6%) and were followed until 31 December 2020. The primary analysis demonstrated superiority for MIS compared to OPEN. The multilevel survival regression analyses confirmed that 5‐year overall survival was higher in MIS with a hazard ratio of 0.874 (95% confidence interval 0.791–0.965), and if excluding pT4 the outcome was similar, with a hazard ratio of 0.847 (95% confidence interval 0.756–0.948).ConclusionThis observational study demonstrated that MIS was favourable to OPEN with regard to 5‐year overall survival. These results support the use of laparoscopic colon cancer surgery in routine practice.
Diabetes distress mediates the relationship between depressive symptoms and glycaemic control among adults with type 2 diabetes: Findings from a multi‐site diabetes peer support intervention
Authors: Qian Yiqing , Emmerling Dane A. , Kowitt Sarah D. , Ayala Guadalupe X. , Cherrington Andrea L. , Heisler Michele , Safford Monika M. , Tang Tricia S. , Thom David H. , Fisher Edwin B. 
Published: February 2023

AbstractAimsDiabetes distress is positively associated with HbA1c and may mediate the relationship between depressive symptoms and HbA1c. This study examined these relationships in a geographically, socioeconomically, and ethnically diverse sample of adults with type 2 diabetes.MethodsUsing data from five US sites evaluating peer support for diabetes management (n = 917), Structural Equation Modeling (SEM) examined whether diabetes distress (four items from Diabetes Distress Scale) mediated the relationship between depressive symptoms (PHQ‐8) and HbA1c. Sites compared interventions of varying content and duration with control conditions. Time from Baseline Assessment to Final Assessment varied from six to 18 months. Site characteristics were controlled by entering site as a covariate along with age, sex, education, diabetes duration, insulin use, and intervention/control assignment.ResultsDepressive symptoms, diabetes distress, and HbA1c were all intercorrelated cross‐sectionally and from Baseline to Final Assessment (rs from 0.10 to 0.57; ps <0.05). In SEM analyses, diabetes distress at Final Assessment mediated the relationship between Baseline depressive symptoms and HbA1c at Final Assessment (indirect effect: b = 0.031, p < 0.001), controlling for Baseline HbA1c and covariates. Parallel analysis of whether depressive symptoms mediated the relationship between Baseline diabetes distress and HbA1c at Final Assessment was not significant.ConclusionsIn this diverse sample, diabetes distress mediated the influence of depressive symptoms on HbA1c but the reverse, depressive symptoms mediating the effect of distress, was not found. These findings add to the evidence that diabetes distress is a worthy intervention target to improve clinical status and quality of life among individuals with type 2 diabetes.
A systematic comparison ofpan‐Trkimmunohistochemistry assays among multiple cancer types
Authors: Haberecker Martina , Töpfer Antonia , Melega Francesca , Moch Holger , Pauli Chantal 
Published: February 2023

AimsNTRK rearranged tumours are rare but can be successfully treated using anti‐TRK‐targeted therapies, making NTRK testing important for treatment choices in patients with advanced cancers. Pan‐Trk immunohistochemistry (IHC) has become a valuable and affordable screening tool in many laboratories. Unfortunately, the choice of antibodies and IHC protocols to investigate biomarkers is not standardised. In this study, we compared the performance of four pan‐Trk IHC methods, using three different clones, primarily in NTRK fusion‐positive tumours.Methods and resultsWe studied the performance of four pan‐Trk IHC methods using three different clones: EPR17341 (Abcam and Ventana), EP1058Y (Abcam) and A7H6R (Cell Signaling) in 22 molecularly confirmed NTRK rearranged tumours. Additionally, selected NTRK fusion‐negative tumours were further included: NTRK mutated (n = 8) and amplified (n = 15) tumours as well as NTRK fusion‐negative tumours driven by other gene fusions, such as ALK, ROS1 and BCOR (n = 20), as well as salivary gland tumours (n = 16). Inter‐rater agreement of three pathologists was additionally calculated, including H‐score. With clone EPR17341 (Abcam in‐house and ready‐to‐use Ventana protocol), all molecularly confirmed NTRK1–3 rearranged tumours were positively detected by immunohistochemistry, while the other clones missed NTRK2–3 rearranged tumours. For the fusion‐negative cohort we found the best performance (least false‐positive cases) using the clone A7H6R (Cell Signalling).ConclusionGiven the therapeutic importance, testing for NTRK rearrangements in daily practice has become necessary and, despite IHC being a fast and affordable tool, using it in routine diagnostics is complicated and requires a high level of expertise.
Seasonality in niche occupation revealed through bird community functional structure in the southern Atlantic rainforest
Authors: Almeida Bia A. , Bochio Gabriela M. , Calsavara Larissa C. , Marques Fernanda C. , dos Anjos Luiz 
Published: February 2023

Seasonal variation in tropical and subtropical systems can have different effects on bird species depending on the resources they use and how they use them. However, despite recent research advances, knowledge of the drivers of the presence and abundance of species in different seasons is still limited for most tropical bird species. In these poorly understood systems, examining seasonal changes in species composition from the perspective of traits related to resource use can provide insight into what resources may be driving bird movements between areas throughout the year and what types of species are more subject to seasonality. Here, we explore bird community seasonality in three forest types (dense, semi‐deciduous and mixed rainforests) subjected to different climatic conditions in one of the world's biodiversity hotspots, the Atlantic Rainforest. We investigated differences between summer and winter in species richness and in the composition of resource‐related species traits (diet, foraging strata and substrates) obtained from the literature. The seasonal differences (summer and winter) between forest types were explored in terms of species and trait composition. We found that the main changes that occurred in bird composition between seasons in the southern Atlantic Rainforest were related to species traits such as diet and foraging strata. In general, the proportion of invertivores was higher in winter than in summer, and in the mixed forest, the forest type exposed to the coldest winters, the proportion of frugivores was lower in winter. Furthermore, species with a more varied diet were better represented in the summer. In general, more generalist species were better represented in the forest type subjected to higher seasonal variations in rainfall. Our results revealed seasonal changes in bird community structure that are related to niche occupation and that were more strongly apparent in the forest type subjected to colder winters.
RETRACTED: A systematic review of life satisfaction and related factors among burns patients
Authors: Parvizi Arman , Haddadi Soudabeh , Ghorbani Vajargah Pooyan , Mollaei Amirabbas , Firooz Mahbobeh , Hosseini Seyed Javad , Takasi Poorya , Farzan Ramyar , Karkhah Samad 
Published: February 2023

AbstractThis systematic review aimed to examine the life satisfaction and related factors among burns patients. A comprehensive systematic search was conducted at the international electronic databases such as Scopus, PubMed, Web of Science, and Persian electronic databases such as Iranmedex, and Scientific Information Database using keywords extracted from Medical Subject Headings such as ‘Burns’, ‘Life satisfaction’, ‘Personal satisfaction’, and ‘Patient satisfaction’ from the earliest to the 1 October 2022. The quality of the studies included in this review was evaluated using the appraisal tool for cross‐sectional studies (AXIS tool). A total of 3352 burn patients in the nine cross‐sectional studies were included in this systematic review. 70.52% of burn patients were male. The mean age of burn patients was 37.47 (SD = 14.73). The mean score of life satisfaction in burn patients based on SWLS was 23.02 (SD = 7.86) out of 35, based on LSI‐A was 12.67 (SD = 4.99) out of 20, and based on the life satisfaction questionnaire was 4.81 (SD = 1.67) out of 7. Factors including time since burn, religion, and constant had a positive and significant relationship with life satisfaction in burn patients. Whereas, factors such as single marital status, age at injury, length of hospital stay, presence of pain, larger total body surface area burn, head and neck burn, functional impairment, family satisfaction, satisfaction with appearance, and previous psychiatric treatment had a negative and significant relationship with life satisfaction in burn patients. In sum, this systematic review showed that burn patients were slightly satisfied with their life. Therefore, health managers and policymakers can improve the quality of life of burn victims by planning psychological counselling and behavioural therapy, and consequently increase their life satisfaction.
Nondestructive detection of adulterated wolfberry (Lycium Chinense) fruits based on hyperspectral imaging technology
Authors: Nirere Adria , Sun Jun , Kama Rakhwe , Atindana Vincent Akolbire , Nikubwimana Felix Didier , Dusabe Keza Dominique , Zhong Yuhao 
Published: February 2023

AbstractIn order to detect adulterants on Lycium Chinense species effectively, a rapid, clean, and nondestructive detection method based on hyperspectral imaging (HSI) technology was conducted in a wavelength range of 400.68–1001.60 nm. Industrial sulfur particles were chosen as a dye to prepare three groups of adulterated L. Chinense samples as the research object. The whole L. Chinense was considered the region of interest. First, a multiple scatter correction (MSC) method was used to preprocess spectra data. The competitive adaptive reweighted sampling (CARS) and linear discriminant analysis approaches were contrasted for optimal extraction of wavelengths characteristic. Then, two models were established: K‐nearest neighbor (KNN) and support vector machine (SVM). Furthermore, the performance accuracies of KNN and SVM models were compared. According to the outcomes, the SVM model built on CARS provided the best classification impact. The accuracy for the prediction set was 98.75%, and the accuracy for the training set was 100%. Also, the kernel parameters c and g of the SVM model were enhanced by genetic algorithm (GA) optimization. The values parameters (c, g) were set at 14.975 and 0.224, respectively, and the results improved by 1.25% at an elapsed time of 1.887 s, with the accuracy reaching 100% on both training and test sets. This study aimed to detect and classify sulfur‐adulterated wolfberries using an improved SVM and HSI. Finally, the results demonstrate that a combination of HSI and the CARS‐GA‐SVM model could be used for the rapid detection of foreign entities' in wolfberry fruits.Practical applicationsDried wolfberry adulteration has a direct link to the overall quality of the fruits, and potentially compromises the health of the fruits consumers. The traditional methods of testing adulterants on Lycium Chinense are arduous, require a lot of time, and are highly impacted by biased elements, necessitating new techniques. HSI technology, on the other hand, is nondestructive, quick/fast, accurate, subjective, reproducible, and pollution‐free. The study findings proved to be recommendable for initiating a feasible mobile system for rapidly detecting adulteration on L. Chinense.