bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread gene flow following range expansion in Anna's Hummingbird
Authors: Adams Nicole E. , Bandivadekar Ruta R. , Battey C. J. , Clark Michael W. , Epperly Kevin , Ruegg Kristen , Tell Lisa A. , Bay Rachael A. 
Published: March 2023

AbstractAnthropogenic changes have altered the historical distributions of many North American taxa. As environments shift, ecological and evolutionary processes can combine in complex ways to either stimulate or inhibit range expansion. Here, we examined the role of evolution in a rapid range expansion whose ecological context has been well‐documented, Anna's Hummingbird (Calypte anna). Previous studies have suggested that theC. annarange expansion is the result of an ecological release facilitated by human‐mediated environmental changes, where access to new food sources have allowed further filling of the abiotic niche. We examined the role of gene flow and adaptation during range expansion from their native California breeding range, north into Canada and east into New Mexico and Texas, USA. Using low coverage whole genome sequencing we found high genetic diversity, low divergence, and little evidence of selection on the northern and eastern expansion fronts. Additionally, there are no clear barriers to gene flow across the native and expanded range. The lack of selective signals between core and expanded ranges could reflect (i) an absence of novel selection pressure in the expanded range (supporting the ecological release hypothesis), (ii) swamping of adaptive variation due to high gene flow, or (iii) limitations of genome scans for detecting small shifts in allele frequencies across many loci. Nevertheless, our results provide an example where strong selection is not apparent during a rapid, contemporary range shift.
Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species
Authors: Dantas‐Queiroz Marcos Vinicius , Hurbath Fernanda , de Russo Godoy Fernanda Maria , Lanna Flávia Mol , Versieux Leonardo M. , Palma‐Silva Clarisse 
Published: March 2023

AbstractMountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.
Mathematical pluralism
Authors: Zalta Edward N. 
Published: March 2023

AbstractMathematical pluralism can take one of three forms: (1) every consistent mathematical theory consists of truths about its own domain of individuals and relations; (2) every mathematical theory, consistent or inconsistent, consists of truths about its own (possibly uninteresting) domain of individuals and relations; and (3) the principal philosophies of mathematics are each based upon an insight or truth about the nature of mathematics that can be validated. (1) includes the multiverse approach to set theory. (2) helps us to understand the significance of the distinguished non‐logical individual and relation terms of even inconsistent theories. (3) is a metaphilosophical form of mathematical pluralism and hasn't been discussed in the literature. In what follows, I show how the analysis of theoretical mathematics in object theory exhibits all three forms of mathematical pluralism.
Tet methylcytosine dioxygenase 1 modulates Porphyromonas gingivalis–triggered pyroptosis by regulating glycolysis in cementoblasts
Authors: Peng Yan , Wang Huiyi , Huang Xin , Liu Heyu , Xiao Junhong , Wang Chuan , Ma Li , Wang Xiaoxuan , Cao Zhengguo 
Published: March 2023

AbstractPorphyromonas gingivalis is involved in the pathogenesis of multiple polymicrobial biofilm–induced inflammatory diseases, including apical periodontitis, and it triggers pyroptosis accompanied by robust inflammatory responses. Tet methylcytosine dioxygenase 1 (TET1), an epigenetic modifier enzyme, has been is correlated with inflammation, though an association of TET1 and P. gingivalis–related pyroptosis in cementoblasts and the molecular mechanisms has not been shown. Our study here demonstrated that P. gingivalis downregulated Tet1 expression and elicited CASP11‐ and GSDMD‐dependent pyroptosis. Additionally, Tet1 mRNA silencing in cementoblasts appeared to result in a more severe pyroptotic phenotype, where levels of CASP11 and GSDMD cleavage, lactate dehydrogenase release, and IL‐1β and IL‐18 production were significantly increased. Moreover, Tet1 overexpression resulted in blockade of pyroptosis activation accompanied by inflammation moderation. Further analyses revealed that TET1 modulated glycolysis, confirmed by the application of the specific inhibitor 2‐deoxy‐d‐glucose (2‐DG). The pyroptosis phenotype enhanced by Tet1 silencing was moderated by 2‐DG upon P. gingivalis invasion. Taken together, these data show the effects and underlying mechanisms of TET1 on pyroptosis and inflammatory phenotype induced by P. gingivalis in cementoblasts, and provides insight into the involvement of P. gingivalis in apical periodontitis and, possibly, other inflammatory diseases.
Stenomitos terricola sp. nov. (Leptolyngbyaceae, Cyanobacteria) from the moist soil of Mt. Gwanggyo, Republic of Korea
Authors: Lee Nam‐Ju , Kim Do‐Hyun , Lee Ok‐Min 
Published: March 2023

SUMMARYStenomitos terricola FBCC‐A190 was collected from soils around the trees of Mt. Gwanggyo, located in Yeongtong‐gu, Suwon‐si, Gyeonggi‐do. S. terricola FBCC‐A190 is a thin and simple filament with a cell length that is longer than its width. It has a thin and firm sheath, exhibiting a blue‐green color. Species belonging to genus Stenomitos is semi‐cryptic species with slight morphological differences from each other. They were confirmed as Stenomitos species by analysis using 16S rRNA and 16S–23S ITS. A monophyletic cluster was formed with the previously reported genus Stenomitos, with 16S rRNA gene sequences sharing similarities of 95.9–97.9% except for S. pantisii TAU‐MAC 4318. In addition, 16S–23S ITS gene sequencing showed tRNAAla, tRNAIle and V2, similar to the previously reported genus Stenomitos. From these results, Stenomitos terricola sp. nov. was proposed as a new species belonging to genus Stenomitos.
The relationship between Th1/Th2 cytokine polarization and milk composition in the postnatal period in Kyrgyz mares and foals
Authors: Istanbullugil Fatih R. , Risvanli Ali , Salikov Ruslan , Bayraktar Metin , Kadiraliyeva Nariste , Zhunushova Aidai , Yilmaz Oznur , Yuksel Burak F. , Turanli Mert , Uz Muhammet , Asinbekovic Mirbek I. 
Published: March 2023

AbstractImmune compatibility between mare and foal is one of the important topics of reproductive immunology. At this point, although there are many studies on antibodies, there are not many publications on the relationship between the cytokine levels of mare, foal and milk and the effects of milk composition on this relationship. Here we investigate the relationship between Th1/Th2 cytokine balance and milk composition in Kyrgyz mares and foals. Samples were taken soon after the foal was born and on days 5, 10 and 20 after birth. Th1 (IFN‐γ, IL‐2, TNF‐α) and Th2 (IL‐4, IL‐5, IL‐10) cytokine levels in blood samples were measured using a commercial ELISA kit. Dry matter, fat, protein and non‐fat dry matter ratios were determined in the mare's milk and colostrum. We detected no Th1/Th2 polarization in the mare's milk on the day of the foal's birth (day 0) and day 10, but there was Th1 polarization on day 5 and Th2 cytokine polarization on day 20. There was no polarization in the blood sera of the mares on days 0, 5, and 10, and Th1 cytokine polarization was also detected on day 20. We detected no Th1/Th2 cytokine polarization in the blood sera of the foals on any of the days. Dry matter (19.66 ± 0.39%), protein (16.56 ± 0.18%), fat (2.13 ± 0.17), and non‐fat dry matter (17.59 ± 0.44%) were higher in colostrum than the other days. When the correlations between cytokine levels in milk samples and milk composition were examined, there was a positive correlation between IL‐5 level and protein ratio on day 10. We detected a positive correlation between IL‐2 level and the fat rate on day 20. There was a positive correlation between the IL‐2 level and the non‐fat dry matter ratio on day 20. Further studies are now needed to determine the relationship between the changes in the composition of mare's milk in the postnatal period and Th1/Th2 cytokine polarization in mares and foals at the time of birth and in the postnatal period. Our finding that protein and fat ratios in mare's milk in the postnatal period are positively correlated with IL‐2 levels should be considered in terms of foal and human nutrition.
High preoperative bradykinin level is a risk factor for severe postoperative hypoxaemia in acute aortic dissection surgery
Authors: Guan XinLiang , Li Lei , Li JinZhang , Jiang WenJian , Li HaiYang , Wang XiaoLong , Han Lu , Liu YuYong , Gong Ming , Zhang HongJia 
Published: March 2023

AbstractSevere hypoxaemia after cardiac surgery is associated with serious complications and a high risk of mortality. The purpose of this study is to investigate the independent risk factors of severe postoperative hypoxaemia in patients with acute Stanford type A aortic dissection. We collected 77 patients with acute Stanford type A aortic dissection who underwent surgical treatment. The primary outcome was severe postoperative hypoxaemia (PaO2/FiO2 ≤ 100 mmHg), and a multivariate logistic regression analysis was performed to assess the independent predictors of risk for this. A mixed‐effects analysis of variance model and a receiver operating characteristic (ROC) curve were generated to evaluate the predictive probabilities of risk factors for severe postoperative hypoxaemia. A total of 36.4% of patients developed severe postoperative hypoxaemia. The multivariate logistic regression analysis identified high preoperative bradykinin level (odds ratio (OR) = 55.918, P < 0.001) and increased body mass index (BMI; OR = 1.292, P = 0.032) as independent predictors of severe postoperative hypoxaemia in patients with acute Stanford type A aortic dissection. The mixed‐effect analysis of variance model and ROC curve indicated that high preoperative bradykinin level and BMI were significant predictors of severe postoperative hypoxaemia (area under the ROC curve = 0.834 and 0.764, respectively). High preoperative bradykinin levels and obesity were independent risk factors for severe postoperative hypoxaemia in patients with acute Stanford type A aortic dissection. For obese patients with high levels of bradykinin before surgery, clinicians should actively take measures to block bradykinin‐mediated inflammatory reactions.
Systemic sclerosis following COVID-19 infection with recurrent corticosteroid-induced scleroderma renal crisis
Authors: Carroll Mitchell , Nagarajah Vanitha , Campbell Sian 
Published: March 2023

Systemic sclerosis is a complex multisystem connective tissue disease resulting in fibrosis of the skin and internal organs. Exposure to corticosteroids can trigger scleroderma renal crisis, a life-threatening complication of the disease. Autoimmune disease following infection with COVID-19 is being increasingly recognised. The mechanisms of post-COVID-19 autoimmunity are likely multifactorial, involving immune dysregulation, molecular mimicry and the development of cross-reactive antibodies. There are currently only two reported cases of systemic sclerosis occurring post-COVID-19 infection.We present the case of a female patient who developed systemic sclerosis post-COVID-19 infection. Following exposure to corticosteroids, the patient developed scleroderma renal crisis complicated by thrombotic microangiopathy, seizures and acute renal failure. Despite an antibody profile not typically associated with renal crisis (anti-topoisomerase positive, anti-RNA-polymerase III negative), the patient developed recurrent renal crisis with repeated exposure to corticosteroid therapy, highlighting the risk of steroid use in all patients with systemic sclerosis.
Fundus topographical distribution patterns of ocular toxoplasmosis
Authors: Hasanreisoglu Murat , Halim Muhammad Sohail , Cakar Ozdal Pinar , Ormaechea Maria Soledad , Kesim Cem , Ozdemir Huseyin Baran , Uludag Gunay , Sredar Nripun , Cankurtaran Mahmut , Liu Xiaoxuan , Denniston Alastair Keith , Rudzinski Marcelo N. , Colombero Daniel N. , Schlaen Bernardo Ariel , Keane Pearse Andrew , Pavesio Carlos , Nguyen Quan Dong 
Published: March 2023

BackgroundTo establish topographic maps and determine fundus distribution patterns of ocular toxoplasmosis (OT) lesions.MethodsIn this retrospective study, patients who presented with OT to ophthalmology clinics from four countries (Argentina, Turkey, UK, USA) were included. Size, shape and location of primary (1°)/recurrent (2°) and active/inactive lesions were converted into a two-dimensional retinal chart by a retinal drawing software. A final contour map of the merged image charts was then created using a custom Matlab programme. Descriptive analyses were performed.Results984 lesions in 514 eyes of 464 subjects (53% women) were included. Mean area of all 1° and 2° lesions was 5.96±12.26 and 5.21±12.77 mm2, respectively. For the subset group lesions (eyes with both 1° and 2° lesions), 1° lesions were significantly larger than 2° lesions (5.52±6.04 mm2vs 4.09±8.90 mm2, p=0.038). Mean distances from foveola to 1° and 2° lesion centres were 6336±4267 and 5763±3491 µm, respectively. The majority of lesions were found in temporal quadrant (p<0.001). Maximum overlap of all lesions was at 278 µm inferotemporal to foveola.ConclusionThe 1° lesions were larger than 2° lesions. The 2° lesions were not significantly closer to fovea than 1° lesions. Temporal quadrant and macular region were found to be densely affected underlining the vision threatening nature of the disease.
Correlating somatic copy number alteration in aqueous humour cfDNA with chemotherapy history, eye salvage and pathological features in retinoblastoma
Authors: Luo Yingxiu , Xu Mingpeng , Yang Ludi , Yao Yiran , Berry Jesse L , Xu Liya , Wen Xuyang , He Xiaoyu , Han Minglei , Fan Xianqun , Fan Jiayan , Jia Renbing 
Published: March 2023

BackgroundThis study determined to probe the potential association between somatic copy number alteration (SCNA) in retinoblastoma (RB) aqueous humour (AH) and pathological high-risk factors, clinical features and previous chemotherapy history.MethodsSingle-centre retrospective cohort study from including 58 AH samples collected from 58 patients diagnosed. Among them, 41 samples were collected after enucleation and 17 samples were collected before intravitreal chemotherapy. SCNAs were accessed by conducting shallow whole-genome sequencing in cell-free (cf) DNA of AH. HRs and ORs were applied to measure risk factors.ResultsCanonical RB SCNAs including 1q gain (87%), 2p gain (50%), 6p gain (76%), 16q loss (69%) were frequently detected. Non-classical RB SCNAs in AH including 17q gain (53%), 19q loss (43%), 7q gain (35%) were also commonly observed. 19q loss was significantly more common in patients with cT3c or worse stage than others (p=0.034). 2p gain(p=0.001) and 7q gain(p=0.001) were both more common in patients with primary enucleation than those with previous chemotherapy. Interestingly, both 2p gain (HR=1.933, p=0.027) and 7q gain (HR=2.394, p=0.005) might predict enucleation. Correlation analysis with pathological features among enucleated eyes showed that 19q loss can predict a higher risk for both massive choroid invasion (OR=4.909, p=0.038) and postlaminar optic nerve invasion (OR=4.250, p=0.043).DiscussionSequencing of AH cfDNA in RB can provide sufficient in vivo information. 19q loss was a potential signature of advanced cases clinically and pathologically.Repeated sampling from eyes receiving sequential chemotherapy should be conducted to evaluate fluctuation of SCNA in future study.
Association between tea consumption and glucose metabolism and insulin secretion in the Shanghai High-risk Diabetic Screen (SHiDS) study
Authors: Zhang Yinan , Bian Zhouliang , Lu Huijuan , Wang Lili , Xu Jinfang , Wang Congrong 
Published: March 2023

IntroductionThe relationship between tea consumption and glucose metabolism remains controversial. This study investigated the associations of tea consumption with impaired glucose regulation, insulin secretion and sensitivity in Shanghai High-risk Diabetic Screen project.Research design and methodsA total of 2337 Chinese subjects were enrolled in the study from 2014 to 2019. Each participant conducted a 75 g oral glucose tolerance test (OGTT) with five-point glucose and insulin level examined. They also completed a nurse-administered standard questionnaire including tea, coffee, and alcohol consumption, smoking habit, physical activity, education, sleep quality, etc.ResultsThe result showed that tea consumption was positively associated with plasma glucose levels during OGTT after adjusting for confounder (Ps <0.05) and was associated with worsening glucose tolerance (OR 1.21, 95% CI 1.01–1.44; p=0.034). Strong tea consumption or long-term tea intake (>10 years) had an increased risk of glucose intolerance (all p<0.05). These associations did not vary in participants drinking green tea. In addition, insulin secretion indexes were decreased 7.0%–13.0% in tea consumption group. Logistic regression analysis showed that tea consumption was independently associated with lower insulin secretion (homeostasis model assessment of β-cell function (HOMA-β) (OR 0.81, 95% CI 0.68–0.97; p=0.021); Stumvoll first-phase index (OR 0.81, 95% CI 0.68–0.97; p=0.020)) in a fully adjusted model. Green tea consumption showed a negative association with insulin secretion (HOMA-β (OR 0.77, 95% CI 0.62–0.96; p=0.019)).ConclusionsTea intake is associated with an increased risk of glucose intolerance in a large high-risk diabetic Chinese population. Habitual tea consumption subjects might have lower pancreatic β-cell function.
Primary placement of low-profile or ‘button’ versus traditional balloon-retention radiologically inserted gastrostomy catheters in adults: a retrospective review
Authors: Al-Balas Hassan , Metwalli Zeyad , Burney Iftikhar , Sada David 
Published: March 2023

ObjectiveDe novo percutaneous placement of radiologically inserted low-profile or ‘button-type’ gastrostomy catheters (LPG) is infrequently reported in adults. This study compares the safety and clinical outcomes of primary percutaneous placement of LPG catheters and traditional balloon-retention gastrostomy catheters (TG) using image guidance at a single institution.DesignThis was a retrospective, single-institution review comparing initial LPG and TG radiologically inserted catheter placements in a 36-month time period. The age, gender, indication, catheter type and method of anaesthesia of 139 consecutive initial gastrostomy placement procedures were recorded. Total catheter days without intervention, major and minor complications, reasons for reintervention, and procedure fluoroscopy times were compared.ResultsDuring the 36-month study period, 61 LPG and 78 TG catheters were placed. Mean total catheter days prior to intervention was 137 days in the LPG group and 128 days in the TG group (p=0.70). Minor complications including cellulitis, pericatheter leakage and early catheter occlusion occurred in 4.9% (3/61) in the LPG group and 9% (7/78) in the TG group (p=0.5). Major complications including early catheter dislodgement and bleeding requiring transfusion (in one patient) occurred in 4.9% (3/61) in the LPG group and 7.7% (6/78) in the TG group (p=0.4). Procedure fluoroscopy time was lower in the LPG group (2.56 min) compared with the TG group (4.21 min) (p<0.005).ConclusionPrimary placement of low-profile or ‘button-type’ gastrostomy catheters is technically feasible with a low complication rate similar to that of traditional radiologically inserted gastrostomy catheters.
Time trends in health-related quality of life assessment and reporting within publications of oncology randomised phase III trials: a meta-research study
Authors: Marandino Laura , Trastu Federica , Ghisoni Eleonora , Lombardi Pasquale , Mariniello Annapaola , Reale Maria Lucia , Aimar Giacomo , Audisio Marco , Bungaro Maristella , Caglio Andrea , Di Liello Raimondo , Gamba Teresa , Gargiulo Piera , Paratore Chiara , Rossi Alessandro , Tuninetti Valentina , Turco Fabio , Perrone Francesco , Di Maio Massimo 
Published: March 2023

ObjectiveTo assess time trends in the inclusion of health-related quality of life (QoL) among study endpoints and in the reporting of QoL results in study publications, randomised phase III oncology trials published between 2017 and 2021 were compared with the trials published in the previous 5 years.Methods and analysisAll issues published between 2012 and 2021 by 11 major journals were handsearched for primary publications of phase III trials in adult patients with solid tumours. Trials published in 2017–2021 were compared with trials published in 2012–2016 for three endpoints: (1) proportion of publications including QoL among endpoints out of all the eligible publications; (2) proportion of publications presenting QoL results out of those including QoL among endpoints and (3) proportion of publications presenting QoL data out of all the eligible publications.Results388 publications between 2017 and 2021 were eligible and compared with 446 publications between 2012 and 2016. QoL was included among endpoints in 67.8% of trials in 2017–2021 vs 52.9% in 2012–2016 (univariate OR 1.87, 95% CI 1.41 to 2.48, p<0.001). QoL results were available in 52.1% in 2017–2021 vs 62.3% in 2012–2016 of primary publications of trials including QoL among endpoints (OR 0.66, 95% CI 0.46 to 0.94, p=0.02). Overall, QoL was analysed and presented in 35.3% of primary publications in 2017–2021 vs 33.0% in 2012–2016 (OR 1.11, 95% CI 0.83 to 1.48, p=0.48).ConclusionsThe proportion of oncology trials including QoL among endpoints increased in 2017–2021 compared with 2012–2016. However, the proportion of primary publications reporting QoL results remains suboptimal.