bluuebunny/crossref_metadata_2025_split huggingface dataset:
C5L2 modulates BDNF production in human dental pulp stem cells via p38α pathway
Authors: Irfan Muhammad , Chung Seung 
Published: January 2023

AbstractTissue injury affects nerve fibers and triggers an immune response, leading to inflammation. The complement system gets activated during inflammatory conditions and has been reported to be involved in the regeneration process. We have demonstrated that the C5a receptor (C5aR) has crucial roles in regeneration and healing processes including nerve sprouting and hard tissue formation. Another C5a-like 2 receptor (C5AR2; C5L2) has been cloned which is still considered controversial due to limited studies. We previously established that C5L2 regulates brain-derived neurotrophic factor (BDNF) secretion in pulp fibroblasts. However, there is no study available on human dental pulp stem cells (DPSCs), especially in the inflammatory context. Stem cell therapy is an emerging technique to treat and prevent several diseases. DPSCs are a great option to be considered due to their great ability to differentiate into a variety of cells and secrete nerve regeneration factors. Here, we demonstrated that C5L2 modulates BDNF secretion in DPSCs. Our results stated that C5L2 silencing through siRNA could increase BDNF production, which could accelerate the nerve regeneration process. Moreover, stimulation with lipopolysaccharide (LPS) enhanced BDNF production in C5L2 silenced DPSCs. Finally, we quantified BDNF secretion in supernatant and cell lysates using ELISA. Our results showed enhanced BDNF production in C5L2 silenced DPSCs and hampered by the p38MAPKα inhibitor. Taken together, our data reveal that C5L2 modulates BDNF production in DPSCs via the p38MAPKα pathway.
Ein steiniger Weg – Komplikationen eines verlorenen Gallensteins
Authors: Ponse Dikyi Joyce , Classen Martina Heim , Jeker Raphael 
Published: January 2023

Zusammenfassung
Anamnese Ein 88-jähriger Patient stellte sich mit seit mehr als 4 Monaten dauerndem wiederkehrendem Fieber, Schwäche und Übelkeit ohne Erbrechen vor. Mehrere Krankenhausaufenthalte folgten, aber der Grund dafür blieb unklar. 11 Jahre zuvor war eine laparoskopische Cholezystektomie erfolgt.
Untersuchung Laborchemisch zeigten sich eine Leukozytose und erhöhtes C-reaktives Protein. Die CT-Untersuchung des Abdomens ergab einen grossen Abszess, der von der intraabdominalen Höhle bis zum Subkutangewebe nahe der Lendenwirbelsäule L2 bis L5 reichte.
Diagnose Vermutet wurde ein intraperitonealer Abszess im Rahmen eines verlorenen Gallensteins bei der Cholezystektomie vor 11 Jahren.
Therapie und Verlauf Der Patient wurde operiert und mit Antibiotika behandelt. Postoperativ erlitt er ein Delir. Nach längerer sekundärer Wundheilung und Antibiotikatherapie war der Patient infektfrei und konnte nach einer Rehabilitation nach Hause entlassen werden.
Folgerung Die Diagnosestellung wurde durch die für geriatrische Patienten häufig atypische Klinik erschwert. Diagnostische Verzögerungen und rezidivierende Hospitalisierungen erhöhen das Morbiditäts- und Letalitätsrisiko. Obwohl der Gallenstein nie geborgen werden konnte, war eine andere Ursache seiner Beschwerden unwahrscheinlich, zumal der Patient seitdem infektfrei blieb.
Treatment Outcomes of Adenoid Cystic Carcinomas of the Head and Neck Region—A Single-Institution Experience
Authors: Rafi Malu , Kumar Rejnish , Thomas Kainickal Cessal , George Nebu Abraham , George Preethi Sara , Ramadas Kunnambath 
Published: January 2023

Objectives This study was undertaken to evaluate the characteristics and treatment outcomes of patients with adenoid cystic carcinomas of the head and neck region treated at a tertiary cancer center in south India.
Materials and Methods This was a retrospective study done on patients treated at the institute between 2004 and 2011. Clinicopathological details and treatment outcomes were captured from the treatment records to estimate the treatment outcomes and factors affecting them.
Results There were a total of 140 patients with mean age of presentation of 46 years and a median follow-up of 65 months. The most common single site of presentation was the oral cavity. One-hundred eighteen patients (84.3%) underwent primary surgical resection in which 38% had negative surgical margins. Ninety-nine patients were given adjuvant radiotherapy and 18 patients received radical radiotherapy, mostly for surgically inaccessible and inoperable tumors.Median time to recurrence and distant metastasis was 37 and 34 months, respectively. The overall survival and disease-free survival estimate using the Kaplan–Meier method were 92.3 and 71.9%, respectively, at 5 years. Surgical removal of the primary tumor and the nodal stage had the most significant impact on the overall survival outcomes of these patients.
Conclusion Surgery remains the most impactful treatment modality in the management of these rare epithelial tumors. The use of adjuvant radiotherapy may help to tackle the issues of perineural spread and inadequate surgical margins in technically difficult sites. Radical radiotherapy also has impressive response rates.
The Effect of Protease-Activated Receptor-1 (PAR-1) Inhibition on Endothelial-Related Biomarkers in Patients with Coronary Artery Disease
Authors: Nilsen Dennis W. T. , Røysland Michelle , Ueland Thor , Aukrust Pål , Michelsen Annika E. , Staines Harry , Barvik Ståle , Kontny Frederic , Nordrehaug Jan Erik , Bonarjee Vernon V. S. 
Published: January 2023

Background Vorapaxar has been shown to reduce cardiovascular mortality in post-myocardial infarction (MI) patients. Pharmacodynamic biomarker research related to protease-activated receptor-1 (PAR-1) inhibition with vorapaxar in humans has short follow-up (FU) duration and is mainly focused on platelets rather than endothelial cells.Aim This article assesses systemic changes in endothelial-related biomarkers during vorapaxar treatment compared with placebo at 30 days' FU and beyond, in patients with coronary heart disease.Methods Local substudy patients in Norway were included consecutively from two randomized controlled trials; post-MI subjects from TRA2P-TIMI 50 and non-ST-segment elevation MI (NSTEMI) patients from TRACER. Aliquots of citrated blood were stored at –80°C. Angiopoietin-2, angiopoietin-like 4, vascular endothelial growth factor, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, E-selectin, von Willebrand factor, thrombomodulin, and plasminogen activator inhibitor-1 and -2 were measured at 1-month FU and at study completion (median 2.3 years for pooled patients).Results A total of 265 consecutive patients (age median 62.0, males 83%) were included. Biomarkers were available at both FUs in 221 subjects. In the total population, angiopoietin-2 increased in patients on vorapaxar as compared with placebo at 1-month FU (p = 0.034). Angiopoietin-like 4 increased (p = 0.028) and plasminogen activator inhibitor-2 decreased (p = 0.025) in favor of vorapaxar at final FU. In post-MI subjects, a short-term increase in E-selectin favoring vorapaxar was observed, p = 0.029. Also, a short-term increase in von Willebrand factor (p = 0.032) favoring vorapaxar was noted in NSTEMI patients.Conclusion Significant endothelial biomarker changes during PAR-1 inhibition were observed in post-MI and NSTEMI patients.
Prediction of antibody binding to SARS-CoV-2 RBDs
Authors: Wang Eric 
Published: January 2023

AbstractSummaryThe ability to predict antibody–antigen binding is essential for computational models of antibody affinity maturation and protein design. While most models aim to predict binding for arbitrary antigens and antibodies, the global impact of SARS-CoV-2 on public health and the availability of associated data suggest that a SARS-CoV-2-specific model would be highly beneficial. In this work, we present a neural network model, trained on ∼315 000 datapoints from deep mutational scanning experiments, that predicts escape fractions of SARS-CoV-2 RBDs binding to arbitrary antibodies. The antibody embeddings within the model constitute an effective sequence space, which correlates with the Hamming distance, suggesting that these embeddings may be useful for downstream tasks such as binding prediction. Indeed, the model achieves Spearman correlation coefficients of 0.46 and 0.52 on two held-out test sets. By comparison, correlation coefficients calculated using existing structure and sequence-based models do not exceed 0.28. The correlation coefficient against dissociation constants of antibodies binding to SARS-CoV-2 RBD variants is 0.46. Additionally, the residue-level escapes are highest in the antibody epitope, correlating well with experimentally measured escapes. We further study the effect of antibody chain use, embedding dimension size and feed-forward and convolutional architectures on the model results. Lastly, we find that the inference time of our model is significantly faster than previous models, suggesting that it could be a useful tool for the accurate and rapid prediction of antibodies binding to SARS-CoV-2 RBDs.Availability and implementationThe model and associated code are available for download at https://github.com/ericzwang/RBD_AB.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
PrioriTree: a utility for improving phylodynamic analyses in BEAST
Authors: Gao Jiansi , May Michael R , Rannala Bruce , Moore Brian R 
Published: January 2023

Abstract

Summary
Phylodynamic methods are central to studies of the geographic and demographic history of disease outbreaks. Inference under discrete-geographic phylodynamic models—which involve many parameters that must be inferred from minimal information—is inherently sensitive to our prior beliefs about the model parameters. We present an interactive utility, PrioriTree, to help researchers identify and accommodate prior sensitivity in discrete-geographic inferences. Specifically, PrioriTree provides a suite of functions to generate input files for—and summarize output from—BEAST analyses for performing robust Bayesian inference, data-cloning analyses and assessing the relative and absolute fit of candidate discrete-geographic (prior) models to empirical datasets.

Availability and implementation
PrioriTree is distributed as an R package available at https://github.com/jsigao/prioritree, with a comprehensive user manual provided at https://bookdown.org/jsigao/prioritree_manual/.
Gas in the myocardium: a fatal presentation of Clostridium perfringens: a case report
Authors: Khan Hafiz Muhammad Waqas , Yousaf Amman , Ahmad Muhammad , Changezi Hameem U 
Published: January 2023

Abstract

Background
Clostridium perfringens is a well-known cause of gas gangrene with a very high mortality rate. Multiple cases of internal organs have been reported in the literature; however, non-traumatic spontaneous gas gangrene due to C. perfringens with solely cardiac involvement in a patient without any risk factors has not been reported before.

Case Summary
A 52-year-old male presented to the emergency department with chest pain and exertional dyspnoea for three days. The patient was haemodynamically stable initially, and the physical examination was unremarkable. Initial laboratory workup revealed elevated D-dimer and troponin levels. Computerized tomography (CT) of the chest was negative for pulmonary embolism but showed a hypodense focus in the cardiac silhouette. Acute coronary syndrome protocol was initiated; however, invasive cardiac workup was negative. The patient had rapid clinical deterioration with development of respiratory failure, shock, and multiorgan failure within 24 h. A transesophageal echocardiogram demonstrated an abnormal echogenic focus, corresponding to CT chest area. Despite aggressive treatment, the patient passed away within 36 h. Later, the patient’s blood culture grew C. perfringens. A limited autopsy showed an abscess cavity in the interventricular septum, pathology of which revealed acute myocarditis and fibrinous pericarditis.

Discussion
Unlike other reported cases of C. perfringens with cardiac abscess, our patient had no known risk factors, and no other organs were involved. We conclude from this case that an air focus on the CT scan in the myocardium can be suggestive of a spontaneous gas gangrene of the myocardium, and the patients should be treated accordingly.
The associations of dental aesthetics, oral health-related quality of life and satisfaction with aesthetics in an adult population
Authors: Närhi Linnea , Mattila Minttu , Tolvanen Mimmi , Pirttiniemi Pertti , Silvola Anna-Sofia 
Published: January 2023

Summary

Aim
The aim of this study was to investigate the gender-specific associations between dental aesthetics, oral health-related quality of life (OHRQoL), and satisfaction with dental aesthetics in an adult population.

Materials and methods
The study population consisted of 1780 individuals (822 males and 958 females) from the Northern Finland Birth Cohort 1966 (NFBC1966). Dental aesthetics were evaluated from digital 3D dental models using the Aesthetic Component (AC) of the Index of Orthodontic Treatment Need (IOTN). Layperson and orthodontist panels evaluated the dental aesthetics of a smaller sample (n = 100). OHRQoL was measured using the Oral Health Impact Profile (OHIP-14) questionnaire. Satisfaction with dental aesthetics was asked with one separate question. Gender-specific analyses consisted of Mann–Whitney U-tests and Spearman’s correlation coefficients.

Results
More than half of the population had an aesthetically acceptable occlusion, and most of the individuals were satisfied with the aesthetics. The most severe aesthetic impairments were associated with the psychological dimensions of OHIP-14. There were significant but weak associations of AC and satisfaction with aesthetics, and satisfaction with aesthetics and OHRQoL. Significant gender differences were found, men having higher mean AC scores but women reporting lower OHRQoL.

Conclusion
At the population level, most of the individuals were satisfied with their aesthetics, despite different dental aesthetic conditions. The most severe aesthetic impairments were associated with decreased psychological well-being, women reporting more impacts compared to men.
The tradeoff strategy between growth and survival in Quercus variabilis seedlings: determining the most limiting resource in the field drive shoot dieback
Authors: Wang Miaomiao , Cheng Zhongqian , Li Guolei , Wang Jiaxi , Uscola Mercedes 
Published: January 2023

Abstract
Shoot dieback is an important survival strategy in juvenile Quercus spp. However, it is unknown how nursery practices can influence the regulatory mechanisms of shoot dieback after planting. Furthermore, there is scarce information about the interactive effects between container depth and nursery fertilization on field seedling performance, and in combination with field weed control. Here, Quercus variabilis seedlings were cultivated the first year in with two container depths (25 cm, D40; 36 cm, D60) and with two nitrogen-loading levels (25, N25; 100 mg seedling−1, N100) in the nursery, and the following year, they were out-planted with/without weed elimination. We evaluated first year seedlings’ functional traits after nursery culture (plant and root morphology and nutritional status) and second year field performance (survival, shoot dieback, growth and nutrient increments), and their relationship. Independently of nursery culture, weed management was an irreplaceable practice to optimize seedling field performance. Seedlings grown in deep containers (D60) showed enhanced field growth and nutrient acquisition and reduced shoot dieback. Fertilization increased N and K loading (content and concentration) in the nursery, but showed no effect in the field. Low quality seedlings (low fertilization and normal container) maintained high survival rates at the expense of increasing shoot dieback rate. Thus, field survival did not differ among seedlings with differing nursery practices. Together, deep container and high N fertilization, increased plant nutritional reserves (content) and improved root system development, consequently, mitigating field shoot dieback. Under our experimental conditions, improved seedling quality by the use of deep container (D60) was sufficient to optimize field seedling performance without weed competition. However, both, deep container and nitrogen loading (D60-N100) were the best nursery practices to optimize seedling success without weed control in the field. Our study highlights that shoot dieback is a paramount trade-off strategy between growth and survival, which should be considered as an important indicator for further evaluating seedling field performance.
Perturbation bounds for (nearly) orthogonally decomposable tensors with statistical applications
Authors: Auddy Arnab , Yuan Ming 
Published: January 2023

Abstract
We develop deterministic perturbation bounds for singular values and vectors of orthogonally decomposable tensors, in a spirit similar to classical results for matrices such as those due to Weyl, Davis, Kahan and Wedin. Our bounds demonstrate intriguing differences between matrices and higher order tensors. Most notably, they indicate that for higher order tensors perturbation affects each essential singular value/vector in isolation, and its effect on an essential singular vector does not depend on the multiplicity of its corresponding singular value or its distance from other singular values. Our results can be readily applied and provide a unified treatment to many different problems involving higher order orthogonally decomposable tensors. In particular, we illustrate the implications of our bounds through connected yet seemingly different high-dimensional data analysis tasks: the unsupervised learning scenario of tensor SVD and the supervised task of tensor regression, leading to new insights in both of these settings.
A numerical approach for solving a class of two-dimensional variable-order fractional optimal control problems using Gegenbauer operational matrix
Authors: Soufivand Farzaneh , Soltanian Fahimeh , Mamehrashi Kamal 
Published: January 2023

AbstractThis study presents a spectral method for solving the two-dimensional variable-order fractional optimal control problems (2D-VOFOCPs). In this work, a dynamic system with variable-order fractional derivatives appears. The Caputo derivative, which is one of the most widely used and essential types of fractional derivatives, has been used to construct operational matrices. The shifted Gegenbauer polynomials are used as orthogonal bases. For this purpose, at first, the control and state functions are approximated by the shifted Gegenbauer polynomials with unknown coefficients. Then, by substituting the approximated functions into initial and boundary conditions, the dynamical system and the objective function, an algebraic equation system is achieved. The solution of the obtained system of the algebraic equation is equivalent to the solution of 2D-VOFOCP. Furthermore, the convergence of the method is studied. Eventually, two numerical examples are presented to illustrate the applicability and accuracy of the proposed method.
Correctly Establishing and Interpreting Oxygenation Status in Sickle Cell Disease
Authors: Lucas Fabienne , Connell Nathan T , Tolan Nicole V 
Published: January 2023

Abstract

Background
As hypoxemia and hypoxia are central elements of disease pathophysiology and disease-related morbidity and mortality in individuals affected by sickle cell disease (SCD), clinical management aims to optimize oxygenation.

Content
Hypoxemia is primarily screened for with pulse oximetry. However, in SCD pulse oximetry can inaccurately reflect arterial saturation, posing the risk of undetected (occult) hypoxemia. Solely relying on pulse oximetry might therefore lead to misdiagnosis or mismanagement, with devastating effects on tissue oxygenation. The interpretation of oxygenation status is multifaceted, and “oxygen saturation” is often used as an umbrella term to refer to distinctly different measured quantities—estimated oxygen saturation (O2Sat), hemoglobin oxygen saturation (SO2) by either pulse oximetry or co-oximetry, and fractional oxyhemoglobin (FO2Hb). While in many clinical situations this ambiguous use is of little consequence, O2Sat, SO2, and FO2Hb cannot be used interchangeably in the setting of SCD, as dyshemoglobins, anemia, cardiopulmonary comorbidities, concomitant medications, and frequent transfusions need to be accounted for. This article describes the parameters that determine blood and tissue oxygen concentration, discusses laboratory method performance characteristics and the correct interpretation of currently available clinical laboratory testing, and reviews the literature on noninvasive vs invasive oxygenation measurements in SCD.

Summary
By correctly establishing and interpreting oxygenation parameters, clinical and laboratory teams can ensure high-quality, equitable healthcare, counteracting systemic exacerbations of health disparities frequently experienced by individuals with SCD.
Comparison of Creatinine, Urea, Ionized Calcium, and Bicarbonate Methods by 2 POC Systems and a Mainframe Chemistry Analyzer
Authors: Toffaletti John G , Handel Elizabeth , Riese Chris , Xu Clarke 
Published: January 2023

Abstract

Background
The i-STAT (iST) and GEM Premier ChemSTAT (ChmST) are point-of-care systems that measure electrolytes, metabolites, acid-base parameters, and hematocrit on blood. We compared results for creatinine, urea (blood urea nitrogen [BUN]), total carbon dioxide (tCo2), and ionized calcium (ion Ca) on blood by the ChmST and iST to Beckman DxC600 (DxC600) results for creatinine and urea on plasma and GEM Premier 5000 (GEM5K) results for ion Ca and tCo2 on blood.

Methods
107 heparinized blood specimens were analyzed on the ChmST and iST systems, with plasma tested by DxC600 for creatinine and BUN and blood tested by GEM5K for ion Ca and tCo2. We evaluated the methods primarily by the mean and SD of the biases at clinically relevant concentrations.

Results
The correlations of ChmST and iST results on blood for creatinine, BUN, ion Ca, and tCo2 correlated to plasma by the DxC600 and to blood by the GEM5K were r ≥ 0.98 for all analytes except for ion Ca on the iST (r = 0.93). The mean and SD of biases were within clinically and analytically acceptable limits for all methods except for tCo2 on the ChmST, which measures bicarbonate with a bicarbonate-sensing electrode. Also, creatinine and BUN by the ChmST were less affected by icterus or hemolysis than were the DxC600 (icterus) and the iST (hemolysis).

Conclusions
The ChmST and iST results on blood demonstrated strong correlations with each other and with the DxC600 results on plasma. We conclude the ChmST provides reliable results for whole blood creatinine, urea, ion Ca, and tCo2.