bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Validation of a Nomogram to Predict the Risk of Blood Transfusion in Orthognathic Patients
Authors: Jiang Fengli , He Jingjing , Wu Huanhuan , Wu Lingsong , Sun Na , Li Mixue , Xing Jiahua , Li Yan , Xu Yujian , Zheng Yang , Chen Youbai , Zhan Sien 
Published: February 2022

Objective:
This study aims to establish a nomogram to predict the probability of blood transfusion in patients with preoperative autologous blood donation before orthognathic surgery.

Methods:
The authors conducted a retrospective case-control study on consecutive orthognathic patients with preoperative autologous blood donation from January 2014 to December 2020. The outcome variable was the actual transfusion of autologous blood (ATAB). Predictors included patients’ demographics, preoperative blood cell test, vital signs, American Society of Anesthesiologists classification, surgical procedure, operation duration, and blood loss. Univariable and multivariable logistic regressions were performed to identify independent risk factors associated with ATAB. A nomogram was constructed to predict the risk for ATAB. The performance of the nomogram was evaluated using the area under the receiver operating characteristic curve, calibration curve and the consistency index.

Results:
A total of 142 patients (75 males and 67 females) with an average age of 22.72 ± 5.34 years donated autologous blood before their orthognathic surgery. Patients in the transfusion group (n = 56) had significantly lower preoperative red blood cell counts (4.74 ± 0.55 × 109/L versus 4.98 ± 0.45 × 109/L, P = 0.0063), hemoglobin (141.48 ± 15.18g/dL versus 150.33 ± 14.73g/dL, P = 0.0008), and hematocrit (41.05% ± 4.03% versus 43.32% ± 3.42%, P= 0.0006), more bimaxillary osteotomies (92.86% versus 56.98%, P < 0.001), longer operation duration (348.4 ± 111.10 minutesversus261.6 ± 115.44 minutes, P < 0.001), and more intraoperative blood loss (629.23±273.06 ml versus 359.53 ± 222.84 ml, P < 0.001) than their counterparts (n = 86) in the non– transfusion group. Univariable and multivariable logistic regression demonstrated that only hemoglobin (adjusted odds ratio [OR] 0.864, 95% confidence interval [CI]:0.76–0.98, P= 0.026), operation procedures (adjusted OR 8.14, 95% CI:1.69–39.16, P = 0.009), and blood loss (adjusted OR 1.006, 95% CI:1.002–1.009, P < 0.001) were independent risk factors for ATAB. The area under the receiver operating characteristic curve of the nomogram was 0.823. The consistency index of the nomogram was 0.823. The calibration curve illustrated that the nomogram was highly consistent with the actual observation.

Conclusions:
The nomogram is a simple and useful tool with good accuracy and performance in predicting the risk for blood transfusion.
A Survey of Factors Influencing Specialization in Plastic Surgery Among Chinese Surgeons
Authors: Liang Xuebing , Sun Sijie , Gu Tianyi , Ma Jiguang , Wang Keming 
Published: February 2022

Abstract:
In recent years, more Chinese surgeons have left other fields to enter plastic surgery. The factors influencing this respe-cialization have not been elicited. The authors aim to elucidate Chinese surgeons’ experience and career satisfaction in this specialty change. Between July and September 2020, the authors conducted an online survey of nonplastic surgeons who received plastic surgery training at an academic center. The survey evaluated their motivation for pursuing their field, practice patterns, and career satisfaction. Responses were compared those who respecialized in plastic surgery with those who did not. A total of 251 nonplastic surgeons completed the survey. The most frequent reasons for pursuing plastic surgery were lifestyle (61.1%), desire to help others (44.4%), and higher compensation (37.3%). Among those who changed fields, employment in academic centers declined from 85% to 51.7%, 70% devoted at least half of their practice to aesthetic surgery, and the median nights on call decreased from 1.54 to 0.38 per week after specializing in plastic surgery. Overall career satisfaction in plastic surgery was significantly higher compared with their former specialties (78.3% versus 28.3%, P 0.05). The authors’ study showed that outflow of surgeons from other specialties to plastic surgery is mainly due to burnout, which erodes physicians’ satisfaction level and the quality of care they are able to provide. The authors highlight the need for reducing burnout in other surgical fields as well as rigorous plastic and aesthetic surgery training for those changing fields to ensure high-quality patient care.
Quantification of the Bimodal Plate-Specific Complication Profile Associated With Reconstruction of Segmental Mandibular Defects With Reconstruction Plate and Soft Tissue Flap: Evidence From Systematic Review
Authors: Rymer Ben C. 
Published: February 2022

Abstract:
Reconstruction of segmental mandibular defects with a mandibular reconstruction plate and separate soft tissue flap can be indicated in certain patients. Whilst this technique can provide acceptable results, its exact longevity and timing of associated complications is poorly understood. This study was designed to quantify and plot in time the complication profile associated with this technique of mandibular reconstruction.
A search of the Medline and PubMed Central databases was conducted using the terms “Mandibulectomy” and “Reconstruction Plate.” Articles reporting total number of plate extrusions and fractures and their postoperative timing were included.
Nine articles were included, representing 265 patients with mandibulectomy defects reconstructed using mandibular reconstruction plates. Of these, 135 were male (62%) and 82 were female (38%). The mean age was 59 years. The predominant pathology was oral cavity Squamous Cell Carcinoma (SCC) (80%). Seventy-three patients (28%) experienced complications (mean follow-up: 24 months), with median time to complication of 3 months. Forty-three plate extrusions (16%), 20 plate fractures (8%) and 10 cases of loosened screws (4%) were reported. A bimodal temporal distribution of complications was found.
Overall, a plate-specific complication rate of 28% was found, confirming a higher incidence of complications in comparison to osseous free flap reconstruction. These occur over a bimodal time distribution, with extrusion occurring earlier than fracture. interference with speech, swallow and dental rehabilitation, and delay of adjuvant therapy are potential consequences. These findings indicate that patients may be better served by more complex reconstructive procedures, to minimize exposure to a frequent and prolonged complication profile.
Effectiveness and safety of PRP on persistent olfactory dysfunction related to COVID-19: towards a new therapeutic hope
Authors: Steffens Younès , Le Bon Serge , Prunier Léa , Rodriguez Alexandra , Lechien Jérôme R. , Saussez Sven , Horoi Mihaela 
Published: February 2022

AbstractOlfactory dysfunction (OD) is a well know symptom of coronavirus disease 2019 (COVID-19), accounting for 48 to 85% of patients. In 1 to 10% of cases, patients develop a chronic olfactory dysfunction (COD,) lasting more than 6 months. Recently, platelet-rich plasma (PRP) was used in patients with non-COVID-19 COD and authors reported encouraging results. In the present study, we investigated the usefulness and safety of PRP injection in 56 patients with COVID-19 COD.Our results showed that PRP in the olfactory cleft can increase the olfactory threshold one month after the injection. Moreover, our results suggest that timing of treatment may be an important factor and that PRP is a safe treatment because no adverse effects were reported throughout the study
Microbiome Toolbox: Methodological approaches to derive and visualize microbiome trajectories
Authors: Banjac Jelena , Sprenger Norbert , Dogra Shaillay Kumar 
Published: February 2022

AbstractSummaryThe gut microbiome changes rapidly under the influence of different factors such as age, dietary changes or medications to name just a few. To analyze and understand such changes we present a microbiome analysis toolbox. We implemented several methods for analysis and exploration to provide interactive visualizations for easy comprehension and reporting of longitudinal microbiome data. Based on abundance of microbiome features such as taxa as well as functional capacity modules, and with the corresponding metadata per sample, the toolbox includes methods for 1) data analysis and exploration, 2) data preparation including dataset-specific preprocessing and transformation, 3) best feature selection for log-ratio denominators, 4) two-group analysis, 5) microbiome trajectory prediction with feature importance over time, 6) spline and linear regression statistical analysis for testing universality across different groups and differentiation of two trajectories, 7) longitudinal anomaly detection on the microbiome trajectory, and 8) simulated intervention to return anomaly back to a reference trajectory.Availability and implementationThe software tools are open source and implemented in Python. The link to the interactive dashboard is https://microbiome-toolbox.herokuapp.com/. For developers interested in additional functionality of the toolbox, the Python package can be downloaded from https://pypi.org/project/microbiome-toolbox/. The toolbox is modular allowing for further extension with custom methods and analysis. The code is available on Github https://github.com/JelenaBanjac/microbiome-toolbox.ContactShaillayKumar.Dogra@rd.nestle.comSupplementary InformationSupplementary data are available at Bioinformatics online.
GMMchi: Gene Expression Clustering Using Gaussian Mixture Modeling
Authors: Liu Ta-Chun , Kalugin Peter N. , Wilding Jennifer L. , Bodmer Walter F. 
Published: February 2022

ABSTRACTMotivationCancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer types suggests the existence of certain “driver mutations,” which likely make up the major contribution to tumors’ selective advantages over surrounding normal tissue and as such are responsible for the most consequential aspects of the cancer cells’ gene expression patterns and phenotypes. We hypothesize that such mutations are likely to cluster with specific dichotomous shifts in the expression of the genes they most closely control, and propose GMMchi, a Python package that leverages Gaussian Mixture Modeling to detect and characterize bimodal gene expression patterns across cancer samples, as a tool to analyze such correlations using 2x2 contingency table statistics.ResultsWe confirm that GMMchi robustly and reliably extracts bimodal patterns from both colorectal cancer (CRC) cell line-derived microarray and tumor-derived RNA-Seq data and verify previously reported gene expression correlates of some well-characterized CRC phenotypes. Using well-defined simulated data, we were able to confirm the robust performance of GMMchi, reaching 85% accuracy with a sample size of n = 90. We were also able to demonstrate a few examples of the application of GMMchi with respect to its capacity to characterize background florescent signal in microarray data, filter out uninformative background probe sets, as well as uncover novel genetic interrelationships and tumor characteristics. Our approach to analysing gene expression analysis in cancers provides an additional lens to supplement traditional continuous-valued statistical analysis by maximizing the information that can be gathered from bulk gene expression data.AvailabilityThe Python package GMMchi and our cell line microarray data used in this paper is available for downloading on GitHub at https://github.com/jeffliu6068/GMMchiContactta-chun.liu@oncology.ox.ac.uk, peter.kalugin@hms.harvard.edu, walter.bodmer@hertford.ox.ac.uk
Robust statistical evaluation of tumor incidences in long-term rodent carcinogenicity studies: the reformulated poly-k trend test
Authors: Hothorn Ludwig A. 
Published: February 2022

AbstractMortality-adjusted tumor rates in long-term carcinogenicity rodent bioassays are commonly evaluated by means of the poly-k=3 Armitage trend test. However, this assumes exactly a linear dose-response curve and the Weibull parameter of k=3 for all tumor sites. These unrealistic assumptions can be circumvented by multiple testing across multiple possible dose-response shapes, multiple Weibull parameters, multiple effect sizes, multiple correlated tumors as well as pairwise and trend tests using the multiple marginal models approach. Based on data examples, different multiple tests are demonstrated using the CRAN R packages multcomp, tukeytrend, coin, MCPAN and multfisher.
Clonally heritable gene expression imparts a layer of diversity within cell types
Authors: Mold Jeff E. , Weissman Martin H. , Ratz Michael , Hagemann-Jensen Michael , Hård Joanna , Eriksson Carl-Johan , Toosi Hosein , Berghenstråhle Joseph , von Berlin Leonie , Martin Marcel , Blom Kim , Lagergren Jens , Lundeberg Joakim , Sandberg Rickard , Michaëlsson Jakob , Frisén Jonas 
Published: February 2022

AbstractCell types can be classified based on shared patterns of transcription. Variability in gene expression between individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. We asked whether long-term, heritable differences in transcription can impart diversity within a cell type. Studying clonal human lymphocytes and mouse brain cells, we uncover a vast diversity of heritable transcriptional states among different clones of cells of the same type in vivo. In lymphocytes we show that this diversity is coupled to clone specific chromatin accessibility, resulting in distinct expression of genes by different clones. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging and disease.
Genomic Surveillance of Salmonella spp. in the Philippines, 2013-2014
Authors: Lagrada Marietta L. , Argimón Silvia , Borlasa Janice B. , Abad Jaywardeen P. , Gayeta June M. , Masim Melissa L. , Olorosa Agnettah M. , Cohen Victoria , Jeffrey Benjamin , Abudahab Khalil , Sia Sonia B. , Hufano Charmian M. , Stelling John , Holden Matthew T.G. , Aanensen David M. , Carlos Celia C. ,   the Philippines Antimicrobial Resistance Surveillance Program
Published: February 2022

ABSTRACTIncreasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. This study aims to utilize whole genome sequencing (WGS) to characterize the population and AMR mechanisms of Salmonella captured by the Philippine Antimicrobial Resistance Surveillance Program (ARSP) and contrast to traditional laboratory methods.We sequenced the whole genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected in the Philippines in 2013–2014. From the genome sequences, we determined the serotype, multilocus sequence type, presence of determinants of antimicrobial resistance and relatedness between isolates. We also compared the genotypic predictions of serotype and AMR to the phenotypic data.AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. In contrast, three quarters of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to resistance to fluoroquinolones. ESBL genes were detected in five genomes that also carried other AMR determinants. The population of S. Typhi was dominated by the likely endemic genotype 3.0, which also caused of a putative local outbreak susceptible to antibiotics. The main NTS clades were global epidemic S. Enteritidis ST11 and the monophasic variant of S. Typhimurium (I 4,[5],12:i:-) ST34, which had frequently been serotyped as S. Typhimurium in the laboratory.This was the first time that Salmonella isolated from the Philippines were characterized by WGS and we provide evidence of its utility for ongoing surveillance at the ARSP.
Neurovascular Uncoupling: Multimodal Imaging Delineates the Acute Effects of MDMA
Authors: Ionescu Tudor M. , Amend Mario , Watabe Tadashi , Hatazawa Jun , Maurer Andreas , Reischl Gerald , Pichler Bernd J. , Wehrl Hans F. , Herfert Kristina 
Published: February 2022

AbstractPsychedelic compounds have attracted increasing interest in recent years due to their therapeutic potential for psychiatric disorders. Methylenedioxymethamphetamine (MDMA) is currently being investigated in clinical trials to treat post-traumatic stress disorder. To understand the acute effects of psychedelic drugs in vivo, functional MR imaging (fMRI) has been widely used in recent years. Notably, fMRI studies have shown that MDMA leads to inhibition of brain activity, challenging earlier hypotheses indicating mainly excitatory effects. However, interpretation of hemodynamic changes induced by psychedelics is challenging because of the potent vascular effects associated with this class of substances. Therefore, this study aimed to investigate the acute effects of MDMA using simultaneous positron emission tomography (PET)/fMRI in rats. For this purpose, hemodynamic changes measured by BOLD-fMRI were related to alterations in glucose utilization and serotonin transporter (SERT) occupancy, investigated using [18F]FDG functional PET (fPET) and [11C]DASB PET.We demonstrate that MDMA induces global hemodynamic decreases accompanied by localized metabolic increases. Elevated metabolism was found primarily in limbic projection areas involved in emotion processing. Concurrent BOLD-fMRI decreases, also found in extracerebral areas, indicate that the BOLD-fMRI reductions observed in the brain are of vascular, non-neuronal origin. We further show that higher SERT occupancy strongly correlates with regional BOLD-fMRI reductions. Therefore, increased serotonin levels induced by SERT blockage may cause a neurovascular uncoupling.Correct understanding of the in vivo mechanism of MDMA not only supports ongoing research but also warrants a reassessment of previous studies on neuronal effects of psychedelics relying on neurovascular coupling.
Lin28b specifies an innate-like lineage of CD8+ T cells in early life
Authors: Watson Neva B. , Patel Ravi K. , Oyesola Oyebola O. , Laniewski Nathan , Grenier Jennifer K. , Wang Jocelyn , Tabilas Cybelle , Yee Mon Kristel J. , Peng Seth P. , Wesnak Samantha P. , Nzingha Kito , Smith Norah L. , Davenport Miles P. , Tait Wojno Elia D. , Scheible Kristin M. , Grimson Andrew , Rudd Brian D. 
Published: February 2022

AbstractThe immune system is stratified into layers of specialized cells with distinct functions. Recently, Lin28b was shown to serve as a master regulator of fetal lymphopoiesis, programming the development of more innate-like lymphocytes in early life. However, it remains unclear whether Lin28b specifies innate functions in more conventional adaptive lymphocytes. In this report, we discovered that Lin28b promotes the development of a more innate-like lineage of CD8+ T cells that is capable of protecting the host against a wide variety of pathogens in the absence of TCR stimulation. Using RNA-seq and ATAC-seq, we found that Lin28b transcriptionally and epigenetically programs CD8+ T cells to be highly responsive to innate cytokines. We also performed scRNAseq and found that the shift from innate-like CD8+ T cells in early life to adaptive CD8+ T cells in adulthood is mediated by changes in the abundance of distinct subsets of cells. Remarkably, the innate CD8+ T cell subset predominates in early life but is also present in adult mice and humans. Collectively, our findings demonstrate that neonatal CD8+ T cells are a distinct lineage of lymphocytes that provide the host with innate defense in early life.One sentence SummaryHigh-dimensional analysis reveals how Lin28b programs neonatal CD8+ T cells for innate defense.
Novel ERR pan-agonists ameliorate heart failure through boosting cardiac fatty acid metabolism and mitochondrial function
Authors: Xu Weiyi , Billon Cyrielle , Li Hui , Hayes Matthew , Yu Keyang , Losby McKenna , Hampton Carissa S. , Adeyemi Christiana M. , Graves Andrea , Nasiotis Eleni , Fu Chen , Welch Ryan , Evans Ronald M. , Pei Liming , Walker John K. , Milosavljevic Aleksandar , Burris Thomas , Zhang Lilei 
Published: February 2022

AbstractCardiac metabolic dysfunction is a hallmark of heart failure. Estrogen related receptors ERRα and ERRγ are essential regulators for cardiac metabolism. Therefore, activation of ERR could be a potential therapeutic intervention for heart failure. However, no natural or synthetic ERR agonist is available to demonstrate their pharmacological effectin vivo. Using a structure-based design approach, we designed and synthesized two structurally distinct pan-ERR agonists, SLU-PP-332 (332) and SLU-PP-915 (915), which significantly improved ejection fraction and ameliorated fibrosis against pressure overload-induced heart failure without affecting cardiac hypertrophy. Mechanistically, a broad-spectrum of metabolic genes were transcriptionally activated by ERR agonists, particularly genes involved in fatty acid metabolism and mitochondrial function, which were mainly mediated by ERRγ. Metabolomics analysis showed significant normalization of metabolic profiles in fatty acid/lipid and TCA/OXPHOS metabolites by 915 in the mouse heart with 6-week pressure overload. Autophagy was also induced by ERR agonists in cardiomycoyte. On the other hand, ERR agonism led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocyte. In summary, ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced heart failurein vivo. Our results provided direct pharmacological evidence supporting the further development of ERR agonists as novel heart failure therapeuticsin vivo.
ScRNA-seq Identified the Metabolic Reprogramming of Human Colonic Immune Cells in Different Locations and Disease States
Authors: Zhao Qiuchen , Zhang Tong , Yang Hao 
Published: February 2022

ABSTRACTDifferent regions and states of the human colon are likely to have a distinct influence on immune cell functions. Here we studied the immunometabolic mechanisms for the spatial immune specialization and the dysregulated immune response during ulcerative colitis at single-cell resolution. We revealed that the macrophages and CD8+ T cells in the lamina propria (LP) of the human colon possessed an effector phenotype and were more activated, while their lipid metabolism was suppressed compared with those in the epithelial (Epi). Also, IgA+ plasma cells accumulated in lamina propria of the sigmoid colon were identified to be more metabolically activated versus those in the cecum and transverse colon, and the improved metabolic activity was correlated with the expression of CD27. In addition to the immunometabolic reprogramming caused by spatial localization colon, we found dysregulated cellular metabolism was related to the impaired immune functions of macrophages, dendritic cells, regulatory T cells, and ILCs in patients with ulcerative colitis. The cluster of OSM+ inflammatory monocytes was also identified to play its role in resistance to anti-TNF treatment, and we explored targeted metabolic reactions that could reprogram them to a normal state. Altogether, this study revealed a landscape of metabolic reprogramming of human colonic immune cells in different locations and disease states, and offered new insights into treating ulcerative colitis by immunometabolic modulation.