bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicopathological and molecular study of 10 salivary gland clear cell carcinomas, with emphasis on rare cases with high grade transformation and occurring in uncommon sites
Authors: Xuan Lanlan , Wang Suxia , Wei Jianguo , Yuan Jianwei , Liu Honggang 
Published: January 2022

Abstract
Background
As a rare salivary gland malignancy, clear cell carcinoma (CCC) is easily misdiagnosed. This study identified the features that allow better recognition of the clinicopathological and molecular characteristics and the prognosis of CCC, focusing on high-grade transformation (HGT) in this tumor and cases arising in uncommon sites.

Methods
Clinicopathological and follow-up data for 10 CCC samples were retrieved. Immunohistochemical (IHC) staining was performed, and fluorescence in situ hybridization (FISH) was used to detect EWSR1 gene rearrangements, EWSR1–ATF1 gene fusions, and MAML2 gene rearrangements.

Results
Histologically, typical CCCs comprised bland polygonal or round cells with clear cytoplasm. In contrast with typical CCCs, HGT tumor cells exhibited nuclear pleomorphism, high nuclear-to-cytoplasmic ratios, high mitotic activity, and necrosis. Rare morphologic features such as pseudopapillae, gland-like spaces, and entrapped ducts were also observed. Occasionally, tumors involving the oral cavity might arise from the overlying epithelium of the mucosal surface. Immunohistochemically, all the cases expressed p63, p40, and CK5/6, while myoepithelial-related markers were uniformly negative in all cases. HGT exhibited a wild type p53 expression pattern. FISH demonstrated EWSR1 rearrangement (10/10) and EWSR1–ATF1 fusion (4/5); however, MAML2 remained intact (0/3).

Conclusions
CCCs with HGT or occurring in uncommon sites are extremely rare. Combining morphology based IHC and molecular detection provided reliable evidence that the HGT component represented a transformation of CCC rather than the coexistence of another tumor and helped differentiating CCCs in uncommon sites from their mimics, avoiding potential misdiagnosis and inappropriate therapy. The overall prognosis for CCCs is good, except for the HGT cases, which needed continued treatment.
Endotheliopathy is associated with slower liberation from mechanical ventilation: a cohort study
Authors: Schønemann-Lund Martin , Itenov Theis S. , Larsson Johan E. , Lindegaard Birgitte , Johansson Pär I. , Bestle Morten H. 
Published: January 2022

Abstract
Background
Endotheliopathy is suggested as pivotal pathophysiology of sepsis and trauma-associated organ failure, but its role in acute respiratory failure is not yet determined. We investigated if endotheliopathy biomarkers at ICU admission are associated with illness severity and clinical outcomes in patients with acute respiratory failure requiring mechanical ventilation.

Methods
We conducted a prospective single-center cohort study including 459 mechanically ventilated adults at ICU admission. Plasma levels of three endotheliopathy biomarkers were measured at ICU admission: Syndecan-1, soluble Thrombomodulin (sTM), and Platelet Endothelial Cell Adhesion Molecule-1 (PECAM-1). The primary outcome was the rate of liberation from mechanical ventilation, which is presented together with the rate of the competing risk of death while still on mechanical ventilation. Secondary outcomes were PaO2/FiO2-ratios on admission and on last measurement in patients dying within five days, and 30-day all-cause mortality. The primary outcome and 30-day all-cause mortality were analyzed using Cox regression, controlled for gender, age, chronic obstructive pulmonary disease, septic shock, heart failure, PaO2/FiO2-ratio at admission, respiratory infection, acute kidney injury, and bilirubin. PaO2/FiO2-ratios were analyzed using linear regression, controlled for age, chronic obstructive pulmonary disease, respiratory infection, and shock.

Results
Patients with high sTM were liberated from mechanical ventilation at a lower rate (adjusted hazard ratio (HR) 0.71, for an increase from the 25th to the 75th percentile, 95% confidence interval (CI) 0.54–0.93, p = 0.01). Patients with high PECAM-1 were liberated from mechanical ventilation at a lower rate, but only during the first 5 days (adjusted HR 0.72, for an increase from the 25th to the 75th percentile, 95% CI 0.58–0.9, p < 0.01). High levels of Syndecan-1 and PECAM-1 were associated with a higher rate of death while still on mechanical ventilation. sTM and PECAM-1 were negatively associated with PaO2/FiO2-ratio at ICU admission and no biomarker was associated with last measured PaO2/FiO2-ratio. High levels of all biomarkers were associated with higher 30-day all-cause mortality.

Conclusion
In acute respiratory failure, endotheliopathy biomarkers are associated with lower rates of liberation from mechanical ventilation, hypoxemia at ICU admission, and 30-day all-cause mortality.

Graphic Abstract
Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease
Authors: Johnson Travis S. , Yu Christina Y. , Huang Zhi , Xu Siwen , Wang Tongxin , Dong Chuanpeng , Shao Wei , Zaid Mohammad Abu , Huang Xiaoqing , Wang Yijie , Bartlett Christopher , Zhang Yan , Walker Brian A. , Liu Yunlong , Huang Kun , Zhang Jie 
Published: February 2022

AbstractWe propose DEGAS (Diagnostic Evidence GAuge of Single cells), a novel deep transfer learning framework, to transfer disease information from patients to cells. We call such transferrable information “impressions,” which allow individual cells to be associated with disease attributes like diagnosis, prognosis, and response to therapy. Using simulated data and ten diverse single-cell and patient bulk tissue transcriptomic datasets from glioblastoma multiforme (GBM), Alzheimer’s disease (AD), and multiple myeloma (MM), we demonstrate the feasibility, flexibility, and broad applications of the DEGAS framework. DEGAS analysis on myeloma single-cell transcriptomics identified PHF19high myeloma cells associated with progression. Availability: https://github.com/tsteelejohnson91/DEGAS.
Inflammatory myopathy occurring shortly after severe acute respiratory syndrome coronavirus 2 vaccination: two case reports
Authors: Vutipongsatorn Kritchai , Isaacs Anthony , Farah Ziad 
Published: January 2022

Abstract
Background
Vaccination remains the cornerstone approach to exiting the current global coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2. The novel messenger ribonucleic acid vaccines offer a high level of protection and are widely used throughout the world. With more people receiving the vaccines, better understanding of their relative safety can be reached. In this report, we describe two patients who developed inflammatory myopathy within 48 hours of receiving the Pfizer BNT162b2 vaccine.

Case presentation
Patient A, a 55-year-old South East Asian woman, presented with a 6-week history of pruritic facial and torso rash and a 1-week history of worsening proximal myopathy. Her rash first developed 2 days after receiving the first dose of BNT162b2 vaccine. Patient B, a 72-year-old Caucasian woman, presented with a 2-week history of proximal myopathy a day after receiving the second dose of BNT162b2 vaccine. Both patients had elevated creatine kinase on admission. Patient A tested positive for anti-Mi-2a antibody and anti-Ro-52 antibody, while Patient B was positive for anti-fibrillarin antibody. Magnetic resonance imaging subsequently confirmed generalized acute muscle inflammation and subcutaneous inflammation consistent with inflammatory myositis. Both patients did not have a previous history or family history of autoimmune disease. Patients A and B were diagnosed with dermatomyositis and inflammatory myositis, respectively. They were initially treated with pulsed intravenous methylprednisolone followed by oral prednisolone. However, as their conditions were resistant to corticosteroids, both eventually received and responded well to intravenous immunoglobulin therapy.

Conclusion
There are previously reported cases of severe acute respiratory syndrome coronavirus 2-induced and other vaccine-related inflammatory myopathies. However, the precise mechanisms are not elucidated. Without more evidence and convincing pathophysiology, it is not possible to conclude that our patients developed inflammatory myopathy because of the vaccine. However, the timing of the disease onset and the lack of previous history raise an important question of this novel messenger ribonucleic acid therapy.
Penile self-amputation due to cannabis-induced psychosis: a case report
Authors: Jengsuebsant Nantanan , Benjachaya Sirapat , Vuthiwong Jaraspong , Tangsuwanaruk Theerapon 
Published: January 2022

Abstract
Background
In recent decades, cannabis has been widely used around the world for medical and recreational purposes, both legally and illegally. Aside from its therapeutic benefits, cannabis exhibits many adverse effects. Psychosis is one of the potentially harmful effects of cannabis.

Case presentation
A 23-year-old Thai man, who reported cannabis use for 2 years and discontinued for 3 months, restarted smoking two bongs (2 g equivalence) of cannabis. Two hours later, he had a penile erection, felt a severe persistent sharp pain in his penis, and reported that his glans looked distorted. Intending to eradicate the pain, he decided to trim the penile skin several times and completely amputated his penis himself using scissors. Cannabis-induced psychosis was diagnosed because symptoms began after cannabis use, without evidence of other substance abuse. To confirm the cannabis exposure, his urine immunoassay was positive for delta-9-tetrahydrocannabinol (Δ9-THC). The distal penis was deemed too dirty and fragile for reconstruction. Bleeding was controlled, penile stump irrigated and debrided, and scrotal urethrostomy was performed by a urologist. After admission and cannabis discontinuation, his delusion and hallucination subsided.

Conclusions
Cannabis-induced psychosis is an adverse effect of cannabis, which may lead to impaired judgement unexpected self-harm. A multidisciplinary team approach, including a primary care physician, an emergency physician, a urologist, and a psychiatrist, is essential when dealing with a patient with cannabis-induced psychosis and a urogenital injury.
Skeletal muscle transcriptomics identifies common pathways in nerve crush injury and ageing
Authors: Staunton C. A. , Owen E. D. , Hemmings K. , Vasilaki A. , McArdle A. , Barrett-Jolley R. , Jackson M. J. 
Published: February 2022

AbstractMotor unit remodelling involving repeated denervation and re-innervation occurs throughout life. The efficiency of this process declines with age contributing to neuromuscular deficits. This study investigated differentially expressed genes (DEG) in muscle following peroneal nerve crush to model motor unit remodelling in C57BL/6 J mice. Muscle RNA was isolated at 3 days post-crush, RNA libraries were generated using poly-A selection, sequenced and analysed using gene ontology and pathway tools. Three hundred thirty-four DEG were found in quiescent muscle from (26mnth) old compared with (4-6mnth) adult mice and these same DEG were present in muscle from adult mice following nerve crush. Peroneal crush induced 7133 DEG in muscles of adult and 699 DEG in muscles from old mice, although only one DEG (ZCCHC17) was found when directly comparing nerve-crushed muscles from old and adult mice. This analysis revealed key differences in muscle responses which may underlie the diminished ability of old mice to repair following nerve injury.
Limonoids from the barks of Chukrasia tabularis and their anti-inflammatory activity
Authors: Shen Jinhuang , Zhang Yifan , Yang Nana , Ma Xinhua , Zhong Tianhua , Zhang Yonghong 
Published: January 2022

AbstractTwo novel phragmalin type limonoids, Tabularisin Q (1) and Chuktabularin Y (18), together with 22 known limonoids have been separated from bark of Chukrasia tabularis. The structures of 1–24 were identified with spectroscopic method (NMR, IR and mass spectrometry) and comparison with literature. The anti-inflammatory activity of all limonoids was assayed in RAW264.7 cells in vitro by evaluating the production of nitric oxide induced by lipopolysaccharide. Limonoids 8, 9, 1, and 18 showed significant anti-inflammatory activity with the inhibitory rates of 4.32, 11.28, 13.13, and 10.40 μm, respectively, and likely to be useful for the development as therapeutic agents for inflammatory diseases.
A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)
Authors: Rasmussen Jacob Agerbo , Villumsen Kasper Rømer , Ernst Madeleine , Hansen Martin , Forberg Torunn , Gopalakrishnan Shyam , Gilbert M. Thomas P. , Bojesen Anders Miki , Kristiansen Karsten , Limborg Morten Tønsberg 
Published: January 2022

AbstractBackgroundAnimal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism.ResultsOur findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid relatedCandidatusMycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence ofCandidatusMycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites.ConclusionOur results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments.
Pleasant touch perception in borderline personality disorder and its relationship with disturbed body representation
Authors: Löffler Annette , Kleindienst Nikolaus , Neukel Corinne , Bekrater-Bodmann Robin , Flor Herta 
Published: February 2022

Abstract
Background
Borderline personality disorder (BPD) is characterized by altered perception of affective stimuli, including abnormal evaluation of nociceptive input. However, whether or not perceptual alterations are present for its positive counterpart, i.e. pleasant touch (PT), has not yet been examined.

Methods
In the present study, we applied standardized PT stimuli to the hands of 25 patients with BPD and 25 healthy controls (HC) and compared their perception. We used the affect-modulated acoustic startle response as a physiological correlate of affective processing. We further explored the effect of PT stimulation on dissociative experiences in BPD.

Results
Compared to HC, BPD perceived PT as less pleasant and less intense. The effect on perceived valence of touch was large even after controlling for the effect of reduced perceived intensity of touch (ƞ2 = .29). We further found qualitative alterations in touch perception in BPD, who rated the touch as significantly rougher and firmer compared to HC. There was a positive correlation between perceived valence of touch and changes in dissociative experiences in terms of body ownership of the stimulated body part from pre to post stimulation, suggesting that a more negative evaluation of touch is associated with an increase in body-related dissociative experiences, while a positive perception of touch might be related to a reduction of these dissociative experiences.

Conclusions
Our results confirm BPD-associated disturbances in the processing of affective somatosensory stimuli and indicate that not only pain perception but also pleasant touch perception is diminished in BPD. We discuss the role of altered touch perception for BPD psychopathology and its potential role for new treatment approaches.
SUV39H1 regulates corneal epithelial wound healing via H3K9me3-mediated repression of p27
Authors: Yang Shuai , Chen Weiwei , Jin Shanshan , Luo Guangying , Jing Xia , Liu Qi , Reinach Peter S. , Qu Jia , Yan Dongsheng 
Published: February 2022

Abstract
Background
Corneal epithelial wound healing (CEWH) is vital for maintaining the integrity and barrier function of the cornea. Although histone modifications mediating gene expression patterns is fundamental in some other tissues, it remains unclear whether these gene regulation patterns underlie CEWH. Suppressor of variegation 3-9 homolog 1 (SUV39H1) plays a vital role in mediating gene silencing via histone H3 trimethylation of lysine 9 (H3K9me3). This study aims to characterize the comprehensive signature of epigenetic modifiers and determine the role of SUV39H1 in CEWH.

Methods
NanoString nCounter technology was used to detect the differentially expressed epigenetic modifiers during CEWH. Bioinformatic analyses were performed to reveal their involvement in this process. After knockdown of SUV39H1 with siRNA transfection, we determined the function of SUV39H1 on cell proliferation and migration in human corneal epithelial cells (HCECs) via MTS, EdU, and wound-healing assay, respectively. Flow cytometry analysis further confirmed the effect of SUV39H1 on the cell cycle of HCECs. Loss-of-function assays for SUV39H1 with siRNA injection or chaetocin assessed the role of SUV39H1 on CEWH in vivo. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blotting characterized the expression of SUV39H1 and its target genes. Chromatin immunoprecipitation assay was used to evaluate the distributions of H3K9me3 marks at the promoters of SUV39H1 target genes.

Results
We first identified 92 differentially expressed epigenetic modifiers and revealed their involvement during CEWH. SUV39H1 was confirmed to be upregulated in response to corneal injury. Its downregulation significantly inhibited HCEC proliferation and retarded in vivo CEWH. Furthermore, knockdown of SUV39H1 upregulated the p27 expression level and reduced H3K9me3 marks at p27 promoter in HCECs. In addition, p27 was remarkably downregulated with elevated H3K9me3 marks at its promoter during in vivo CEWH.

Conclusions
SUV39H1 plays a critical role in regulating corneal epithelial cell proliferation via H3K9me3-mediated suppression of p27 during CEWH. Our findings suggest that epigenetic modifiers such as SUV39H1 can be potential therapeutic approaches to accelerate corneal repair.
Heterozygous POLG variant Ser1181Asn co-segregating in a family with autosomal dominant axonal neuropathy, proximal muscle fatigability, ptosis, and ragged red fibers
Authors: Dohrn Maike F. , Heller Corina , Zengeler Diana , Obermaier Carolin D. , Biskup Saskia , Weis Joachim , Nikolin Stefan , Claeys Kristl G. , Schöne Ulrike , Beijer Danique , Winter Natalie , Achenbach Pascal , Gess Burkhard , Schulz Jörg B. , Mulahasanovic Lejla 
Published: February 2022

AbstractBy whole-exome sequencing, we found the heterozygous POLG variant c.3542G>A; p.Ser1181Asn in a family of four affected individuals, presenting with a mixed neuro-myopathic phenotype. The variant is located within the active site of polymerase gamma, in a cluster region associated with an autosomal dominant inheritance. In adolescence, the index developed distal atrophies and weakness, sensory loss, afferent ataxia, double vision, and bilateral ptosis. One older sister presented with Charcot-Marie-Tooth-like symptoms, while the youngest sister and father reported exercise-induced muscle pain and proximal weakness. In none of the individuals, we observed any involvement of the central nervous system. Muscle biopsies obtained from the father and the older sister showed ragged-red fibers, and electron microscopy confirmed mitochondrial damage. We conclude that this novel POLG variant explains this family’s phenotype.
Criteria of tracking vortex surfaces in turbulent-like flows
Authors: Han Zishuo , Yang Yue 
Published: February 2022

AbstractWe propose criteria of tracking vortex surfaces in complex flows based on the vortex-surface field (VSF). The criteria characterize the accuracy and Lagrangian tracking performance of the numerical VSF solution, and determine the time period when the vortex surface tracking is satisfactory. Moreover, we develop a turbulent-like flow combining large-scale coherent structures in the Taylor–Green flow and small-scale turbulent structures in homogeneous isotropic turbulence (HIT). From tracking of vortex surfaces during the effective tracking period, we find that the imposed HIT disturbance significantly wrinkles vortex surfaces. Subsequently, the wrinkled vortex tube with large vorticity magnitude tends to be further twisted, contributing to energy cascade, while the wrinkling is mitigated in the region with small vorticity magnitude.
Can magnetic resonance imaging predict preoperative consistency and vascularity of intracranial meningioma?
Authors: ElBeheiry Ahmed A. , Fayed Ahmed A. , Alkassas Ahmed H. , Emara Doaa M. 
Published: February 2022

Abstract
Background
Meningiomas are considered the most common primary intracranial neoplasms. The surgical resection is the main curative therapy. Evaluation of meningioma consistency and vascularity is important before surgery to be aware about the difficulties that neurosurgeon will face during resection, the possibility of total resection and to determine which equipment will be suitable for surgery. The purpose of this study was to identify the relationship between the MRI predictors of meningioma consistency [utilizing tumor/cerebellar peduncle T2-weighted imaging intensity (TCTI) ratios] as well as tumor vascularity (utilizing arterial spin labeling perfusion) in correlation with intraoperative findings. The study was carried out on 40 patients with MRI features of intracranial meningiomas. Non-contrast conventional MRI followed by arterial spin labeling MR perfusion and post contrast sequences were done for all cases. Final diagnosis of the cases was established by histopathological data while consistency and vascularity was confirmed by operative findings.

Results
According to surgical data, the studied cases of intracranial meningiomas were classified according to tumor consistency into 19 cases (47.5%) showing soft consistency, 14 cases (35%) showing intermediate consistency and 7 cases (17.5%) showing firm/hard consistency. TCTI ratio was the most significant MRI parameter in correlation with operative consistency of meningiomas, with soft lesions showing TCTI ranging from 1.75 to 2.87, intermediate consistency lesions TCTI ranging from 1.3 to 1.6, and firm lesions TCTI ranging from 0.9 to 1.2. According to intraoperative vascularity, cases were classified into 27 cases (67.5%) showing hypervascularity, 6 cases (15%) showing intermediate vascularity and 7 cases (17.5%) showing hypovascularity. Arterial spin labeling (ASL) was the most significant MRI parameter in correlation with operative vascularity of meningiomas, with hypervascular lesions showing normalized cerebral blood flow (n-CBF) ranging from 2.10 to 14.20, intermediately vascular lesions ranging from 1.50 to 1.60, and hypovascular lesions ranging from 0.70 to 0.90.

Conclusions
TCTI ratio showed good correlation with intraoperative meningioma consistency. ASL MR perfusion as a noninvasive technique is a reliable method to predict vascularity of meningioma in cases where IV contrast is contraindicated.