bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lateral Neck Radiography in Preoperative Evaluation of Adenoid Hypertrophy
Authors: Soldatova Liuba , Otero Hansel J. , Saul David A. , Barrera Christian A. , Elden Lisa 
Published: December 2019

Objective: To assess the value of lateral neck radiographs in quantifying adenoid hypertrophy to help guide treatment decisions in patients with symptoms of nasal obstruction. Study Design: Retrospective review. Methods: Quantitative radiologic grading of adenoids was correlated with the intraoperative grading to select cases in agreement between the two methods. The percent airway obstruction was calculated as a ratio of adenoid size to the size of the nasopharyngeal airway near the level of the choanae on the lateral neck radiographs for adenoidectomy cases in which radiographic and intraoperative grading of adenoid size were in agreement. Results: A total of 426 adenoidectomy cases with preoperative lateral neck radiographs were reviewed (M:F = 254:172 for age range 9 months to 16 years), and only cases in agreement between radiographic and intraoperative adenoid grading were included in radiographic analysis (N = 234). The percent airway obstruction values were significantly different between “severely obstructive” (N = 137, mean = 94.71, SD = 6.55, range [72.00; 100.00]) and “moderately obstructive” adenoid categories (N = 97, mean = 78.53, SD = 6.91, range [63.67; 98.08]), not only within clinically relevant age groups (1-3 years, 4-7 years, 8-15 years), but also for the entire data set (95% CI [14.41; 17.95], P < .0001). “Mildly obstructive” category was omitted due to small sample size (N = 4). Conclusion: Lateral neck radiographs can provide useful supplemental information on the degree of nasopharyngeal airway obstruction when other clinical findings do not clearly point toward adenoid hypertrophy as a primary cause of nasal obstruction. In our data set, a 65% nasopharyngeal airway obstruction represents a value two standard deviations below the mean for “moderately” obstructive adenoid category, and can be viewed as a simplified cut-off to indicate that the degree of adenoid enlargement is clinically relevant. This cut-off value can assist in evaluation of patients with symptoms of nasal obstruction. Level of Evidence: 4
Jet Ventilation in the Pregnant Patient with Airway Stenosis: Surgical Safety and Outcomes
Authors: Heichel Philip D. , Jacobsen Christian P. , Llamas Luis L. , Simpson C. Blake , Lott David G. , Verma Sunil , Dominguez Laura M. 
Published: December 2019

Objective: To review pregnancy outcomes and the safety of jet ventilation use in the gravid patient undergoing surgical airway intervention. Methods: A multi-institutional retrospective review of medical records was performed to identify women who underwent low-frequency jet ventilation during pregnancy for surgical treatment of airway stenosis. Postoperative complications were noted, and patients were interviewed regarding pregnancy outcomes. Results: Six women were included in this series. No immediate complications relating to anesthesia or surgical intervention were noted in five of the six women. One patient with a well-known history of uncontrolled seizures experienced seizure activity postoperatively. One patient returned to the operating room at a later date for debridement of tracheal crusts. Five mothers delivered via cesarean section and one via spontaneous vaginal delivery. The mean gestation age was 37.3 weeks. One of the six infants delivered prematurely and three were delivered at low birth weight. Three of the six infants required elevated care immediately post-delivery but, at present, all are in good health. Conclusion: Low-frequency jet ventilation and surgical management of airway stenosis should be recognized as a safe treatment option in the gravid patient. Surgical intervention should not be delayed in patients with severe symptoms, particularly given the potential risk associated with prolonged corticosteroid use. Level of evidence: 4
Intra-articular Injection of Culture-Expanded Mesenchymal Stem Cells Without Adjuvant Surgery in Knee Osteoarthritis: A Systematic Review and Meta-analysis
Authors: Kim Seong Hwan , Djaja Yoshi Pratama , Park Yong-Beom , Park Jung-Gwan , Ko Young-Bong , Ha Chul-Won 
Published: December 2019

Background: Although many clinical studies have assessed the efficacy of mesenchymal stem cells (MSCs) in knee osteoarthritis, evidence on their efficacy remains unclear owing to heterogeneity of cell entity and concomitant procedures. Purpose: To determine the efficacy of culture-expanded MSCs in knee osteoarthritis in terms of clinical outcome and cartilage repair via meta-analysis of randomized controlled trials (RCTs) without adjuvant surgery. Study Design: Meta-analysis. Methods: PubMed, Embase, the Cochrane Library, CINAHL, and Scopus were searched from inception to December 31, 2018. RCTs with culture-expanded MSCs for treating knee osteoarthritis were included. Studies with adjuvant surgery or cell concentrate were excluded. Quality was assessed by the Cochrane Collaboration risk-of-bias tool. For meta-analysis, data on clinical outcomes were measured using a visual analog scale (VAS) and the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and data on cartilage repair were measured using the Whole-Organ Magnetic Resonance Imaging Score (WORMS); categorization related to improvement was extracted. Results: Six RCTs (203 patients) were included. Two studies were deemed to have a low risk of bias. In pooled analysis, the only significant difference was in the VAS score (mean difference, –13.55; 95% CI, –22.19 to −4.9). In cumulative pain analysis with VAS and WOMAC pain scores, there was significant improvement after treatment (standardized mean difference, –0.54; 95% CI, –0.85 to −0.23). There was no significant difference in cartilage repair assessed by magnetic resonance imaging (standardized mean difference, 0.11; 95% CI, –0.51 to 0.73), WORMS (standardized mean difference, 1.68; 95% CI −14.84 to 18.21), or categorical results (odds ratio, 1.56; 95% CI, 0.32-7.59). Conclusion: Intra-articular injection of culture-expanded MSCs without adjuvant surgery can improve pain for patients experiencing knee osteoarthritis at short-term follow-up (6-12 months). However, evidence regarding function and cartilage repair remains limited.
Associations of Metabolic Syndrome and Its Components with the Risk of Incident Knee Osteoarthritis Leading to Hospitalization: A 32-Year Follow-up Study
Authors: Konstari Sanna , Sääksjärvi Katri , Heliövaara Markku , Rissanen Harri , Knekt Paul , Arokoski Jari P. A. , Karppinen Jaro 
Published: December 2019

Objectives To examine whether metabolic syndrome or its individual components predict the risk of incident knee osteoarthritis (OA) in a prospective cohort study during a 32-year follow-up period. Design The cohort consisted of 6274 participants of the Mini-Finland Health Survey, who were free from knee OA and insulin-treated diabetes at baseline. Information on the baseline characteristics, including metabolic syndrome components, hypertension, elevated fasting glucose, elevated triglycerides, reduced high-density lipoprotein, and central obesity were collected during a health examination. We drew information on the incidence of clinical knee OA from the national Care Register for Health Care. Of the participants, 459 developed incident knee OA. In our full model, age, gender, body mass index, history of physical workload, smoking history, knee complaint, and previous injury of the knee were entered as potential confounding factors. Results Having metabolic syndrome at baseline was not associated with an increased risk of incident knee OA. In the full model, the hazard ratio for incident knee OA for those with metabolic syndrome was 0.76 (95% confidence interval [0.56, 1.01]). The number of metabolic syndrome components or any individual component did not predict an increased risk of knee OA. Of the components, elevated plasma fasting glucose was associated with a reduced risk of incident knee OA (hazard ratio 0.71, 95% confidence interval [0.55, 0.91]). Conclusions Our findings do not support the hypothesis that metabolic syndrome or its components increase the risk of incident knee OA. In fact, elevated fasting glucose levels seemed to predict a reduced risk.
Student-athlete concussion disclosure and coach communication within collegiate athletics
Authors: Milroy Jeffrey J , Wyrick David L , Sanders Lindsey , Refisteck Erin , Beamon Emily 
Published: December 2019

Background Between 1.6 and 3.8 million sports- and recreation-related concussions occur in the United States annually. Reports indicate that a significant number of athletes who have experienced symptoms of a potential sport-related concussion did not disclose their symptoms. Aims The purpose of this study was to investigate the impact of coach communication about concussion disclosure on student-athlete intentions to disclose symptoms of a concussion and encourage another student-athlete to disclose their concussion symptoms. Methods A total of 2881 student-athletes completed a web-based survey during Fall of 2016. Multiple linear regression was conducted to primarily investigate the relationship between coach communication and intentions to disclose concussion symptoms. Secondarily, biological sex, year in school, athletic division, and sport category was also assessed. Results Coach communication predicted greater intentions to disclose symptoms to their coach, athletic trainer/sports medicine sports medicine staff member and encourage another athlete to disclose their symptoms of a concussion. Biological sex and sport category also predicted intentions to disclose concussion symptoms. Discussion Findings from this study provide support for the important role coaches play in an athlete’s regarding concussion safety and introduces preliminary evidence suggesting the impact of coach communication on athlete intentions to disclose concussion symptoms to a coach or athletic trainer/sports medicine staff member. Conclusion Future studies and behavioral interventions ought to consider the inclusion of coach communication or other coach-related variables when exploring concussion disclosure among athletes.
Regulation of Salivary Peptidoglycan Recognition Protein 1 in Adolescents
Authors: Raivisto T. , Heikkinen A.M. , Silbereisen A. , Kovanen L. , Ruokonen H. , Tervahartiala T. , Haukka J. , Sorsa T. , Bostanci N. 
Published: December 2019

Introduction: Peptidoglycan recognition protein 1 (PGLYRP1), a member of peptidoglycan recognition proteins, is known to be involved in the proinflammatory response toward bacterial infections. Recently, PGLYRP1 was identified as a ligand for triggering receptor expressed on myeloid cells 1 (TREM-1). Although PGLYRP1 is involved in immune and inflammatory responses, its levels in initial stages of periodontal disease in adolescents are currently unknown. Objectives: We aimed to investigate salivary levels of PGLYRP1 and its correlation with TREM-1, polymorphonuclear leukocyte elastase (PMN elastase), and an active matrix metalloproteinase 8 (aMMP-8) in adolescents. Methods: Whole saliva samples (n = 537) were collected from 15- to 16-y-old adolescents at Kotka Health Center, Finland, prior to periodontal examination, including measurement of periodontal pocket depth (PPD), visible plaque index (VPI), and bleeding on probing (BOP). Adolescents, clustered as periodontally healthy, gingivitis, or subclinical periodontitis, were tested for salivary levels of TREM-1, PGLYRP1, and PMN elastase by enzyme-linked immunosorbent assay and aMMP-8 by a time-resolved immunofluorometric assay (IFMA). Results: Salivary levels of PGLYRP1 and aMMP-8 were significantly higher in adolescents with subclinical periodontitis and gingivitis compared to individuals with healthy periodontium. TREM-1 and PMN elastase levels were higher in adolescents with subclinical periodontitis compared to healthy individuals but did not reach significance. PGLYRP1 correlated positively with BOP, PPD, VPI, aMMP-8, and TREM-1. Conclusions: Elevated PGLYRP1 levels in adolescents with gingivitis and subclinical periodontitis and its positive correlation with TREM-1 and aMMP-8 may indicate an association of PGLYRP1 with initial stages of periodontal disease. Sex and poor oral hygiene but not smoking are also associated with higher levels of PGLYRP1. However, PGLYRP1 has a lower discriminating capacity and is therefore a less reliable marker alone in the diagnosis of initial stages of periodontal disease in adolescents. Knowledge Transfer Statement: PGLYRP1, a member of peptidoglycan recognition proteins, is a ligand for TREM-1. Elevated PGLYRP1 levels in adolescents with gingivitis and subclinical periodontitis and its positive correlation with TREM-1 and aMMP-8 may indicate an association of PGLYRP1 with initial stages of periodontal disease. However, it has a lower discriminating capacity and is therefore a less reliable marker alone in the diagnosis of periodontal disease in adolescents.
Blocking the PD-1/PD-L1 axis enhanced cisplatin chemotherapy in osteosarcoma in vitro and in vivo
Authors: Liu Xiaoqiang , He Shaoya , Wu Huaming , Xie Hui , Zhang Tao , Deng Zhongliang 
Published: December 2019

Abstract
Background
The blocking of the programmed cell death protein (PD-1)/programmed death-ligand 1 (PD-L1) axis has been found to have an anticancer activity against various types of cancer by enhancing T cell immunity, while there are no studies linking the PD-1/PD-L1 axis to chemotherapy drugs in osteosarcoma (OS). The present study aimed to investigate the effects of blocking PD-1/PD-L1 axis on the cisplatin chemotherapy in OS in vitro and in vivo.

Methods
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was applied to detect PD-L1 mRNA in OS tissues. Cell proliferation and apoptosis were measured by Cell Counting Kit-8 (CCK-8) and flow cytometry assays, respectively. In vivo, the syngeneic mice were treated with cisplatin and anti-PD-1 antibody alone or jointly.

Results
In this study, it revealed that PD-L1 mRNA was highly expressed in OS tissues. Further inhibitory evaluation showed that the K7M2-LV cells (PD-L1 overexpression) co-cultured with PD-1+ lymphocytes could promote K7M2 cell proliferation. Meanwhile, the combination of anti-PD-1 antibody and cisplatin significantly decreased the proliferation and increased the apoptosis of K7M2 cells in a co-culture system. In vivo, the combination of anti-PD-1 antibody and cisplatin significantly inhibited tumor growth, while the mechanisms did not involve regulatory T cells.

Conclusion
The present data suggested that the blocking of PD-1/PD-L1 axis had a positive prognostic value, which can enhance the chemotherapeutic effect of cisplatin in OS. These findings provide a rationale for utilizing PD1/PD-L1 blocking antibodies as a single agent to cure refractory OS in patients receiving cisplatin treatment.
Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)
Authors: Jiao Yulian , Hu Qiutao , Zhu Yan , Zhu Longfei , Ma Tengfei , Zeng Haiyong , Zang Qiaolu , Li Xuan , Lin Xinchun 
Published: December 2019

Abstract
Background
Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear.

Results
In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo.

Conclusions
This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.
MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks
Authors: Lin Yang-Ming , Chen Ching-Tai , Chang Jia-Ming 
Published: December 2019

Abstract
Background
Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An accurate tandem mass spectrum prediction tool is thus crucial in expanding the peptide space and increasing the coverage of spectral library search.

Results
We propose MS2CNN, a non-linear regression model based on deep convolutional neural networks, a deep learning algorithm. The features for our model are amino acid composition, predicted secondary structure, and physical-chemical features such as isoelectric point, aromaticity, helicity, hydrophobicity, and basicity. MS2CNN was trained with five-fold cross validation on a three-way data split on the large-scale human HCD MS2 dataset of Orbitrap LC-MS/MS downloaded from the National Institute of Standards and Technology. It was then evaluated on a publicly available independent test dataset of human HeLa cell lysate from LC-MS experiments. On average, our model shows better cosine similarity and Pearson correlation coefficient (0.690 and 0.632) than MS2PIP (0.647 and 0.601) and is comparable with pDeep (0.692 and 0.642). Notably, for the more complex MS2 spectra of 3+ peptides, MS2PIP is significantly better than both MS2PIP and pDeep.

Conclusions
We showed that MS2CNN outperforms MS2PIP for 2+ and 3+ peptides and pDeep for 3+ peptides. This implies that MS2CNN, the proposed convolutional neural network model, generates highly accurate MS2 spectra for LC-MS/MS experiments using Orbitrap machines, which can be of great help in protein and peptide identifications. The results suggest that incorporating more data for deep learning model may improve performance.
Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information
Authors: Lan Chaowang , Peng Hui , Hutvagner Gyorgy , Li Jinyan 
Published: December 2019

Abstract
Background
A long noncoding RNA (lncRNA) can act as a competing endogenous RNA (ceRNA) to compete with an mRNA for binding to the same miRNA. Such an interplay between the lncRNA, miRNA, and mRNA is called a ceRNA crosstalk. As an miRNA may have multiple lncRNA targets and multiple mRNA targets, connecting all the ceRNA crosstalks mediated by the same miRNA forms a ceRNA network. Methods have been developed to construct ceRNA networks in the literature. However, these methods have limits because they have not explored the expression characteristics of total RNAs.

Results
We proposed a novel method for constructing ceRNA networks and applied it to a paired RNA-seq data set. The first step of the method takes a competition regulation mechanism to derive candidate ceRNA crosstalks. Second, the method combines a competition rule and pointwise mutual information to compute a competition score for each candidate ceRNA crosstalk. Then, ceRNA crosstalks which have significant competition scores are selected to construct the ceRNA network. The key idea, pointwise mutual information, is ideally suitable for measuring the complex point-to-point relationships embedded in the ceRNA networks.

Conclusion
Computational experiments and results demonstrate that the ceRNA networks can capture important regulatory mechanism of breast cancer, and have also revealed new insights into the treatment of breast cancer. The proposed method can be directly applied to other RNA-seq data sets for deeper disease understanding.
The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features
Authors: Wang Lingling , Abu-Doleh Anas , Plank Johanna , Catalyurek Umit V. , Firkins Jeffrey L. , Yu Zhongtang 
Published: December 2019

Abstract
Background
Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. However, they remain poorly understood due to the lack of definitive direct evidence without influence by prokaryotes (including symbionts) in co-cultures or the rumen. In this study, we used RNA-Seq to characterize the transcriptome of Entodinium caudatum, the most predominant and representative rumen ciliate species.

Results
Of a large number of transcripts, > 12,000 were annotated to the curated genes in the NR, UniProt, and GO databases. Numerous CAZymes (including lysozyme and chitinase) and peptidases were represented in the transcriptome. This study revealed the ability of E. caudatum to depolymerize starch, hemicellulose, pectin, and the polysaccharides of the bacterial and fungal cell wall, and to degrade proteins. Many signaling pathways, including the ones that have been shown to function in E. caudatum, were represented by many transcripts. The transcriptome also revealed the expression of the genes involved in symbiosis, detoxification of reactive oxygen species, and the electron-transport chain. Overall, the transcriptomic evidence is consistent with some of the previous premises about E. caudatum. However, the identification of specific genes, such as those encoding lysozyme, peptidases, and other enzymes unique to rumen ciliates might be targeted to develop specific and effective inhibitors to improve nitrogen utilization efficiency by controlling the activity and growth of rumen ciliates. The transcriptomic data will also help the assembly and annotation in future genomic sequencing of E. caudatum.

Conclusion
As the first transcriptome of a single species of rumen ciliates ever sequenced, it provides direct evidence for the substrate spectrum, fermentation pathways, ability to respond to various biotic and abiotic stimuli, and other physiological and ecological features of E. caudatum. The presence and expression of the genes involved in the lysis and degradation of microbial cells highlight the dependence of E. caudatum on engulfment of other rumen microbes for its survival and growth. These genes may be explored in future research to develop targeted control of Entodinium species in the rumen. The transcriptome can also facilitate future genomic studies of E. caudatum and other related rumen ciliates.