bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Analysis Tool for Continuous Glucose Monitor Data
Authors: Olawsky Evan , Zhang Yuan , Eberly Lynn E , Helgeson Erika S , Chow Lisa S 
Published: July 2021

Background: With the development of continuous glucose monitoring systems (CGMS), detailed glycemic data are now available for analysis. Yet analysis of this data-rich information can be formidable. The power of CGMS-derived data lies in its characterization of glycemic variability. In contrast, many standard glycemic measures like hemoglobin A1c (HbA1c) and self-monitored blood glucose inadequately describe glycemic variability and run the risk of bias toward overreporting hyperglycemia. Methods that adjust for this bias are often overlooked in clinical research due to difficulty of computation and lack of accessible analysis tools. Methods: In response, we have developed a new R package rGV, which calculates a suite of 16 glycemic variability metrics when provided a single individual’s CGM data. rGV is versatile and robust; it is capable of handling data of many formats from many sensor types. We also created a companion R Shiny web app that provides these glycemic variability analysis tools without prior knowledge of R coding. We analyzed the statistical reliability of all the glycemic variability metrics included in rGV and illustrate the clinical utility of rGV by analyzing CGM data from three studies. Results: In subjects without diabetes, greater glycemic variability was associated with higher HbA1c values. In patients with type 2 diabetes mellitus (T2DM), we found that high glucose is the primary driver of glycemic variability. In patients with type 1 diabetes (T1DM), we found that naltrexone use may potentially reduce glycemic variability. Conclusions: We present a new R package and accompanying web app to facilitate quick and easy computation of a suite of glycemic variability metrics.
Effectiveness of 2-year treatment with aripiprazole long-acting injectable and comparison with paliperidone palmitate
Authors: Mason Katy , Barnett Joshua , Pappa Sofia 
Published: July 2021

Background: The pragmatic management of psychotic disorders is more complex than that delivered in a controlled trial environment. Therefore, this study aims to evaluate the real-world effectiveness of aripiprazole long-acting injectable (ALAI) and compare it with another commonly used long-acting anti-psychotic, once-monthly paliperidone palmitate (PP1M). Methods: This naturalistic, independent 4-year mirror image study compared the mean number and length of hospital admissions 2 years before and 2 years after treatment initiation with ALAI. Retention rates, discontinuation reasons and level of adherence were also recorded. Furthermore, indirect comparisons were made between treatment outcomes on ALAI and PP1M. Results: A total of 109 eligible patients with a severe mental illness (65% with schizophrenia and 35% with other diagnosis) commenced on ALAI and 173 patients (69% with schizophrenia and 31% with other diagnoses) initiated on PP1M were included. Of these, 37% on ALAI and 34% on PP1M stopped treatment at 2 years; retention rates were most favourable for the schizophrenia group on PP1M. Patients were more likely to discontinue due to lack of effectiveness on ALAI and due to tolerability issues on PP1M. Those who continued for 2 years on ALAI ( n = 69), demonstrated an overall decrease of 84% in the mean number and 88% in the mean length of hospital admissions compared with the 2 years before initiation. Although patients on ALAI appeared to have a significantly higher bed occupancy the 2-year period before initiation than patients on PP1M, the reductions in hospitalizations were comparable across both cohorts after 2 years of treatment. Conclusions: The introduction of ALAI had a substantial impact on long-term clinical outcomes in this naturalistic cohort; more than half of patients continued treatment and had no admission during 2 years of follow up. There were no significant differences in hospitalisation rates between patients on ALAI and PP1M at 2 years.
Free Tissue Transfer for Repair of Chronic Esophageal Perforations
Authors: Helton Matthew , Gardner James Reed , Dunlap Quinn , Pait T. Glenn , Sunde Jumin , Vural Emre , Moreno Mauricio Alejandro 
Published: July 2021

ObjectiveAnterior cervical discectomy and fusion have become a common intervention for cervical spine stabilization. However, complications can cause life‐threatening morbidity. Among them, esophageal perforation is associated with severe morbidity, including dysphagia, malnutrition, and infection with the potential development of mediastinitis. Presentation is variable but often results in chronic morbidity. Herein we examine our experiences in the management of esophageal perforation with microvascular free tissue transfer.Study DesignRetrospective review from January 2013 to September 2020.SettingSingle academic tertiary care center.MethodsThis study comprised all patients (age, 41‐73 years) undergoing free tissue transfer for the repair of chronic esophageal perforation secondary to anterior cervical discectomy and fusion at an academic tertiary care center. Four patients underwent repair via vastus lateralis myofascial onlay grafting for defects ≤2 cm in greatest dimension, while 1 patient underwent a fasciocutaneous radial forearm free flap repair of an 11 × 5–cm defect.ResultsDefect location ranged from hypopharynx to cervical esophagus. Mean operative time was 6.2 hours; the average length of stay for all patients was 6.6 days. Of 5 patients, 1 required additional hardware placement for spine stabilization. All patients underwent gastrostomy tube placement to bypass the surgical site during healing, and all eventually resumed an oral diet postoperatively. Recurrent fistula occurred in 1 of 5 patients. No flap failures were encountered in the study population.ConclusionVastus lateralis myofascial onlay grafting and fasciocutaneous radial forearm free flap are robust, relatively low‐morbidity interventions with a high success rate for definitive repair of chronic esophageal perforation. Repair should be undertaken in concert with a spine surgeon for management of the cervical spine.
Analysis of the Peak Systolic Velocity in the Transplant Renal Artery Anastomosis to Determine Normal Values in Patients Without Graft Dysfunction
Authors: Luna Cibele , Hassan Farooq , Scortegagna Eduardo , Castillo Rosa Patricia 
Published: July 2021

Objective: The primary purpose is to define the mean renal artery anastomosis peak systolic velocity (RAA PSV) and the renal artery anastomosis to external iliac artery ratio (RAA-to-EIA) of renal transplant recipients without graft dysfunction. Moreover, to determine associations with type of vascular anastomosis and type of graft. Materials and Methods: This is a single-center retrospective analysis of kidney transplant recipients. Recorded variables included recipient age, type of vascular anastomosis, type of graft, RAA PSV, and external iliac artery PSV (EIA PSV). Such variables were evaluated on different postoperative follow-up periods. Results: There was a high degree of reliability between the RAA PSV and EIA PSV ( P < .001). The mean RAA PSV was 174 cm/s ± 72.9 cm/s with 95% confidence interval (CI) (162.2 cm/s-185.5 cm/s]. Conclusion: This study highlights the importance of determining the normal range of RAA PSV and showed that a high PSV does not necessarily indicate dysfunction.
Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing
Authors: Filer Dayne L. , Kuo Fengshen , Brandt Alicia T. , Tilley Christian R. , Mieczkowski Piotr A. , Berg Jonathan S. , Robasky Kimberly , Li Yun , Bizon Chris , Tilson Jeffery L. , Powell Bradford C. , Bost Darius M. , Jeffries Clark D. , Wilhelmsen Kirk C. 
Published: July 2021

Abstract
Background
As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number variants (CNVs) often get overlooked or obscured by under-powered data collection. Many groups have developed methodology for detecting CNVs from ES, but existing methods often perform poorly for small CNVs and rely on large numbers of samples not always available to clinical laboratories. Furthermore, methods often rely on Bayesian approaches requiring user-defined priors in the setting of insufficient prior knowledge. This report first demonstrates the benefit of multiplexed exome capture (pooling samples prior to capture), then presents a novel detection algorithm, mcCNV (“multiplexed capture CNV”), built around multiplexed capture.

Results
We demonstrate: (1) multiplexed capture reduces inter-sample variance; (2) our mcCNV method, a novel depth-based algorithm for detecting CNVs from multiplexed capture ES data, improves the detection of small CNVs. We contrast our novel approach, agnostic to prior information, with the the commonly-used ExomeDepth. In a simulation study mcCNV demonstrated a favorable false discovery rate (FDR). When compared to calls made from matched genome sequencing, we find the mcCNV algorithm performs comparably to ExomeDepth.

Conclusion
Implementing multiplexed capture increases power to detect single-exon CNVs. The novel mcCNV algorithm may provide a more favorable FDR than ExomeDepth. The greatest benefits of our approach derive from (1) not requiring a database of reference samples and (2) not requiring prior information about the prevalance or size of variants.
Factors affecting in-hospital mortality of non-tuberculous mycobacterial pulmonary disease
Authors: Tanaka Goh , Jo Taisuke , Tamiya Hiroyuki , Sakamoto Yukiyo , Hasegawa Wakae , Matsui Hiroki , Fushimi Kiyohide , Yasunaga Hideo , Nagase Takahide 
Published: July 2021

Abstract
Background
The incidence and prevalence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) are reportedly increasing in many parts of the world. However, there are few published data on NTM-PD-related death. Using data from a national inpatient database in Japan, we aimed in this study to identify the characteristics of patients with NTM-PD and clinical deterioration and to identify risk factors for in-hospital mortality.

Methods
We examined data from the Diagnosis Procedure Combination (DPC) database in Japan from July 2010 to March 2014. We extracted data for HIV-negative NTM-PD patients who required unscheduled hospitalization. We evaluated these patients’ characteristics and performed multivariable logistic regression analysis to identify risk factors for all-cause in-hospital mortality.

Results
A total of 16,192 patients (median age: 78 years; women: 61.2%) were identified. The median body mass index (BMI) was 17.5 kg/m2 (IQR 15.4–20.0). All cause In-hospital death occurred in 3166 patients (19.6%). The median BMI of the patients who had died was 16.0 kg/m2 (IQR 14.2–18.4). Multivariable analysis revealed that increased mortality was associated with male sex, lower BMI, lower activities of daily living scores on the Barthel index, hemoptysis, and comorbidities, including pulmonary infection other than NTM, interstitial lung disease, pneumothorax, and malignant disease.

Conclusions
We found associations between being underweight and having several comorbidities and increased in-hospital mortality in patients with NTM-PD. Preventing weight loss and management of comorbidities may have a crucial role in improving this disease’s prognosis.
Ferroptosis-related gene signature predicts the prognosis in Oral squamous cell carcinoma patients
Authors: Li Hongyu , Zhang Xiliu , Yi Chen , He Yi , Chen Xun , Zhao Wei , Yu Dongsheng 
Published: July 2021

Abstract
Background
The prognosis of oral squamous cell carcinoma (OSCC) patients is difficult to predict or describe due to its high-level heterogeneity and complex aetiologic factors. Ferroptosis is a novel form of iron-dependent cell death that is closely related to tumour growth and progression. This study aims to clarify the predictive value of ferroptosis-related genes (FRGs) on the overall survival(OS) of OSCC patients.

Methods
The mRNA expression profile of FRGs and clinical information of patients with OSCC were collected from the TCGA database. Candidate differentially expressed ferroptosis-related genes (DE-FRGs) were identified by analysing differences between OSCC and adjacent normal tissues. A gene signature of prognosis-related DE-FRGs was established by univariate Cox analysis and LASSO analysis in the training set. Patients were then divided into high- and low-risk groups according to the cut-off value of risk scores, A nomogram was constructed to quantify the contributions of gene signature and clinical parameters to OS. Then several bioinformatics analyses were used to verify the reliability and accuracy of the model in the validation set. Finally, single-sample gene set enrichment analysis (ssGSEA) was also performed to reveal the underlying differences in immune status between different risk groups.

Results
A prognostic model was constructed based on 10 ferroptosis-related genes. Patients in high-risk group had a significantly worse OS (p < 0.001). The gene signature was verified as an independent predictor for the OS of OSCC patients (HR > 1, p < 0.001). The receiver operating characteristic curve displayed the favour predictive performance of the risk model. The prediction nomogram successfully quantified each indicator’s contribution to survival and the concordance index and calibration plots showed its superior predictive capacity. Finally, ssGSEA preliminarily indicated that the poor prognosis in the high-risk group might result from the dysregulation of immune status.

Conclusion
This study established a 10-ferroptosis-releated gene signature and nomogram that can be used to predict the prognosis of OSCC patients, which provides new insight for future anticancer therapies based on potential FRG targets.
Ultrasound-guided implantation of radioactive 125I seed in radioiodine refractory differentiated thyroid carcinoma
Authors: Chen Wei , Luo Yu kun , Zhang Ying , Song Qing , Tang Jie 
Published: July 2021

Abstract
Background
Treatment for radioiodine refractory differentiated thyroid carcinoma (RR-DTC) is challenging. The purpose of this study was to assess the efficacy and safety of ultrasound-guided implantation of radioactive 125I-seed in radioiodine refractory differentiated thyroid carcinoma.

Methods
Thirty-six cervical metastatic lymph nodes (CMLNs) diagnosed with RR-DTC from 18 patients were enrolled in this retrospective study. US and contrast-enhanced ultrasound (CEUS) examinations were performed before implantation. Follow-up comprised US, CEUS, thyroglobulin (Tg) level and routine hematology at 1–3, 6, 9 and 12 months and every 6 months thereafter. The volumes of the nodules were compared before implantation and at each follow-up point. The volume reduction rate (VRR) of nodules was also recorded.

Results
The median volume of the nodules was 523 mm3 (148, 2010mm3) initially, which decreased significantly to 53mm3 (0, 286mm3) (P < 0.01) at the follow-up point of 24 months with a median VRR as 95% (86,100%). During the follow-up period (the range was 24–50 months), 25 (69%) nodules had VRR greater than 90%, of which 12 (33%) nodules had VVR ≈ 100% with unclear structures and only 125I seed images were visible in the US. At the last follow-up visit, the serum Tg level decreased from 57.0 (8.6, 114.8) ng/ml to 4.9 (0.7, 50.3) ng/ml, (P < 0.01).

Conclusion
US-guided 125I seed implantation is safety and efficacy in treating RR- DTC. It could be an effective supplement for the comprehensive treatment of thyroid cancer.
Cortical thickness distinguishes between major depression and schizophrenia in adolescents
Authors: Zhou Zheyi , Wang Kangcheng , Tang Jinxiang , Wei Dongtao , Song Li , Peng Yadong , Fu Yixiao , Qiu Jiang 
Published: July 2021

Abstract
Background
Early diagnosis of adolescent psychiatric disorder is crucial for early intervention. However, there is extensive comorbidity between affective and psychotic disorders, which increases the difficulty of precise diagnoses among adolescents.

Methods
We obtained structural magnetic resonance imaging scans from 150 adolescents, including 67 and 47 patients with major depressive disorder (MDD) and schizophrenia (SCZ), as well as 34 healthy controls (HC) to explore whether psychiatric disorders could be identified using a machine learning technique. Specifically, we used the support vector machine and the leave-one-out cross-validation method to distinguish among adolescents with MDD and SCZ and healthy controls.

Results
We found that cortical thickness was a classification feature of a) MDD and HC with 79.21% accuracy where the temporal pole had the highest weight; b) SCZ and HC with 69.88% accuracy where the left superior temporal sulcus had the highest weight. Notably, adolescents with MDD and SCZ could be classified with 62.93% accuracy where the right pars triangularis had the highest weight.

Conclusions
Our findings suggest that cortical thickness may be a critical biological feature in the diagnosis of adolescent psychiatric disorders. These findings might be helpful to establish an early prediction model for adolescents to better diagnose psychiatric disorders.
Application of failure mode and effects analysis (FMEA) to improve medication safety in the dispensing process – a study at a teaching hospital, Sri Lanka
Authors: Anjalee J. A. L. , Rutter V. , Samaranayake N. R. 
Published: July 2021

Abstract
Background
Failure mode and effects analysis (FMEA) is a prospective, team based, structured process used to identify system failures of high risk processes before they occur. Medication dispensing is a risky process that should be analysed for its inherent risks using FMEA. The objective of this study was to identify possible failure modes, their effects, and causes in the dispensing process of a selected tertiary care hospital using FMEA.

Methods
Two independent teams (Team A and Team B) of pharmacists conducted the FMEA for two months in the Department of Pharmacy of a selected teaching hospital, Colombo, Sri Lanka. Each team had five meetings of two hours each, where the dispensing process and sub processes were mapped, and possible failure modes, their effects, and causes, were identified. A score for potential severity (S), frequency (F) and detectability (D) was assigned for each failure mode. Risk Priority Numbers (RPNs) were calculated (RPN=SxFxD), and identified failure modes were prioritised.

Results
Team A identified 48 failure modes while Team B identified 42. Among all 90 failure modes, 69 were common to both teams. Team A prioritised 36 failure modes, while Team B prioritised 30 failure modes for corrective action using the scores. Both teams identified overcrowded dispensing counters as a cause for 57 failure modes. Redesigning of dispensing tables, dispensing labels, the dispensing and medication re-packing processes, and establishing a patient counseling unit, were the major suggestions for correction.

Conclusion
FMEA was successfully used to identify and prioritise possible failure modes of the dispensing process through the active involvement of pharmacists.
Tooth brushing performance in adolescents as compared to the best-practice demonstrated in group prophylaxis programs: an observational study
Authors: Eidenhardt Zdenka , Ritsert Alexander , Shankar-Subramanian Sadhvi , Ebel Stefanie , Margraf-Stiksrud Jutta , Deinzer Renate 
Published: July 2021

Abstract
Background
Research indicates that adolescents may have difficulties to adopt the tooth brushing recommendations delivered in prophylaxis programs. However, it is not clear whether these difficulties are seen amongst the entire age range of adolescence (10–19 years) or only occur at certain developmental stages of the adolescence. The present study analyzes the tooth brushing performance of adolescents and compares it to the best-practice of tooth brushing demonstrated during prophylaxis programs.

Methods
A random sample of N = 66 adolescents, comprising 10-year-olds (n = 42) and 15-year-olds (n = 24), were asked to perform oral hygiene to the best of their abilities in front of a tablet camera. Videos were analyzed for tooth brushing duration, location, and brushing movements, and the difference between the actual and expected behaviour was tested for consistency using repeated measures ANOVAs and Student’s t-tests. For the direct comparison across different age groups, already available data from 12- and 18-year-olds were reanalysed.

Results
The average brushing time (mean ± SD) of the 10-year-olds and 15-year-olds was 195.8 s (74.6 s) and 196.1 s (75.8 s), respectively. Regardless of age, the adolescents distributed their brushing time unevenly across the inner, outer and occlusal surfaces. The inner surfaces in particular were neglected to a considerable extent, as no age group spent more than 15.8% of the total brushing time on them. Furthermore, all age groups showed a high proportion of horizontal movements on the inner and outer surfaces, regardless of the movements instructed for the respective surfaces.

Conclusion
Even if adolescents brush to the best of their abilities, they neglect or skip one or many of the tooth surfaces. The reasons for the lack of compliance to tooth brushing instructions are discussed in light of the methods used in prophylaxis programs and the influence of parents.
CBCT evaluation of root canal morphology and anatomical relationship of root of maxillary second premolar to maxillary sinus in a western Chinese population
Authors: Yan Yujia , Li JingLin , Zhu Hualing , Liu Jun , Ren Jiayin , Zou Ling 
Published: July 2021

Abstract
Background
To evaluate the root anatomy, root canal morphology and the anatomical relationship between the roots and maxillary sinus of maxillary second premolars by CBCT in a western Chinese population.

Methods
A total of 1118 CBCT scans of the maxillary second premolars were collected from West China Hospital of Stomatology, Sichuan University. Information below were measured on axial, coronal and sagittal sections, recorded and evaluated properly: the number of roots and canals, the morphology of canal system classified by Vertucci standard, the inter-orifice distance of canal orifices, the curvature of each canal and the distance from root tip to maxillary sinus floor.

Results
Among the 1118 teeth, 94.2% (1053) are single-rooted and 55.1% (616) have one canal. Type I (55.1%) is the commonest root canal morphology followed by Type II (31.9%). The mean inter-orifice distance (IOD) for multi-canal teeth ranging from 2.72 ± 0.32 to 3.41 ± 0.11 mm. Of 1622 canals, 38.8% (630) curvature are mesiodistal and 30.9% (501) are straight canals. The distance from root tip to maxillary sinus floor increased with age and the mean distance of single-rooted ones is 2.47 ± 3.45 mm.

Conclusions
All kinds of canal morphology category can be detected in maxillary second premolars. The IOD might be a predictable factor for root canal morphology. Roots of maxillary second premolars are related to maxillary sinus which should be treated carefully.