bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concordance Analysis of the 23-Gene Expression Signature (myPath Melanoma) With Fluorescence In Situ Hybridization Assay and Single Nucleotide Polymorphism Array in the Analysis of Challenging Melanocytic Lesions: Results From an Academic Medical Center
Authors: Castillo Stephanie A. , Pham Anh K. , Dagrosa Alicia T. , Yan Shaofeng , Barton Dorothea T. , Lefferts Joel A. , Linos Konstantinos 
Published: July 2020

Background:
Fluorescence in situ hybridization (FISH) and single nucleotide polymorphism (SNP) arrays are well-established molecular tests for the analysis of challenging melanocytic lesions. A 23-gene expression signature (GES), marketed as myPath Melanoma, is a recently introduced molecular test that categorizes melanocytic lesions as “benign,” “malignant,” and “indeterminate.” There are few studies on the concordance between FISH, SNP, and GES in the analysis of melanocytic lesions.

Methods:
A single-institution retrospective analysis of 61 contiguous cases of challenging melanocytic lesions with molecular analysis by 2 or more techniques. The primary objective was to determine the intertest agreement, which was calculated as percent agreement. A secondary objective was to determine the combined-test performance, that is, the frequency of obtaining a successful test (a test with an abnormal or normal, benign or malignant result) when 2 or more molecular tests were performed.

Results:
Of the 61 cases, 58 cases were submitted for analysis using the GES assay, 44 cases were submitted for FISH analysis, and 21 cases were submitted for SNP array analysis. Percent agreement between GES and FISH array was 50.9% (18/34), which improved to 69.7% (18/23) when indeterminate/equivocal results were excluded. Similarly, percent agreement between GES and SNP array was 57.1% (8/14); this improved to 77.8% (7/9) when indeterminate/equivocal results were excluded. In 44% of cases submitted for GES and FISH and in 39% of cases submitted for GES and SNP, one test was successful and the other was not.

Conclusion:
For challenging melanocytic lesions, the choice of a molecular test is consequential as the GES assay correlated with FISH and SNP arrays approximately only half of the time. This improved when cases with indeterminate/equivocal results were excluded from the calculations. The combined-test analysis supports the utility of conducting more than one molecular test, as this increased the odds of obtaining a successful test.
Low medication adherence is associated with decline in health-related quality of life: results of a longitudinal analysis among older women and men with hypertension
Authors: Peacock Erin , Joyce Cara , Craig Leslie S. , Lenane Zachary , Holt Elizabeth W. , Muntner Paul , Krousel-Wood Marie 
Published: July 2020

Objective:
The aim of this study was to determine the association of low antihypertensive medication adherence with decline in health-related quality of life (HRQOL) over 1 year.

Methods:
We used data from older men and women with hypertension (n = 1525) enrolled in the Cohort Study of Medication Adherence among Older Adults. Adherence was measured using the validated self-report four-item Krousel-Wood Medication Adherence Scale (K-Wood-MAS-4) (low adherence = score ≥1) and prescription refill-based proportion of days covered (PDC) (low adherence = PDC < 0.80). We defined decline in HRQOL as a decrease in Mental Component Summary (MCS) or Physical Component Summary (PCS) score (from the RAND 36-Item Health Survey 1.0 administered at two time points – at the time of adherence assessment and 1 year later) equivalent to the minimal important difference (MID) for each respective summary score, calculated as the average of MID estimates derived from distribution and anchor-based approaches.

Results:
The prevalence of low adherence was 38.6% using the K-Wood-MAS-4 and 23.9% using PDC. On the basis of mean MID estimates of 4.40 for MCS and 5.16 for PCS, 21.8 and 25.2% of participants experienced a decline in MCS and PCS, respectively, over 1 year. Low adherence was associated with a decline in MCS for K-Wood-MAS-4 [prevalence ratio = 1.32, 95% confidence interval (95% CI) 1.08–1.62, P = 0.008], but not PDC (prevalence ratio  = 1.17, 95% CI 0.94–1.47, P = 0.168). Low adherence was not associated with decline in PCS (K-Wood-MAS-4: prevalence ratio  = 0.95, 95% CI 0.79–1.16; PDC: prevalence ratio  = 1.10, 95% CI 0.90–1.35).

Conclusion:
Low self-report medication adherence is associated with decline in mental HRQOL over 1 year in older adults with hypertension.
Adjustable Ptosis Correction via Posterior Levator Advancement With Minimal Superior Tarsectomy
Authors: Tran Ann Q. , DeMaria Lauren N. , Nair Archana A. , Tooley Andrea A. , Godfrey Kyle J. , Lisman Richard D. 
Published: July 2020

Purpose:
To report the surgical technique and outcomes for adjustable ptosis correction using a posterior levator advancement with minimal superior tarsectomy.

Methods:
A retrospective single-center study was conducted on patients who underwent adjustable ptosis repair via posterior levator advancement with minimal superior tarsectomy by a single surgeon from 2002 to 2018. Patients with greater than 1 mm asymmetry between eyes or contour abnormalities underwent nonsurgical adjustment in the office within 6 days of surgery.

Results:
A total of 79 patients (146 eyelids) were included in this study. The patients were female (67%), underwent bilateral surgery (87%) with mean age of 63 years (range, 20–92). The mean improvement in marginal reflex distance 1 at postoperative month 1 was 2.56 ± 1.04 mm (p ≤ 0.0001). Postoperative symmetry of 1 mm or less between eyes was achieved in 96.6% of patients. Only 8 eyes (5.4%) underwent in-office adjustment postoperatively. No demographic or clinical differences were noted in eyes that required adjustments. Postoperative complications included dry eyes that resolved by 3 months (13.6%), suture cyst (1.4%), corneal abrasion (1.4%), and persistent eyelid edema (1.4%). Surgical revision was required in 2.8% of eyes.

Conclusions:
The adjustable posterior levator advancement with minimal superior tarsectomy is an effective surgical technique for ptosis repair with the added benefit of in-office adjustability to correct minor asymmetries.
Impedance Values Do Not Correlate With Speech Understanding in Cochlear Implant Recipients
Authors: Prenzler Nils K. , Weller Tobias , Steffens Melanie , Lesinski-Schiedat Anke , Büchner Andreas , Lenarz Thomas , Warnecke Athanasia 
Published: July 2020

Objective:
To evaluate a possible correlation between impedance values and speech perception after cochlear implantation.

Study Design:
Retrospective chart review.

Setting:
Tertiary referral center.

Patients and Intervention:
All patients implanted with a MedEl Flex28 device in our department with complete audiometric data (Freiburger monosyllabic testing at 65 dB, Hochmaier–Schulz–Moser testing in quiet and in 10 dB noise) and impedance measurements at the 1-year refitting appointment were enrolled in this study. Further inclusion criteria were age > 17 years, native speakers, and no use of electric-acoustic-stimulation.

Main Outcome Measures:
Mean values for impedances were calculated over all electrode contacts and separately for basal, medial, and apical regions. These data were correlated statistically (Pearson's correlation) with speech testing results. Furthermore, groups of patients with extreme values were built and compared against each other and against the rest of the collective.

Results:
Impedance values did not correlate significantly with speech performance in any of the audiometric tests neither for all electrode contacts nor for specific clusters of contacts. Patients with the lowest impedances did not perform statistically different than patients with the highest impedances in any condition.

Conclusion:
To our knowledge, this is the first data on a possible correlation between impedances and speech perception. The extent of the impedances as a benchmark for a good performance in speech discrimination tests could not be verified. Further prospective studies, possibly with more precise diagnostic tools, should be carried out to define the value of impedance measurements for cochlear implantation provision.
Accuracy of the WatchBP O3 device for ambulatory blood pressure monitoring according to the new criteria of the ISO81060-2 2018 protocol
Authors: Fania Claudio , Lazzaretto Ilaria , Fontana Umberto , Palatini Paolo 
Published: July 2020

Objective
The aim of the study was to determine the accuracy of the Microlife WatchBP O3 monitor for ambulatory blood pressure (BP) measurement according to the new ISO81060-2 2018 protocol.

Methods
The WatchBP O3 was first tested in 97 subjects from the general population (mean age, 71.3 years; 48 men) using four cuffs of different sizes. In a second study, 36 subjects (mean age, 72.9 years; 18 men) underwent stress testing on a cycle ergometer in order to increase their heart rate by 15% or more.

Results
In the general population, the mean device–observer difference was 1.3 ± 3.2 mmHg for systolic BP and was 0.7 ± 3.2 mmHg for diastolic BP. These data were in agreement with criterion 1 of the protocol standard requirements (≤5 ± 8 mmHg). Also, criterion 2 was satisfied being the SDs of the 97 participants well below the maximum values required by the protocol (6.82 and 6.90 mmHg, respectively). During the ambulatory monitoring study, the average heart rate increase was 20.3% (range 15.4–28.9%). The mean device–observer difference was 1.5 ± 2.8 mmHg for systolic BP and was 1.7 ± 2.6 mmHg for diastolic BP. Also, these data were in agreement with criterion 1 of the protocol.

Conclusions
These data show that the Microlife WatchBP O3 monitor satisfied the ISO 81060-2:2018 standard requirements for a general population across a wide range of arm sizes and that also the protocol criteria for validation of devices intended for ambulatory BP monitoring were fulfilled.
Mental Health Factors Associated With Fatigue in Mexican Patients With Inflammatory Bowel Disease
Authors: Fresán Orellana Ana , Parra Holguín Norma N. , Yamamoto-Furusho Jesus K. 
Published: July 2020

Goals:
The aim of this study was to describe mental health factors associated with the development of fatigue in inflammatory bowel disease (IBD) patients.

Background:
IBD includes ulcerative colitis and Crohn’s disease. Patients with chronic diseases can present fatigue differently and qualitatively more severely than those typically represented by healthy populations.

Study:
This was a cross-sectional study in which 200 Mexican patients were attending the Inflammatory Bowel Disease Clinic at the National Institute of Medical Sciences and Nutrition. All patients answered 3 instruments: the first IBD-fatigue, HADS (Hospital Anxiety and Depression Scale), and PSQI (Pittsburgh Sleep Quality Index). The statistical analysis was carried out in the statistical program SPSS v 24.

Results:
The percentage of fatigue in our patients was 55.5% (n=111) for mild-moderate fatigue, 31.5% (n=63) for severe fatigue, and only 13% (n=26) had no fatigue. Sleep disturbance and sleep latency were the most important predictors of fatigue in IBD patients.

Conclusions:
Sleep quality and depression have an impact on fatigue in Mexican patients with IBD. It is important for multidisciplinary management to reduce these symptoms and improve the quality of life of patients with IBD.
Low prevalence of upper endoscopic gastrointestinal findings despite high frequency of alarm symptoms at the time of diagnosis in adult coeliac disease
Authors: Maimaris Stiliano , Schiepatti Annalisa , Gabrielli Gian Marco , Costetti Martina , Costa Stefania , Sanders David S , Zingone Fabiana , Carroccio Antonio , Ciacci Carolina , Di Sabatino Antonio , Biagi Federico 
Published: July 2020

Objectives
Exclusion of organic disorders involving the upper gastrointestinal (UGI) is a mandatory step before considering a biopsy-avoidance diagnostic strategy for adult coeliac disease. We aim to evaluate the prevalence of alarm symptoms and coincidental UGI endoscopic findings at the time of diagnosis of coeliac disease. To develop consensus criteria to identify patients with coeliac disease requiring a gastroscopy and to evaluate whether alarm symptoms prompting gastroscopy were predictive of endoscopic findings.

Methods
Presenting symptoms and UGI endoscopic findings at diagnosis of coeliac disease were collected retrospectively in 278 adult patients with coeliac disease diagnosed in Pavia between January 1999 and December 2017. A panel of experts developed criteria to evaluate which clinical scenarios warrant gastroscopy, which was then applied retrospectively to patients diagnosed in Pavia.

Results
At least one alarm symptom was present in 177/278 patients, 121/278 met our criteria for gastroscopy. Major UGI endoscopic findings included 3 cases of autoimmune atrophic gastritis, 19 oesophagitis and 20 Helicobacter pylori infections. No organic disorders were found. Prevalence of major endoscopic findings did not differ between patients who met our criteria and those who did not.

Conclusions
Despite the high prevalence of alarm symptoms at diagnosis, coincident major UGI endoscopic findings are rare in adult coeliac disease. These results may be relevant for future developments in coeliac disease diagnosis in adults.
Sim for Life: Foundations—A Simulation Educator Training Course to Improve Debriefing Quality in a Low Resource Setting
Authors: Robinson Traci , Santorino Data , Dube Mirette , Twine Margaret , Najjuma Josephine N. , Cherop Moses , Kyakwera Catherine , Brenner Jennifer , Singhal Nalini , Bajunirwe Francis , Wishart Ian , Lin Yiqun , Lorentzen Helge , Lutnæs Dag Erik , Cheng Adam 
Published: July 2020

Introduction
Despite the importance of debriefing, little is known about the effectiveness of training programs designed to teach debriefing skills. In this study, we evaluated the effectiveness of a faculty development program for new simulation educators at Mbarara University of Science and Technology in Uganda, Africa.

Methods
Healthcare professionals were recruited to attend a 2-day simulation educator faculty development course (Sim for Life: Foundations), covering principles of scenario design, scenario execution, prebriefing, and debriefing. Debriefing strategies were contextualized to local culture and focused on debriefing structure, conversational strategies, and learner centeredness. A debriefing worksheet was used to support debriefing practice. Trained simulation educators taught simulation sessions for 12 months. Debriefings were videotaped before and after initial training and before and after 1-day refresher training at 12 months. The quality of debriefing was measured at each time point using the Objective Structured Assessment of Debriefing (OSAD) tool by trained, calibrated, and blinded raters.

Results
A total of 13 participants were recruited to the study. The mean (95% confidence interval) OSAD scores pretraining, posttraining, and at 12 months before and after refresher were 18.2 (14.3–22.1), 26.7 (22.8–30.6), 25.5 (21.2–29.9), and 27.0 (22.4–31.6), respectively. There was a significant improvement from pretraining to posttraining (P < 0.001), with no significant decay from posttraining to 12 months (P = 0.54). There was no significant difference in OSAD scores pre– versus post–refresher training at 12 months (P = 0.49).

Conclusions
The Sim for Life Foundations program significantly improves debriefing skills with retention of debriefing skills at 12 months.
Systematic identification of modifiable risk factors and drug repurposing options for Alzheimer’s disease: Mendelian randomization analyses
Authors: Wu Chong , Wu Lang , Wang Jingshen , Lin Lifeng , Li Yanming , Lu Qing , Deng Hong-wen 
Published: July 2020

AbstractIntroductionSeveral Mendelian randomization studies have been conducted, which identified multiple risk factors for Alzheimer’s disease (AD). However, they typically focus on a few pre-selected risk factors.MethodsTwo-sample Mendelian randomization (MR) study was used to systematically examine the potential causal associations of 1,054 risk factors/medical conditions and 28 drugs with the risk of late- onset AD. To correct for multiple comparisons, the false discovery rate was set at <0.05.ResultsThere were strong evidence of a causal association between glioma risk, reduced trunk fat-free mass, lower education levels, lower intelligence and a higher risk of AD. For 28 investigated treatments (such as antihypertensive drugs), we found limited evidence for their associations.ConclusionMR found robust evidence of causal associations between glioma, trunk fat-free and AD. Our study also confirms that higher educational attainment and higher intelligence are associated with a reduced risk of AD.
Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19
Authors: Basile K , McPhie K , Carter I , Alderson S , Rahman H , Donovan L , Kumar S , Tran T , Ko D , Sivaruban T , Ngo C , Toi C , O’Sullivan MV , Sintchenko V , Chen S C-A , Maddocks S , Dwyer DE , Kok J 
Published: July 2020

ABSTRACTBackgroundThe detection of SARS-CoV-2 by real-time polymerase chain reaction (PCR) in respiratory samples collected from persons recovered from COVID-19 does not necessarily indicate shedding of infective virions. By contrast, the isolation of SARS-CoV-2 using cell-based culture likely indicates infectivity, but there are limited data on the correlation between SARS-CoV-2 culture and PCR. Here we review our experience using SARS-CoV-2 culture to determine infectivity and safe de-isolation of COVID-19 patients.Methods195 patients with diverse severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and ICU [n=5]). SARS-CoV-2 PCR positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was documented, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) values of the day four PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined as a Ctsample - Ctculture value of ≥3.FindingsOf 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ctsample values <32, including in 28/181 (15%), 19/42 (45%) and 9/11 samples (82%) collected from outpatients, inpatients and ICU patients, respectively. The mean duration from symptom onset to culture positivity was 4.5 days (range 0-18 days). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (p<0.001) and ICU patients (p<0.0001) compared with outpatients, and in samples with lower Ctsample values.ConclusionSARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.
Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations
Authors: Sarkar Rakesh , Mitra Suvrotoa , Chandra Pritam , Saha Priyanka , Banerjee Anindita , Dutta Shanta , Chawla-Sarkar Mamta 
Published: July 2020

AbstractAccumulation of mutations within the genome is the primary driving force for viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility as well as antigenic shift to escape host immunity, which might compromise the efficacy of vaccines and antiviral drugs. Therefore, we aimed at genome-wide analyses of circulating SARS-CoV-2 viruses for the emergence of novel co-existing mutations and trace their spatial distribution within India. Comprehensive analysis of whole genome sequences of 441 Indian SARS-CoV-2 strains revealed the occurrence of 33 different mutations, 21 being distinctive to India. Emergence of novel mutations were observed in S glycoprotein (7/33), NSP3 (6/33), RdRp/NSP12 (4/33), NSP2 (2/33) and N (2/33). Non-synonymous mutations were found to be 3.4 times more prevalent than synonymous mutations. We classified the Indian isolates into 22 groups based on the co-existing mutations. Phylogenetic analyses revealed that representative strain of each group divided themselves into various sub-clades within their respective clades, based on the presence of unique co-existing mutations. India was dominated by A2a clade (55.60%) followed by A3 (37.38%) and B (7%), but exhibited heterogeneous distribution among various geographical regions. The A2a clade mostly predominated in East India, Western India and Central India, whereas A3 clade prevailed in South and North India. In conclusion, this study highlights the divergent evolution of SARS-CoV-2 strains and co-circulation of multiple clades in India. Monitoring of the emerging mutations would pave ways for vaccine formulation and designing of antiviral drugs.
Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide
Authors: Yin Rui , Luo Zihan , Kwoh Chee Keong 
Published: July 2020

AbstractA newly emerging novel coronavirus appeared and rapidly spread worldwide and World Health Organization declared a pandemic on March 11, 2020. The roles and characteristics of coronavirus have captured much attention due to its power of causing a wide variety of infectious diseases, from mild to severe on humans. The detection of the lethality of human coronavirus is key to estimate the viral toxicity and provide perspective for treatment. We developed alignment-free machine learning approaches for an ultra-fast and highly accurate prediction of the lethality of potential human-adapted coronavirus using genomic nucleotide. We performed extensive experiments through six different feature transformation and machine learning algorithms in combination with digital signal processing to infer the lethality of possible future novel coronaviruses using previous existing strains. The results tested on SARS-CoV, MERS-Cov and SARS-CoV-2 datasets show an average 96.7% prediction accuracy. We also provide preliminary analysis validating the effectiveness of our models through other human coronaviruses. Our study achieves high levels of prediction performance based on raw RNA sequences alone without genome annotations and specialized biological knowledge. The results demonstrate that, for any novel human coronavirus strains, this alignment-free machine learning-based approach can offer a reliable real-time estimation for its viral lethality.