bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vaginal Intraepithelial Neoplasia: A Retrospective Study of Treatment and Outcomes Among a Cohort of UK Women
Authors: Field Alexander , Bhagat Nanak , Clark Sharon , Speed Tracey , Razvi Khalil 
Published: December 2019

Objectives
The aim of the study was to analyze the clinical features of women found to have vaginal intraepithelial neoplasia (VaIN), the treatment modalities that they were offered, and clinical outcomes after treatment and follow-up.

Materials and Methods
This is a retrospective review of all cases of biopsy-proven or treated VaIN occurring for a 15-year period at Southend University Hospital, United Kingdom.

Results
Eighty-eight cases of VaIN were identified. The age range was from 24 to 76 years, and 39% of cases were low grade (VaIN 1) and 60% high grade (VaIN 2 and 3). Sixty-five percent of patients had either already undergone or would go on to have treatment for cervical intraepithelial neoplasia. Of those with low-grade disease, 86% were managed conservatively with a 97% success rate. Similarly, with high-grade disease, 77% were managed with laser treatment with a success rate of 76% for primary treatment. Of the 6 cases of high-grade disease treated conservatively, 50% subsequently needed active treatment. There was 1 case of progression to vaginal cancer (1.3%).

Conclusions
Vaginal intraepithelial neoplasia remains an uncommon premalignant condition. It can affect women of all ages and is commoner in those who are immunosuppressed. Observation of low-grade disease is safe and the abnormality often resolves spontaneously. For persistent disease or higher-grade abnormalities, there are many treatment options but laser vaporization is the most commonly used. However, because of the nature of VaIN, recurrence is common even after treatment and further management can be challenging. The overall rate of malignant progression is small but protracted follow-up may be necessary.
Harmonizing Nutritional Therapies for Pediatric Inflammatory Bowel Disease
Authors: Picoraro Joseph A. , Akabas Sharon R. , LeLeiko Neal S. 
Published: December 2019

ABSTRACTUses of nutritional therapies for inflammatory bowel disease (IBD) are of tremendous interest to the lay and professional communities. This interest currently outweighs the scientific basis for deciding on a particular therapy for any given patient. Some nutritional therapies have credible reports, in peer‐review journals, validating their use for some patients. The broad pediatric gastroenterology community in the United States has, however, been unable or unwilling to agree on the details necessary to disseminate the most effective therapies with adequate reliability and validity to implement these interventions successfully. The well‐established importance of the appropriate use of nutritional interventions for the treatment of undernutrition and maintenance of optimal nutrition is not an issue. A consensus and widely applicable solution for nutrition as therapy for IBD is, however, not imminent. In the interim, we aim to help the science‐based reader to evaluate manuscripts appearing in our journals and to use this information to make rational, informed therapeutic decisions. We outline the current limited evidence base and make recommendations to advance the field of nutritional therapy in IBD.
Should Obesity Be Considered a Contraindication for Prepectoral Breast Reconstruction?
Authors: Banuelos Joseph , Abu-Ghname Amjed , Vyas Krishna , Sharaf Basel , Nguyen Minh-Doan T. , Harless Christin , Manrique Oscar J. , Martinez-Jorge Jorys , Tran Nho V. 
Published: December 2019

Background:
Prepectoral implant-based reconstruction reemerged as a viable approach following recent advances in reconstructive techniques and technology. To achieve successful outcomes, careful patient selection is critical. Obesity increases the risk of complications and has been suggested as a relative contraindication for prepectoral breast reconstruction.

Methods:
Retrospective chart review of patients who underwent immediate two-stage implant-based reconstruction at the authors’ institution was performed. Only women having a body mass index of 30 kg/m2 or greater were included. Patient demographics, operative details, and surgical outcomes of prepectoral and subpectoral reconstruction were compared.

Results:
One hundred ten patients (189 breasts) who underwent prepectoral and 83 (147 breasts) who underwent subpectoral reconstruction were included. Complications were comparable between the two groups. Twelve devices (6.4 percent), including implants and tissue expanders, required explantation in the prepectoral group, and 12 devices (8.2 percent) required explantation in the subpectoral group (p =0.522). Final implant-based reconstruction was achieved in 180 breasts (95.2 percent) in the prepectoral group and 141 breasts (95.9 percent) in the subpectoral group. Regardless of type of reconstruction (prepectoral or subpectoral), for each point increase in body mass index, the odds of complications and device explantation increased by 3.4 percent and 8.6 percent, respectively; and the optimal cutoff to predict higher complications and explantation rates was a body mass index of 34.8 kg/m2 and 34.1 kg/m2, respectively.

Conclusions:
Obesity increases complications and failure rates in a positive correlation; however, complications and final reconstruction rates are comparable between the prepectoral and subpectoral groups. The authors believe that obesity should not be a contraindication for prepectoral breast reconstruction but that care should be taken in patients with a body mass index above 35 kg/m2.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
A Simple Standardized Three-Dimensional Anthropometry for the Periocular Region in a European Population
Authors: Guo Yongwei , Schaub Friederike , Mor Joel M. , Jia Renbing , Koch Konrad R. , Heindl Ludwig M. 
Published: December 2019

Background:
The three-dimensional surface imaging system is becoming more common in plastic surgeries. However, few studies have assessed three-dimensional periocular structures and surgical outcomes. This study aimed to propose a standardized three-dimensional anthropometric protocol for the periocular region, investigate its precision and accuracy, and determine the three-dimensional periocular anthropometric norms for young Caucasians.

Methods:
Thirty-nine healthy young Caucasians (78 eyes) were enrolled. Three-dimensional facial images were obtained with a VECTRA M3 stereophotogrammetry device. Thirty-eight measurements in periocular regions were obtained from these images. Every subject underwent facial surface capture twice to evaluate its precision. A paper ruler was applied to assess its accuracy.

Results:
Sixty-three percent of measurements in linear distances, curvatures, angles, and indices were found to reach a statistically significant difference between sexes (p ≤ 0.05, respectively). Across all measurements, the average mean absolute difference was 0.29 mm in linear dimensions, 0.56 mm in curvatures, 1.67 degrees in angles, and 0.02 in indices. In relative error of magnitude, 18 percent of the measurements were determined excellent, 51 percent very good, 31 percent good, and none moderate. The mean value of the paper-ruler scale was 10.01 ± 0.05 mm, the mean absolute difference value 0.02 mm, and the relative error of magnitude 0.17 percent.

Conclusions:
This is the first study to propose a detailed and standardized three-dimensional anthropometric protocol for the periocular region and confirm its high precision and accuracy. The results provided novel metric data concerning young Caucasian periocular anthropometry and determined the variability between sexes.
Protective Effects of Micronized Fat against Ultraviolet B–Induced Photoaging
Authors: He Anqi , Wang Lu , Wang Qiang , Luan Wenjie , Qi Fazhi 
Published: December 2019

Background:
Autologous fat grafting has long been an essential technique in cosmetic and reconstructive surgery. Here, the authors report the advantages of a new device for preparing micronized fat, and they also investigated the therapeutic potential of micronized fat against ultraviolet B–induced photoaging.

Methods:
Micronized fat aliquots were prepared through a connector device with trifoliate blades. The histologic structure and viability of the prepared fat samples were evaluated by calcein AM/propidium iodide staining. The levels of growth factor were measured by enzyme-linked immunosorbent assay, and flow cytometry was used to detect the ratio of adipose-derived mesenchymal stem cells to stromal vascular fraction. The authors also evaluated the effects of micronized fat transplantation through immunohistochemistry and Masson trichrome staining in an animal model of photoaging.

Results:
The micronized fat had a normal histologic structure and viable adipocytes. It had a higher level of hepatocyte growth factor compared with the control group, and its ratio of adipose-derived mesenchymal stem cells to stromal vascular fraction was also higher than in the control fat preparations. Transplantation of micronized fat preparations in the animal model of photoaging produced increased skin neovascularization, epidermal cell proliferation, and dermal collagen density.

Conclusions:
The authors’ results demonstrated that the novel device produced micronized fat easily, which can condense adipose tissue. This micronized fat was easy to use with smaller cannulas. It mitigated the signs of cutaneous photoaging and was superior to control fat. Contrary to previous reports, normal histologic structures and viable adipocytes were noted in the micronized fat.
Objective Measures of Sleep Apnea and Actigraphy-Based Sleep Characteristics as Correlates of Subjective Sleep Quality in an Epidemiologic Study: The Jackson Heart Sleep Study
Authors: Johnson Dayna A. , Javaheri Sogol , Guo Na , Champion Cora L. , Sims Jeraline F. , Brock Michelene P. , Sims Mario , Patel Sanjay R. , Williams David R. , Wilson James G. , Redline Susan 
Published: December 2019

ABSTRACT

Objective
Self-reported “sleep quality” often is assessed in epidemiologic studies. However, the bases for variation in sleep quality is not fully understood. We quantified the extent to which subjective sleep quality was related to sleep disorders and sleep characteristics among 795 African American adults.

Method
Between 2012 and 2016, participants underwent home sleep apnea testing and 1-week actigraphy (estimating sleep duration, efficiency, fragmentation, latency). Sleep quality, insomnia and restless legs syndrome symptoms, sleepiness, and physician diagnosis of sleep disorders were self-reported. We fit linear regression models to determine the extent to which subjective and objective sleep measures as well as depressive symptoms and anxiety were related to subjective sleep quality.

Results
After adjustment for covariates, worse sleep quality scores were associated with insomnia and restless legs syndrome symptoms, sleep apnea, physician diagnosis of a sleep disorder, and actigraphy-based fragmented sleep, lower sleep efficiency, and shorter sleep duration. Insomnia symptoms explained the most variance in subjective sleep quality, 21%. Other sleep measures each explained 3% to 7% and psychosocial factors explained 8% to 9% of the variance in subjective sleep quality after adjustment for confounders.

Conclusions
The weak associations of sleep quality with sleep disorders and objectively measured sleep disturbances are consistent with concepts of “sleep health” as a multidimensional construct. Sleep quality is a patient-centered outcome that provides unique information over objective measurements of sleep disturbances.
Reliability and Diagnostic Accuracy of a New Vaginal Dynamometer to Measure Pelvic Floor Muscle Strength
Authors: Romero-Cullerés Georgia , Peña-Pitarch Esteban , Jané-Feixas Cecilia , Vilaseca-Grané Anna , Montesinos Jesus , Arnau Anna 
Published: December 2019

Aims
Assess the intrarater and interrater reliabilities and diagnostic accuracy of a new vaginal dynamometer to measure pelvic floor muscle (PFM) strength in incontinent and continent women.

Methods
A test-retest reliability study including 152 female patients. Exclusion criteria: history of urge urinary incontinence, prolapse of pelvic organ, pregnancy, previous urogynecological surgery, severe vaginal atrophy, or neurological conditions. The examination comprised digital assessment using the modified Oxford scale (MOS) and dynamometry measurements with a new prototype hand-held dynamometer. The MOS score ranges from 0 to 5: 0, no contraction; 1, flicker; 2, weak; 3, moderate; 4, good; 5, strong. Examinations were performed by a physiatrist, a physiotherapist and a midwife. The rest period between each rater measurement was 5 minutes. Assessment of intrarater and interrater reliability was calculated with the intraclass correlation coefficient.

Results
One hundred twenty-two incontinent women and 30 continent women were included. Scores between 0 and 2 in MOS were recorded in 72% of incontinent women versus 20% in continent patients (P < 0.001). Intrarater reliability of the dynamometer was 0.942 (95% confidence interval [CI], 0.920–0.958) and the interrater reliability was 0.937 (95% CI, 0.913–0.954). The analysis of variance analysis showed significant differences in PFM strength across digital assessment categories. The post-hoc analysis showed statistical differences between adjacent categories of MOS 1–2 and 2–3. The diagnostic accuracy showed an area under the curve of 0.82 (95% C,: 0.75–0.89), 0.87 (95% CI, 0.81–0.92), and 0.83 (95% CI, 0.77–0.90) for the physiatrist, midwife, and physiotherapist, respectively.

Conclusions
The results obtained show a good reliability and validity of this new vaginal dynamometer to quantify PFM strength.
A Cadaveric Simulation Model to Teach Suture Placement During Sacrospinous Ligament Fixation
Authors: Evans Sarah Keenan Larkin , Myers Erinn M. , Anderson-Montoya Brittany , Vilasagar Smitha , Tarr Megan E. 
Published: December 2019

Objectives
The objectives of this study were to describe a cadaveric simulation model designed to teach sacrospinous ligament fixation (SSLF) and to assess trainee performance, comfort, and skill with suture placement.

Methods
Nine invited participants from 3 institutions participated in cadaveric simulation training, consisting of a didactic lecture, technical demonstrations, and supervised execution of suture placement. Trainee self-perceived knowledge and confidence levels of SSLF were assessed before and after the educational intervention. Suture placement was assessed by expert faculty pelvic reconstructive surgeons. The number of attempts required by trainees for an anatomically safe suture placement was recorded. Participants completed a postintervention satisfaction survey.

Results
All 9 participants correctly identified where an SSLF suture should be placed on a printed image before the educational intervention, but only 33% achieved anatomically safe suture placement on the first attempt (mean ± SD, 2.88 ± 2.10 attempts). Four participants (44%) reported comfort with independently performing SSLF before the course. Of these, three (75%) required more than 1 attempt for successful suture placement. Mean ± SD distance of SSLF suture from the ischial spine was 1.90 ± 0.59 cm. All participants reported that they found the training helpful in learning the surgical steps and anatomy related to SSLF and would recommend it to others.

Conclusions
A cadaveric simulation teaching model led to improved trainee-reported confidence with the operative steps and anatomy related to SSLF. Participants’ prior knowledge of procedural steps and anatomy did not always transfer to adequate procedural skills for safe suture placement, suggesting the need for further simulation practice for fellow trainees.
Enhanced Cancer Subtyping via Pan-Transcriptomics Data Fusion, Monte-Carlo Consensus Clustering, and Auto Classifier Creation
Authors: Linton-Reid Kristofer , Clifford Harry , Thompson Joe Sneath 
Published: December 2019

ABSTRACTSubtyping of tumor transcriptome expression profiles is a routine method used to distinguish tumor heterogeneity. Unsupervised clustering techniques are often combined with survival analysis to decipher the relationship between genes and the survival times of patients. However, the reproducibility of these subtyping based studies is poor. There are multiple reports which have conflicting subtype and gene-survival time relationship results. In this study, we introduce the issues underlying the lack of reproducibility in transcriptomic subtyping studies. This problem arises from the routine analysis of small cohorts (< 100 individuals) and use of biased traditional consensus clustering techniques. Our approach carefully combines multiple RNA-sequencing and microarray datasets, followed by subtyping via Monte-Carlo Consensus Clustering and creation of deep subtyping classifiers. This paper demonstrates an improved subtyping methodology by investigating pancreatic ductal adenocarcinoma. Importantly, our methodology identifies six biologically novel pancreatic ductal adenocarcinoma subtypes. Our approach also enables a degree of reproducibility, via our pancreatic ductal adenocarcinoma classifier PDACNet, which classical subtyping studies have failed to establish.
The association of DNA methylation with body mass index: distinguishing between predictors and biomarkers
Authors: Reed Zoe E. , Suderman Matthew J. , Relton Caroline L. , Davis Oliver S.P. , Hemani Gibran 
Published: December 2019

AbstractBackgroundDNA methylation is associated with body mass index (BMI), but it is not clear if methylation scores are biomarkers for extant BMI, or predictive of future BMI. Here we explore the causal nature and predictive utility of DNA methylation measured in peripheral blood with BMI and cardiometabolic traits.MethodsAnalyses were conducted across the life course using the ARIES cohort of mothers (n=792) and children (n=906), for whom DNA methylation and genetic profiles and BMI at multiple time points (3 in children at birth, in childhood and in adolescence, 2 in mothers during pregnancy and in middle age) were available. Genetic and DNA methylation scores for BMI were derived using published associations between BMI and DNA methylation and genotype. Causal relationships between methylation and BMI were assessed using Mendelian randomisation and cross-lagged models.ResultsThe DNA methylation scores in adult women explained 10% of extant BMI variance. However, less extant variance was explained by scores generated in the same women during pregnancy (2% BMI variance) and in older children (15-17 years; 3% BMI variance). Similarly, little extant variance was explained in younger children (at birth and at 7 years; 1% and 2%, respectively). These associations remained following adjustment for smoking exposure and education levels. The DNA methylation score was found to be a poor predictor of future BMI using linear and cross-lagged models, suggesting that DNA methylation variation does not cause later variation in BMI. However, there was some evidence to suggest that BMI is predictive of later DNA methylation. Mendelian randomisation analyses also support this direction of effect, although evidence is weak. Finally, we find that DNA methylation scores for BMI are associated with extant cardiometabolic traits independently of BMI and genetic score.ConclusionThe age-specific nature of DNA methylation associations with BMI, lack of causal relationship, and limited predictive ability of future BMI, indicate that DNA methylation is likely influenced by BMI and might more accurately be considered a biomarker of BMI and related outcomes than a predictor. Future epigenome-wide association studies may benefit from further examining associations between early DNA methylation and later health outcomes.
Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline
Authors: Straub Daniel , Blackwell Nia , Fuentes Adrian Langarica , Peltzer Alexander , Nahnsen Sven , Kleindienst Sara 
Published: December 2019

AbstractOne of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is DNA- or RNA-based 16S rRNA (gene) amplicon sequencing. Subsequent bioinformatics analyses are required to extract valuable information from the high-throughput sequencing approach. However, manifold bioinformatics tools complicate their choice and might cause differences in data interpretation, making the selection of the pipeline a crucial step.Here, we compared the performance of most widely used 16S rRNA gene amplicon sequencing analysis tools (i.e. Mothur, QIIME1, QIIME2, and MEGAN) using mock datasets and environmental samples from contrasting terrestrial and freshwater sites. Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times less false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), while there was still room for improvement e.g. imperfect sequence recovery (recall up to 87%) or detection of additional false sequences (precision up to 72%). Furthermore, we found that microbial diversity estimates and highest abundant taxa varied among analysis pipelines (i.e. only one in five genera was shared among all analysis tools) when analyzing environmental samples, which might skew biological conclusions.Our findings were subsequently implemented in a high-performance computing conformant workflow following the FAIR (Findable, Accessible, Interoperable, and Re-usable) principle, allowing reproducible 16S rRNA gene amplicon sequence analysis starting from raw sequence files. Our presented workflow can be utilized for future studies, thereby facilitating the analysis of high-throughput DNA- or RNA-based 16S rRNA (gene) sequencing data substantially.ImportanceMicroorganisms play an essential role in biogeochemical cycling events across the globe. Phylogenetic marker gene analysis is a widely used method to explore microbial community dynamics in space and time, to predict the ecological relevance of microbial populations, or to identify microbial key players in biogeochemical cycles. Several computational analysis methods were developed to aid 16S rRNA gene analysis but choosing the best method is not trivial. In this study, we compared popular analysis methods (i.e. Mothur, QIIME1 and 2, and MEGAN) using samples with known microbial composition (i.e. mock community samples) and environmental samples from contrasting habitats (i.e. groundwater, soil, sediment, and river water). Our findings provide guidance for choosing the currently optimal 16S rRNA gene sequencing analysis method and we implemented our recommended pipeline into a reproducible workflow, which follows highest bioinformatics standards and is open source and free to use.